Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges

A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e⁻ with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955–969, 1997     

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: II. Electrostatic potentials inside the molecular van der Waals envelope

In part I of this series, the PESP (parameterized electrostatic potential) method was described and applied to the calculation of electrostatic-potential-derived charges for a wide variety of organic and inorganic systems. Based on PRDDO/M wave functions and parameterized against ab initio MP2/6-31G** calculations, PESP is an order of magnitude faster than ab initio STO-3G calculations, while achieving a level of accuracy that rivals that of far more sophisticated ab initio methods. In this study, the application of the PESP method to the high potential regions of molecules containing H, C, N, O, F, P, S, Cl, and Br is described. For a collection of 48 molecules and 55 distinct lone pair minima, PESP yields the location and depth of lone pair minima to an average accuracy (relative to MP2/6-31G**) of 0.03 Å and 2.5 kcal/mol, respectively. Similarly, the location and well depths of minima in the π regions of organic molecules are calculated to an accuracy of 0.08 Å and 1.5 kcal/mol. PESP electrostatic potential maps are, in some cases, virtually indistinguishable from those obtained at the MP2/6-31G** level. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1682–1693, 1997     

Double carbon-halogen bond in the compounds H2CX+, H2CCX+, and H2BCX (X = F, Cl)

The structure of formaldehyde and ketene analogs H₂CX and H₂CCX (X = O, F⁺, Ne²⁺, S, Cl⁺, Ar²⁺), and also of boron-containing compounds H₂BCX (X = F, Cl), was studied by ab initio [CCD(full)/6-311+G**] and DFT (B3LYP/6-311+G**) calculations. In all the halogen-containing species except H₂BCF, a double carbon-halogen bond is formed.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 10, 2004, pp. 1649–1654.Original Russian Text Copyright © 2004 by Minyaev, Gribanova.This revised version was published online in April 2005 with a corrected cover date.     

Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation

A combined ab initio SCF supermolecule and molecular mechanics investigation is carried out on the binding energetics of the divalent cations Mg²⁺, Ca²⁺, Zn²⁺, and Cd²⁺ to a series of the most common ligand functional groups found in biomolecules. The SCF binding energy components are resolved using the restricted variational space method.¹ The results show that the SIBFA molecular mechanics (SMM) procedure² reproduces the ab initio binding energies and total energy variations as a function of intermolecular variables. The model also reproduces the selectivity energetics for exchange reactions. Thus, the SMM procedure can be used without reparametrization to describe the coordination energetics of complex molecules including those subject to coordination changes. The energetic properties of divalent cation-hexahydrate complexes are compared as examples of a complete, realistic coordination system. The hexahydrates exhibit strong nonadditive effects typical of dication coordination. Nevertheless, these energetics are satisfactorily reproduced by the SMM procedure. © 1996 John Wiley & Sons, Inc.     

Approximate molecular electrostatic potentials from semiempirical wavefunctions

Approximate molecular electrostatic potentials (MESPs) are calculated with the asymptotic density model (ADM) on the basis of semiempirical wavefunctions generated by the SINDO1 method. The approximate MESP is adjusted to obtain good agreement with the exact MESP from 6–31G^* ab initio calculations for small molecules. This form of the MESP is used for the study of the reactivity of small and medium size silicon clusters with 5 to 45 atoms. Special attention is given to the reactivity of various Si₄₅ structures proposed in the literature. © 1997 by John Wiley & Sons, Inc.     

Quantum-Chemical Study of the Electronic Structure of the Complex Ions [Ru(NH3)5pyz]2 + and [Ru(CN)5pyz]3 - in Solution

The hydration shell of the complex ions [Ru(NH₃)₅pyz]^{2 +} and [Ru(CN)₅pyz]^{3 -} was simulated on the basis of ab initio Hartree-Fock calculations in the supermolecular approximation, within the framework of the multicavity polarizable continuum model. In calculations of the spectral characteristics of complexes with a pronounced nonuniformity of electron density distribution, it is primarily necessary to take into account the shift of energy levels of particular fragments under the action of the electrostatic potential produced by the solvation surrounding. Consideration of the charge transfer between the complex and the outer-sphere water molecules has no significant effect on the calculated electronic spectrum; the transferred electron density is below 1e.     

Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.     

Theoretical study of intermolecular potential energy surface for HCl dimer: Example of nonspherical atom–atom exchange repulsion interaction

The intermolecular part of the potential energy surface for the HCl dimer has been studied with ab initio quantum chemical methods. An intermolecular potential, based on quantum chemical calculations has been constructed. The interaction energy consists of electrostatic, induction, and dispersion terms calculated from the monomer properties of the interacting molecules and an exchange repulsion term. The latter term was parameterized from the results of the quantum chemical calculations and estimates of the electrostatic and induction energies. It was found necessary to use nonspherical atom–atom exchange repulsion interaction parameters, and the parameters describing the deviation from spherical behavior could be obtained from the expectation values of r² for the electrons assigned to an atom. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1816–1825, 1998     

Effect of metal cations [Li+, Na+, K+, Be2+, Mg2+, and Ca2+] on the structure of 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole: A theoretical investigation

Density functional theory calculations were performed at the B3LYP/6‐311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ (Mⁿ⁺, hereinafter), with 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole. A total of 60 initial structures were designed and optimized, of which 51 optimized structures were found, which could be divided into two different types: monodentate complexes and bidentate complexes. In the cation‐heteroatom complex, bidentate binding is generally stronger than monodentate binding, and of which the bidentate binding with five‐membered ring structure has the strongest interaction. Energy decomposition revealed that the total binding energies mainly come from electrostatic interaction for alkaline metal ion complexes and orbital interaction energy for alkaline earth metal ion complex. In addition, the electron localization function analysis show that only the Be? O and Be? N bond are covalent character, and others are ionic character. © 2012 Wiley Periodicals, Inc.     

Ab initio studies of the protonation of CO,N2 and NO+: Calculation of the minimum energy reaction paths

Ab initio molecular orbital calculations employing a 4-31G basis set have been used to study the minimum energy paths for the formation of HCO⁺, COH⁺, and HCOH²⁺ from CO by protonation. The protonation of N₂ to give NNH⁺ and HNNH²⁺ and of NO⁺ to form HNO²⁺ and NOH²⁺ have also been investigated. All species formed have linear equilibrium geometries and the minimum energy path for approach of the proton is along the line-of-centers of the heavy atoms. Energy barriers to the formation of the various species are given, where appropriate, and changes in geometry, ordering of molecular orbitals and orbital occupancy are discussed.     

Accurate modeling of the intramolecular electrostatic energy of proteins

The (?, ψ) energy surface of blocked alanine (N-acetyl–N′-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.     

OH stretching force constants in complexes of water with F−, Cl−, Li+ ions and LiF,LiCl ion pairs by 6-31G ab initio MO calculations

Ab initio MO calculations using 6-31G and 6-31 + G (for complexes with F⁻ and LiF) basis sets have been carried out for complexes of H₂O (monomer and dimer) with F⁻, Cl⁻, Li⁺ ions as well as with LiF and LiCl ion pairs for the evaluation of the OH stretching force constants. The changes in force constants are discussed in terms of molecular interactions, cooperativity effect and interionic electrostatic interactions. It is noticed that the cooperativity effect also operates through ionic bonds in symmetrically hydrated ion pairs and that OH stretching force constants are found to increase in the case of solvent bound ion pairs and symmetrically hydrated halide ions showing anticooperativity effect.     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.     

An Ab Initio MO Study on Orbital Interaction and Charge Distribution in Alkali Metal Aqueous Solution: Li+, Na+, and K+

The analysis of the orbital interaction between an alkali metal ion and the surrounding solvent molecules is performed for aqueous solutions of Li⁺, Na⁺, and K⁺, by means of the ab initio MO method with the aid of the quantum mechanical (QM)/molecular mechanics (MM) method. A total of 171 water molecules are included for each system. The effect of Li⁺ orbitals reaches as far as 6 Å 7 Å for Na⁺; and 9 Å for K⁺. This effect is caused by the orbital interactions between the valence orbitals of an alkali metal ion and of the surrounding water molecules. The electrostatic interaction and the orbital interaction must not be neglected. The difference in the effect between the alkali metal ions originates from the difference in the valence orbital extensions of the alkali metal ions.     

Force field parameters for carbohydrates

A new set of force field parameters for carbohydrates is reported. The parameter set is based on the CHARMM22 force field of Karplus and co-workers. The parameterization is based on newly performed high-level ab initio calculations [MP2/6-311 + G (2d, 2p)/ /6-31G**] of fragment molecules. A good agreement of the modified force field and ab initio data is achieved, which is demonstrated with a variety of molecules. © 1996 by John Wiley & Sons, Inc.     

Isoelectronic changes in energy of quark atoms and molecules via the Levy equation

Summary Z-transition state calculations based on the Levy equation suggest that the isoelectronic changes in energy of quark atoms,Q, (ordinary atoms with extra nuclear charge in units of ±1/3 and/or ±2/3) can be expressed quantitatively in terms of the electrostatic potential at the nucleus of an isoelectronic ordinary atom. Numerical tests within the local density functional theory are presented for the quark atoms of Li-F. Theab initio MO (molecular orbital) calculations using STO-5G basis on the C₂ molecule and its quark derivatives lead to similar conclusions.     

Combined application of pair potentials and the MM2 force field for the modeling of ionophores

Complexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li⁺, Na⁺, K⁺, Mg²⁺, and Ca²⁺ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K⁺ complex of 18-crown-6 is presented. For more flexible ligands the introduction of three-body correction terms of the pair potentials seems necessary.     

Three-body nonadditive effects for hydrogen bonded water molecules: SCF study of hydrated species including H2S and various metal ions

The relative importance of purely nonadditive three-body terms in solvated systems is assessed through ab initio LCAO –MO –SCF studies of hydrogen bonded structures containing two or more water molecules plus a solvate species. Among the latter the cases of Li⁺, Ca²⁺, and Mg²⁺ ions (of biological interest for aminoacid release processes in membrane transport) and of HDS molecules (of industrial importance in processes for the production of heavy water) are studied.