Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes

The PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C-1s core binding energies and ¹H-NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4-disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.     

Reduced basis set for the gold atom in cluster complexes

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.     

A CNDO/INDO molecular orbital formalism for the elements H to Br. applications

The CNDO/INDO molecular orbital formalism introduced in the preceding paper has been applied to a large number of atom combinations up to bromine under the inclusion of the first transition metal series. The results are compared with experimental data (geometries, ionization potentials, dipole moments) or with the results of sophisticatedab initio calculations (one electron energies, net charges, atomic populations). The semiempirical model reproduces for a wide range of molecules the experimental andab initio data with remarkable success.     

Quantum chemistry investigation on the active site of Mn-SOD

In this paper, we carried out a theoretical study on the active site structures of the Mn-SOD with ab initio Hartree–Fock SCF method, and analyzed the molecular orbital energies, charges and atomic orbital contribution to the frontier molecular orbital.     

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

A method is presented for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems. Atoms are characterized by their orbital electronegativities. In the calculation only the connectivities of the atoms are considered. Thus only the topology of a molecule is of importance. Through an iterative procedure partial equalization of orbital electronegativity is obtained. Excellent correlations of the atomic charges with core electron binding energies and with acidity constants are observed. This establishes their value in predicting experimental data.     

An approximate relation between Wigner-Seitz-type one-electron Hamiltonians and complete Hamiltonians for molecules and solids

Summary The relation between the sum of Wigner-Seitz-type one-electron Hamiltonians of all electrons in a system (any molecule or solid) and the complete Hamiltonian for the system is deduced. According to this relation, the total energy for an electronic configuration may be formulated approximately as a quadratic function of the atomic charges defined for the configuration added to the sum of the energies of occupied orbitals. This formula is necessary for evaluating the system's total energy, using the orbital energies calculated from the Wigner-Seitz-type potential (called the linkage of embedded atomic fields (LEAF)), and is also useful for analyzing and understanding electronic structures, reactivities, and other properties of molecules and solids.     

Non-empirical quantum chemical calculations of the structure of a homologous series of N-alkylpyridinium cations

The results of non-empirical quantum chemical calculations of geometric parameters, total energies, partial atomic charges, dipole moments, energies of frontier molecular orbitals obtained within second order Möller-Plesset perturbation theory in the MP2/6-31G(d,p) approximation are presented for a homologous series of N-alkyl pyridinium cations containing from 1 to 16 carbon atoms in the hydrocarbon radical. Differences are found in the electronic structure of lower and higher homologues.     

铁超氧化物歧化酶活性中心结构研究

对氧化型、还原型及非活性形式铁超氧化物歧化酶Fe-SOD活性中心进行了量子化学计算和比较。在HF方法及LANL2DZ基组水平上获得了分子轨道能量、电荷分布以及原子轨道对前沿分子轨道贡献的信息。结果表明, Fe-SOD酶的活性形式的活性中心易于接受超氧自由基(O2- )的进攻而完成其生理功能。     

Theoretical study of ketenimine: Geometry,electronic properties,force constants and barriers to inversion and rotation

Non-empirical calculations of the structure and properties of ketenimine have been performed using nine Gaussian basis sets. Values for the bond lengths and angles, HOMO and LUMO energies, atomic charges, overlap populations, dipole moments, bond energies, force constants and barriers to nitrogen inversion and internal rotation are predicted.     

A theoretical study of potential energy surface and some chemo-physical descriptors of Aspirin,Coupling the rotation of the ester and carboxyl groups

In this paper, the effect of the simultaneous rotation of the carboxyl (COOH) and ester (R'COOR) functional groups on the potential energy surface (PES) of aspirin is studied. Relative energies are reported at the HF/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. To understand the activity and selected electrophilic attack sites, electric dipole moments, atomic charges, HOMO-LUMO energy gap, natural bond orbital (NBO), and molecular electrostatic potential (MEP) analyses, as well as the main structural parameters of the identified conformers, are studied at the same theoretical level. Finally, an NBO analysis is used to demonstrate charge transfer between lone pairs and localized bonds.     

Comparison of atomic charges derived via different procedures

Atomic charges were obtained from ab initio molecular orbital calculations using a variety of procedures to compare them and assess their utility. Two procedures based on the molecular orbitals were examined, the Mulliken population analysis and the Weinhold–Reed Natural Population Analysis. Two procedures using the charge density distribution were included; the Hirshfeld procedure and Bader's Atoms in Molecules method. Charges also were derived by fitting the electrostatic potential (CHELPG) and making use of the atomic polar tensors (GAPT). The procedures were first examined for basis set independence, and then applied to a group of hydrocarbons. The dipole moments for these molecules were computed from the various atomic charges and compared to the total SCF dipole moments. This was followed by an examination of a series of substituted methanes, simple hydrides, and a group of typical organic compounds such as carbonyl derivatives, nitriles, and nitro compounds. In some cases, the ability of the charges to reproduce electrostatic potentials was examined. © John Wiley & Sons, Inc.     

Charge distributions and multipole moments in molecules

The consideration of multipole moments is suggested as a new criterion for the validity of assignments of atomic charges in molecules. The total quadrupole and octupole moments generated by our definition of atomic charges are compared with the exact moments of the underlying wavefunction for various basis sets in selected diatomics. The analysis includes also total overlap and total dipole moment partitioning as well as 1σ MO overlap partitioning. All considerations together allow us to assess the validity of our charge definition as compared to Mulliken's and Löwdin's and the quality of the basis set.     

A charge-conserving approximation method for ab initio calculations

A new method is presented for approximate ab initio calculations in quantum chemistry. It is called CCAM (charge conserving approximation method). The calculation method does not include the use of empirical parameters. We use Slater type orbitals as basis set, replacing STO's by STO-2G functions to evaluate three- and four-center integrals and making the STO-2G two-orbital charge distributions have the same total charge as STO. The results are presented for test calculations on five molecules. In view of these results, CCAM is better than ab initio calculations over STO-6G in the results on total energies, kinetic energies and occupied orbital energies. In atomic populations, dipole moments and unoccupied orbital energies, CCAM is also satisfactory. We estimate that CCAM would be as fast as ab initio calculations over STO-2G in evaluating molecular integrals.     

DNA碱基的电子相关效应

分别在Hartree-Fock和二级Moller-Plesset微扰理论MP2的电子相关校正水平, 用6-31G^*^*基函数对四种DNA碱基胞嘧啶、胸腺嘧啶、鸟嘌呤和腺嘌呤的能量、偶极矩、电荷分布和分子静电势等性质进行了系统的从头计算研究。其中, 采用Z矢量方法在波函数中加入MP2级别的电子相关校正; 分别用Mulliken布居分析、静电势导出电荷CHELPG以及自然布居分析NPA方法计算分子中原子电荷。在上述计算结果的基础上, 系统地分析了DNA碱基的电子相关效应。     

Waugh-型镍钼杂多酸的量子化学计算

采用半经验INDO法，完成了Waugh-型镍钼杂多酸（NH44）6〔NIMO9O32〕·6H2O的量子化学计算，得到146个成键轨道和78个反键轨道，轨道能级，电荷和键序等数据。通过对这些数据的分析，表明杂多酸分子中端氧和Ni都可能为化学活性中心，各原子轨道在分子轨道中都占有一定比例，其HOMO和LUMO能级皆为负值，其体系具有进一步接受电子的能力。这些结论与实验事实一致。     

Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors

Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon—carbon rather than carbon—nitrogen bonds. © 1997 by John Wiley & Sons, Inc.     

Atomic dipole moments calculated using analytical molecular second-moment gradients

We have implemented analytical second-moment gradients for Hartree-Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.     

密度泛函理论下的分子电负性(Ⅳ)──大环分子的总能量和电荷分布的直接计算

以密度泛函理论表述的电负性定义及其均衡原理为基础,提出了一个修正电负性均衡方法(MEEM),可直接用于计算各类分子的总能量和原子电荷分布。通过对3个较大环状分子18-crown-6,24-crown-8和24-cryptand的实际计算,发现其计算结果与从头计算结果接近。     

A comparison of molecular orbital and crystal field calculations of ferric heme compounds

In this paper molecular orbital and crystal field calculations of some properties of five coordinated ferric heme proteins are compared. In particular, choosing hemin as an example, we have compared the following quantities: single orbital energies, electron repulsion energies, term energies, electron population of the Fe d orbitals, net atomic charges and the electric field gradient at the Fe nucleus calculated from the two models. Smaller term energy intervals between low lying sextet, doublet and quartet states, and an electric field gradient of opposite sign and three times the magnitude appear to be predicted from the MO calculation. These and other results are discussed in some detail.     

Calculation of core-level electron spectra of ionic liquids

On the example of 40 ion pairs (5 cations times 8 anions), this study demonstrates how the core-level binding energy values can be calculated and used to plot theoretical spectra at low computational cost using density functional theory methods. Three approaches for obtaining the binding energy values are based on delta Kohn–Sham (ΔKS) calculations, 1s KS orbital energies, and atomic charges. The ΔKS results show reasonable agreement with the available experimental X-ray photoelectron data. The 1s KS orbital energies correlate well with the ΔKS results. Atomic charge correlation with ΔKS is improved by accounting for the charges of neighboring atoms. Assignment of binding energies to atoms and the applicability of the mentioned methods to model systems of ionic liquids are discussed.