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  • 1990-1994  (852)
  • 1965-1969  (37)
  • 1860-1869
  • Biochemistry  (768)
  • Insulin
  • 1
    Electronic Resource
    Electronic Resource
    Effect of systemic insulin on protein kinetics in postoperative cancer patients (1994)
    Springer
    Annals of surgical oncology 1 (1994), S. 321-328 
    Details
    ISSN: 1534-4681
    Keywords: Insulin ; TPN ; Protein kinetics ; Amino acids ; Nutrition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Background: Cancer cachexia is a significant cause of postoperative morbidity and mortality in patients with tumors of the upper gastrointestinal tract. Standard parenteral nutrition (TPN) has failed to alter this. The anabolic effect of insulin has been well documented, and its positive effect on protein economy in cancer patients has been recently demonstrated. This study examines the effect of high-dose insulin and parenteral nutrition on protein kinetics in postoperative cancer patients. Methods: Eleven patients underwent surgery for pancreatic, esophageal, or gastric carcinoma. Postoperatively, patients received standard TPN for 4 days (1 g/kg/day amino acids, 1,000 kcal/day dextrose, 100 g/day lipid), and hyperinsulinemic parenteral nutrition for 4 days (same as standard TPN plus 1.44 U/kg/day regular human insulin) in a crossover design. All patients received both treatments, and the order of treatment was determined randomly. Euglycemia was maintained during insulin infusion via a variable 30% dextrose infusion. Patients underwent protein metabolic studies after each treatment period and rates of whole body and skeletal muscle protein synthesis, breakdown, and net balance were determined by radioisotopic tracer methods using14C-leucine and3H-phenylalanine. Results: Compared with standard TPN (STD), hyperinsulinemic TPN (INS) resulted in a significant increase in skeletal muscle protein synthesis (INS: 52.04±10.22 versus STD: 26.06±6.71 nmol phe/100 g/min, p〈0.05) and net balance of protein (INS: 7.75±4.61 versus STD: −15.10±6.44 nmol phe/100 g/min, p〈0.01), but no difference in skeletal muscle protein breakdown (INS: 44.29±11.54 versus STD: 41.17±5.89 nmol phe/100 g/min). Whole-body net balance of protein also significantly increased with insulin-based TPN, compared with standard TPN (INS: 0.04±0.05 versus STD: −0.08±0.07 µmol leu/kg/min, p〈0.05), but no difference in whole-body protein synthesis (INS: 2.52±0.15 versus STD: 2.49±0.15 µmol leu/kg/min) or whole-body protein breakdown (INS: 2.48±0.16 versus STD: 2.58±0.19 µmol leu/kg/min) was observed. Patients received significantly more calories during the hyperinsulinemic TPN period than during the standard TPN period. There was no difference in total, essential, or branched-chain amino acids, and no difference in serum free fatty acids, triglycerides, or cholesterol was observed between the two treatment periods. Conclusion: High-dose insulin in conjunction with hypercaloric parenteral nutrition causes improved skeletal muscle protein synthesis, skeletal muscle protein net balance, and whole-body protein net balance compared with standard TPN in postoperative cancer patients.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02303571
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  • 2
    Electronic Resource
    Electronic Resource
    Study on growth hormone and insulin secretion in myotonic dystrophy (1994)
    Springer
    Journal of molecular medicine 72 (1994), S. 508-511 
    Details
    ISSN: 1432-1440
    Keywords: Myotonic dystrophy ; Growth hormone ; Growth hormone releasing hormone ; Insulin ; C-Peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Growth hormone (GH) levels were measured in 12 patients with myotonic dystrophy (MD; 7 men and 5 women, aged 21–49 years) and 14 volunteers after administration of 100 μg GH-releasing hormone (GHRH; 1–29). A 75-g oral glucose tolerance test was carried out to determine glucose, insulin, plasma C-peptide, and urinary C-peptide. The GH level in six MD patients responded normally to GHRH (group I), with a peak of 17.1 ± 1.46 μg/l, compared withcontrols (27.8 ± 19.6 μg/l, NS), and that in the other six patients responded subnormally, with a peak of 3.15 ± 1.46 μg/l, lower than in controls and in group I patients (P 〈 0.001). In group I the insulin response to the glucose tolerance test showed hyperinsulinism and was lower than that in group II patients; stimulated C-peptide was also higher in group II than in group I and in controls; urinary C-peptide levels were parallel to those in previous data. In all MD patients there were a negative correlation between absolute values of GH response to GHRH and insulin response to glucose tolerance test (r = - 0.79, P 〈 0.001). Our data suggest that the failure in GH release and peripheral insulin action is due to a generalized defect in cellular membrane function in MD patients.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00207479
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  • 3
    Electronic Resource
    Electronic Resource
    Age-related changes in the haematology of young koalas (Phascolarctos cinereus) up to one year old (1994)
    Springer
    Comparative clinical pathology 4 (1994), S. 146-151 
    Details
    ISSN: 1433-2981
    Keywords: Biochemistry ; Development ; Haematology ; Koala
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Haematology and biochemistry of captive pouch young and back young koalas from 165 days to one year old were studied. Distinct changes with age were observed. Packed cell volume, haemoglobin, erythrocyte count, MCV and total plasma protein where lowest in the youngest animals less than 180 days old. Reticulocytes were highest in this age group. Haematological values differed from those of adult animals. Lymphocytosis occurred, especially between 210–330 days of age. Intense erythropoiesis was indicated by reticulocytosis and the presence of erythrocyte granular inclusions, anisocytosis and poikilocytosis on blood films, particularly up to 330 days of age. Microcytosis present on blood films throughout the study period could not be explained by iron deficiency.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00798355
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  • 4
    Electronic Resource
    Electronic Resource
    Tissue insulin contents in nesidioblastosis. Report of two cases (1994)
    Springer
    Pediatric surgery international 9 (1994), S. 353-356 
    Details
    ISSN: 1437-9813
    Keywords: Nesidioblastosis ; Insulin ; Radioimmunoassay ; Immunohistochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We present two cases of nesidioblastosis, a common cause of persistent hypoglycemia in infancy that, if inadequately treated, can lead to mental retardation. Tissue insulin data obtained from both radioimmunoassay and immunohistochemistry are presented. In each case, the insulin content correlated well with the quantity of insulinpositive cells in each portion of the pancreas. However, the insulin content varied from case to case and from portion to portion of the same pancreas. Thus, discrepancies in clinical results in nesidioblastosis may be due to variability of insulin content in the resected pancreas.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01685999
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  • 5
    Electronic Resource
    Electronic Resource
    Immunocytochemical and ultrastructural heterogeneities of normal and glibenclamide stimulated pancreatic beta cells in the rat (1994)
    Springer
    Virchows Archiv 425 (1994), S. 305-313 
    Details
    ISSN: 1432-2307
    Keywords: Rat ; Pancreatic beta cells ; Immunocytochemistry ; Ultrastructure ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract When studied morphologically in semi-thin sections in the rat in vivo, pancreatic beta cells displayed heterogeneous immunoreactivities for insulin and amylin, depending on the islet size and the intra-islet position of the beta cells. In larger islets, cortical beta cells (beta cells with contacts with all islet cell types and with the exocrine parenchyma) which are located in the periphery were more densely immunostained for insulin and amylin than medullary beta cells (beta cells with contacts only with other beta cells) which are located in the centre of the islet. Ultrastructurally, these findings were accompanied by differences in the number of secretory granules and mitochondria. Beta cells in small islets and at extra-islet sites exhibited a dense immunoreactivity. After administration of glibenclamide, immunoreactivities for insulin and amylin were diminished in a time-dependent manner, decreasing first in medullary and thereafter in cortical beta cells of larger islets. Ultrastructurally, the beta cells exhibited the typical signs of stimulation. A minority of beta cells in small islets and all beta cells in extra-islet locations remained unchanged. Thus pancreatic beta cells under basal and stimulatory conditions in vivo exhibit heterogeneity in hormone content and in ultrastructural features. These differences may represent the basis for a functional heterogeneity of the insulin secretory response of the individual beta cell both in vivo and in vitro in states of normal and impaired insulin secretion. As heterogeneity was observed only among beta cells in islets, while single beta cells surrounded by acinar cells exhibited no changes in insulin immunoreactivity, interactions between beta cells as well as between beta cells and other endocrine cells may be critical for expression of heterogeneity within the beta cell population.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00196154
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  • 6
    Electronic Resource
    Electronic Resource
    Transgenic mice overproducing islet amyloid polypeptide have increased insulin storage and secretion in vitro (1994)
    Springer
    Diabetologia 37 (1994), S. 725-728 
    Details
    ISSN: 1432-0428
    Keywords: Insulin ; islet amyloid polypeptide ; pancreas ; secretion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary To determine whether chronic overproduction of islet amyloid polypeptide alters beta-cell function, we studied a line of transgenic mice which overexpress islet amyloid polypeptide in their beta-cells. At 3 months of age, these transgenic mice had greater pancreatic content of both islet amyloid polypeptide and insulin. Further, basal and glucose-stimulated secretion of both islet amyloid polypeptide and insulin were also elevated in the perfused pancreas of the transgenic animals. These findings demonstrate that chronic overproduction and secretion of islet amyloid polypeptide are associated with increased insulin storage and enhanced secretion of insulin in vitro. This increase in insulin storage and secretion may be due to a direct effect of islet amyloid polypeptide on the beta-cell or a betacell adaptation to islet amyloid polypeptide-induced insulin resistance.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00417699
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  • 7
    Electronic Resource
    Electronic Resource
    Effect of metformin on insulin-stimulated glucose transport in isolated skeletal muscle obtained from patients with NIDDM (1994)
    Springer
    Diabetologia 37 (1994), S. 826-832 
    Details
    ISSN: 1432-0428
    Keywords: Insulin ; metformin ; 3-0-methylglucose transport ; non-insulin-dependent diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Metformin has been demonstrated to lower blood glucose in vivo by a mechanism which increases peripheral glucose uptake. Furthermore, the therapeutic concentration of metformin has been estimated to be in the order of 0.01 mmol/l. We investigated the effect of metformin on insulin-stimulated 3-0-methylglucose transport in isolated skeletal muscle obtained from seven patients with non-insulin-dependent diabetes mellitus (NIDDM) and from eight healthy subjects. Whole body insulin-mediated glucose utilization was decreased by 45% (p〈0.05) in the diabetic subjects when studied at 8 mmol/l glucose, compared to the healthy subjects studied at 5 mmol/l glucose. Metformin, at concentrations of 0.1 and 0.01 mmol/l, had no effect on basal or insulin-stimulated (100 ΜU/ml) glucose transport in muscle strips from either of the groups. However, the two control subjects and three patients with NIDDM which displayed a low rate of insulin-mediated glucose utilization (〈20 Μmol·kg−1·min−1), as well as in vitro insulin resistance, demonstrated increased insulin-stimulated glucose transport in the presence of metformin at 0.1 mmol/l (p〈0.05). In conclusion, the concentration of metformin resulting in a potentiating effect on insulin-stimulated glucose transport in insulin-resistant human skeletal muscle is 10-fold higher than the therapeutic concentrations administered to patients with NIDDM. Thus, it is conceivable that the hypoglycaemic effect of metformin in vivo may be due to an accumulation of the drug in the extracellular space of skeletal muscle, or to an effect of the drug distal to the glucose transport step.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00404340
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  • 8
    Electronic Resource
    Electronic Resource
    Differences in umbilical cord insulin and birth weight in non-diabetic pregnancies of women from different ethnic groups in New Zealand (1994)
    Springer
    Diabetologia 37 (1994), S. 930-936 
    Details
    ISSN: 1432-0428
    Keywords: Insulin ; C-peptide ; fructosamine ; triglyceride ; birthweight ; fatty acid ; non-insulin-dependent diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Many ethnic groups at high risk of non-insulin-dependent diabetes mellitus are hyperinsulinaemic by early adult life. This study assessed whether such hyperinsulinaemia is present at birth. Cross sectional comparisons of maternal biochemistry, umbilical cord biochemistry and neonatal anthropometry were made between one ‘low risk’ and three ‘high risk’ ethnic groups, without diabetes in pregnancy in Auckland, New Zealand. The study comprised 123 European, Polynesian (Maori and Pacific Islands) and Indian normal pregnancies. Indian mothers were the smallest, with the highest insulin and non-esterified fatty acid concentrations. Polynesian mothers were the most obese with a higher fructosamine concentration. From these pregnancies, Indian neonates were smaller, slimmer, with the highest cord triglyceride (0.6 mmol/l vs 0.4 mmol/l, p〈0.01), and lowest cord insulin concentrations (7.1 mU/l vs 8.6 mU/l (European), 9.2 mU/l (Polynesian), p〈0.05). Polynesian babies had a high cord insulin: C-peptide ratio (52.5 mU/nmol vs 44.4 mU/ nmol (European), 44.1 mU/nmol (Indian), p=0.05). Although reduced intrauterine growth may contribute to the excess of diabetes and heart disease in Indians, it cannot explain the excess of diabetes in Polynesians. Exposure to minor relative maternal hyperglycaemia in the mother and abnormal neonatal insulin handling (as demonstrated by the higher insulin: C-peptide ratio) may be of long-term significance in Polynesians.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00400950
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  • 9
    Electronic Resource
    Electronic Resource
    Differential effects of insulin and insulin-like growth factor-I in the femoral tissues of rats with skeletal unloading (1994)
    Springer
    Calcified tissue international 55 (1994), S. 363-367 
    Details
    ISSN: 1432-0827
    Keywords: Skeletal unloading ; Bone formation ; Insulin ; Insulin-like growth factor-I ; Rat femur
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract The alteration of bone metabolism in the femur of rats with skeletal unloading for 4 days was investigated. Skeletal unloading was designed using the model of hindlimb hang in rats. Skeletal unloading caused a significant decrease in femoral weight, calcium, and phosphorus contents in the metaphysis but not diaphysis. Also, the unloading induced a significant decrease of zinc content, alkaline phosphatase activity, and deoxyribonucleic acid (DNA) content in the femoral diaphysis and metaphysis. When the femoraldiaphyseal and metaphyseal tissues from normal and skeletal-unloading rats were cultured in the presence of insulin (10-9 and 10-8 M) for 24 hours in vitro, the hormonal effect to increase alkaline phosphatase activity and DNA content in the diaphysis, but not metaphysis, was lost in the bone tissues from unloading rats. However, the culture with insulin-like growth factor-I (IGF-I; 10-8 and 10-7 M) produced a significant increase of alkaline phosphatase activity and DNA content in both the diaphyseal and metaphyseal tissues from normal and unloading rats. These results demonstrate that skeletal unloading causes an impairment of insulin effect, but not IGF-I effect, on bone metabolism in femoral tissues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00299316
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  • 10
    Electronic Resource
    Electronic Resource
    Insulin and growth in chronic renal failure (1994)
    Springer
    Pediatric nephrology 8 (1994), S. 309-312 
    Details
    ISSN: 1432-198X
    Keywords: Glucose ; Insulin ; Growth ; Chronic renal failure ; Uremia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We studied glucose metabolism using the hyperglycemic technique in a cross-section of 23 children (15 pubertal, 8 prepubertal) with stable chronic renal failure as a possible cause of their poor growth. Linear growth was expressed as growth velocity standard deviation score (GVSDS). GVSDS correlated with glucose disposal rate but not with insulin sensitivity index in the pubertal (r=0.87,P〈0.001) and prepubertal (r=0.86,P〈0.02) children with chronic renal failure. Thirteen children were followed longitudinally during medical suppression of hyperparathyroidism with dietary phosphate restriction and high-dose phosphate binders. Following significant suppression of serum parathyroid hormone (PTH) levels back to the normal range (932±240 ng/l to 199±50 ng/l), GVSDS, glucose disposal rate and insulin secretion all increased significantly (P〈0.01), with no change in insulin sensitivity index and renal function. The changes in GVSDS correlated with the changes in glucose disposal rate (r=0.86,P〈0.02) and with the changes in insulin secretion (r=0.80,P〈0.01). However, the changes in GVSDS did not correlate with the changes in PTH. The hypothesis that insulin may be more important than PTH in the pathogenesis of growth failure in chronic renal disease deserves further investigation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00866344
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  • 11
    Electronic Resource
    Electronic Resource
    Survey on the pharmacodynamics of the new antipsychotic risperidone (1994)
    Springer
    Psychopharmacology 114 (1994), S. 9-23 
    Details
    ISSN: 1432-2072
    Keywords: Risperidone ; Antipsychotics ; 5-HT2 antagonism ; D2 antagonism ; Pharmacology ; Receptor binding ; Biochemistry ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review reports on the pharmacodynamics of the new antipsychotic risperidone. The primary action of risperidone is serotonin 5-HT2 receptor blockade as shown by displacement of radioligand binding (Ki: 0.16 nM), activity on isolated tissues (EC50:0.5 nM), and antagonism of peripherally (ED50: 0.0011 mg/kg) and centrally (ED50:0.014 mg/kg) acting 5-HT2 receptor agonists in rats. Risperidone is at least as potent as the specific 5-HT2 receptor antagonist ritanserin in these tests. Risperidone is also a potent dopamine D2 receptor antagonist as indicated by displacement of radioligand binding (Ki: 1.4 nM), activity in isolated striatal slices (IC50: 0.89 nM), and antagonism of peripherally (ED50: 0.0057 mg/kg in dogs) and centrally acting D2 receptor agonists (ED50: 0.056–0.15 mg/kg in rats). Risperidone shows all effects common to D2 antagonists, including enhancement of prolactin release. However, some central effects such as catalepsy and blockade of motor activity occur at high doses only. Risperidone is 4–10 times less potent than haloperidol as a central D2 antagonist in rats and it differs from haloperidol by the following characteristics: predominant 5-HT2 antagonism; LSD antagonism; effects on sleep; smooth dose-response curves for D2 antagonism; synergism of combined 5-HT2/D2 antagonism; pronounced effects on amphetamine-induced oxygen consumption; increased social interaction; and pronounced effects on dopamine (DA) turnover. Risperidone displays similar activity at pre- and postsynaptic D2 receptors and at D2 receptors from various rat brain regions. The binding affinity for D4 and D3 receptors is 5 and 9 times weaker, respectively, than for D2 receptors; interaction with D1 receptors occurs only at very high concentrations. The pharmacological profile of risperidone includes interaction with histamine H1 and α-adrenergic receptors but the compound is devoid of significant interaction with cholinergic and a variety of other types of receptors. Risperidone has excellent oral activity, a rapid onset, and a 24-h duration of action. Its major metabolite, 9-hydroxyrisperidone, closely mimics risperidone in pharmacodynamics. Risperidone can be characterized as a potent D2 antagonist with predominant 5HT2 antagonistic activity and optimal pharmacokinetic properties.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02245439
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  • 12
    Electronic Resource
    Electronic Resource
    Assessment of the labelling index of cohorts of the pancreatic islet cell population in phenobarbitone-treated male rats using a double immunohistochemical technique for 5-bromo-2′-deoxyuridine and pancreatic hormones (1994)
    Springer
    Archives of toxicology 69 (1994), S. 52-58 
    Details
    ISSN: 1432-0738
    Keywords: Key words Cell proliferation ; Pancreas ; 5-Bromo-2′-deoxyuridine (BrdU) ; Immunohistochemistry ; Hormones ; Insulin ; Glucagon ; Somatostatin ; Phenobarbitone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  A previous study demonstrated that administration of phenobarbitone to male AP Wistar rats for up to 7 days caused alterations in labelling indices (LIs) in several different tissues (including a reduction of the endocrine pancreas population LI) as determined by immunohistochemical visualisation of 5-bromo-2′-deoxyuridine (BrdU) incorporation into S-phase nuclei. The primary objective of this study was to determine whether treatment with phenobarbitone influenced the replicative states of specific cohorts of the islet (of Langerhans) cell population or generated a uniform depression of LI. Quantitation of the LIs of individual islet cell cohorts was achieved by utilisation of a dual immunohistochemical staining method for BrdU and islet hormones (insulin, glucagon and somatostatin) using a sequential peroxidase anti-peroxidase (PAP)/alkaline phosphatase anti-alkaline phosphatase (APAAP) method employing diaminobenzidine and New Fuchsin chromogens, respectively. We observed reductions, increases and no change in LIs of insulin-, glucagon- and somatostatin-positive cells, respectively. We conclude that the decreased LI of the insulin-positive cohort was not countered entirely by the LI increase in the glucagon-positive cohort due to the larger size of the former. Furthermore, the effects of phenobarbitone treatment are not manifested generally in the islet cell population but in the insulin- and glucagon-positive cohorts only. The causation of these effects is unknown but is likely to be due to enhanced carbohydrate and hormone metabolism. We believe that the visualisation and quantitation of replicating cells in specific hormone-positive cohorts of the islet cell population provide opportunities for understanding the influence of xenobiotics and disease processes on pancreatic function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002040050137
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  • 13
    Electronic Resource
    Electronic Resource
    Painfulness of needle and jet injection in children with diabetes mellitus (1994)
    Springer
    European journal of pediatrics 153 (1994), S. 409-410 
    Details
    ISSN: 1432-1076
    Keywords: Key words     Children ; Diabetes ; Insulin ; Jet injection ; Pain
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract      The aim of this study was to investigate whether insulin application by jet injector is less painful than by needle. Pain was scored by 41 diabetic and seven healthy volunteers after injections with both methods. Injections by jet were no less painful than those by needle but produced several local side-effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01983402
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  • 14
    Electronic Resource
    Electronic Resource
    Comparative studies on the dynamics of crosslinked insulin (1994)
    Springer
    European biophysics journal 23 (1994), S. 177-187 
    Details
    ISSN: 1432-1017
    Keywords: Molecular dynamics simulation ; Insulin ; Crosslinked insulin ; Single chain insulin ; Active conformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Molecular dynamics simulations were carried out on an insulin crosslinked between the N-terminal A chain and the C-terminal B chain to form a so-called mini-proinsulin: N α -A1-N ε -B29-diaminosuberoyl insulin (DASI). To investigate the influence of crosslinking on the dynamics of the insulin moiety, the bridge was removed from a transient DASI structure and simulation was carried on independently with the then unlinked (ULKI) as well as with the crosslinked species. The effects of crystal packing and quaternary interactions were checked by simulating both types of monomers and dimers known from the hexamer structure. All simulations were compared to previous ones of native insulin. DASI shows general similarity to the native simulations in most parts of the structure. Deviations are visible in the segments to which the bridge is directly connected, i.e. their flexibility is reduced. Upon removal of the bridge the ULKI simulations reapproach those of native insulin. The influence of the bridge spreads over the whole molecule, but all of its main structural features remain intact. The simulations suggest that the displacement of the C-terminal B chain of native insulin, considered important for receptor interaction, is prevented by the bridge, which also partially shields some binding residues. This is in accordance with the poor biological potency of A1-B29-crosslinked insulins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01007609
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  • 15
    Electronic Resource
    Electronic Resource
    Muscle phosphoglycerate mutase (PGAM) deficiency in the first Caucasian patient: biochemistry, muscle culture and31P-MR spectroscopy (1994)
    Springer
    Journal of neurology 241 (1994), S. 289-294 
    Details
    ISSN: 1432-1459
    Keywords: PGAM deficiency ; Myopathy ; Biochemistry ; Muscle culture ; 31P-MR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphoglycerate mutase (PGAM) deficiency has been so far identified in only six patients, five of these being African Americans. We report the results of clinical, morphological, biochemical, muscle culture and31P-MR spectroscopy studies in the first Caucasian patient with muscle PGAM deficiency. A 23-year-old man had a 10-year history of cramps after physical exertion with one episode of pigmenturia. Neurological examination and EMG study were normal. ECG and echocardiography revealed hypertrophy of the interventricular septum and slight dilatation of the left chambers of the heart. Muscle biopsy revealed increased glycogen content and some accumulation of mitochondria. Muscle PGAM activity was markedly decreased (6.5% and 9.7% of control value in two different biopsies). Citrate synthase and other mitochondrial respiratory chain enzyme activities were much higher than normal. In contrast to the marked decrease of PGAM activity observed in muscle biopsy, total enzyme activity in the patient's aneural muscle culture was normal, being represented exclusively by BB isoenzyme. The deficiency of PGAM-MM isoenzyme was reproduced in the patient's innervated muscle culture. Muscle31P-MR spectroscopy showed accumulation of phosphomonoesters only on fast “glycolytic” exercise. On “aerobic” exercise, Vmax, calculated from the work-energy cost transfer function, showed an increase consistent with the morphological and biochemical evidence of mitochondrial proliferation. This might represent a sort of compensatory aerobic effort in an attempt to restore muscle power.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00868435
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  • 16
    Electronic Resource
    Electronic Resource
    Glucose kinetics during prolonged exercise in euglycaemic and hyperglycaemic subjects (1994)
    Springer
    Pflügers Archiv 426 (1994), S. 378-386 
    Details
    ISSN: 1432-2013
    Keywords: Glucose oxidation ; Glucose infusion ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To determine the limits to oxidation of exogenous glucose by skeletal muscle, the effects of euglycaemia (plasma glucose 5 mM, ET) and hyperglycaemia (plasma glucose 10 mM, HT) on fuel substrate kinetics were evaluated in 12 trained subjects cycling at 70% of maximal oxygen uptake (VO2, max) for 2 h. During exercise, subjects ingested water labelled with traces of U-14C-glucose so that the rates of plasma glucose oxidation (R ox) could be determined from plasma 14C-glucose and expired 14CO2 radioactivities, and respiratory gas exchange. Simultaneously, 2-3H-glucose was infused at a constant rate to estimate rates of endogenous glucose turnover (R a), while unlabelled glucose (25% dextrose) was infused to maintain plasma glucose concentration at either 5 or 10 mM. During ET, endogenous liver glucose R a (total R a minus the rate of infusion) declined from 22.4±4.9 to 6.5±1.4 μmol/min per kg fat-free mass [FFM] (P〈0.05) and during HT it was completely suppressed. In contrast, R ox increased to 152±21 and 61±10 μmol/min per kg FFM at the end of HT and ET respectively (P〈0.05). HT (i. e., plasma glucose 10 mM) and hyperinsulinaemia (24.5±0.9 μU/ml) also increased total carbohydrate oxidation from 203±7 (ET) to 310±3 μmol/min per kg FFM (P〈0.0001) and suppressed fat oxidation from 51±3 (ET) to 18±2 μmol/min per kg FFM (P〈0.0001). As the rates of oxidation at more physiological euglycaemic concentrations of glucose were limited to 92±9 μmol/ min per kg FFM, and were similar to those reported when carbohydrate is ingested, the results of the current study suggest that the concentrations of glucose and insulin normally present during prolonged, intense exercise may limit the rate of muscle glucose uptake and oxidation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00388300
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    Electronic Resource
    Electronic Resource
    Structure-activity relationship of covalently dimerized insulin derivatives: correlation of partial agonist efficacy with cross-linkage at lysine B29 (1994)
    Springer
    Naunyn-Schmiedeberg's archives of pharmacology 350 (1994), S. 213-217 
    Details
    ISSN: 1432-1912
    Keywords: Insulin ; Dimerized insulin derivatives ; Insulin receptor antagonists ; Glucose transport ; 3T3-L1 cells
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The effects of 7 covalently dimerized insulin derivatives on glucose transport in differentiated 3T3-L1 cells were investigated. Symmetric cross-linkage at lysine B29 with a bridge of 2 (oxalyl), 8 (suberoyl) or 12 (dodecanedioyl) carbon atoms produced derivatives with essentially unaltered receptor binding affinity but largely reduced intrinsic activity. Regardless of the chain length, these derivatives inhibited the effect of submaximal insulin concentrations. Insulin derivatives cross-linked at phenylalanine 131 or asymmetrically at 131/1129 were full agonists of the insulin receptor. When lysine B29 was cross-linked with the inactive desoctapeptide(B23-B30)insulin at phenylalanine B1, the intrinsic activity of the resulting dimer was lower than that of insulin, but higher than that of the symmetric B29-dimers. It is concluded that linkage at the B29-lysines, and not at the B1-phenylalanine, leads to partial agonism of dimerized insulin derivatives, regardless of the length of the crosslinker.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00241099
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  • 18
    Electronic Resource
    Electronic Resource
    The effect of a ventral medial hypothalamic lesion on the insulin-induced hypotensive response in normal rats (1994)
    Springer
    Acta diabetologica 31 (1994), S. 91-97 
    Details
    ISSN: 1432-5233
    Keywords: Insulin ; VMH ; Cardiovascular response ; VMH lesion ; Blood pressure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The cardiovascular responses to insulin-induced hypoglycemia were studied in normal and ventral medial hypothalamic (VMH)-lesioned rats. The goal of this study was to investigate the role of the VMH in mediating the insulin-induced decreases in cardiovascular tone. Male Wistar rats were anesthetized with urethane/chloralose. Following the induction of anesthesia, the trachea, femoral artery, and femoral vein were cannulated. The femoral artery was attached to a pressure transducer for cardiovascular monitoring. The cardiovascular activity was recorded using a Modular Instruments Micro 5000 signal processing system. The mean arterial pressure and pulse pressures and heart rate were evaluated. In control studies, a stable plasma glucose and blood pressure were obtained with urethane/chloralose anesthesia for the duration of the experiments. Insulin (2.0 or 5.0 U/kg) significantly decreased the plasma glucose as well as the blood pressure. In VMH-lesioned rats, the lesions were accomplished by radiofrequency, and the cardiovascular response to insulin-induced hypoglycemia was investigated 1 or 6 weeks later. There was no difference in the cardiovascular response to insulin-induced hypoglycemia between the low or high insulin dose after 1 week in VMH-lesioned animals. The low dose after 6 weeks in VMH-lesioned animals did not produce a change in the mean arterial pressure response compared with controls. The pulse pressure was higher than in the sham-lesioned animals, and the plasma glucose response was greater. The high dose after 6 weeks in VMH-lesioned animals in contrast to sham-lesioned animals led to an increased cardiovascular response instead of a decrease. We propose that the decrease in cardiovascular activity in response to insulin-induced hypoglycemia in normal animals can be attributed to a direct or indirect effect on vascular dilation as well as possibly to an inhibition of sympathetic firing. However, it appears that insulin increases the vascular dilation as well as the parasympathetic tone after 1 week in the VMH-lesioned animals, similar to the findings in sham-lesioned animals. However, after 6 weeks, the insulin-induced decreased cardiovascular tone is minimal. Thus, we believe hat the VMH does not have a direct effect in modulating the insulin-induced decrease in cardiovascular tone, but its destruction appears to influence other regulatory centers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00570542
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  • 19
    Electronic Resource
    Electronic Resource
    Hypoxia and training-induced adaptation of hormonal responses to exercise in humans (1994)
    Springer
    European journal of applied physiology 68 (1994), S. 303-309 
    Details
    ISSN: 1439-6327
    Keywords: Catecholamines ; Insulin ; Growth hormone ; ACTH ; Erythropoietin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To establish whether or not hypoxia influences the training-induced adaptation of hormonal responses to exercise, 21 healthy, untrained subjects [26 (2) years, mean (SE)] were studied in three groups before and after 5 weeks' training (cycle ergometer, 45 min· day−1, 5 days· week−1). Group 1 trained at sea level at 70% maximal oxygen uptake ( $$\dot V$$ O2max), group 2 in a hypobaric chamber at a simulated altitude of 2500 m at 70% of altitude $$\dot V$$ O2max, and group 3 at a simulated altitude of 2500 m at the same absolute work rate as group 1. Arterial blood was sampled before, during and at the end of exhaustive cycling at sea level (85% of pretraining of $$\dot V$$ O2max). $$\dot V$$ O2 increased by 12 (2)% with no significant difference between groups, whereas endurance improved most in group 1 (P 〈 0.05). Training-induced changes in response to exercise of noradrenaline, adrenaline, growth hormone, β-endorphin, glucagon, and insulin were similar in the three groups. Concentrations of erythropoietin and 2,3-diphosphoglycerate at rest did not change over the training period. In conclusion, within 5 weeks of training, no further adaptation of hormonal exercise responses takes place if intensity is increased above 70% $$\dot V$$ O2max. Furthermore, hypoxia per se does not add to the training-induced hormonal responses to exercise.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00571448
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  • 20
    Electronic Resource
    Electronic Resource
    Insulin synthesis in chick embryo retinas during development (1994)
    Springer
    Neurochemical research 19 (1994), S. 821-825 
    Details
    ISSN: 1573-6903
    Keywords: Insulin ; chick embryo ; retina ; development ; HPLC analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Retinas of chick embryos contain insulin (1) and further, are capable of synthesizing it, as demonstrated by incubating retinas at different ages (7th–18th day) with [3H]leucine. The synthesized radioactive insulin was isolated and assayed by means of a HPLC procedure. The synthesis of insulin was found to be highest in the youngest retinas studied (day 7), afterwards it declined with age except for an increment found at 14–15 day. Explants of chick embryo retinas, cultured in vitro, rapidly degraded insulin. Nevertheless, the content of immunoreactive insulin in retinal explants diminished slowly with the age of culture, so that, after 8 days of incubation, it was about 60% of the content found in the retinas at the beginning of incubation. This was proof that cultured explants are capable of efficiently synthesizing insulin. The synthesized [3H]insulin was released from explants into the medium. This was evident also after 6–8 days in culture.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00967450
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  • 21
    Electronic Resource
    Electronic Resource
    Insulin family growth factors have specific effects on protein synthesis in preimplantation mouse embryos (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Molecular Reproduction and Development 37 (1994), S. 398-406 
    Details
    ISSN: 1040-452X
    Keywords: Preimplantation embryo ; Insulin ; IGFs ; Protein synthesis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Previously constructed protein databases for two stages of preimplantation mouse embryogenesis, the compacted eight-cell stage and the fully expanded blastocyst stage, have been used to analyze the effects of insulin, IGF-I, and IGF-II on protein synthesis in these developmental stages. Proteins were labeled by placing, for 2 hr, synchronous cohorts of 35-50 embryos into human tubal fluid (HTF) medium containing L-[35S]-methionine (1 mCi/ml) in the presence or absence of one of the growth factors. The embryos were then washed with medium and lysed. Samples were processed for 2-D gel analysis. For each embryonic stage and each growth factor, four or five experimental replicates were done and the gel images were compared using the PDQUEST system. Using the computer-assisted analysis, we were able to identify proteins that showed a statistically significant (P 〈 0.05) change in synthesis. At the eight-cell stage of development insulin caused increased synthesis of two proteins and decreased synthesis in three proteins. Insulin-treated blastocyst stage embryos exhibited an increased synthesis in eight proteins and decreased synthesis for one protein. The effect of IGF-I at the eight-cell stage of development was mostly inhibitory; the synthesis of only one protein increased and the synthesis of five proteins showed a decrease. Similar results were obtained with blastocyst stage embryos; four proteins demonstrated an increase in synthesis while 14 proteins showed a decrease. Eight-cell stage embryos incubated with IGF-II had seven proteins with a decreased synthesis, although in blastocyst stage embryos, nine proteins showed increased synthesis. However, seven IGF response proteins were found to be proteins that showed significant changes in isotope incorporation during the eight-cell to blastocyst stage of development (Shi et al., 1993). In all, 54 proteins were affected, and these were unique; thus, protein synthesis in preimplantation mouse embryos is influenced by insulin and the IGFs, and further, each growth factor affects specific proteins. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrd.1080370406
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  • 22
    Electronic Resource
    Electronic Resource
    Morphological effects of diabetes on the granular ducts and acini of the rat submandibular gland (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Microscopy Research and Technique 27 (1994), S. 61-70 
    Details
    ISSN: 1059-910X
    Keywords: Salivary gland ; Diabetes ; Insulin ; Electron microscopy ; Streptozotocin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Natural Sciences in General
    Notes: Effects of experimental diabetes on rat submandibular glands have been documented, but earlier reports suggested that diabetes caused an extensive cellular degeneration and a replacement of the parenchymal cells by fibrous connective tissue. Such observations, however, are difficult to reconcile with the relatively normal physiological responsiveness of the gland (Anderson and Suleiman, 1989). This study, therefore, reexamined the histological, histochemical and ultrastructural effects of streptozotocin-induced diabetes on rat submandibular glands. The tissues were examined at 3 weeks, and 3 and 6 months after the induction of diabetes, and compared with glands from age-matched controls by both light and electron microscopy. Light microscopically, the proportional volumes of the acini and granular ducts remained constant in control rats at about 48% and 38% respectively. In diabetic animals the volume density of the acini increased progressively to 62%, whereas that of the granular ducts decreased to 20%. The diameter and number of granular ducts were reduced in diabetic animals, but acinar cell profile area was only affected 6 months after the induction of diabetes. Ultrastructurally, there was an accumulation of lipid in the acinar cells and, with increasing duration of diabetes, the number of autophagic structures in both the acini and the granular ducts increased. Although there was evidence of some cellular degeneration it was never excessive. Morphometry showed that the volume density of secretory granules within the acinar cells was unaffected, but there was a significant reduction in the volume density of secretory granules within the granular ducts. Thus, in the rat submandibular gland the greatest effect of streptozotocin-induced diabetes was to cause hypotrophic changes in the cells of the granular ducts. The relative contributions of a direct effect of insulin insufficiency and the hypogonadal effects of diabetes, however, are not known. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jemt.1070270105
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  • 23
    Electronic Resource
    Electronic Resource
    Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 12-22 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150103
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  • 24
    Electronic Resource
    Electronic Resource
    Newton-Raphson optimization of the explicitly correlated Gaussian functions for calculations of the ground state of the helium atom (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 54-60 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150107
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  • 25
    Electronic Resource
    Electronic Resource
    General parameterization of a reaction field theory combined with the boundary element method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 90-104 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150111
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  • 26
    Electronic Resource
    Electronic Resource
    Conformation and reactivity of α-oxo-ketenes: Ab initio and semiempirical (AM1, PM3) calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 132-143 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150203
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  • 27
    Electronic Resource
    Electronic Resource
    Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 200-207 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150210
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  • 28
    Electronic Resource
    Electronic Resource
    A ring-bracing approach to computer-assisted ligand design (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150213
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  • 29
    Electronic Resource
    Electronic Resource
    Force field calculations (MM3) on glyoxal, quinones, and related compounds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 251-268 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150302
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  • 30
    Electronic Resource
    Electronic Resource
    A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 313-321 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Effective core potential (ECP) and full-electron (FE) calculations for MoS4-2, MoO4-2, and MoOCl4 compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo—L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo—L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150306
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  • 31
    Electronic Resource
    Electronic Resource
    Ab initio study of low-lying electronic states of the PF2 radical (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 346-350 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150309
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  • 32
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150310
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  • 33
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    Transferable semiempirical quadratic force fields: The case of polythiophene and shorter oligomers (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 405-423 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150405
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    Announcements (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 475-475 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150411
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    On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 507-523 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast computer algorithm is presented for complete analytical calculation of van der Waals surfaces and volumes. Connolly's analytical algorithms, computing second- and third-order atomic spheres overlaps, are shown to give insufficient numerical approximations of the exact van der Waals surfaces and volumes. The presented algorithm computes overlaps of any order. Practical situations frequently involve six-order overlaps. Analytical computed surfaces and volumes of 63 chemicals are compared with Monte Carlo measured values. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 36
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    ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 488-506 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150601
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  • 38
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    Direct search methods for the molecular conformation problem (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 627-632 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150606
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  • 39
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    Triazene proton affinities: A comparison between density functional, Hartree-Fock, and post-Hartree-Fock methods (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 875-892 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high-level Hartree-Fock and Møller-Plesset (MP) calculations for triazene (HN=NNH2) and formyl triazene (HN=NNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
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  • 40
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    Cluster analysis of molecular conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 899-916 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150811
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    D-CICADA: A software for conformational PES elucidation on network of workstationsThis work is dedicated to Professor M. Kratochvíl on the occasion of his seventieth birthday. (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 937-946 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low-energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D-CICADA, and results have been compared to those of the sequential version. D-CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150904
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  • 42
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    Long-time overdamped Langevin dynamics of molecular chains (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 997-1012 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a novel algorithm of constrained, overdamped dynamics to study the long-time properties of peptides, proteins, and related molecules. The constraints are applied to an all-atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high-frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 103 times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150908
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    Decomposition analyses of the intermolecular interaction energies in two π—π stacking complexes: Quinhydrone and N,N,N′, N′-tetramethyl-P-diaminobenzene-chloranil complex (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1013-1018 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′-tetramethyl-p-diaminobenzene-chloranil complex, the stacking conformations are different from each other. The former prefers the half-stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150909
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  • 44
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    A force field for monosaccharides and (1 → 4) linked polysaccharides (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1019-1040 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10-12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water-saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D-glucose and D-mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D-glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150910
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  • 45
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    A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1302-1310 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC-SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier-crossing ability of large-step Monte Carlo. Using calculations on double-well potentials and long simulations (108 steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n-pentane, we find that MC-SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n-pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151111
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  • 46
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    Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1321-1330 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 14 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540151202
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    A variational biorthogonal valence bond method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1357-1364 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The details of a simple and efficient scheme for performing variational biorthogonal valence bond calculations are presented. A variational bound on the energy functional is obtained through the use of a complete configuration expansion in a well-chosen subset of orbitals. The resultant wave functions are clearly dominated by the covalent (spin-coupled) structures, with a negligible contribution from ionic structures. The orbitals obtained compare favorably with overlap enhanced atomic orbitals obtained by other valence bond approaches. The method is illustrated by calculations on water and dioxygen difluoride. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151205
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  • 48
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    Stability of two-dimensional crystalline aggregates of a protein studied by molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151109
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  • 49
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    Linear dependency in the refinement of force constants with the Jacobian method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1291-1301 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Jacobian method in the refinement of force constants is studied. Theoretical and experimental frequencies and other observables, νs, are matched by minimizing ΣsWs(νsexp - νsth)2, where s = 1, 2, 3,…, proceeds over all normal modes and isotopes, and Ws are weighting factors. Modification of the theoretical frequencies is accomplished with the Jacobian matrix, J, with elements Jsi = ∂νs/∂ki involving each force constant or associated parameter, ki, i = 1, 2, 3,…, by Δν = JΔk. The parameters are adjusted directly with Δk = (JTWJ)-1(JW) Δν, where W is a diagonal matrix which weights the frequencies. The linear dependence problem must be addressed prior to inversion of JTWJ. The approach entails diagonalization of JT WJ, analysis of the components of the eigenvectors associated with zero and small eigenvalues, identification of the linearly dependent parameters, successive elimination of selective parameters, and a repeat of this procedure until linear dependency is removed. The Jacobian matrices are obtained by differencing the frequencies when the parameters are varied and by numerical and analytical evaluation of the derivative of the potential. The unitary transformation, U, used to calculate J = UT (∂F/∂k)U or J = UT (ΔF/Δk)U, is obtained from the diagonalization of the Hessian, Fmn = ∂2ν/∂pm∂qn, where p, q = x, y, z are the Cartesian coordinates for atoms m, n = 1, 2, 3,…, at the initial value of ki, i = 1, 2, 3,⃜ The accuracy of and the ability to evaluate the Jacobian matrix by these methods are discussed. Applications to CH4, H2CO, C2H4, and C2H6 are presented. Linearly dependent and ill-conditioned parameters are identified and removed. The procedure is general for any observable quantity. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151110
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  • 50
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    Algorithms for clustering molecular dynamics configurations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1331-1340 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151203
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    Application of a high-performance, special-purpose computer, GRAPE-2A, to molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1372-1376 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151207
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    Hydrating peptides using a sprouting technique (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 23-27 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X-PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley & Sons, Inc.
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    Simulations of the solution structure of HIV-1 protease in the presence and absence of bound zinc (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 61-71 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Zinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV-1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion-protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV-1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn+2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150108
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  • 54
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    Electronic Resource
    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150201
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    Parallel algorithm for calculating ro-vibrational states of diatomic molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 144-148 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we develop and implement an algorithm for calculating the rovbrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p-version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150204
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    Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 162-182 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150207
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    Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 28-43 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher-order multipole moments. The second is an acceleration of the calculations by the particle-particle and particle-mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1-1 kcal/mol, much smaller than the 30-kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150105
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    Canonical numerical methods for molecular dynamics simulations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 72-79 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We consider the application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard-Jones interaction potential. To accomplish this comparative study of canonical and noncanonical integrators, we computed thermodynamic and structural quantities. Our results indicate that noncanonical methods, with one exception, fail miserably to conserve energy and as a consequence give poor estimates of the other quantities. Also, higher-order canonical methods may offer an advantage over the Störmer/Verlet method. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150109
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    Free energy derivatives: A new method for probing the convergence problem in free energy calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 105-123 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration-type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window-type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150112
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    Free energy of solvation of a small Lennard-Jones particle (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 149-154 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular dynamics (MD) and Monte Carlo (MC) free energy calculations, the choices of the thermodynamic paths from state a to state b affect the accuracy of the result and the efficiency of the programs. Most of the problems occur at the initial stages of growing in a new particle into a solvent. Based on statistical mechanical perturbation theory, an accurate and efficient direct calculation of inserting a small Lennard-Jones particle into solvent is derived. This eliminates the need for calculation of the initial stages of growing in a new particle by MD or MC simulation. Examples are given to show the utility of direct calculation. The recommended procedure is to use direct calculation for a small Lennard-Jones particle and then use MD or MC simulations to calculate the ΔG of changing the small Lennard-Jones particle into the target molecule. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150205
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    Preconditioners for distance matrix algorithms (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 227-232 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A recent gradient algorithm in nonlinear optimization uses a novel idea that avoids line searches. This so-called spectral gradient algorithm works well when the spectrum of the Hessian of the function to be minimized has a small range or is clustered. In this article, we find a general preconditioning method for this algorithm. The preconditioning method is applied to the stress function, which arises in many applications of distance geometry, from statistics to finding molecular conformations. The Hessian of stress is shown to have a nice block structure. This structure yields a preconditioner which decreases the amount of computation needed to minimize stress by the spectral gradient algorithm. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150212
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    Conformational sampling of hydrocarbon and lipid chains in an orienting potential (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 208-226 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Distribution Biased Monte Carlo (DBMC) sampling procedure is developed for the efficient generation of chain conformations in the oriented environment of lipid membranes and other liquid crystalline systems. Conformations of the sn-1 chain of dipalmitoyl phosphatidylcholine (DPPC) were generated by independently sampling torsion angles from continuous distributions in an orienting potential based on a Marcelja mean field; depending on the chain position, the convergence in the deuterium order parameters (SCD) was 100 to 3000 times more efficient with DBMC than with Brownian dynamics. Optimization using joint distribution and torsional potentials of mean force yielded a further threefold increase in sampling efficiency. Overall chain tilt was included using Euler angle rotations and a separate field strength for the anchor. A segmental DBMC procedure was used to generate a set of complete DPPC conformations with well-converged conformationally averaged SCD consistent with experimental values. These conformations show considerable flexibility, not only in the hydrocarbon tails, but additionally in both the glycerol and head-group portions of the lipid. An appendix compares DBMC with a number of other Monte Carlo and stochastic dynamics algorithms using the example of a bistable oscillator, and illustrates the tuning of parameters for optimal convergence. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150211
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    Molecular simulation of alkyl boronic acids: Molecular mechanics and solvation free energy calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 333-345 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics force-field parameters for alkyl boronic acids. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150308
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150401
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    Modulation of intramolecular proton transfer by electronic excitation and environment: 2-Pyridone as a case study (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 395-404 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150404
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    MRD-CI studies of vertical excitation energies of unsaturated hydrocarbon molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 424-432 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Systematic MRD-CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet-singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO-3G results. On an absolute scale, the AM1/MRD-CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between -1.0 and 1.0 eV. The STO-3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ-correlation effects through second-order Epstein-Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150406
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150501
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    New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 524-531 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150505
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    A truncated Newton minimizer adapted for CHARMM and biomolecular applications (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 532-552 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the adaptation of the truncated Newton minimization package TNPACK for CHARMM and biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate-gradient technique for solving the Newton equations. The structure of the problem - sparsity of the Hessian - is exploited for preconditioning. Experience with the new version of TNPACK is presented on a series of molecular systems of biological and numerical interest: alanine dipeptide (N-methyl-alanyl-acetamide), a dimer of N-methyl-acetamide, deca-alanine, mellitin (26 residues), avian pancreatic polypeptide (36 residues), rubredoxin (52 residues), bovine pancreatic trypsin inhibitor (58 residues), a dimer of insulin (99 residues), and lysozyme (130 residues). Detailed comparisons among the minimization algorithms available in CHARMM, particularly those used for large-scale problems, are presented along with new mathematical developments in TNPACK. The new TNPACK version performs significantly better than ABNR, the most competitive minimizer in CHARMM, for all systems tested in terms of CPU time when curvature information (Hessian/vector product) is calculated by a finite-difference of gradients (the numeric option of TNPACK). The remaining derivative quantities are, however, evaluated analytically in TNPACK. The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10-8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150506
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    Direct one-index transformations in multiconfiguration response calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 573-579 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The evaluation of gradient vectors of a general operator with one-index, double-one-index, or higher-order one-index transformed integrals is a key operation in multiconfiguration response theory calculations. We describe an integral-driven direct algorithm that carries out this operation efficiently without pretransforming the integrals. The use of this algorithm leads to a considerable reduction in disk space and timing. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150602
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    Interaction between carbon dioxide and naphthalene: A molecular modeling approach (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 580-587 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The formation of a charge-transfer complex between carbon dioxide and naphthalene was studied using a molecular modeling program, with the aim of studying the solubility of naphthalene in supercritical carbon dioxide. The orbitals involved in the formation of the complex were studied using MINDO/3 as the semi-empirical method. A solvent cage was constructed, and the maximum number of carbon dioxide molecules to surround naphthalene was found to be 20. The heat of interaction of the complex was obtained using MINDO/3. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150603
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    Atomic orbital basis sets for molecular interactions (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 653-661 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a general approach to the parametrization of linear combinations of Gaussian atomic orbitals, useful for atomic and molecular interactions. We use a Gaussian transform method and Gauss-Legendre quadratures to express hydrogenic atomic orbitals, with varying effective charges, in terms of Gaussian-type orbitals. This procedure provides well-defined rules for calculating exponent factors and combination coefficients of the linear combinations of Gaussians in problems where nuclear distances may vary over large ranges during interactions. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150609
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150701
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    Internal dynamics of a globular protein under external force field (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 684-703 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The inelastic neutron-scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low-frequency internal dynamics, 〈 200 cm-1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron-derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150703
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    Fast geometry optimization using a modified extended Hückel method: Results for molecules containing H, C, N, O, and F (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 733-746 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi-Newton Broyden-Fletcher-Goldfarb-Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree-Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150706
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  • 76
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    High-precision atomic computations from finite element techniques: Second-order correlation energies for Be, Ca, Sr, Cd, Ba, Yb, and Hg (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 782-790 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have applied the FEM-MP2 method (an implementation of the p-version finite element technique within the framework of second-order Møller-Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second-order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed-shell elements. The FEM-MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 10 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150710
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  • 77
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    Analysis of the ring-form tautomers of psicose with MM3 (92) (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 561-570 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By nuclear magnetic resonance (NMR), the four ring forms of psicose, α-and β-pyranose and α- and β-furanose, have almost equal concentrations in aqueous solution. Prediction of this equilibrium by molecular mechanics tests both the balance within the force field and the methods for including the many degrees of freedom in the system. For both the α- and β-furanoses, each of 410 different ring shapes was studied in combination with 37 combinations of staggered side-group orientations. Of these, 48 and 57 initial combinations of side-group orientations contributed to the α- and β-furanose energy surfaces. The pyranoses were analyzed in two steps. First, the 38 characteristic ring conformations were optimized with the 63 staggered side-group combinations. All combinations that gave the lowest energy at one or more of the 38 shapes (20 combinations for α-pyranose, 15 for β-pyranose) were then optimized with 4912 different ring forms. Ring conformations were generated by fixing nonadjacent ring atoms (two for furanose rings, three for pyranoses) at increments of 0.1 Å from the plane of the remaining three atoms. At a dielectric constant of 4.0, prediction was in fair agreement with the NMR results. Model northern and southern conformers contribute to the furanose equilibrium, and both chairs are important for α-psicopyranose. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150508
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    Application of genetic algorithms in molecular modeling (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 588-595 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150604
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  • 79
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    New implementation of a program to calculate correlated band structures of polymers: An application to the band structure of polyparaphenylene (PPP) (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 814-819 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program has recently been implemented with the aim of extending quasi-particle (QP) band structure calculations to polymers with larger unit cells. The theoretical background is briefly reviewed and the new algorithm described, which has been optimized for machines with vector processors. To illustrate the usefulness of this technique, calculations have been performed on polyparaphenylene (PPP) using a double-zeta basis set. The calculated QP band gap between the valence and conduction bands is 2.3 eV, which compares favorably with the experimental value of 2.8 eV. The self-consistent field (SCF) result with the same double-zeta basis set is 8.7 eV. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150803
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  • 80
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    Explicitly correlated Gaussian functions with r122n factors for calculations of the ground state of the helium atom (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 893-898 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions with r122n exp( - βr122) factors have been used in variational calculations of the ground state of the helium atom. Additional correlation factors in the form of even powers of rij were introduced to the Gaussian functions with exponential correlation components by differentiating these functions with respect to the correlation exponent β. The algorithm of this method and its computational implementation is described. A number of calculations were performed for the ground state of helium atom to test the performance of the basis sets comparising different numbers of the Gaussians with the exp( - βr122) and r122 exp( - βr122) correlation factors. The numerical results indicate that including functions with r122 factors does not lead to improved results, contrary to what was anticipated initially. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150810
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  • 81
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150901
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  • 82
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    Structure of disiloxane: A semiempirical and Post-Hartree-Fock study (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 925-936 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The semiempirical (MNDO, AM1, and PM3) and ab initio predicted structure of disiloxane is studied with a series of basis sets and inclusion of electron correlation at MP2, MP3, MP4, CCD, CCSD, and CCSD(T) levels. The calculated molecular geometry and barrier to linearization of the Si—O—Si bond angle are compared with previous theoretical and experimental values. Our results show that the calculated barrier to linearization is very sensitive to the number of polarization functions in the basis set. We also investigate the coupling between the Si—O—Si bond angle and the Si—O bond length and calculate the Mulliken and electrostatic potential-derived charges. For comparison purposes we also calculate the molecular geometry, the barrier to linearization of the Si—O—Si bond angle, and the atomic charges in hexamethyldisiloxane. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150903
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  • 83
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    Principal component analysis of dipeptides (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 963-980 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Principal component analysis applied to a set of dipeptides illustrates how changes in families of parameters act in concert to produce overall molecular structural changes. Principal component analysis is an eigenvalue-eigenvector analysis whereby the parametric sensitivity coefficient matrix is manipulated to produce weighted principal components, which reveal the variant and invariant directions in the parameter space. This analysis summarizes the sensitivity results by revealing interdependence among the parameter values with regard to their role in controlling the molecular structure. An analysis of the principal components reveals hidden relationships among the parameters. Thus, those parameters, which were thought to be of controlling significance with respect to the molecular structure, may, in fact, not be (or vice versa) due to cooperative parametric interactions; as a result, the parameters of significance in a sequence of dipeptides are identified. In general, for the dipeptides studied, there is mutual exclusion of dominant parameters between the sets of invariant and variant eigenvectors. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150906
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  • 84
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    Application of the multiple computer automated structure evaluation methodology to a quantitative structure-activity relationship study of acidity (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1041-1050 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We applied the Multiple Computer Automated Structure Evaluation (Multi-CASE) program to the analysis of the relationship between the structure of 2464 organic acids and their (first) pKa values. By using the self-created expert dictionary of molecular attributes pertinent to acidity, the program could make successful a priori prediction of the acidity of new organic compounds. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150911
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  • 85
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    Conformational sensitivity analysis of FKBP-FK506/rapamycin complexes (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1074-1090 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Sensitivity analysis techniques are applied to the FKBP-FK506 and FKBP-rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the φ, ψ, and χ1 torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151004
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  • 86
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    Incorporation of bond-length constraints in Monte Carlo simulations of cyclic and linear molecules: Conformational sampling for cyclic alkanes as test systems (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1121-1126 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple method for incorporating bond-length constraints in Monte Carlo simulations of cyclic and linear molecules is described. As an example, the conformational behavior of five even-numbered cyclic alkanes is studied using Monte Carlo simulation and the MM2 force field. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151008
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  • 87
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    The use of Fraga's potential with AM1 atomic point charges in the evaluation of spectral shifts: Application to TICT molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1139-1150 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fraga potential calculations with atomic point charges and geometrical parameters calculated from AM1 calculations have been used to calculate spectral shifts upon electronic excitation in twisted intramolecular charge transfer (TICT) systems due to intermolecular interactions. Changes of atomic polarizabilities have also been taken into account. Present calculations deal with absorption transitions of the p-N,N-dimethylaminobenzonitrile (DMABN) surrounded by methane, water, acetone, or acetonitrile solvent molecules. The methodology permits us to evaluate the influence of the solvent molecule on DMABN dimethylamino motions and to find the most stable conformation of a cluster configuration which can lead to a blue or red shift. The results have been compared with the experimental work of Warren et al.7 and confirm their analysis. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151010
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  • 88
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    Force field for computation of conformational energies, structures, and vibrational frequencies of aromatic polyesters (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 752-768 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A CFF931 all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150708
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  • 89
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    Expanding molecular dynamics simulations to the NMR time scale. I. Studies of conformational interconversions of 1, 1-difluoro-4, 4-dimethylcycloheptane using MM3-MD (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 769-781 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1-difluoro-4,4-dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist-chair 〈 twist-boat 〈 twist-chair) were not observed. The axial-equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2-like rotations, where C2-like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2-like axis in the simulated process, mostly because the C2-like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2-like symmetry of the twist-chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial-equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial-equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150709
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  • 90
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    Hybrid Monte Carlo: An efficient algorithm for condensed matter simulation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 838-846 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150805
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  • 91
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    An optimized AM1/MST method for the MST-SCRF representation of solvated systems (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 847-857 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water-induced dipoles computed at the 6-31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150806
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  • 92
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151101
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  • 93
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    Gaussian multipoles in practice: Electrostatic energies for intermolecular potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1187-1198 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented for calculating the total electrostatic interaction energies between molecules from ab initio monomer wave functions. This approach differs from existing methods, such as Stone's distributed multipole analysis (DMA), in including the short-range penetration energy as well as the long-range multipolar energy. The monomer charge densities are expressed as distributed series of atom-centered functions which we call Gaussian multipoles; these are analogous to the distributed point multipoles used in DMA. Our procedure has been encoded in the GMUL program. Calculations have been performed on the formamide/formaldehyde complex, a model system for N—H … O hydrogen bonding in biological molecules, and also on guanidinium/benzene, modeling amino/aromatic interactions in proteins. We find that the penetration energy can be significant, especially in its contribution to the variation of the electrostatic energy with interaction geometry. A hybrid method, which uses Gaussian multipoles for short-range atom pair interactions and point multipoles for long-range ones, allows the electrostatic energies, including penetration, to be calculated at a much reduced cost. We also note that the penetration energy may provide the best route to an atom-atom anisotropic model for the exchange-repulsion energy in intermolecular potentials. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151102
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  • 94
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    Reversed stereochemical preference in binding of Ro 31-8959 to HIV-1 proteinase: A free energy perturbation analysis (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1241-1253 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ro 31-8959 is a highly potent inhibitor of HIV-1 proteinase in phase III clinical trials for treatment of AIDS. It is also the first subnanomolar inhibitor that demonstrated reversed stereochemical preference at the central hydroxyl group. Free energy perturbation calculations have been carried out to rationalize the preference for the R-diastereomer by consideration of two models of the (weaker) S-diastereomer. In the first model, the central hydroxyl group makes only one hydrogen bond with the active site aspartates, whereas the hydroxyl group in the second model makes at least three strong hydrogen bonds. Using the first model, the free energy difference in binding of Ro 31-8959 and its S-diastereomer is calculated to be 3.4 kcal/mol, which is in close agreement with the experimental value. Although the second model has a more favorable interaction with the active site aspartates compared to the first model, it has a higher energy N-axial conformation at the decahydroisoquinoline group in P1′. We show here that the two contributions cancel each other and the two models of S-diastereomer are predicted to have equivalent binding. The stereochemical preference in a hydroxyethylamine series of inhibitors appears to be affected by both intermolecular and intramolecular (conformational) energies. The binding data on the proline containing inhibitors are rationalized based on these results. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151106
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  • 95
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    Algorithm to infer the structures of molecular formulas within a reaction pathway (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1266-1277 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MECHEM is a computer aid for elucidation of reaction pathways that was developed over the last 5 years. The program searches systematically and comprehensively for the simplest multistep reaction pathways (or mechanisms) that are consistent with the experimental constraints formulated by the experimentalist, any ad hoc assumptions, and the program's internal theory. Previous articles have reported the basic pathway-generation algorithm and another algorithm that tests the structural soundness of individual steps. This article introduces an algorithm to solve another basic problem: Given a multistep pathway containing a mixture of molecular structures and formulas, assign possible structures to the formulas while obeying (and exploiting) the constraint imposed by the pathway steps. With this new algorithm, MECHEM is now approaching competence as an interactive tool for elucidating some catalytic reaction pathways, which is the current chemical focus. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151108
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  • 96
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    Electronic Resource
    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151201
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  • 97
    Electronic Resource
    Electronic Resource
    Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1311-1318 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential7 was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151112
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  • 98
    Electronic Resource
    Electronic Resource
    Variational biorthogonal valence bond descriptions of 1,3-dipoles (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1365-1371 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The variational biorthogonal valence bond method is applied to the π-electrons of six 1,3-dipoles (CH2N2, HCNO, CH2NHO, N2O, O3, NO2). The results are compared with those from other valence bond techniques, including a detailed comparison with the spin-coupled valence bond approach. For CH2N2, HCNO, CH2NHO, and N2O, zwitterionic structures are predicted and it is shown that the variational biorthogonal valence bond method leads to orbitals and configuration weights which are essentially indistinguishable from those of the spin-coupled valence bond method. However, for O3 and NO2 the techniques give contradictory results. The biorthogonal valence method predicts O3 and NO2 to be spin-paired diradicals. Evidence from other calculations on O3 is discussed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151206
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  • 99
    Electronic Resource
    Electronic Resource
    Ab initio study of some CH3OCXYCH2 radicals: The influence of anomeric effects on their structure and their stability (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1341-1356 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized equilibrium geometries and rotational transition structures for CH3OCH XCH2 (X = H, F, CH3, NH2) and CH3OCF2CH2 radicals are obtained by using unrestructed Hartree-Fock (UHF) and second-order Møller-Plesset perturbation (UMP2) theory; a standard 6-31G* basis set is used for geometry optmizations; single-point energies for all stable rotamers are obtained at the UMP4/6-31 + G*//UMP2/6-31G* level. By analysis of rotamers, it is apparent that an anomeric effect exists for X = F and to a lesser extent for X = NH2. Several isodesmic reactions have been studied for the purpose of obtaining theoretical heats of formation and stabilization energies (SE) of these β substituted radicals and their α isomers; the examination of computed SE shows that in the case of CH3OCHFCH2 and CH3OCF2CH2 radicals, a significant extra stabilization induced by the anomeric effect occurs. The question of nO → σCX* negative hyperconjugation in β-substituted radicals was explored with the aid of natural bond orbital (NBO) energetic analysis; it appears that nO → σCF* delocalization plays a predominant role in the conformational preference and stabilization of β fluoro derivatives; on the other hand, the stabilization arising from the oxygen lone pair into the σCN(H2)* orbital does not appear to be the key factor in the conformational preference of the CH3OCHNH2CH2 radical. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151204
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  • 100
    Electronic Resource
    Electronic Resource
    An algorithm for packing regular multistrand polypeptide structures by energy minimization (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1414-1428 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum-energy regular structures of three-stranded (L-Ala)8, three-stranded (L-Val)6, five-stranded (L-Ile)6, and the regular and truncated three-stranded (Gly-L-Pro-L-Pro)4 triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151211
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