Ab Initio Molecular Electrostatic Potential Research Articles

Prelude to molecular dynamics: Topography‐driven gaussian charge models

AbstractA new strategy to develop Gaussian charge models (GCMs) for molecules like ammonia, water, ethene, hydrogen sulfide, formaldehyde and benzene is presented. These molecular models comprising of positive point charges and negative Gaussian charge distributions (GCDs), which represent nuclei and continuous electron charge distribution, are found to correctly represent the ab initio Molecular Electrostatic Potential (MESP) and reproduce its essential topographical features of corresponding molecules. The models use optimized parameters: positive charges at nuclei, negative charges on GCDs, Gaussian exponent and centers. The Potential Energy Surface (PES) of water dimer has been explored using water GCMs. A good agreement has been found between PES obtained using GCMs and wave function. The Gaussian models correctly predict structure of benzene‐water complex. It is thus recommended to use GCMs for molecular dynamic simulations.

Multipole models of sulphur for accurate anisotropic electrostatic interactions within force fields

Nowadays, as computing has become much more available, a fresh momentum has been observed in the field of re-visioning and re-parameterizing the usual tools, as well as estimating for the incorporation of new qualitative capabilities, aimed at making more accurate and reliable predictions in drug discovery processes. Inspired by the success of modelling the electrostatic part of the halogen bonding (XB) by means of the distributed multipole expansion, a study is presented which attempts to extend this approach to a tougher case of σ-hole interaction: sulphur-based chalcogen bonding. To that end, 11 anisotropic models have been derived and tested for their performance in the reproduction of reference ab initio molecular electrostatic potential. A careful examination resulted in three models which have been selected for further examination as a part of the molecular mechanics force field (GAFF). The combined force field was used to estimate inter- and intra-molecular interactions for the molecular systems, capable of differentiating the binding from the σ-hole and other directions. The anisotropic models proposed were generally able to correct the wrong predictions of the sulphur models based only on isotropic charges and, thus, are a promising direction for further development of the refined electrostatics force fields.

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core.

Halogen bonding (XB) is a new promising interaction pattern in medicinal chemistry. It has predominantly electrostatic nature - high electrostatic potential anisotropy. However to fully unleash the potential of XB in rational drug design fast and robust empirical methods of XB description should be developed. Current approaches rely heavily on ab initio calculation for each molecule studied. Thus fast prediction of electrostatic parameters for description of XB for arbitrary organic molecules is of paramount importance to promptly establish QSAR/QSPR, virtual screening and molecular docking pipelines suitable for today's agile development requirements. The two most promising approaches to describe anisotropic electrostatic models - the extra point (EP) charge model and the multipole expansion (ME) model - were studied on their ability (1) to describe ab initio molecular electrostatic potential (MEP) and (2) to produce parameters that can be predicted for each molecule empirically rather than estimated via ab initio calculations. The reference ab initio MEP was calculated for a set of 730 substituted halobenzenes. Parameters for anisotropic electrostatics of both empirical models (EP and ME) studied were extracted from ab initio MEP. The FreeWilson and Hansch type QSPR models relating XB parameters with aromatic substituents were built and analyzed, providing the guidelines for further development.

Core–shell potential‐derived point charges

The present work details the development of a core-shell model for the purposes of obtaining potential-derived point charges from the ab initio molecular electrostatic potential. In contrast to atomic point charge models, the core-shell model decomposes all atoms into a core with static charge located at a fixed atomic position and a shell with variable charge and position. The optimization of shell charges and positions is discussed. The core-shell model was found to significantly improve description of the ab initio electrostatic potential when compared to potential-derived net atomic point charge models as well as distributed multipoles with contributions up to atomic quadrupole moments. The core-shell model was found to produce similar results as the Weller-Williams lone-pair model and differences in the implementation of the models are discussed.

Application of error‐ranked singular value decomposition for the determination of potential‐derived atomic‐centered point charges

The present work provides a detailed investigation on the use of singular value decomposition (SVD) to solve the linear least-squares problem (LLS) for the purposes of obtaining potential-derived atom-centered point charges (PD charges) from the ab initio molecular electrostatic potential (V(QM)). Given the SVD of any PD charge calculation LLS problem, it was concluded that (1) all singular vectors are not necessary to obtain the optimal set of PD charges and (2) the most effective set of singular vectors do not necessarily correspond to those with the largest singular values. It is shown that the efficient use of singular vectors can provide statistically well-defined PD charges when compared with conventional PD charge calculation methods without sacrificing the agreement with V(QM). As can be expected, the methodology outlined here is independent of the algorithm for sampling V(QM) as well as the basis set used to calculate V(QM). An algorithm is provided to select the best set of singular vectors used for optimal PD charge calculations. To minimize the subjective comparisons of different PD charge sets, we also provide an objective criterion for determining if two sets of PD charges are significantly different from one another.

Fast tools for calculation of atomic charges well suited for drug design1

Two novel approaches to construct empirical schemes for partial atomic charge calculation were proposed. The charge schemes possess important benefits. First, they produce both topologically symmetrical and environment dependent charges. Second, they can be parameterised to reasonably reproduce ab initio molecular electrostatic potential (MEP), which guarantees their successful use in molecular modelling. To validate the approaches, the parameters of the proposed charge schemes were fitted to best reproduce MEP simultaneously on grids around a set of 227 diverse organic compounds. The residual errors in MEP reproduction due to calculated atomic charges were compared to those due to charges from known charge schemes. 1Presented at CMTPI 2007: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Moscow, Russia, September 1–5, 2007).

Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets

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.

Near ab initio quality molecular electrostatic potential maps using hybridization displacement charges at PM3 level and effects of geometrical changes in amino groups

Charge distributions, dipole moments, and molecular electrostatic potentials (MEP) around several molecules consisting of carbon, nitrogen, oxygen, fluorine, sulfur, and chlorine atoms were studied using the PM3 semiempirical method and the results compared with those obtained using ab initio calculations at the RHF/6-31G** level. Thus it is shown that relative MEP values near different atoms can be obtained using hybridization displacement charges (HDC) obtained by employing PM3 density matrices that usually agree quite satisfactorily with the ab initio ones. Further, positions of ab initio MEP minima are correctly located and the corresponding relative MEP values usually correctly predicted using the PM3(HDC) charges distributed continuously in three dimensions according to the forms of squares of valence s atomic orbitals. The necessary parameters for HDC calculations using the PM3 method were optimized. It is shown how within the frameworks of both PM3 and AM1 methods the π electrons or lone pairs associated with amino group nitrogen atoms and ring atoms can be satisfactorily treated in different situations. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 299–312, 2001

Electrostatic potential mapping using hybridization displacement charge: Atomic parameters and transferability of charge and potential

Molecular electrostatic potential (MEP) maps and MEP-derived charges for certain molecules were studied by the ab initio approach using the 6-31G basis set. These results were used to obtain the parameters (K and ζ) for fluorine, sulfur, and chlorine required for the hybridization displacement charge (HDC) calculations employing the MNDO and AMI methods. The HDC combined with Löwdin charges, distributed continuously in three-dimension spherically and symmetrically, were shown to reproduce ab initio MEP features of molecules fairly well. This method of computing the MEP was applied to two molecules of pharmacological importance, namely, dimaprit and mustard gas. It is shown by studying the cis and trans forms of two amino acids that transferability of the MEP is appreciably less acceptable than that of charges in going from one conformation to the other. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 149–156, 1998

Molecular Dynamics Modeling of Clay Minerals. 1. Gibbsite, Kaolinite, Pyrophyllite, and Beidellite

A molecular dynamics model for clays and the oxide minerals is desirable for studying the kinetics and thermodynamics of adsorption processes. To this end, a valence force field for aluminous, dioctahedral clay minerals was developed. Novel aspects of this development include the bending potential for octahedral O−Al−O angles, which uses a quartic polynomial to create a double-well potential with minima at both 90° and 180°. Also, atomic point charges were derived from comparisons of ab initio molecular electrostatic potentials with X-ray diffraction-based deformation electron densities. Isothermal−isobaric molecular dynamics simulations of quartz, gibbsite, kaolinite, and pyrophyllite were used to refine the potential energy parameters. The resultant force field reproduced all the major structural parameters of these minerals to within 1% of their experimentally determined values. Transferability of the force field to simulations of adsorption onto clay mineral surfaces was tested through simulations of Na+, Ca2+, and hexadecyltrimethylammonium (HDTMA+) in the interlayers of beidellite clays. The new force field worked rather well with independently derived nonbonded parameters for all three adsorbates, as indicated by comparisons between experimental and molecular-dynamics-predicted d(001) layer spacings of the homoionic beidellites.

Molecular electrostatic potential and field as descriptors of hydrogen bonding and molecular activity. Effects of hybridization displacement charge

Molecular electrostatic potential (MEP) and field (MEF) maps have been studied for certain epoxides, ethers and nitriles. The MNDO method was used to optimize geometries of the molecules fully. Hybridization displacement charges (HDC) recently defined by us, which preserve atomic contributions to molecular hybridization dipole moment, were combined with the Mulliken and Löwdin charges to compute the MEP and MEF maps. Linear correlation coefficients between our MEP and MEF values and the observed hydrogen bond accepting parameters (β) for ethers and nitriles, and the corresponding ab initio MEP values for epoxides were found to be quite high (> 0.9). Thus it has been shown that combination of HDC with the Mulliken and Löwdin charges usually improves the quality of MEP and MEF maps appreciably in comparison with those computed using the Mulliken and Löwdin charge distributions alone. Furthermore, the study demonstrates great utility of MEP and MEF in describing hydrogen bonding and molecular activity.

Reply to Comment on “Computing molecular electrostatic potentials with the PRISM algorithm”

This Reply clarifies the similarities and differences between our work and that of Gadre et al. in computing ab initio molecular electrostatic potentials. The principal advance described by us was to cast the PRISM algorithm for two-electron repulsion integrals in a form suitable for the calculation of molecular electrostatic potentials.

Computing molecular electrostatic potentials with the PRISM algorithm

The PRISM integral algorithm has been applied to the computation of the ab initio molecular electrostatic potential and its derivatives. Implementational details which are relevant to the additional efficiency of the algorithm in the electrostatic case are discussed. On a range of machines, CPU timings of the PRISM electrostatic properties program, which is included in the GAUSSIAN 92 quantum chemistry package, reveal a dramatic performance increase (in some cases more than two orders of magnitude) over other commonly used electrostatic programs (GAUSSIAN 90, GAMESS, MOPAC ESP, CHELPG). In addition, timings are reported for a particularly large electrostatic potential evaluation job on the six base-pair oligonucleotide CTCGAG (C 116H 138N 46O 68P 10 10−.

Topography-driven electrostatic charge models for molecules

A new method has been proposed for the generation of charge models for use in molecular interaction studies. These models have been developed so as to reproduce the essential topographical features of the corresponding ab initio molecular electrostatic potential. This has been achieved via the fitting of variable parameters in the model, such as point charges and their location, as well as the charge on the diffuse “floating” Gaussian, its exponent and center. Test applications to H 2O and NH 3 are reported.

Molecular recognition of amiloride analogs: a molecular electrostatic potential analysis. 1. Pyrazine ring modifications.

Ab initio molecular electrostatic potential (MEP) patterns are used to determine the electrostatic requirements for the formation of a stable blocking complex between amiloride analogs and the epithelial sodium channel of Rana ridibunda. MEP maps calculated in the 3-21G(*) and STO-3G basis sets for amiloride and analogs with pyrazine ring modifications are used to interpret differences in the microscopic rate constants for analog-channel binding determined by Li et al. MEP maps of the protonated analogs are correlated to differences in the value of kon, the microscopic association constant. Those analogs with kon values similar to amiloride are found to have a MEP maximum that is localized over the side chain, as well as strong, distinguishing minima in the MEP pattern off the carbonyl oxygen and positions 3, 4, and 5 of the pyrazine ring. MEP maps of a model-encounter complex (protonated analog and formic acid anion) are correlated to differences in koff, the microscopic dissociation constant. The major conclusions of this work are that (1) a stable blocking complex is formed with analogs which have a deep, localized minimum off the 6 position of the pyrazine ring, (2) the stability of the blocking complex is directly related to the depth of that minimum, (3) substitution at position 5 affects not only the depth but also the location and size of the minimum off position 6, and (4) steric factors may influence the optimal binding of the 6-position ligand to the ion channel. The MEP analysis also suggests that the distance between the proton donors of the chelating guanidinium moiety and the deep, localized minimum off position 6 of the pyrazine ring may define an important spatial requirement for all those analogs which form a stable blocking complex with the channel.

Molecular structure and dynamics of serotonin

The electronic structure and low-energy conformations of the protonated serotonin molecule were examined by quantum mechanical and molecular mechanical calculations based on the AMBER force field. The flexibility and internal motions of the molecule, which may be important for its mode of receptor interaction, were examined by molecular dynamics simulations in vacuo and in aqueous solution. Two crystal structures and four computed serotonin structures were used as starting points in the calculations. Both gauche and anti conformers were observed during molecular dynamics simulations in aqueous solution, but only gauche conformers of serotonin were observed in vacuo. The simulations demonstrated that the side chain conformation may adjust in order to fit into a receptor binding site. Energy refined gauche conformers had lowest molecular energies both in vacuo and in aqueous solution. Ab initio molecular electrostatic potentials were calculated in 4 layers surrounding the molecule and projected into net atomic point charges. The effect of the hydroxyl group in lowering the molecular electrostatic potentials around the phenyl ring was highly dependent on the conformation of the side chain. Conformers with an extended side chain had significantly lower electrostatic potentials over the phenyl ring than those with a folded conformation.

A quantum chemical study of the enzymatic deamination of benzoadenine derivatives

A theoretical study is presented, where, by using both ab initio and semi-empirical methodologies, the properties of benzoadenine derivatives as substrates of adenosine deaminase are discussed. The results suggest that lin-benzoadenine and lin-benzoadenosine can be recognized with an affinity similar to that of adenosine, but only if they are introduced about 0.12 nm deeper inside the active site of the enzyme than the natural substrate adenosine. This fact implies the existence of non-linear hydrogen bonds inside the active site of adenosine deaminase. Ab initio molecular electrostatic potential values suggest that these hydrogen bonds can exist, and have stability similar to that of linear hydrogen bonds. Finally, the great rate of deamination of lin-benzoadenine, comparable with that of adenosine despite the absence of the ribose, is explained in the context of the hypothesis that the protonation at the N1 atom is the rate-determining step of the whole deamination reaction.

Relationships between the activity of some H 2-receptor agonists of histamine and their ab initio molecular electrostatic potential (MEP) and electron density comparison coefficients

From an analysis of the ab initio molecular electrostatic potential (MEP) maps of some H 2-receptor agonists of histamine in their essential trans—trans conformations, for both neutral and cationic species, a good relationship between H 2-activity data and the MEP minima located at the N π nitrogen atom of the imidazole ring is predicted. From these data it appears easy to define a threshold value according to which the H 2-agonists may be classified as being strongly or weakly active. While the MEP values appear to be a good parameter for activity prediction, in this case, the comparison of electron densities does not give any additional useful information.

Study of Hydration Inhibitors on Aluminum Oxide Using Tunneling Spectroscopy and Molecular Electrostatic Potential Calculations

Inelastic electron tunneling and ab initio molecular electrostatic potential calculations have been used to investigate the bonding of several phosphonate based hydration inhibitors adsorbed on aluminum oxide. Results are reported for phosphoric acid (PA), methylphosphonic acid (MPA), hydroxylmethylphosphonic acid (HMP), and nitrotrismethylphosphonic acid (NTMP). Tunneling spectra were taken for PA, HMP, and NTMP and the observed frequencies compared to values obtained from FTIR, IR, and Raman spectra of similar compounds. Upward shifts in the P=O and P‐O‐(H) stretch frequencies indicated that the phosphonates bond to the aluminum oxide surface through the phosphonate group. Ab initio quantum mechanical molecular electrostatic potentials (QMEP's) were calculated for PA, MPA, and HMP. Analysis of these results provided a means to understand on a molecular level the known variations in effectiveness for each of the inhibitors investigated.

Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid

Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid