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Forti F, Barril X, Luque FJ, Orozco M. Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian. J Comput Chem 2008; 29:578-87. [PMID: 17705247 DOI: 10.1002/jcc.20814] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The need to simulate large-sized molecules or to deal with large series of compounds is a challenging topic in computational chemistry, which has stimulated the development of accurate semiempirical methods, such as the recently reported Recife Model 1 (RM1; J Comput Chem 2006, 27, 1101). Even though RM1 may prove to be of value simply due to the enhanced quantitative accuracy in gas phase, it is unclear how the new parameters optimized for RM1 affect the suitability of this semiempirical Hamiltonian to study chemical processes in condensed phases. To address this question, we report the parametrization of the MST/RM1 continuum model for neutral solutes in water, octanol, chloroform and carbon tetrachloride, and for ions in water. The results are used to discuss the transferability of the solvation parameters implemented in previous MST/AM1 and MST/PM3 models.
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Affiliation(s)
- Flavio Forti
- Facultat de Farmàcia, Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, Av. Diagonal 643, E-08028, Barcelona, Spain
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2
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Tishchenko O, Truhlar DG. Global Potential Energy Surfaces with Correct Permutation Symmetry by Multiconfiguration Molecular Mechanics. J Chem Theory Comput 2007; 3:938-48. [DOI: 10.1021/ct600315h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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3
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Thiel W. Perspectives on Semiempirical Molecular Orbital Theory. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470141526.ch10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Horn AHC, Clark T. Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets. J Mol Model 2006; 13:381-92. [PMID: 16924559 DOI: 10.1007/s00894-006-0137-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 06/23/2006] [Indexed: 11/28/2022]
Abstract
The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159-168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol(-1), respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively.
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Affiliation(s)
- Anselm H C Horn
- Computer Chemie Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Alemán C, Luque F, Orozco M. Suitability of the PM3-derived molecular electrostatic potentials. J Comput Chem 2004. [DOI: 10.1002/jcc.540140706] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Tasi G, Kiricsi I, Förster H. Representation of molecules by atomic charges: A new population analysis. J Comput Chem 2004. [DOI: 10.1002/jcc.540130310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Curutchet C, Salichs A, Barril X, Orozco M, Javier Luque F. Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study. J Comput Chem 2003; 24:32-45. [PMID: 12483673 DOI: 10.1002/jcc.10155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study examines the transferability of fragmental contributions to the octanol/water partition coefficient. As a previous step, we report the parameterization of the AM1 and PM3 versions of the MST model for n-octanol. The final AM1 and PM3 MST models reproduce the experimental free energy of solvation and the octanol/water partition coefficient (log P(ow)) with a root-mean-square deviation of around 0.7 kcal/mol and 0.5 (in units of log P), respectively. Based on this parameterization, an NNDO-based procedure is presented to dissect the free energy of transfer between octanol and water in contributions directly associated with specific atoms or functional groups. The application of this procedure to a set of representative molecular systems illustrates the dependence of the log P(ow) fragmental contribution due to electronic, hydrogen bonding, and steric effects, which cannot be easily accounted for in simple additive-based empirical schemes. The results point out the potential use of theoretical methods to refine the fragmental contributions in empirical methods.
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Affiliation(s)
- C Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, Barcelona 08028, Spain
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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9
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Leboeuf M, Köster AM, Jug K, Salahub DR. Topological analysis of the molecular electrostatic potential. J Chem Phys 1999. [DOI: 10.1063/1.479749] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Marynick DS. Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(199705)18:7<955::aid-jcc7>3.0.co;2-q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Rameau JP, Devillers J, Declercq JP, Chauviere G, Perie J. Molecular structure of 2-Amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazol (Megazol) and related compounds: A concerted study using X-ray crystallography, molecular mechanics, and semiempirical methods. Struct Chem 1996. [DOI: 10.1007/bf02281230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches. J Comput Chem 1996. [DOI: 10.1002/(sici)1096-987x(19960115)17:1<87::aid-jcc8>3.0.co;2-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Molecular Electrostatic Potentials from Density Functional Theory. THEORETICAL AND COMPUTATIONAL CHEMISTRY 1996. [DOI: 10.1016/s1380-7323(96)80042-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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14
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Orozco M, Luque FJ. Generalization of the Molecular Electrostatic Potential for the Study of Noncovalent interactions. THEORETICAL AND COMPUTATIONAL CHEMISTRY 1996. [DOI: 10.1016/s1380-7323(96)80044-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Cummins PL, Gready JE. Thermodynamic integration calculations on the relative free energies of complex ions in aqueous solution: Application to ligands of dihydrofolate reductase. J Comput Chem 1994. [DOI: 10.1002/jcc.540150704] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Cummins PL, Gready JE. The electrostatic potential in the semiempirical molecular orbital approximation. Chem Phys Lett 1994. [DOI: 10.1016/0009-2614(94)00617-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Wang B, Ford GP. Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations. J Comput Chem 1994. [DOI: 10.1002/jcc.540150210] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Alhambra C, Luque FJ, Orozco M. Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials. J Comput Chem 1994. [DOI: 10.1002/jcc.540150103] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Alem�n C, Luque FJ, Orozco M. A new scaling procedure to correct semiempirical MEP and MEP-derived properties. J Comput Aided Mol Des 1993. [DOI: 10.1007/bf00125328] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Cummins PL, Gready JE. Computer-aided drug design: a free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase. J Comput Aided Mol Des 1993; 7:535-55. [PMID: 8294945 DOI: 10.1007/bf00124361] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of 8-methylpterins and 8-methyl-N5-deazapterins to dihydrofolate reductase (DHFR). Methyl-substitution at the 5, 6 and 7 positions in the N-heterocyclic ring gives rise to a variety of ring substituent patterns and biological activity: several of these methyl derivatives of the 8-methyl parent compounds (8-methylpterin and 8-methyl-N5-deazapterin) have been identified as substrates or inhibitors of vertebrate DHFR in previous work. The calculated free energy differences reveal that the methyl-substituted compounds are thermodynamically more stable than the primary compounds (8-methylpterin and 8-methyl-N5-deazapterin) when bound to the enzyme, due largely to hydrophobic hydration phenomena. Methyl substitution at the 5 and/or 7 positions in the 6-methyl-substituted compounds has only a small effect on the stability of ligand binding. Furthermore, repulsive interactions between the 6-methyl substituent and DHFR are minimal, suggesting that the 6-methyl position is optimal for binding. The results also show that similarly substituted 8-methylpterins and 8-methyl-N5-deazapterins have very similar affinities for binding to DHFR. The computer simulation predictions are in broad agreement with experimental data obtained from kinetic studies, i.e. 6,8-dimethylpterin is a more efficient substrate than 8-methylpterin and 6,8-dimethyl-N5-deazapterin is a better inhibitor than 8-methyl-N5-deazapterin.
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Affiliation(s)
- P L Cummins
- Department of Biochemistry, University of Sydney, N.S.W., Australia
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Orozco M, Luque F. Molecular interaction potential: A new tool for the theoretical study of molecular reactivity. J Comput Chem 1993. [DOI: 10.1002/jcc.540140512] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cummins PL, Gready JE. Novel mechanism-based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: a comparison of theory and experiment for 8-methylpterin and 6,8-dimethylpterin. Proteins 1993; 15:426-35. [PMID: 8460112 DOI: 10.1002/prot.340150409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism-based pterins, 8-methylpterin and 6,8-dimethylpterin, to dihydrofolate reductase (DHFR), with cofactor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8-dimethylpterin is thermodynamically more stable than DHFR.NADPH.8-methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8-dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH-dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8-dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8-methylpterin. The kinetic data suggest a value of 6.6 +/- 0.2 for the pKa of the active site Glu-30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1-10 microM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8-methylpterin and 6,8-dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kcal/mol.
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Affiliation(s)
- P L Cummins
- Department of Biochemistry, University of Sydney, N.S.W., Australia
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Merz KM. Analysis of a large data base of electrostatic potential derived atomic charges. J Comput Chem 1992. [DOI: 10.1002/jcc.540130609] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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