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  • 1990-1994  (182)
  • 1965-1969
  • 1860-1869
  • 1991  (182)
  • Biochemistry  (158)
  • Insulin
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular life sciences 47 (1991), S. 270-272 
    ISSN: 1420-9071
    Keywords: Insulin ; potassium ; hyperkalemia ; portal vein ; glucose
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The effect of hyperkalemia on insulin secretion remains undefined. We evaluated portal and peripheral insulin levels in anesthetized dogs after infusions of KCl. The mean maximal increase in peripheral plasma potassium at infusion rates of 0.2 mEq/kg/h was 0.68±0.20 mEq/l. There were no significant increases in either portal or peripheral insulin levels. In contrast, in six dogs whose plasma potassium concentration increased in each case by more than 2.0 mEq/l (infusion rate of 0.5 mEq/kg/h), portal insulin levels increased fivefold (p〈0.05). We conclude that only marked increases in plasma potassium concentration stimulate pancreatic insulin secretion.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular medicine 69 (1991), S. 31-36 
    ISSN: 1432-1440
    Keywords: (D-)ribose ; Glucose ; Insulin ; C-peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary D-ribose was given orally and/or intravenously to nine healthy subjects at doses ranging from 83.3 to 222.2 mg/kg per hour for at least four hours. The serum ribose level increased in a dose-dependent manner to maximum concentrations of 75 to 85 mg/dl. The serum glucose level decreased after the beginning of continuous ribose administration and was reduced as long as ribose was being administered. The oral or intravenous administration of 166.7 mg/kg per hour of ribose resulted in a 25% decrease in serum glucose. Higher intravenous doses of ribose did not provoke a further decrease in serum glucose concentration. Oral administration of 166.7 mg/kg per hour led to an increase in serum insulin concentrations from a mean of 8.4 (range 6.4–11.5) to 10.4 (range 6.3–15.4) μU/ml (p〈0.05). In contrast, intravenous administration did not change serum insulin concentrations significantly. The serum c-peptide concentration remained unchanged regardless of treatment. We conclude that the variations in plasma insulin concentrations do not account for the observed decrease in mean serum glucose concentrations accompanying D-ribose administration.
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  • 3
    ISSN: 1432-0428
    Keywords: Insulin ; glucose ; obesity ; glucose disposal ; insulin secretion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Insulin responses to intravenous glucose infusion and glucose utilization during hyperinsulinaemic euglycaemic clamp were determined in a large homogeneous group of 65-year-old male subjects. Twenty-eight had untreated Type 2 (non-insulin-dependent) diabetes mellitus and the remaining 44 control subjects had a normal glucose tolerance. Diabetic patients with abdominal obesity displayed peripheral insulin resistance in combination with defective insulin secretion, whereas non-obese diabetic patients showed only a secretory defect. Thus, Type 2 diabetes in obese and non-obese elderly male subjects may take two forms where the cause of hyperglycaemia differs.
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  • 4
    ISSN: 1432-0428
    Keywords: Insulin ; glucose ; insulin resistance ; man ; glucotoxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In vitro and in vivo studies have suggested that metabolic deterioration can be induced by hyperglycaemia per se. The effect of 53 h of 2.2 mg glucose · kg ideal body weight−1· min−1 was examined in four normal male subjects. This produced overnight hyperglycaemia of 6.0 mmol/l on the two nights of the study compared with 4.7 mmol/l on the control night (p〈0.05). In response there was a sustained, two-fold increase in basal plasma insulin (p〈0.005) and C-peptide (p〈0.05) levels. After two days of hyperglycaemia an increased Beta-cell response was demonstrated in response to an additional glucose infusion stimulus (estimated Beta-cell function median of 84% on the control day to 100% after two days glucose infusion). Plasma insulin and C-peptide responses to a 10.0 mmol/l hyperglycaemic clamp increased over the two days of the study (insulin from median 48 mU/l to 73 mU/l and C-peptide from median 2.0 pmol/ml to 2.6 pmol/ml). Glucose tolerance to the additional glucose infusion stimulus improved, suggesting that the increased insulin response during hyperglycaemia was enhancing peripheral glucose uptake. The calculated peripheral insulin sensitivity was unchanged during the hyperglycaemic clamp. Thus, in response to the two days of basal hyperglycaemia, both the basal and stimulated Beta-cell responses were enhanced and there was no evidence for ‘glucose toxicity’ to the Beta-cells.
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  • 5
    ISSN: 1432-0428
    Keywords: Insulin ; hepatic clearance ; receptor recycling ; receptor-mediated endocytosis ; physiological model ; mouse liver perfusion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary After perfusion of mouse livers with A14-125I-insulin for designated intervals, an acid-wash technique was employed to separately measure the surface-bound (Xs) and intracellular (Xi) A14-125I-insulin, as well as intracellular degradation products (Xdeg) of labelled insulin. From the perfusate concentrations (Cp) of A14-125I-insulin, the apparent intrinsic hepatic clearance of labelled insulin at a high dose (0.2 nmol/l) was shown to be 60% smaller than that at a low dose (0.018 nmol/l), indicating that the cellular uptake of insulin is remarkably nonlinear at the concentration range examined. From the time courses of Cp, Xs, Xi and Xdeg, the hepatic insulin disposition was shown to be largely accounted for by the receptor-mediated endocytosis. The observed data at the low dose were analysed to estimate biochemical parameters, (i.e., total receptor number, endocytotic rate constant and intracellular degradation rate constant) according to “receptor-recycling” and “non-receptor-recycling” models, using a computer-aided optimization procedure. The “receptor-recycling” model could not only adequately explain the Cp, Xs, Xi and Xdeg at the low dose, but also predict the Cp at the high dose. On the other hand, a “non-receptor-recycling” model, in which recycling of receptors was not assumed, could also explain the observed data at the low dose, but failed to predict the Cp at the high dose, indicating that the receptor recycling process is necessary to explain the hepatic insulin clearance at high insulin concentrations, at which hepatic insulin clearance should be limited by the rate of receptor recycling. However, the applicability of our model might be limited within the physiologic insulin concentrations, because of the negative co-operativity of insulin-receptor interaction and a high-capacity, non-degradative and more rapidly recycling pathway for receptors that may occur at high concentrations of insulin. In conclusion, we have developed a mathematical model of hepatic insulin clearance and distribution under physiological conditions, including receptor binding, receptor-mediated endocytosis and receptor recycling, which has been so far demonstrated using isolated hepatocytes.
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  • 6
    ISSN: 1432-0428
    Keywords: Insulin ; C-peptide ; Glucagon ; Pancreas ; Transplantation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary It has been established that successful pancreas transplantation in Type 1 (insulin-dependent) diabetic patients results in normal but exaggerated phasic glucose-induced insulin secretion, normal intravenous glucose disappearance rates, improved glucose recovery from insulin-induced hypoglycaemia, improved glucagon secretion during insulin-induced hypoglycaemia, but no alterations in pancreatic polypeptide responses to hypoglycaemia. However, previous reports have not segregated the data in terms of the length of time following successful transplantation and very little prospective data collected over time in individual patients has been published. This article reports that in general there are no significant differences in the level of improvement when comparing responses as early as three months post-operatively up to as long as two years post-operatively when examining the data cross-sectionally in patients who have successfully maintained their allografts. Moreover, this remarkable constancy in pancreatic islet function is also seen in a smaller group of patients who have been examined prospectively at various intervals post-operatively. It is concluded that successful pancreas transplantation results in remarkable improvements in Alpha and Beta cell but not PP cell function that are maintained for at least one to two years.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Diabetologia 34 (1991), S. 144-149 
    ISSN: 1432-0428
    Keywords: Insulin ; insulin-like growth factor I ; euglycaemic clamping ; glucose metabolism ; lipogenesis ; glycogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The acute metabolic actions of insulin-like growth factor I were studied in anaesthetized adult rats and its potency was compared to that of insulin. Following an i. v. bolus injection of insulin-like growth factor I a dose-dependent decrease of blood glucose and serum non-esterified fatty acid concentrations was noted with a potency of about 2% that of insulin. Stimulation of total body glucose disposal during euglycaemic clamping required ∼ 50times higher insulin-like growth factor I serum concentrations to achieve an identical half-maximal response. A similar difference in potency was observed for the stimulatory action on 2-de-oxyglucose uptake and on glycogen formation in skeletal muscle. Lipogenesis in epididymal fat pads was increased dose-dependently by both hormones requiring approximately 30 times higher half-maximally effective serum concentrations of insulin-like growth factor I. These data demonstrate that insulin-like growth factor I exerted acute insulin-like metabolic actions in vivo with low potency. These effects were probably mediated via insulin receptors. A preferential stimulation of glucose metabolism in skeletal muscle was not observed.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Diabetologia 34 (1991), S. 868-876 
    ISSN: 1432-0428
    Keywords: Insulin ; fetal rat hepatocytes ; glycogen ; endocytosis ; degradation ; retroendocytosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary We studied insulin processing and hepatic glycogenesis in cultured hepatocytes isolated from rat fetuses of 17, 19, and 21 days of gestation. Steady-state insulin binding increased by 250% between days 17 and 19, from 145±8 to 361±52 fmol/mg protein, and by an additional 40% (405±69 fmol/mg protein) by 21 days of gestation. At 37°C, 125I-insulin was rapidly (t1/2〈5 min) internalized by hepatocytes at all three ages, reaching maximal levels (63–76% of the total cell-associated radioactivity) by 15 min. 125I-labelled degradation products appeared rapidly (t1/2〈15 min) within the cells. Yet, the majority (68–77%) of the intracellular radioactivity consisted of intact 125I-insulin, even after 4 h at 37°C. Hepatocytes pre-loaded with 125I-insulin and then acid-stripped of surface-bound radioactivity, rapidly released both intact 125I-insulin (retroendocytosis) and its radiolabelled degradation products. While intact insulin was initially released more rapidly (t1/2〈6 min), and reached a plateau after 15–30 min, the degradation products continued to accumulate in the medium for at least 4 h. Methylamine inhibited intracellular 125I-insulin degradation at all three gestational ages and also blocked insulin-stimulated glycogenesis in 19- and 21-day hepatocytes, without altering basal glycogen synthesis. Insulin-stimulated glycogenesis was not induced in 17-day fetal rat hepatocytes in control or methylamine-treated cultures. We conclude that both degradative and retroendocytotic pathways for processing insulin are present in fetal rat hepatocytes by 17 days of gestation. Further, insulin-receptor processing was functionally related to the glycogenic action of insulin in responsive 19- and 21-day fetal rat hepatocytes
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  • 9
    ISSN: 1432-0428
    Keywords: Insulin ; insulin analogues ; insulin-like growth factors ; proliferation ; vascular smooth muscle cells
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Binding and growth promoting effects of insulin, insulin analogues modified in the B chain, proinsulin, insulin-like growth factor-I and -II were studied in cultured rat aortic smooth muscle cells. Specific binding of125I-insulin was 0.9±0.2% of total 125I-insulin added, and the IC50-value was estimated to 8.9 pmol/1. The insulin analogue B10 Asp tended to be more potent than insulin in displacing 125I-insulin, B28 Asp was equipotent, B9 Asp/B27 Glu was approximately 100 times less potent and insulin-like growth factor-I more than 1000 times less potent than insulin. Specific binding of 125I-insulin-like growth factor-I after 4 h incubation at 10 °C was five times higher than the specific binding of insulin (4.4±0.4% of total 125I-insulin-like growth factor-I added), and the IC50-value was 0.3 nmol/l. Insulin was approximately 500 times less potent than insulin-like growth factor-I in displacing 125I-insulin-like growth factor-I. The insulin analogue B10 Asp was slightly more potent and analogue B28 Asp was equipotent with insulin. Analogue B9 Asp/B27 Glu was ten times less potent and proinsulin was more than ten times less potent than insulin. The order of potency was similar for 3H-thymidine incorporation into DNA: insulin-like growth factor-I 〉 B10 Asp 〉 insulin-like growth factor-II 〉 insulin 〉 B28 Asp 〉 B9 Asp/B27 Glu 〉 proinsulin. The maximal effect of insulin-like growth factor-I on 3H-thymidine incorporation was 71±16% higher than the maximal effect of insulin. The maximal effect of insulin-like growth factor-II was at least as high as the effect of insulin-like growth factor-I. Furthermore, the maximal effect of B10 Asp was 62±10% higher than the maximal effect of insulin. Insulin-like growth factor-I and B10 Asp tended to increase cell number more than insulin. In conclusion, this study shows that insulin analogues interact with different potencies with receptors for insulin and insulin-like growth factor-I in vascular smooth muscle cells and that insulin-like growth factors and the insulin analogue B10 Asp have more pronounced growth effects than insulin. Substitution of the amino acid Asp for His at position B10 in insulin makes the molecule more similar to insulin-like growth factor-I, chemically and probably also biologically.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 150 (1991), S. 339-342 
    ISSN: 1432-1076
    Keywords: Glucose tolerance ; Turner syndrome ; Insulin ; GIP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract There is a well documented increase in the incidence of abnormal glucose tolerance in patients with Turner syndrome. To elucidate the pathophysiology of this phenomenon, we studied the serum concentrations of gastric inhibitory polypeptide (GIP) — as probably the most important hormonal factor of the entero-insular axis — in relation to impaired glucose tolerance in this syndrome. Oral glucose tolerance tests were performed in 12 Turner patients with simultaneous determination of plasma glucose, insulin and GIP. An impaired glucose tolerance (iGT) was found in four patients with a chronological age between 12.3 and 14.9 years. These patients were compared with found Turner patients of similar age and weight and a normal glucose tolerance (nGT). The highest insulin level occurred 90 min after stimulation in the patients with iGT compared to 30 min in the nGT group. Interestingly, the total areas under the insulin curves were not different. Stimulated plasma GIP concentrations and the areas under the GIP curves wer significantly lower in iGT compared to nGT patients. A disturbed entero-insular axis might contribute to the delayed — rather than diminished — release of insulin in patients with Turner syndrome and impaired glucose tolerance.
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    European journal of clinical pharmacology 40 (1991), S. 379-381 
    ISSN: 1432-1041
    Keywords: Insulin ; glibenclamide ; C-peptide ; insulin catabolism ; diabetes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary In eight patients with uncomplicated non insulin dependent diabetes mellitus, serum insulin levels, serum C-peptide levels and blood glucose levels were measured before and after oral administration of glibenclamide 0.1 mg/kg body weight and a test meal, or after a test meal alone. The rise in serum insulin levels persisted longer after glibenclamide. The initial rise in serum insulin was of the same magnitude in both situations, as was the rise in serum C-peptide levels during the entire 5 h study. It is concluded that glibenclamide is able to maintain a more protonged increase in serum insulin levels by inhibiting the degradation of insulin in the vascular endothelial cells of the liver. The inhibition contributes to the blood glucose lowering effect of glibenclamide.
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 150 (1991), S. 554-556 
    ISSN: 1432-1076
    Keywords: Diabetes ; Insulin ; Therapy ; Child
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The aim of our study was to assess whether a non-invasive insulin injector could improve the metabolic control of ten diabetic children complaining of painful injections with syringe and needle. The cumulative study period amounted to 1347 days. Whereas a non-significant rise in insulin needs was observed (from 0.98±0.03 to 1.03±0.06 units/kg per day, mean ± sem), mean HbA1c value remained unchanged (8.9%±0.4% vs 9.0%±0.5%). Jet injections were felt as less painful than those using syringe and needle (nine out of ten cases). This advantage was hampered by side-effects in eight out of ten cases such as episodes of glycoketonuria (six out of ten cases) leading to hospitalization in three patients. Other side-effects included inability to adjust injection pressure (four out of ten cases) and technical failure requiring an exchange of injector in five cases. The four children with most serious problems were significantly younger (P=0.009) than other subjects. In conclusion, this type of injector should be discouraged in young diabetic children. For older children and adolescents, it may be an alternative to syringe and needle provided repeated detailed information and tight medical supervision is available.
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Journal of cancer research and clinical oncology 117 (1991), S. 416-420 
    ISSN: 1432-1335
    Keywords: Pancreas cancer ; Insulin ; Somatostatin ; Growth ; Colony formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The effects of insulin and somatostatin on the growth and the colony formation of two human pancreatic cancer cell lines, BxPC-3 and SOJ-6, were studied. The BxPC-3 cell line (American Type Culture Collection no. CRL 1687) was derived from a moderately differentiated pancreatic adenocarcinoma. The SOJ-6 cell line is a subclone of SOJ that was initiated from ascites of a well-differentiated pancreatic adenocarcinoma. Both cell lines express fetoacinar pancreatic antigen, an antigen that might be associated with early transformation stages. However, these lines have different proliferation and tumoral powers. SOJ-6 cells showed an almost twofold higher division rate over BxPC-3 cells when cultured in RPMI-1640 medium containing 10% fetal bovine serum. The tumorigenic degree of SOJ-6 cells, as assessed by tumor growth in nude mice, was about three times greater than that of BxPC-3. The in vitro growth of BxPC-3 cells was significantly promoted by insulin, and was slightly inhibited by somatostatin, whereas the growth of SOJ-6 cells was not influenced by these hormones. Using a clonogenic assay in soft agar, the average ratio of colony numbers formed by SOJ-6 and BxPC-3 was about 10/1, indicating a good correlation between the colony formation and tumorigenic degree in vivo. In this test, the number of colonies formed by BxPC-3 cells was increased about twofold in insulin-supplemented medium. On the other hand, somatostatin inhibited the colony formation by a factor of four to six. However, no hormonal modulation of the colony formation of SOJ-6 cells was observed. Our data show that pancreatic cancer cell lines respond differently to pancreatic hormones, and suggest that this may be correlated to a tumour stage or a tumour type.
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 1 (1991), S. 237-246 
    ISSN: 1573-5001
    Keywords: Linear prediction ; Heteronuclear correlation ; 2D NMR spectra ; Protein ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Linear prediction has been used to extrapolate the t1 domain of natural abundance1H−13C correlated two-dimensional (2D) FIDs of insulin. The FIDs were obtained by two different heteronuclear correlation experiments, one that utilizes heteronuclear multiple-quantum coherence during t1, and one that utilizes13C single-quantum coherence. It is shown that the enhancement of the resolution and sensitivity in the F1 dimension of the Fourier transform spectrum that results from the linear prediction extrapolation allows the t1 domain to be confined to a relatively short time period where the signal intensity is at maximum. In particular, it is found that the enhancement thus obtained is sufficiently good to allow an observation of the difference between the F1 line widths in the single-quantum and double-quantum coherence spectra.
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  • 15
    ISSN: 1432-5233
    Keywords: Insulin ; C-peptide ; Glucose ; Glipizide ; Non-insulin-dependent diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The effect of a rapid-acting sulphonylurea, glipizide, on the dose-response relationship between the β-cell response (insulin and C-peptide secretion) and the ambient plasma glucose concentration was examined in 12 healthy and 6 non-insulin-dependent diabetic subjects. The subjects participated in two sets of experiments which were performed in random order: (A) four hyperglycaemic clamp studies, during which the plasma glucose concentration was raised for 120 min by 1 (only in healthy subjects), 3, 7, and 17 mmol/l; and (B) the same four hyperglycaemic clamp studies preceded by ingestion of 5 mg glipizide. All subjects participated in a further study, in which glipizide was ingested and the plasma glucose concentration was maintained at the basal level. In control subjects in the absence of glipizide, the firstphase plasma insulin response (0–10 min) increased progressively with increasing plasma glucose concentration up to 10 mmol/l, above which it tended to plateau. Glipizide augmented the first-phase insulin response without changing the slope of the regression line relating plasma insulin to glucose concentrations. The second-phase plasma insulin response (20–120 min) increased linearly with increasing hyperglycaemia (r=0.997). Glipizide alone increased the plasma insulin response by 180 pmol/l. A similar increase in plasma insulin response following glipizide was observed at each hyperglycaemic step, indicating that glipizide did not affect the sensitivity of the β-cell to glucose. First-phase insulin secretion was reduced in the type 2 (non-insulin-dependent) diabetic patients, and was not influenced by glipizide. The dose-response curve relating second-phase insulin secretion to the ambient plasma glucose concentration was significantly (P〈0.001) flatter in the diabetic patients than in the control subjects. Glipizide alone increased the plasma insulin response by 60 pmol/l without changing the slope of the dose-response curve. It is concluded that, in both type 2 diabetic patients and healthy subjects: (A) sulphonylurea augments glucose-stimulated second-phase insulin secretion without changing the sensitivity of the β-cell to glucose; (B) first-phase insulin secretion is reduced in non-insulin-dependent diabetic patients with fasting hyperglycaemia and is not influenced by sulphonylurea.
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  • 16
    ISSN: 1432-0878
    Keywords: B cells ; Insulin ; Catecholamine ; synthesizing enzymes ; Immunohistochemistry ; Chicken
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The identity of the monoamine which produces a very weak formaldehyde-induced fluorescence in some pancreatic islet cells was studied by fluorescence microscopy and immunohistochemistry either on the same tissue section or on serial tissue sections of tissue from male chickens. Pancreatic islet cells showing this very weak formaldehyde-induced fluorescence react immunohistochemically with antisera directed against insulin, aromatic L-amino acid decarboxylase and dopamine beta-hydroxylase and therefore appear to be islet B cells producing insulin and noradrenaline.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Cell & tissue research 265 (1991), S. 261-273 
    ISSN: 1432-0878
    Keywords: Endocrine pancreas ; Immunization ; Insulin ; Glucagon ; Somatostatin ; Electron microscopy ; Rabbit (Chinchilla, Ch: b Ch)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary An active or passive immunization against hormones and the subsequent neutralization of hormones by circulating antibodies is a valuable tool for the identification of hormonal action. To recognize presumed local (autocrine, paracrine) effects exerted by pancreatic hormones, the endocrine pancreas of rabbits was investigated electron-microscopically after long-term immunization against glucagon or somatostatin. Glucagon immunization resulted in hyperplasia and hypertrophy of glucagon- (A-) cells and in their increased metabolic activities: They showed prominent nucleoli, increased amounts of endoplasmic reticulum, Golgi areas, and mitochondria. These changes were paralleled by alterations in secretion granules (increased size, decreased hormonal content), increased numbers of lysosomes (crinophagic bodies), and an increment of the filamentous system. Basically, these findings point to an autocrine regulation of A-cells. Following somatostatin immunization, somatostatin- (D-) cells were hyperplastic but unchanged in their metabolic state. Instead, insulin-(B-) cells and A-cells exhibited equivalents of increased cellular activities (parameters, see above). This stimulation most probably is caused by cancelled paracrine (inhibitory) effects of somatostatin. The changes observed after both immunizations were differently expressed in morphologically heterogeneous islet types (size, angioarchitecture, cellular composition, microtopology of the various cell types). It is concluded, therefore, that the regulation of islets is not uniform. Autocrine and paracrine effects exerted by islet hormones are of different significance in individual islets, or they interfere differently with other regulatory signals.
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  • 18
    ISSN: 1619-1560
    Keywords: Postprandial hypotension ; Elderly ; Carbohydrate ; Neurotensin ; Catecholamines ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Previous studies have demonstrated that blood pressure falls postprandially in fit elderly subjects, the greatest changes occurring after meals with a high carbohydrate content. To evaluate the influence of the type of carbohydrate on postprandial blood pressure, the effects of equivalent energy content (2.4 MJ) high complex (starch) and high simple (monosaccharide) carbohydrate meals were studied in seven healthy elderly subjects. Blood pressure, heart rate, autonomic function, plasma catecholamines, insulin and neurotensin levels were measured pre- and postprandially. Greater falls in supine and erect systolic blood pressure occurred after the high simple than the high complex carbohydrate meal (p 〈 0.05). No differences were found in supine or erect diastolic blood pressure, heart rate or in any of the biochemical parameters measured between the meal types. It is concluded that a simple carbohydrate meal results in a greater postprandial fall in blood pressure than an equivalent energy complex carbohydrate meal in the elderly, although the mechanisms for these changes are unknown.
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  • 19
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    European journal of applied physiology 62 (1991), S. 286-291 
    ISSN: 1439-6327
    Keywords: High altitude ; Cortisol ; Insulin ; Growth hormone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Concentrations of glucose, lactic acid, free fatty acid (FFA), insulin, cortisol and growth hormone (GH) in the blood were monitored in 15 euglycaemic men (sojourners, SJ) at sea level (SL) and while at altitudes of 3500 m and 5080 m, in acclimatised low landers (ALL) and in high altitude natives (HAN). In SJ, blood glucose and insulin concentrations showed a significant increase on the 3rd and 7th day after arrival at high altitude (HA), thereafter returning to sea level values and remaining the same during the entire period of their stay at 3500 m. Subsequently, on arrival at higher altitude (5080 m) the glucose concentrations again showed an increase over the preceding values and returned to SL values on day 41 while at 5080 m. A significant increase in cortisol concentrations was seen on day 3 after arrival at HA and the increased levels were maintained until day 21 at 3500 m. The cortisol concentrations on day 30 after arrival at 5080 m came down to SL values and remained unchanged thereafter. No appreciable change in GH and FFA was seen during the sojourn at HA. On the other hand, blood lactic acid concentration decreased significantly. There was no difference between the fasting glucose concentrations in ALL at 3500 m and in HAN at 3500 m and 4200 m compared to values of SJ at SL, whereas ALL at 4200 m had higher glucose values. Concentrations of plasma insulin and GH in ALL and HAN were higher than the values of SJ at SL, whereas cortisol values did not show any difference. These observations indicated that at HA the glucose values were high for the insulin concentration observed and might have been due to increased secretion of GH by the pituitary gland.
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  • 20
    ISSN: 1439-6327
    Keywords: Endurance conditioning ; Aerobic fitness ; Lipoproteins ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Two experiments were carried out to compare the cardiorespiratory and metabolic effects of cross-country skiing and running training during two successive winters. Forty-year-old men were randomly assigned into skiing (n = 15 in study 1,n = 16 in study 2), running (n = 16 in study 1 andn = 16 in study 2) and control (n = 17 in study 1 andn = 16 in study 2) groups. Three subjects dropped out of the programme. The training lasted 9–10 weeks with 40-min exercise sessions three times each week. The training intensity was controlled at 75%–85% of the maximal oxygen consumption (VO2max) using portable heart rate metres and the mean heart rate was 156–157 beats·min−1 in the training groups. In the pooled data of the two studies the mean increase in theVO2max (in ml·min−1·kg−1) on a cycle ergometer was 17% for the skiing group, 13% for the running group and 2% for the control group. The increase inVO2max was highly significant in the combined exercise group compared to the control group but did not differ significantly between the skiing and running groups. The fasting serum concentrations of lipoproteins and insulin did not change significantly in any of the groups. These results suggested that training by cross-country skiing and running of the same duration and intensity at each session for 9–10 weeks improved equally the cardiorespiratory fitness of untrained middle-aged men.
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  • 21
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    European journal of applied physiology 63 (1991), S. 48-51 
    ISSN: 1439-6327
    Keywords: Insulin ; Hyperglycemia ; Hyperinsulinemia ; Human subjects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The purpose of the present investigation was to examine the effects of hyperglycoemia induced by supramaximal exercise on blood glucose homeostasis during submaximal exercise following immediately after. Six men were subjected to three experimental situations; in two of these situations, 3 min of high-intensity exercise (corresponding to 112, SD 1%VO2 max) was immediately followed by either a 60-min period of submaximal exercise (68, SD 2%VO2 max) or a 60-min resting period. In the third situation, subjects performed a 63-min period of submaximal exercise only. There were no significant differences between the heurt rates, oxygen uptakes, and respiratory exchange ratios during the two submaximal exercise bouts (〉 15 min) whether or not preceded by supramaximal exercise. The supramaximal exercise was associated within 10 min of the start increases (P〈0.05) in blood glucose, insulin, and lactate concentrations. This hyperglycemia was more pronounced when subjects continued to exercise submaximally than when they rested (at 7.5 min;P〈0.05). There was a more rapid return to normal exercise blood glucose and insulin values during submaximal exercise compared with rest. The data show that the hyperinsulinemia following supramaximal exercise is corrected in between 10–30 min during submaximal exercise following immediately, suggesting that this exercise combination does not lead to premature hypoglycemia.
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  • 22
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    European journal of applied physiology 63 (1991), S. 417-423 
    ISSN: 1439-6327
    Keywords: Energy expenditure ; Thermogenesis ; Epinephrine ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The contribution of insulin (3.6 pmol sd kg body mass−1·min−1 to adrenaline-induced (0.164 nmol · kg fat free mass−1·min−1) thermogenesis was studied in ten postabsorptive healthy volunteers using two sequential protocols. Variables considered were oxygen consumption as well as carbon dioxide production, heart rate, blood pressure, plasma concentrations of glucose, insulin, glycerol, free fatty acids,β-HO-butyrate and lactate. Adrenaline increased plasma concentrations of glucose, glycerol, free fatty acids, andβ-HO-butyrate, and heart rate and metabolic rate during normo-insulinaemia [61.3 (SEM 6.6) pmol·−1]. Similar effects were observed during hyperinsulinaemia [167.9 (SEM 18.7) pmol·−1], but the effect of adrenaline on oxygen consumption was reduced. On average, metabolic rate increased by 12.9% during normo-insulinaemia and by 8.9% during hyperinsulinaemia. We concluded that relative hyperinsulinaemia resulted in decreased adrenaline-induced thermogenesis and therefore increased whole body anabolism.
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  • 23
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    European journal of applied physiology 63 (1991), S. 242-249 
    ISSN: 1439-6327
    Keywords: Atropine ; Glucose ; Fructose ; Dietary thermogenesis ; Insulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Muscarinic blockade by atropine has been shown to decrease the thermic effect of a mixed meal, but not of intravenous glucose. To further delineate the mechanisms involved in the atropine-induced inhibition of thermogenesis after a meal, plasma substrate and hormone concentrations, energy expenditure (EE) and substrate oxidation rates were measured before and during a continuous glucose infusion (44.4 μmol·kg−1·min−1) with or without atropine. After 2 h of glucose infusion, a 20-g oral fructose load was administered while the glucose infusion was continued. Plasma insulin concentrations attained a plateau at 596 (SEM 100) pmol·l−1 after 120 min of glucose infusion and were not affected by muscarinic blockade; plasma glucose concentrations peaked at 13.3 (SEM 0.5) mmol·l−1 at 90 min and decreased progressively thereafter; no difference was observed with or without atropine. Plasma free fatty acid and glucagon concentrations, with or without atropine, were both decreased to 201 (SEM 18) μmol·l−1 and 74 (SEM 4) ng·l−1, respectively, after 2 h of glucose infusion, and were not further suppressed after oral fructose. Carbohydrate oxidation rates (CHOox) increased to 20.8 (SEM 1.4) μmol·kg−1·min−1 and lipid oxidation rates (Lox) decreased to 1.5 (SEM 0.3) μmol·kg−1·min−1 between 90 and 120 min after the beginning of glucose infusion and were not affected by atropine. Glucose-induced thermogenesis was similar with [6.5% (SEM 1.4%) of basal EE] or without [6.0% (SEM 1.0%), NS) muscarinic blockade during the 30 min preceding fructose ingestion. During the second half-hour after fructose ingestion, atropine infusion inhibited markedly the stimulation of CHOox [+2.8 (SEM 1.0) μmol·kg−1·min−1 vs +6.9 (SEM 1.0) μmol·kg−1·min−1, saline, P〈0.02] and the suppression of Lox [−0.8 (SEM 0.2) μmol·kg−1·min−1 vs −1.4 (SEM 0.2) μmol·kg−1·min−1, saline, P〈0.05]. Carbohydrate-induced thermogenesis during the second half-hour after fructose ingestion, increased to 13.0% (SEM 2.0%) without atropine and was suppressed to 7.7% (SEM 1.9%) (P〈 0.05, vs saline) with atropine. It was concluded that muscarinic blockade suppressed the increase of thermogenesis observed after oral fructose, but not during intravenous glucose infusion and that this suppression occurred independently of alterations of plasma insulin concentrations.
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  • 24
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    Pharmacy world & science 13 (1991), S. 123-126 
    ISSN: 1573-739X
    Keywords: Alkylation ; Antineoplastic agents ; Biochemistry ; Cytotoxicity ; Oxidation-reduction ; Quinones
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Quinones can be metabolized by various routes: substitution or reductive addition with nucleophilic compounds (mainly glutathione and protein thiol groups), one-electron reduction (mainly by NADPH: cytochrome P-450 reductase) and two-electron reduction (by D,T-diaphorase). During reduction semiquinone radicals and hydroquinones are formed, which can transfer electrons to molecular oxygen, resulting in the formation of reactive oxygen intermediates and back-formation of the parent quinone (redox cycling). Reaction of semiquinones and reactive oxygen intermediates with DNA and other macromolecules can lead to acute cytotoxicity and/or to mutagenicity and carcinogenicity. The enhanced DNA-alkylating properties of certain hydroquinones are exploited in the bioreductive alkylating quinones. Acute cytotoxicity of quinones appears to be related to glutathione depletion and to interaction with mitochondria and subsequent disturbance of cellular energy homoeostasis and calcium homoeostasis. These effects can to a certain extent be predicted from the electron-withdrawing and electron-donating effects of the substituents on the quinone nucleus of the molecule. Prediction of cytostatic potential remains much more complicated, because reduction of the quinones and the reactivity of the reduction products with DNA are modulated by the prevailing oxygen tension and by the prevalence of reducing enzymes in tumour cells.
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  • 25
    ISSN: 1434-9949
    Keywords: Ossein-Hydroxyapatite Compound ; Bone Remodeling ; Biochemistry ; Histomorphometry ; Ewe
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Ossein-hydroxyapatite compound (OHC) is a protein-mineral complex derived from bovine bone. Its effects on bone remodeling were studied in old ewes which have seasonal variations in bone remodeling. Seven animals received 200 mg OHC/kg b.w./day for 90 days from July to September. The control group consisted of 7 untreated animals followed for the same period of time. OHC was administered through a fistula into the fourth stomach. A significant decrease of bone histomorphometric parameter values was noted in controls at the end of the experiment, due to seasonal variations: the cancellous eroded perimeter decreased by 45%, the osteoblastic perimeter by 60% and the bone formation rate at the cell level by 20%. In contrast, in the treated-group, these parameters tended to increase or did not change. In conclusion, counteracting the significant seasonal reduction of bone remodeling in ewes, OHC seems able to stimulate directly or indirectly bone metabolism, especially when osteoblast activity is reduced and may partly prevent the seasonal reduction of bone turnover.
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  • 26
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    Molecular Reproduction and Development 29 (1991), S. 253-258 
    ISSN: 1040-452X
    Keywords: Embryos ; Insulin ; ICM ; Trophectoderm ; Receptor ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Insulin specifically stimulates protein synthesis in compacted mouse embryos on days 3 and 4 after fertilization, with an EC50 of 0.5 pM (Harvey and Kaye, 1988). The identity of the receptor mediating this short-term effect of insulin was further examined by dose-response studies with IFG-1 and by using a specific anti-insulin receptor antiserum that has no appreciable cross-reaction with IGF-1 receptors. IGF-1 caused a maximum 40% stimulation of protein synthesis after 4 h exposure (similar to the response to insulin) with an EC50 of 150 pM IGF-1. The insulin receptor-specific antiserum, or IgGs isolated from it, also stimulated protein synthesis at dilutions as high as 1:1,000 to the same degree as insulin (∼40%). This agonistic action of the insulin receptor antiserum, the EC50 of 150 pM for IGF-1, and the previously established EC50 of 0.5 pM for insulin, all with similar maximal stimulation, strongly support the conclusion that the short-term metabolic stimulation of mouse blastocysts by insulin is mediated by insulin receptors. Immunosurgical isolation of inner cell masses before and after exposure to 1.7 pM insulin (sufficient to stimulate only the insulin receptor) showed that insulin stimulates protein synthesis in these cells as well as in the trophectoderm cells of the blastocyst. This finding suggests that in intact blastocysts, insulin may travel across the trophectoderm to the inner cell mass, acting anabolically on both tissues. Analysis of the agonistic effect of the B-10 antiserum showed there was no evidence of an unresponsive subpopulation of embryos.
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  • 27
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    Journal of Computational Chemistry 12 (1991), S. 175-179 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This is a study of the effect of data structures and algorithms on parallelism and vectorization for the molecular dynamics package GROMOS. About 80% of the computing time (for the GROMOS benchmark) is spent on the nonbonded interactions, and an important issue is the method that is used for finding all pairs of atoms (actually atom groups) which are within a given cutoff radius of each other. Favored by the authors of GROMOS is the use of the (Verlet) neighbor list with direct calculation of all distances. Substantial restructuring of their code for the nonbonded interactions has resulted in a speedup of a factor 6.9 for the eight-processor Alliant FX/8 through the use of concurrent subroutine calls. Vectorization gave a further improvement of 30%. However, the direct calculation of all distances does not scale up linearly with the number of atoms. (Nor would neighbor lists be needed if cutoffs were abandoned in favor of such techniques as the fast multipole method). Therefore an alternative GROMOS subroutine that implements the “gridcell plus linked list” approach without a neighbor list was also rewritten and tested. This resulted in the discovery of an apparent flaw in an early study of the relative merits of the two algorithms. It is observed that actually the neighbor list version of GROMOS is not much faster.
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  • 28
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.
    Additional Material: 7 Tab.
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  • 29
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    Journal of Computational Chemistry 12 (1991), S. 147-166 
    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 modeling program AMBER 3.0 was used to study the conformations adopted by the C8-substituted guanosine adduct of the carcinogen N-2-acetylaminofluorene (AAF), called dGuo-AAF. This conformational study was extended to the hexamer d(CGCGCG)2 in the Z form, modified by AAF at guanine G4 with the carcinogen situated at the helix exterior in two different orientations (named ZAAF-5′ and ZAAF-3′). Considering the importance of electrostatic interactions in case of charged molecules like nucleic acids, minimization and molecular dynamics (MD) were performed using different electrostatic parameters (dielectric functions and scale factors). For that purpose, a subroutine allowing the use of a sigmoidal distance-dependent dielectric function εcal has been added to the program. For dGuo-AAF, the results show a great importance of the starting conformation and of the force field parameters on the minimization and MD behaviors. For the AAF-modified Z-DNA, the results display a pronouned dependence on the choice of the set of electrostatic parameters as well. With the distance-dependent dielectric function ε = r, the force field parameters favor the formation of intramolecular H bonds, which can lead to important distortions of Z-DNA. The use of ε = 4r or ε = εcal attenuates effectively such a tendency, except in full MD simulations. The dielectric function εcal is computing intense, but often similar results are obtained with ε = 4r, especially with the use of the BELLY option. AAF appears to prefer the ZAAF-5′ conformation, i.e., with the fluorene ring stacking on the sugar phosphate backbone of the following 5′ C-G bases. Such a conformation is further stabilized by an intramolecular hydrogen bond between the amino group of the 3′ cytosine and the carbonyl group of AAF. The fluorene ring, although mobile around its long axis, does not flip-flop between its two main orientations, ZAAF-5′ and ZAAF-3′. The presence of the AAF does not prevent the ZI to ZII transitions. Whatever the electrostatic parameters, the presence or absence of AAF, the cytosine sugars stay in the C2′-endo pucker domain. In unmodified Z-DNA, the guanine sugars stay in the C3′-endo region, except for the terminal guanines which transit to the C2′endo region. In modified Z-DNA, the sugar of the modified guanine behaves as a terminal guanine sugar.
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  • 30
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    Journal of Computational Chemistry 12 (1991), S. 690-696 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents theoretical calculations on bond energies for the first-row diatomics C2, CN, CO, CF, N2, NO, NF, O2, FO, and F2, which vary in bond order from one to three. The atomic-centered basis functions are systematically augmented with bond functions (BFs), which range in composition from (sp) to 2(spd), to determine the basis set which yields a dissociation energy closest to the experimental De. A strong correlation is found to exist between the bond order and the number of BFs required in the optimum basis set. Based on these results, we are able to predict the optimum composition of the BF basis which should be added to a DZP-quality AO basis set for a case in which only the bond order is known. These optimized BF basis sets are shown in the accompanying article to give more accurate potential curves than larger basis sets without bond functions.
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  • 31
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    Journal of Computational Chemistry 12 (1991), S. 731-741 
    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 harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in-plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1-3 Since only a fraction of the 2N - 3 in-plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N - 3 in-plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
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  • 32
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    Journal of Computational Chemistry 12 (1991), S. 839-843 
    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 calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3-methyl-1-butene is not in agreement with experimental data. In order to reparametrize the Csp2-Csp3-Csp-Csp3 torsional angle, 3-methyl-1-butene and 1-butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6-31G* and MP3/6-31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3-methyl-1-butene and 1-butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.
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  • 33
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    Journal of Computational Chemistry 12 (1991), S. 880-884 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vibrational spectra were obtained for the structurally similar compounds 2-methylbutyronitrile and 3-methyl-1-pentyne, and vibrational assignments were made with the aid of normal coordinate calculations. Molecular mechanics calculations were also made, and each compound was shown to exist as a mixture of three conformers, with the most stable conformer being the one with the two methyl groups trans to each other. Results of the calculations are given.
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  • 34
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    Journal of Computational Chemistry 12 (1991), S. 909-912 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.
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  • 35
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    Journal of Computational Chemistry 12 (1991), S. 868-871 
    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 is presented for calculating the solvent accessible surface area of proteins using a three-dimensional grid. Since it requires only calculations based on single atomic positions, the algorithm is easy to be vectorized. It has been implemented on ST100 and may also be implemented on supercomputers like the CRAY or the CYBER. Results on several proteins indicate that its deviation from that of the Shrake-Rupley algorithm is very small while the computation time is much reduced.
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  • 36
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    Journal of Computational Chemistry 12 (1991), S. 885-890 
    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 use of principal components as a basis for a graphical procedure to analyze polar tensor data is proposed. Molecular orbital and experimental polar tensor data for all possible sign combinations of the ∂p/∂Qj of CHCl3 and CDCl3 are represented graphically as principal component scores facilitating sign selection for the ∂p/∂Qj. The graphs are particularly useful in analyzing an apparent conflict in ∂p/∂Qj sign choices based on the isotopic invariance criterion and molecular orbital results for the A1 symmetry species of these molecules. The numerical impacts of individual sign ambiguities for the ∂p/∂Qj on the polar tensor data are measured by the variances associated with the principal components. Assuming the ∂p/∂Qj sign sets with indeterminate signs provide replicated results for the polar tensor elements, their errors are estimated and compared with errors obtained previously by propagating intensity uncertainties through the polar tensor equations.
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  • 37
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    Journal of Computational Chemistry 12 (1991), S. 913-917 
    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 novel method to calculate electrostatic charges is proposed. Partial charges are fitted to reproduce the electrostatic potential of a distributed multipole series without explicitly evaluating electrostatic potentials. The calculation is economical and results in charges reflecting the symmetry properties of charge centers and being independent of molecular orientation.
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  • 38
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    Journal of Computational Chemistry 12 (1991), S. 1129-1133 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MM2-87 calculations have been performed on C60 (buckminsterfullerence; footballene) and C70 with full energy minimization. The steric energies for C60 and C70 were computed to be 179.9 and 177.9 kcal/mol, respectively. The heats of formation for C60 is found to be more stable than C60. The two bond lengths for C60 were computed to be 1.393 and 1.444 Å. Eight different bond lengths were found for C70 ranging from 1.386 to 1.452 Å. Bond angles, dihedral angles, and moments of inertia are also reported for the compounds.
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  • 39
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    Journal of Computational Chemistry 12 (1991), S. 1065-1076 
    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 Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below -10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below -10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.
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  • 40
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    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 41
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    Journal of Computational Chemistry 12 (1991), S. 1187-1197 
    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 developed a method for building up accurate electrostatic models for polypeptides, based on a distributed multipole representation of the SCF charge densities for the dipeptides (CH3.CO.NH.CHR.CO.NH.CH3) of the naturally occurring amino acids. It is based on the observation that each peptide residue has almost the correct formal charge (0, ±1). We find that the variations in the backbone charge distributions (excluding proline) with sidechain have a negligible effect on the predicted electrostatic potential around the residue. However changes in the atomic multipoles with the torsion angles (φ, ψ, χ) are more significant, and may need to be taken into account if electrostatic potential close to the residue is required to high accuracy. This type of DMA peptide library provides more accurate, more theoretically based, estimates of the electrostatic potential around polypeptides than current models.
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  • 42
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    Journal of Computational Chemistry 12 (1991), S. 180-185 
    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 consequences of substitution of fluorine for the para hydrogen of a phenylalanine residue in ribonuclease-S were investigated by conformational energy calculations using the AMBER force field. Both the fluorine-containing protein and the corresponding nonfluorinated material were subjected to conformational adjustment through energy minimization and the minimum energy structures so defined were compared. Fluorine substitution leads to small alterations in many atomic positions in the protein, with adjustments at at sites more than 0.5 nm from the fluorine appearing to be somewhat larger than those within the immediate vicinity of the fluorine. Several atoms proximate to the fluorine atom were observed to move toward the fluorine while others in the same vicinity move away. The greater bulk of the fluorine atom and the strongly different electronic properties of fluorine compared to hydrogen thus appear to be insufficient to cause a consistent, unidirectional change in nearest-neighbor interactions upon introduction of a fluorine atom into a protein structure. Virtually all changes in atomic positions that are predicted by these calculations would be barely detectable by a crystallographic study with a resolution of 0.2 nm.
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  • 43
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    Journal of Computational Chemistry 12 (1991), S. 220-230 
    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 for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB2 molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian-type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two-dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two-dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.
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  • 44
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    Journal of Computational Chemistry 12 (1991), S. 266-270 
    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 formula is presented for calculating the approximate partition function of a hindered internal rotational mode of a polyatomic molecule. The formula gives useful accuracy over the whole range from harmonic oscillator to hindered rotator to free rotator.
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  • 45
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    Journal of Computational Chemistry 12 (1991), S. 292-300 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Various algorithms for solving the Solomon equations describing nuclear Overhauser effects (nOes) in NMR spectroscopy have been compared. The applicability of the eigenvalue/eigenvector and the numerical integration approaches have been investigated. The eigenvalue/eigenvector approach is not a computationally efficient means of simulating nOe experiments in which a saturating radiofrequency field is applied during the time course. For experiments in which nOes develop in the absence of an RF field, this approach should only be used in simulating a full NOESY spectrum. Integration schemes have been found to be more efficient at simulating nOe experiments in which the nOe evolves in the presence of a saturating field, at simulating a partial set of initial perturbation experiments and at simulating a few rows or columns in a NOESY spectrum. Various integration schemes were applied to a two-spin system for which an analytic solution is available and to a model B-DNA oligonucleotide hexamer. The previously unused Taylor series algorithm was found to be superior to the Euler, midpoint, and fourth-order Runge-Kutta methods with regard to integration accuracy/computation time. An adaptive step size control routine for the Taylor series integration scheme was developed. Integration schemes can be speeded up in a simple fashion by introducing a distance cutoff for the dipolar interaction. Using a cutoff of 8 Å the Taylor series algorithm was able to compute the NOESY spectrum more rapidly than the eigenvalue/eigenvector algorithm for large spin systems at short mixing times. At longer mixing times the eigenvalue/eigenvector approach becomes the more efficient scheme.
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  • 46
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    Journal of Computational Chemistry 12 (1991), S. 359-368 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Effects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α-helix of deca-alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one-to-one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm-1 and those in the DAS with frequencies less than 164 cm-1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very-low-frequency normal modes in the CCS with frequencies less than 128 cm-1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low-frequency motions are concerned. Based on the results of calculation, mechanical property of the α-helix of deca-alanine is discussed.
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  • 47
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    Journal of Computational Chemistry 12 (1991), S. 742-745 
    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 C-C glycol bond rotational energy in ethylene diacetate as a polyester model was compared using the semiempirical method AM1 and an ab initio method with an STO-3G basis set. The results were qualitatively much different depending on the method used. Ab initio calculations showed the expected minima at 180 and near 60 (69.6) degrees dihedral angle with maxima at 0 and 120 degrees. The AM1 rotational curve indicated an apparent minimum at a 90 degree dihedral angle, a shallow, apparent maximum at 180 degrees and an apparent maximum at 0 degrees which could not be confirmed as minima or maxima via frequency calculations. Ethylene diacetate analog compounds with one or two ester oxygens replacing methylene group(s) gave curves with AM1 having the general shape for ethylene diacetate by the ab initio method, indicating a parameterization problem for the otherwise very useful AM1 to correctly handle a compound with only two carbons between the two electronegative oxygen atoms thus rendering this method currently unsuitable for examination of rotational energy barriers of such polyester model compounds.
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  • 48
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    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 49
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    Journal of Computational Chemistry 12 (1991), S. 918-922 
    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 topological procedure is described that is able to detect cavities of all shapes and sizes in a system of interpenetrating spheres. The procedure is coupled to an analytic algorithm for computing surface areas and volumes, but as such, involves only logical operations and is therefore not subject to numerical imprecision. Its application to the identification of internal cavities in molecular systems is illustrated.
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  • 50
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    Journal of Computational Chemistry 12 (1991), S. 1198-1210 
    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 purpose of this study is to design a technique that generates a variable van der Waals-like surface for any desired charge density value of a molecule. The method is based on the recognition that for each fixed density value, within a wide range, certain shape features of the electron density contours are approximately invariant under configuration rearrangements, such as bending and stretchings in polyatomic molecules. These invariants appear in the form of spherical regions in space around the nuclei, where no density contours of a given level set value enter. These regions, the so-called invariant cores, behave as approximately transferable quasi-atomic spherical surfaces. We have evaluated these cores in molecules, and also approximated them in terms of the electron density of isolated atoms. The properties of these quasi-atomic surfaces allow one to design a scale of variable atomic radii based on the size of the transferable isodensity spheres. In this work we provide a detailed description of the dependence of the diameters of these spheres on the electron density values. We show that, by using this scale of radii, it is possible to design fused-sphere molecular models that closely mimic isodensity surfaces for a whole range of density values. The results discussed here allow one to relate molecular size with charge density. We propose the use of these scales for the construction of more realistic van der Waals model surfaces when studying molecular shape in the context of computer-assisted molecular modeling.
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  • 51
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    Journal of Computational Chemistry 12 (1991), S. 1232-1236 
    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 carried out free energy perturbation calculations on the relative solvation free energy of cis- and trans-N-methyl-acetamide (NMA). Experimentally, the solvation free energy difference has been found to be near zero. Using 6-31G* ab initio electrostatic potential derived charges for both the cis and trans conformations, we calculate a solvation free energy difference of 0.1 ± 0.1 kcal/mol. Using the 6-31G* charges derived for the trans conformation for both the cis and trans models leads to a solvation free energy difference of 0.9 ± 0.1 kcal/mol, compared to the value of 2.2 kcal/mol determined for the OPLS model for trans-NMA.
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  • 52
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    Journal of Computational Chemistry 12 (1991), S. 1270-1277 
    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 description of vector/parallel algorithms for the molecular dynamics (MD) simulation of macromolecular systems on multiple processor, shared-memory computers is presented. The algorithms encompass three computationally intensive portions of typical MD programs: (1) the evaluation of the potential energies and forces, (2) the generation of the nonbonded neighbor list, and (3) the satisfaction of holonomic constraints. We implemented the algorithms into two standard programs; CHARMM and AMBER, and obtained near linear speedups on eight processors of a Cray Y-MP for cases (1) and (2). For case (3) the SHAKE method demonstrated a speedup of 6.0 on eight processors while the matrix inversion method demonstrated 6.4. For a system of water molecules the performance improvement over the standard scalar SHAKE subroutine in AMBER ranged from a factor of 165 to greater than 2000.
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  • 53
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Dissociation energies and potential energy surface features for the carbon clusters C2 to C10 are compared with ab initio or experimental results for the semiempirical methods MINDO/3, MNDO, AM1, and PM3. Quite surprisingly, MINDO/3 gives a rather good account of the various structures and electronic states, unlike the other three methods. MINDO/3 tends towards systematic overestimates of binding energies, the other methods to systematic gross underestimates. Reparametrization of the diatomic parameters α, βs, and βp for exact reproduction of the experimental data for C3 results in much improved values for binding energies, but fails to correct the state splittings. Also reparametrizing Uss, Upp, ζs, and ζp to reproduce the ab initio linear-rhombic energy difference in C4 results in a much improved description of the other states. For the linear structures, computed harmonic frequencies with the latter parameters are in surprisingly good agreement with experimental or correlated ab initio data, where available; experimental values are consistently overestimated by about 40 cm-1. Other results are comparable in quality to good ab initio treatments. The experimental IR bands at 2128 and 1892 cm-1, formerly assigned to C9, should be reassigned to linear C7. The intense 1997 cm-1 feature almost certainly belongs to C9; bands at 1952 and 1197 cm-1 both belong to linear C6. Tentative assignments of bands in the 1600-1850 cm-1 region to various cyclic structures of C6, C8, and C10 have been made. As such, this suggests a new and promising procedure for the theoretical study of large molecules in general, and of large clusters in particular.
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  • 54
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Carefully calibrated large-scale nonempirical CI computations have been performed for the isotropic hyperfine splittings of the t-butyl radical. The results have been used to interpret the effects of out-of-plane vibration of the radical center, with and without coupling to methyl rotations, on the observed splitting at the radical center. In particular, the value computed under rotation-inversion is 39 G, in good agreement with the ESR result of 45 G.
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  • 55
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    Journal of Computational Chemistry 12 (1991), S. 254-265 
    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 self-consistent-field molecular-orbital (SCF MO) Hartree-Fock (HF) calculations using the STO-3G, 6-31G, and 6-31G* basis sets, were performed to model quasi-tetrahedral silicon species in silicon dioxide. Mostly nine-atom clusters, [Si(OH)4]qt, with charge number qt = 0 or + 1, were studied. The positions of the Si and O atoms were varied to achieve minimum total energies, while the protons were held fixed in the O-(neighboring)Si direction to simulate the rigid crystal surroundings. The α-quartz-type local symmetry C2 was found to be retained for the neutral cluster, but not for the ionic one. The unrestricted HF calculations indicate that the latter paramagnetic centre, (qt = +1), has its spin population almost entirely on one short-bonded oxygen ion bonded weakly to its neighboring Si, and is quite high in energy (9.55 eV with 6-31G) compared to the diamagnetic centre (qt = 0). The ionization energy is much higher than the self-trapping potential of the polaronic hole, a fact which may account for the failure so far to observe a [SiO4]+1 center in quartz by means of continuous-wave electron paramagnetic resonance spectroscopy. Calculations on the [SiO4]+1 center agree well with ultraviolet spectra, and with the [hole portion of a] proposed radiation-induced exciton in quartz. The hole in [Si(OH)4]+1 can be shifted from a short-bonded to a long-bonded oxygen to give the excited state [Si(OH)4]es+1. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [Si(OSiH3)4]qt. Comparisons with the known isoelectronic species [AlO4]0 were carried out.
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  • 56
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    Journal of Computational Chemistry 12 (1991), S. 141-146 
    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 IPPP-CLOPPA method is used to study the origin of the difference between exo-exo and endo-endo vicinal interproton couplings in norbornane and norbornene. The main pathway defining such couplings is found to be determined by the corresponding C—H bonds and antibonds. For this reason they can be considered to be transmitted through space. Contributions from excitations involving MOs of bridge 7 and the C—H endo and exo bonds and antibonds are found to be negligible in both compounds. Even though bridges 5-6 and 7 are not included in the coupling pathway, they influence the structure of endo and exo C—H bonds, and thus cause the nonequivalence of endo-endo and exo-exo couplings. Results obtained with the NNBI method are compared to those of IPPP-CLOPPA.
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  • 57
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    Journal of Computational Chemistry 12 (1991), S. 209-214 
    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 modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.
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  • 58
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    Journal of Computational Chemistry 12 (1991), S. 248-253 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several unique advantages of the Le Verrier-Fadeev-Frame method for the characteristic polynomials of graphs over the method proposed by Zivković recently based on the Givens-Householder method are described. It is shown that the Givens-Householder method proposed by Zivković, by itself fails for directed graphs, signed graphs, and complex nonhermetian graphs requiring extensive modifications to the Householder algorithm through the double + random shift QR procedure requiring more computations than claimed. Furthermore, the QR procedure does not always converge and requires random shifts. To the contrary, it is shown that the Le Verrier-Fadeev-Frame method does not require any such modifications or random shifts and takes less total CPU times when both algorithms are run using vector processors. Hence it is demonstrated that the Le Verrier-Frame algorithm is efficient and superior in its universal and direct applicability to all graphs requiring no further modifications (directed, signed, and complex).
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  • 59
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    Journal of Computational Chemistry 12 (1991), S. 271-275 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy difference calculations have been performed by the “slow growth” method of thermodynamic integration of the AMBER 3.0 molecular dynamics program for the mutation of a conformationally restricted threonine dipeptide, N-acetyl threonyl-N-methylamide, to the corresponding alanyl dipeptide. By varying the total simulation length, it has been determined that precise free energy values are obtained only for simulations of greater than 100 ps total simulation time length. By varying the starting configurations for simulations of the same length, it has been determined that averaging the free energies obtained from shorter simulations may not give precise answers. Possible reasons for this behavior are discussed.
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  • 60
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    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 61
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    Journal of Computational Chemistry 12 (1991), S. 301-309 
    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 several variants of methods for the automatic search of optimum geometries of solutes via ab initio SCF procedures. The physical meaning of geometry optimization in solution is discussed. Advantages and disadvantages of the different variants are shown making use of calculations on the HF dimer with different basis sets, supplemented by information on the computational times. Suggestions for the most convenient strategies (which in part depend on the nature of the solute) are also done.
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  • 62
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    Journal of Computational Chemistry 12 (1991), S. 527-535 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New local graph invariants, “regressive vertex degrees” (which are slightly augmented vertex degrees) are introduced on the basis of decreasing contributions of more remote vertexes to the classical vertex degrees. Several such invariants are proposed (BRi(t), ERi(t), SRi(t)) where t (either t = 1 or t = 2) is an operator expressing the attenuation with increasing topological distance, according to formula (1) or (2). With the aid of these new local invariants, new topological indices (global graph invariants), Y (namely BY, EY or SY) are introduced and exemplified. Their ability to express the branching and to order alkanes is investigated. An appendix gives some recursive relationships for computing these indices.
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  • 63
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    Journal of Computational Chemistry 12 (1991), S. 342-349 
    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 in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis (e-ΔE/kT) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal-Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf-Gen reads the history file and extracts all low energy conformations visited during the run.
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    Journal of Computational Chemistry 12 (1991), S. 620-626 
    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 protocol to replace “10-12” hydrogen bonding function with the “6-12” form to reproduce hydrogen bond distances, energies, and geometries in molecular mechanics calculations is described. The 6-12 function was least-squares fit to the normally employed 10-12 form of the function for the hydrogen bond types of the Weiner et al. force field by iterating over the A and B coefficients. A weighting function was used to fit the curves in the most critical areas. The 6-12 hydrogen bond model was compared with the Weiner et al. force field, OPLS/AMBER fore field, and quantum mechanical calculations on two simple systems, the water dimer and the chloride-water interaction. The 6-12 model produced structures, energies, and geometries that were consistent with the other molecular mechanics calculations and showed reasonable agreement to the quantum mechanical results for the water dimer. The 6-12 model was also compared with normal calculations using a 10-12 model on several representative systems. The results indicate that the 6-12 function, when substituted by the procedure outlined in this work, yields structures and hydrogen bond properties that are similar to the normal 10-12 model.
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    Journal of Computational Chemistry 12 (1991), S. 421-426 
    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 effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.
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  • 66
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    Journal of Computational Chemistry 12 (1991), S. 446-453 
    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 SCF-MO Hartree-Fock calculations were performed using the STO-3G, 6-31G, and 6-31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine-atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the C—O bond lengths are appreciably longer than typical C—O bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed-proton model by 6.80 eV with the 6-31G* basis set. The free-H model compared favorably with the x-ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α-quartz. In the fixed-H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H-F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6-31G) compared to the diamagnetic neutral one. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Gō-Scheraga algorithm to produce rigid-geometry chain closures for polypeptide chains (N. Gō and H.A. Scheraga, Macromolecules, 3, 178, 1970) has been updated to allow each residue in the chain to adopt different bond lengths or bond angles. A treatment of five-residue local chain deformations is presented in detail. For chain sections shorter than five residues in length, it is shown that satisfactory closures may be obtained by direct fitting, indicating that the rigid-geometry approximation is adequate to model even short sections of chains having perturbed local geometry. The new implementation of the algorithm has been applied to several problems in protein structure determination and molecular modeling. The first of these is the problem of finding standard-geometry closures for short regions of chains having irregular geometry. It is shown that standard-geometry closures which superimpose well upon the coordinates of the irregular structures may be obtained routinely for chain sections that are five amino acid residues or more in length. Another application of the algorithm is to generate a large number of closures for a short segment of a protein chain, as a method to search the conformational space of this segment. The latter application should prove useful in studies in which the conformation of some region of a given protein has not been determined experimentally. Such applications include the modeling of proteins which have a sequence homology to a crystallized protein, and modeling regions of crystallized proteins which are not well-defined in electron density maps.
    Additional Material: 5 Ill.
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  • 68
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    Journal of Computational Chemistry 12 (1991), S. 560-564 
    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 general theory of three-electron Hylleraas-Configuration-Interaction method using linear correlation factors of the form rij has been implemented for molecular systems using cartesian Gaussians as basis sets. A brief review of the theory and the form of the three-electron integrals is presented. Additionally, a table of numerical values of some selected three-electron integrals is given. Results from test calculations on H3 using the full form of the theory are presented for some simple basis sets. A discussion of the computational problems that need to be overcome before this approach is competitive with traditional methods is included.
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  • 69
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    Journal of Computational Chemistry 12 (1991), S. 606-610 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Geometry optimization directly in Cartesian coordinates using the EF and GDIIS algorithms with standard Hessian updating techniques is compared and contrasted with optimization in internal coordinates utilizing the well known Z-matrix formalism. Results on a test set of 20 molecules show that, with an appropriate initial Hessian, optimization in Cartesians is just as efficient as optimization in internals, thus rendering it unnecessary to construct a Z-matrix in situations where Cartesians are readily available, for example from structural databases or graphical model builders.
    Additional Material: 1 Ill.
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  • 70
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    Journal of Computational Chemistry 12 (1991), S. 627-634 
    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 two techniques for implementing a new method of simulating an entire virion. Earlier computer simulations of a capsid protein revealed large edge effects due to the use of free standing boundaries. Because of the size of a given protomer, conventional three-dimensional periodic boundary conditions would be extremely wasteful. This would require an extremely large number of solvent molecules, and therefore would be computationally feasible for only a fragment of the entire virion. The new method employs non-space-filling computational cells in molecular modeling and molecular dynamics with the boundary conditions based on the icosahedral group. The method is general and could be used for any molecular system with a point group symmetry. With this method, the dynamical and spatial intra and interprotomer correlations can be studied at atomic levels. The technique is applicable to any virion with icosahedral symmetry. A sample calculation involving a geometry optimization of the human rhinovirus coat proteins is given to demonstrate the technique.
    Additional Material: 7 Ill.
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  • 71
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    Journal of Computational Chemistry 12 (1991), S. 675-680 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation (ΔHf) and proton affinities (PA) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the AM1 and PM3 semiempirical methods. The following substitutents are considered: NO2, CN, CF3, CHO, F, Cl, COCH3, H, CH3, OCH3, SCH3, NH2, and N(CH3)2. The results are compared with the experimental data. Both methods reproduce the ΔHf with comparble accuracy; the rms deviations are 4.1 (AM1) and 4.5 kcal/mol (PM3) for the free bases and 9.5 (AM1) and 9.7 kcal/mol (PM3) for their conjugated acids. The PA are systematically underestimated by both methods, but AM1 appears to be clearly better than PM3 for reproducing the experimental values. The rms deviations for AM1 and PM3 are 5.1 and 9.6 kcal/mol, respectively. This is due to a cancellation of systematic errors in the calculated ΔHf in the AM1 case and to a summation of the errors in the PM3 case. Both methods correctly reproduce conformations of the molecules under consideration.
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  • 72
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    Journal of Computational Chemistry 12 (1991), S. 697-704 
    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 the current practice of quantum chemistry, it is not clear whether corrections for basis set superposition errors should be applied to the calculation of potential energy curves, in order to improve agreement with experimental data. To examine this question, spectroscopic parameters derived from theoretical potential curves are reported for the homonuclear diatomics C2, N2, O2, and F2, using a configuration interaction method. Three different basis sets were used, including double zeta plus polarization, triple zeta plus double polarization, and double zeta polarization augmented by bond functions. The bond function basis sets, which were optimized in the preceding paper to obtain accurate dissociation energies, also gave the most accurate parameters. The potential curves were then corrected for basis set superposition error using the counterpoise correction, and the spectroscopic parameters were computed again. The BSSE-corrected curves showed worse agreement with experiment for all properties than the original (uncorrected) curves. The reasons for this finding are discussed. In addition to the numerical results, some problems in the application of the BSSE correction to basis sets containing bond functions are shown. In particular, there is an overcounting of the lowering due to the bond functions, regardless of which type of correction is applied. Also, genuine BSSE affects cannot be separated from energy-lowering effects due to basis set incompleteness, and we postulate that it is the latter which is strongly dominant in the calculation of covalent potential curves. Based on these arguments, two conclusions follow: (1) application of BSSE corrections to potential curves should not be routinely applied in situations where the bonding is strong, and (2) appropriate use of bond functions can lead to systematic improvement in the quality of potential curves.
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  • 73
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    Journal of Computational Chemistry 12 (1991), S. 970-980 
    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 outline a search for optimal parameters involving heteroatoms for use in multivariate regression analysis in structure-property and structure-activity studies. The problem consists of determining optimal numerical values for the diagonal elements of the adjacency matrix in graphs with atoms of different kind. In particular we consider weighted paths as the basic molecular descriptors and search for optimal parameters for carbon atom and oxygen atom in a correlation of molecular structure with isomeric variations in the boiling points of hexanols. Standard error is taken as the criterion for the selection of the optimal parameters. The weighting algorithm restricts the diagonal entries to values greater than -1. The selection of positive diagonal values leads to reducing the path numbers and the negative values lead to enlarging the role of path numbers relative to the zero diagonal values implied by simple graphs in which heteroatoms are not discriminated. A systematic search for optimal parameters for alcohols gave for carbon atom and oxygen atom diagonal entries: x = 1.50 and y = -0.85 respectively when a single path number is used as a descriptor and x = -0.15 and y = -0.94 when two path numbers are used. The parameters derived for 17 hexanols have been successively applied to 37 heptanols demonstrating thus transferability of the parameters.
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  • 74
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    Journal of Computational Chemistry 12 (1991), S. 1008-1013 
    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 Simulated Annealing method using a quantum mechanical potential energy surface is used to study the interactions of molecules and the formation of clusters. The results obtained for a range of systems are in good agreement with other theoretical calculations and experimental data where available.
    Additional Material: 7 Ill.
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  • 75
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    Journal of Computational Chemistry 12 (1991), S. 1058-1064 
    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 definition and implementation of a rigorous two-electron integral bound based on Schwarz' inequality both for gradient and hessian calculations is presented. Tests demonstrate the advantages of this easily implemented and effective bound.
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  • 76
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    Journal of Computational Chemistry 12 (1991), S. 1089-1096 
    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 virial theorem for molecules is shown to have two different forms, one employing the energy gradient the other involving the Hellmann-Feynman force. While the former VT can be fulfilled by a uniform scaling of the basis set, the latter cannot be satisfied in certain basis sets, and can give unrealistic results in others. The scaling procedure is applied to molecules at nonstationary points on the potential energy surface and it is found that energy components can change substantially, especially at short bondlengths, while the change in total energy is small. The effects on molecular properties are also small.
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  • 77
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    Journal of Computational Chemistry 12 (1991), S. 1118-1124 
    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 theorem of Gutman et al. (1983) is applied to calculate the number of spanning trees in the carbon-carbon connectivity-network of the recently diagnosed C60-cluster buckminsterfullerene. This “complexity” turns out to be approximately 3.75 × 1020 and it is found necessary to invoke the device of modulo arithmetic and the “Chinese Remainder Theorem” in order to evaluate it precisely on a small computer. The exact spanningtree count for buckminsterfullerene is 375 291 866 372 898 816 000, or, 225 × 34 × 53 × 115 × 193. A “ringcurrent” calculation by the method of McWeeny may be based on any desired one of this vast number of spanning trees.
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  • 78
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    Journal of Computational Chemistry 12 (1991), S. 1223-1231 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Given a reaction mechanism we show how a symbolic computation approach can be used to develop the kinetic equations by identifying the reaction scheme with an equivalent matrix. Our method is also applicable in cases where the stoichiometric matrix approach fails. The specific algorithm that is written applies to schemes where individual reactions are at most ternary, but the way to generalize the procedure is also discussed. By using symbolic computing it is possible to determine general properties of the system. We demonstrate this by showing how to use the matrix to determine the system's conservation laws, which in turn can be used to reduce the number of equations in the system. As another application it is shown how to determine some of the species which have a zero equilibrium state. To illustrate the procedure, example reaction schemes are investigated.
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  • 79
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    Journal of Computational Chemistry 12 (1991), S. 1260-1264 
    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 powerful algorithm for calculating conjugated-circuit expectations for planar graphs is enunicated. The utility for systematizing quantitative resonance-theoretic computations on conjugated hydrocarbons, and related species, is emphasized.
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  • 80
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    Journal of Computational Chemistry 12 (1991), S. 844-849 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Application of Allinger's MM2/MM3 force fields to molecules of real interest is frequently hindered by the lack of parameters for various heterocyclic systems and for poly-functionalized molecules. A common approach to this problem is to manually choose missing parameters “by analogy” with those that are part of the force field's internal parameter set. Naturally, this is generally attempted only by those possessing extensive experience with force fields. In order to use the MM2/MM3 force fields to study herbicides, an algorithm has been developed to automate this process for the non MM2 specialist. Using a set of “relative cost” criteria for atom type replacement, the algorithm searches the force field parameter set and selects the most appropriate parameters for a given molecule whose MM2 output file contains “missing parameter” errors. The program selects parameter error messages from a standard MM2 output file, finds analogous parameters, asks the user to verify their appropriateness and creates a standard MM2 parameter deck for the molecule of interest.
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  • 81
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    Journal of Computational Chemistry 12 (1991), S. 872-879 
    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 modified the MM2(80) molecular mechanics force field for alcohols and ethers to reproduce geometric trends predicted by ab initio calculations with the 4-21G basis set. The results obtained with the modified force field are consistent with experimental evidence.
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  • 82
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    Journal of Computational Chemistry 12 (1991), S. 1134-1141 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heavy atom and deuterium isotope effects for the hydride transfer from formate to carbon dioxide were determined using MNDO, AM1, and PM3 semiempirical methods and the ab initio RHF/3-21G*, 3-21 + G, 6-31G*, and 6-31 + G* basis sets. Frequencies were also determined for ground state structures using 6-31G* basis set at the MP2 level of theory. The calculated isotope effects compared favorably with the experimentally determined values of Hermes et al. (Biochemistry, 23, 5479 (1984)). The calculated ground state frequencies were high for most vibrational modes as compared with measured values, however some ab initio methods underestimate the carbon hydrogen stretching frequencies. The heavy atom isotope effects were influenced to a large extent by the excitation factor, the mass factor and the moment of inertia factor of the Bigeleisen equation.
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  • 83
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    Journal of Computational Chemistry 12 (1991), S. 36-41 
    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 procedure is presented which allows a more economical representation of the potential produced by orbital charge distributions in which the orbitals are expanded in terms of a finite set of polynomial Gaussian functions. The basic idea is that the products of pairs of Gaussian basis functions, on which the charge distributions are expanded, are expressed in terms of a new basis set of optimally chosen single Gaussian functions. Such a procedure has been tested in a particular case and a few possible applications have been suggested.
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  • 84
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    Journal of Computational Chemistry 12 (1991), S. 106-112 
    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 vectorized computer code is developed for the enumeration of walks through the matrix power method for directed graphs. Application of this code to several graphs is considered. It is shown that the coefficients in the generating functions for signed graphs are much smaller in magnitude. It is shown that self-avoiding walks on some graphs can be enumerated as a linear combination of walk GFs of directed paths and rooted-directed paths.
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  • 85
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    Journal of Computational Chemistry 12 (1991), S. 126-134 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Higher ionization energies were calculated with PM3, AM1, and MNDO for three series of molecules, representative small molecules, molecules containing heteroatoms, and sterically congested alkenes. Values from PM3, AM1, and MNDO were compared to experimental values. In most instances, the semiempirical calculations correctly predict the ordering of higher ionization energies. In the absence of steric hindrance, MNDO is the method of choice. Within groups of molecules, AM1 performs better on hydrocarbons, especially twisted hydrocarbons, than PM3. PM3 commonly gives sigma orbitals which are too high in energy compared to related pi orbitals. PM3 performed better than AM1 with molecules containing oxygen, but failed to give the correct geometry for hydrogen peroxide.
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  • 86
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    Journal of Computational Chemistry 12 (1991), S. 276-282 
    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 improved gradient-based algorithm is presented for the determination of the minimum energy point on the crossing seam hypersurface between two arbitrary potential energy hypersurfaces. The Hessian matrix is updated employing the gradient information. The method is demonstrated in a study of some representative cases including charge-transfer states of a typical molecular-device molecule (a rigid spiro π - σ - π molecular cation) with, as well as without, an external electric field.
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  • 87
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    Journal of Computational Chemistry 12 (1991), S. 310-319 
    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 mechanics energy minimizer is presented whose main features are the “floating blocks” and “isles” option, the “a-NOE” distance inequality constraints and the variable storage first derivative minimization method. The program possibilities are illustrated by examples of molecular docking, energy barrier estimation, modeling of infinite structures, and DNA bending simulations.
    Additional Material: 10 Ill.
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  • 88
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    Journal of Computational Chemistry 12 (1991), S. 215-219 
    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 algorithm for efficient evaluation of two-electron repulsion integrals (ERIs) using uncontracted geometrical-type Gaussian basis functions is presented. Integrals are evaluated by the Habitz and Clementi method. The use of uncontracted geometrical basis sets allows grouping of basis functions into shells (s, sp, spd, or spdf) and processing of integrals in blocks (shell quartets). By utilizing information common to a block of integrals, this method achieves high efficiency. This technique has been incorporated into the KGNMOL molecular interaction program. Representative timings for a number of molecules with different basis sets are presented. The new code is found to be significantly faster than the previous program. For ERIs involving only s and p functions, the new algorithm is a factor of two faster than previously. The new program is also found to be competitive when compared with other standard molecular packages, such as HONDO-8 and Gaussian 86.
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  • 89
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    Journal of Computational Chemistry 12 (1991), S. 237-247 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General mathematical solutions to excluded volume constrained problems in computational chemistry are reported. The solutions have been used to create a new family of molecular modeling algorithms to facilitate the study of molecular interactions in condensed phases. The new algorithms, collectively known as Molecular Silverware, are for the most part interactive and designed for packing, solvating, and sampling molecules embedded in simple or complex topological environments. Multifolded, disconnected, or porous molecular structures are permitted. Molecular Silverware assists the preparation of Monte Carlo and molecular dynamics simulations at a small fraction of the total simulation time. Primary targets for applications include the study of molecular recognition mechanisms and the selective binding of DNA, RNA, peptides, saccharides and other biopolymers in solution as well as the prediction of phase separation behavior and physical properties of non-crystalline condensed phases such as bulk polymers, polymer blends, organic liquids, membranes, micelles, gels, crosslinked networks, glasses, and amorphous heterogeneous catalysts. As a result of this new approach to excluded volume constraints, the computer simulation of noncrystalline condensed phases is no longer hampered by the lack of a general and efficient method for the creation and configurational sampling of small and large molecular assemblies at high densities.
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  • 90
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    Journal of Computational Chemistry 12 (1991), S. 283-291 
    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 program OPKINE is presented for the study of reaction mechanisms and multicomponent analysis in dynamic conditions. This program is written in FORTRAN-77 for IBM 30/90 and VAX 8300 computers, and permits the simultaneous evaluation of both rate constants and initial reagent concentrations or, alternatively, rate constants and sensitivities. Up to 20 kinetic curves, with up to 400 points each, can be treated to evaluate up to 40 parameters. Integration of the system of differential equations is performed by means of the Runge-Kutta-Fehlberg method. OPKINE is provided with the Simplex, and modified versions of the Davidon-Fletcher-Powell and Gauss-Newton-Marquardt optimization methods. A Monte Carlo procedure to search for the seeds is also available. Simulated experiments have been used to check the performances of the program. Complex kinetic mechanisms and mixtures of a large number of analytes can be managed with good results.
    Additional Material: 4 Ill.
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  • 91
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    Journal of Computational Chemistry 12 (1991), S. 350-358 
    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 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.
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  • 92
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    Journal of Computational Chemistry 12 (1991), S. 410-415 
    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 energy minimization in the computer program PACK established for investigating interactions of secondary structures in proteins was based on the finite deference method. It is well known that a minimizer of finite difference method is less efficient than that of analytical gradient method. In this article the equations of the analytical energy gradients for a multiple chain system have been derived and they can be directly incorporated into the PACK program. The revised version, PACK/2, thus obtained is much more efficient. Energy minimizations carried out on the theoretical models of 4-helix bundle, sheet-sheet packing, and β-barrel indicated that the CPU times were reduced 15- to 20-fold if the revised PACK/2 algorithm was used. In general, the more complicated the computed structure was, the more significantly the computation time was reduced. Furthermore, for the cases demonstrated here, the final minimized energies were always lower than those obtained by the original version of PACK, indicating that a better packing structure was achieved by means of the revised program PACK/2.
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  • 93
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    Journal of Computational Chemistry 12 (1991), S. 435-445 
    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 algorithm is presented for the numerical solution of the Poisson-Boltzmann equation by the finite difference method of successive over-relaxation. Improvements include the rapid estimation of the optimum relaxation parameter, reduction in number of operations per iteration, and vector-oriented array mapping. The algorithm has been incorporated into the electrostatic program DelPhi, reducing the required computing time by between one and two orders of magnitude. As a result the estimation of electrostatic effects such as solvent screening, ion distributions, and solvation energies of small solutes and biological macromolecules in solution, can be performed rapidly, and with minimal computing facilities.
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  • 94
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 487-504 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article summarizes the detailed equations for the time-dependent Hartree-Fock treatment of nonlinear properties for perturbations made up of a static electric field and an oscillating field. Explicit expressions for all nonlinear processes up to third order are obtained in terms of the density matrices at the same order. For processes at second and third order in perturbation, expressions in terms of lower order quantities are also obtained by applying the (2n + 1) theorem of perturbation theory. The corresponding computer implementation in the HONDO program is described.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 546-559 
    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 primary and secondary first and second derivatives of the NMR isotropic chemical shift with respect to bond length modification have been calculated in the gauge invariant atomic orbital (GIAO) perturbed Hartree-Fock approach for some 177 first-row nuclei in 63 molecules using the mixed basis heavy:6-311G(d)/hydrogen:4-31. The shift derivative with respect to multiple bond length changes correlates linearly with the shift itself while changes involving single bonds behave differently. Agreement between experimental derivatives and those calculated theoretically is good but the calculations show that second derivatives as well as both types of secondary effects cannot always be neglected. The correlation between the shift derivative and the isotropic shift indicates an exponential variation of the chemical shift with bond length near the vicinity of the equilibrium structure for multiple bonds.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 376-384 
    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 approach is presented for performing geometry optimization for stationary points on potential energy hypersurfaces with equality constraints on the internal coordinates of a polyatomic system. The working equations are the same as for unconstrained Newton-Raphson optimization in Cartesian coordinates except that projection operators are applied to the gradient and Hessian to enforce the constraints. Two reactive systems with different kinds of constraints are treated as examples: OH + H2 → OH3≠ → H2O + H with one constrained OH bond distance and CH3 + H2 → CH5≠ → CH4 + H with one constrained H—C—H bond angle in the CH3 group or with one constrained bond distance and one simultaneously constrained bond angle. In each case we optimized all reactants and products as well as the saddle point, all subject to the constraints.
    Additional Material: 3 Tab.
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991) 
    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
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991) 
    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
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 664-674 
    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 strategy for the determination of force parameters is presented. The equilibrium values appearing in the force field equations representing the “stretching” and “bending” of bonds are directly determined from quantum mechanical calculations without geometrical restrictions. The determination of the force parameters is carried out by means of a rigorous fitting between the quantum mechanic and the molecular mechanical energy variations arising from the perturbation of the geometric variables. The strategy presented here has been incorporated into a computer program named PAPQMD, which was developed in order to provide nonquantum mechanical experts with a powerful tool for the determination of approximate force parameters. The program was developed upon the assumption that force parameters are not universal, but they strongly depend on the molecular environment. This implies that the parametrization procedure should be done in a molecular model close to the molecule or molecules to be studied by means of molecular mechanical or dynamic methods, and consequently, it is no longer supposed that the variation of one geometrical parameter does not affect the rest of the molecular geometry. PAPQMD performs the fitting between molecular mechanics and quantum mechanical energies considering all the perturbations that the modification in one geometric variable causes in all the others, enabling the parametrization even of large molecules. The ability of our method to reproduce experimentally derived force parameters is discussed and compared with the widely used Hopfinger's strategy. The study of the behavior of PAPQMD and Hopfinger's strategies for reproducing the force parameters of two complex molecules demonstrates the superiority of the methodology presented here.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 746-750 
    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 for solving the protein docking problem is presented. Many tentative dockings are first generated by requiring a hole on the surface of one protein to match a knob on the surface of the other. All the tentative dockings are then applied. The initial configurations thus generated are further optimized. The optimization is facilitated by giving a discrete representation to the protein interior and a double-layer discrete representation to the protein surface. The algorithm presented correctly predicts the association of trypsin with its inhibitor as well as that of the α and β subunits in hemoglobin.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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