Molecular modeling of geometries, charge distributions, and binding energies of small, druglike molecules containing nitrogen heterocycles and exocyclic amino groups in the gas phase and in aqueous solution

Brian R. White, Carston R. Wagner, Donald G. Trahlar, Elizabeth A. Amin

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Abstract

We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and fifteen are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1 H-2-(aminomethyl) pyrazine and 1 H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31 +G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to use the well-validated charge model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations, followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation was used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without the CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 druglike ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER.

Original languageEnglish (US)
Pages (from-to)1718-1732
Number of pages15
JournalJournal of Chemical Theory and Computation
Volume4
Issue number10
DOIs
StatePublished - Oct 14 2008

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Molecular modeling
Charge distribution
Binding energy
charge distribution
field theory (physics)
Nitrogen
binding energy
Gases
vapor phases
aqueous solutions
nitrogen
Molecules
Geometry
geometry
Solvation
molecules
Methotrexate
Pyrazines
solvation
Water

Cite this

@article{b9ffd38145394ef1a2f9d0e987e40de7,
title = "Molecular modeling of geometries, charge distributions, and binding energies of small, druglike molecules containing nitrogen heterocycles and exocyclic amino groups in the gas phase and in aqueous solution",
abstract = "We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and fifteen are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1 H-2-(aminomethyl) pyrazine and 1 H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31 +G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to use the well-validated charge model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations, followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation was used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without the CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 druglike ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER.",
author = "White, {Brian R.} and Wagner, {Carston R.} and Trahlar, {Donald G.} and Amin, {Elizabeth A.}",
year = "2008",
month = "10",
day = "14",
doi = "10.1021/ct8000766",
language = "English (US)",
volume = "4",
pages = "1718--1732",
journal = "Journal of Chemical Theory and Computation",
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TY - JOUR

T1 - Molecular modeling of geometries, charge distributions, and binding energies of small, druglike molecules containing nitrogen heterocycles and exocyclic amino groups in the gas phase and in aqueous solution

AU - White, Brian R.

AU - Wagner, Carston R.

AU - Trahlar, Donald G.

AU - Amin, Elizabeth A.

PY - 2008/10/14

Y1 - 2008/10/14

N2 - We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and fifteen are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1 H-2-(aminomethyl) pyrazine and 1 H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31 +G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to use the well-validated charge model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations, followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation was used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without the CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 druglike ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER.

AB - We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and fifteen are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1 H-2-(aminomethyl) pyrazine and 1 H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31 +G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to use the well-validated charge model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations, followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation was used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without the CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 druglike ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER.

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