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  • 1
    ISSN: 0948-5023
    Keywords: Cocaine ; Electrostatic potential ; Ester hydrolysis ; Molecular orbital calculations ; Transition state ; Catalytic antibodies ; Transition state analogs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Semiempirical molecular orbital calculations have been performed for the first step in the alkaline hydrolysis of the neutral benzoylester of cocaine. Successes, failures, and limitations of these calculations are reviewed. A PM3 calculated transition state structure is compared with the PM3 calculated structure for the hapten used to induce catalytic antibodies for the hydrolysis of cocaine. Implications of these calculations for the computer–aided design of transition state analogs for the induction of catalytic antibodies are discussed.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 4595-4606 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The complete basis set methods CBS-4, CBS-QB3, and CBS-APNO, and the Gaussian methods G2 and G3 were used to calculate the gas phase energy differences between six different carboxylic acids and their respective anions. Two different continuum methods, SM5.42R and CPCM, were used to calculate the free energy differences of solvation for the acids and their anions. Relative pKa values were calculated for each acid using one of the acids as a reference point. The CBS-QB3 and CBS-APNO gas phase calculations, combined with the CPCM/HF/6-31+G(d)//HF/6-31G(d) or CPCM/HF/6-31+G(d)//HF/6-31+G(d) continuum solvation calculations on the lowest energy gas phase conformer, and with the conformationally averaged values, give results accurate to 〈fraction SHAPE="CASE"〉12 pKa unit. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 95 (1991), S. 5085-5089 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 349-360 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The PM3 quantum-mechanical method has been used to study large water clusters ranging from 8 to 42 water molecules. These large clusters are built from smaller building blocks. The building blocks include cyclic tetramers, pentamers, octamers, and a pentagonal dodecahedron cage. The correlations between the strain energy resulting from bending of the hydrogen bonds formed by different cluster motifs and the number of waters involved in the cluster are discussed. The PM3 results are compared with TIP4P potential and ab initio results. The number of net hydrogen bonds per water increases with the cluster size. This places a limit on the size of clusters that would fit the Benson model of liquid water. Many of the 20-mer clusters fit the Benson model well. Calculations of the ion cluster (H2O)40(H3O+)2 reveal that the m/e ratio obtainable by mass spectrometry experiments can uniquely indicate the conformation of the 20 water pentagonal dodecahedron cage present in the larger clusters. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 83-93 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The potential energy surface for the first step of the alkaline hydrolysis of methyl acetate was explored by a variety of methods. The conformational search routine within SPARTAN was used to determine the lowest energy AM1 and PM3 structures for the anionic tetrahedral intermediate. Ab initio single point and geometry optimization calculations were performed to determine the lowest energy conformer, and the linear synchronous transition (LST) method was used to provide an initial structure for transition state optimization. Transition states were obtained at the AM1, PM3, 3-21G, and 3-21 + G levels of theory. These transition states were compared with the anionic tetrahedral intermediates to examine the assumption that the intermediate is a good model for the transition state. In addition, the Cramer/Truhlar SM3 solvation model was used at the semiempirical level to compare gas phase and aqueous alkaline hydrolysis of methyl acetate. © 1995 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 103-112 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A computationally efficient procedure for modeling the alkaline hydrolysis of esters is proposed based on calculations performed on methyl acetate and methyl benzoate systems. Extensive geometry and energy comparisons were performed on the simple ester methyl acetate. The effectiveness of performing high level single point ab initio energy calculations on the geometries obtained from semiempirical and ab initio methods was determined. The AM1 and PM3 semiempirical methods are evaluated for their ability to model the transition states and intermediates for ester hydrolysis. The Cramer/Truhlar SM3 solvation method was used to determine activation energies. The most computationally efficient way to model the transition states of large esters is to use the PM3 method. The PM3 transition structure can then be used as a template for the design of haptens capable of inducing catalytic antibodies. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 89-104 
    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 PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F 〉 O 〉 N and acceptor strength follows the order N 〉 O 〉 F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H---N bond to be the strongest and the N-H---F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1326-1332 
    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 PM3 quantum-mechanical method is able to model the magic water clusters (H2O)20 and (H2O)21H+. Results indicate that the H3O+ ion is tightly bound within the (H2O)20 cluster by multiple hydrogen bonds, causing deformation to the symmetric (H2O)20 pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H2O)21H+ clusters are presented. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 95-107 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ability of the PM3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of PM3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA-pdT, pdG-pdC, and pdG(syn)-pdC are presented and discussed. The PM3 method is the first of the parameterized NDDO quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson-Crick base pairing are 0.1-0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′—C5′ bond (γ), and the C5′—O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. PM3 calculations reveal that many of the most stable conformations are stabilized by intramolecular C—H≡O hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT-pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the PM3 method for the four bases in the dT-pdA duplex. PM3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the PM3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The PM3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 51-59 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Over the past 7 years, the enediyne anticancer antibiotics have been widely studied due to their DNA cleaving ability. The focus of these antibiotics, represented by kedarcidin chromophore, neocarzinostatin chromophore, calicheamicin, esperamicin A, and dynemicin A, is on the enediyne moiety contained within each of these antibiotics. In its inactive form, the moiety is benign to its environment. Upon suitable activation, the system undergoes a Bergman cycloaromatization proceeding through a 1,4-dehydrobenzene diradical intermediate. It is this diradical intermediate that is thought to cleave double-stranded DNA through hydrogen atom abstraction. Semiempirical, semiempirical CI, Hartree-Fock ab initio, and MP2 electron correlation methods have been used to investigate the inactive hex-3-ene-1,5-diyne reactant, the 1,4-dehydrobenzene diradical, and a transition state structure of the Bergman reaction. Geometries calculated with different basis sets and by semiempirical methods have been used for single-point calculations using electron correlation methods. These results are compared with the best experimental and theoretical results reported in the literature. Implications of these results for computational studies of the enediyne anticancer antibiotics are discussed. © 1995 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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