Quantum chemical study of electronic and structural properties of retinal and some aromatic analogs

The electronic and structural properties of retinal and four analogs were studied using semiempirical, ab initio Hartree-Fock, and density functional theory methods with the aim to evaluate the effects caused by some structural modifications in the ring bound to the polyenic chain and compared with the all-E-trans-retinal molecule. Therefore, some properties such as bond lengths, bond angles, atomic charges derived from electrostatic potential charges from electrostatic potential using grid based method as well as frontier orbitals of the polyenic chain were analyzed. Furthermore, the transition energies of the molecules were also calculated using the Zerner's intermediate neglect of differential overlap-spectroscopic, time-dependent Hartree-Fock, and time-dependent density functional theory methods. The results indicate that in spite of the structural modifications of retinal derivatives in comparison with all-E-trans-retinal, their properties seem similar. Thus, these molecules may behave similarly to all-E-trans-retinal and possibly be attempted in the search of novel molecular devices.     

Electronegativity and inductive and mesomeric parameters of atomic groups: A semiempirical quantum chemical estimation

The electronegativity, the inductive parameter, and the mesomeric dipole moments of substituents depend on the electronic structure characteristics of organic molecules calculated by the CNDO/2, INDO, MINDO, MINDO/3, MNDO, and AMI methods. It is shown that the electronegativity as well as the inductive and mesomeric characteristics of atomic groups may be estimated by semiempirical quantum chemical methods.     

New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron-porphyrin system was needed. In this study, two models with a five-coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree-Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron-porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three-dimensional structures determined by X-ray diffraction and extended X-ray absorption fine-structure experiments. From these results, atomic charges and force-field parameters for molecular mechanics and molecular dynamics calculations were obtained.     

On the relation between the formal atomic charges and total molecular energies

It is shown that the total SCF molecular energies are fairly well reproduced by the sum of electrostatic potentials exerted on the nuclei calculated in the point-charge approximation. Hence, there is a very simple relation between the total energies and formal atomic charges in molecules. The semiempirical SCC-MO charges have the same performance as the ab initio DZ ones.     

On heteroaromaticity of nucleobases. Bond lengths as multidimensional phenomena

Three hundred and nine carbon-carbon, carbon-nitrogen, and carbon-oxygen pi-bond lengths in high precision crystal structures of 31 purine and pyrimidine nucleobases were related to the Pauling pi-bond order, its analogues corrected to crystal packing effects, the numbers of non-hydrogen atoms around the bond, and the sum of atomic numbers of the bond atoms. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) demonstrated that the bond lengths in the nucleobases are three-dimensional phenomenon, characterized by nine distinct classes of bonds. Bond lengths predicted by Linear Regression models, Pauling Harmonic Potential Curves, Multiple Linear Regression, Principal Component, and Partial Least Squares Regression were compared to those calculated by molecular mechanics, semiempirical, and ab initio methods using PCA-HCA procedure on the calculated bond lengths, statistical parameters, and structural aromaticity indices. Incorporation of crystal packing effects into bond orders makes multivariate models to be competitive to semiempirical results, while further improvement of quantum chemical calculations can be achieved by geometry optimization of molecular clusters.     

A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods

Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.     

Molecular size and conformational effects on oligophenylene's electronic and vibrational properties

Electronic and vibrational properties of phenylene‐based oligomers from biphenyl P2P to para‐sexiphenil P6P, and their dependence on torsion angle are calculated using semiempirical quantum mechanic (AM1, ZINDO/S) and ab initio linear combination of atomic orbitals methods. The systematic relations between molecular size and geometry, and numerous molecular properties have been established, providing the basis both for the spectroscopic identification of different structures that could appear during material processing and for tailoring of devices with desired properties. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1783–1794, 2006     

Determination of one-centre core integrals from the average energies of atomic configurations

One-center core integrals for valence orbitals are determined from the experimental average energies of neutral atomic configurations from Li through Zn. These values are compared with those estimated from CNDO /1, “INDO /1”, CNDO /2, “INDO /2” and with theoretical values calculated from a pseudo-potential method. The agreement is good between values obtained from neutral atoms and from the psuedo-potential calculation except for the 3d orbitals of the transition elements where the theoretically calculated integrals over single ξ functions are not realistic. These two methods reproduce both term and average configuration energies for the first two rows of atoms; the semiempirical method reliably reproduces them for the third row. The CNDO /1 and INDO /1 methods underestimate atomic energies, while the CNDO /2 and INDO /2 procedures fail rather poorly. The propriety of using core integrals estimated semiempirically in molecular orbital calculations is discussed.     

The dynamics of gallamine: A potent neuromuscular blocker. A determination by quantum mechanics and molecular dynamics (i) in vacuo studies

The potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.     

Correlation of singlet-triplet gaps for aryl carbenes calculated by MINDO/3, MNDO,AM1, and PM3 with Hammett-type substituent constants

Heats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4-dimethyl-1,4-dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet-triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ⁺ constants. Good correlations with σ⁺ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C-C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.     

Dipole preserving and polarization consistent charges

A method for estimating dipole preserving and polarization consistent (DPPC) charges is described, which reproduces exactly the molecular dipole moment as well as the local, atomic hybridization dipoles determined from the corresponding wave function and can yield accurate molecular polarization. The method is based on a model described by Thole and van Duijnen and a new feature is introduced to treat molecular polarization. Thus, the DPPC method offers a convenient procedure to describe molecular polarization in applications using semiempirical models and ab initio molecular orbital theory with relatively small basis functions such as 6‐31+G(d,p) or without inclusion of electron correlation; these methods tend to underestimate molecular polarizability. The trends of the DPPC partial atomic charges are found to be in good accord with those of the CM2 model, a class IV charge analysis method that has been used in a variety of applications. The DPPC method is illustrated to mimic the correct molecular polarizability in a water dimer test case and in water‐halide ion complexes using the explicit polarization (X‐Pol) potential with the Austin model 1 Hamiltonian. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

A theoretical study of the nitrogen—graphite system

The chemisorption of atomic and molecular nitrogen on the basal plane of graphite has been studied by both semiempirical and non-empirical Hartree—Fock methods employing finite cluster models.

Geometric and energetic parameters obtained by semiempirical and non-empirical methods are generally in good agreement. Among the different chemisorption sites considered, nitrogen atoms are found to prefer a two-fold coordination site, and only in this case has any evidence been found for an exothermic process. No evidence of dissociative chemisorption has been found in the case of molecular nitrogen, whose preferred orientation changes from nearly vertical to nearly horizontal on approaching the surface. Molecular adsorption is strongly endothermic at the Hartree—Fock level, so that the only possible interaction occurs through dispersion forces, which are not taken into account in our computations, but can be well represented by model potentials.     

Analysis of the Conformational Composition of 2-Alkyl-4-phenyl-1,3,2-oxazaborinanes

The empirical MM2 and semiempirical AM1 methods were used to calculate the energy of model 2-methyl-4-phenyl-1,3,2-oxazaborinane with full optimization of the molecular geometry. Comparison of the experimental coupling constants for the 2-isobutyl analog and calculated coupling constants as well as the data for the relative energy of the individual conformers indicated that these compounds form a multicomponent equilibrium system containing sofa and a family of half-chair forms.     

Valence-bond calculations on ZNO and HGO using integrals computed through the semiempirical AM1 method

Valence-bond calculations have been carried out on ZnO and HgO using a basis set of Slatertype atomic orbitals and the one- and two-electron integrals as computed in the semiempirical AM 1 molecular orbital method. The zero differential overlap approximation has been used to calculate integrals between atomic orbital Slater determinants using the rules for matrix elements between determinants formed by orthogonal orbitals. Diabatic and adiabatic curves have been analyzed for the two systems, and results compared with molecular orbital AM 1 results. © 1992 John Wiley & Sons, Inc.     

Solvatons. II. Aqueous dissociation of hydrides in the MINDOS approximation

A simple electrostatic model of solvation is presented which allows the interaction with solvent to be included systematically within semiempirical SCF calculations. Solvent effects are incorporated into the Hamiltonian for a solute molecule through a series of imaginary particles, solvatons, which represent the oriented solvent distribution around the solute.The proposed model is based on an algorithm for approximating the enthalpy of solvation of each atomic center from its charge in the molecular system and the experimental hydration enthalpies of its various ions. The calculated atomic solvation energy of one center is then modified to include the interaction with other charged atomic centers in the molecule. The method, developed here for the MINDO/3 approximation, has been applied to the calculation of the aqueous dissociation of a series of hydrides. In general, it leads to fairly accurate solvation enthalpies andpK _a values when applied to systems with fixed molecular geometries. A general discussion of the problems associated with the development of a solvation model within a semiempirical framework is also presented.     

Efficient multipole model and linear scaling of NDDO-based methods

Fast growth of computational costs with that of the system's size is a bottleneck for the applications of traditional methods of quantum chemistry to polyatomic molecular systems. This problem is addressed by the development of linear (or almost linear) scaling methods. In the semiempirical domain, it is typically achieved by a series of approximations to the self-consistent field (SCF) solution. By contrast, we propose a route to linear scalability by modifying the trial wave function itself. Our approach is based on variationally determined strictly local one-electron states and a geminal representation of chemical bonds and lone pairs. A serious obstacle previously faced on this route were the numerous transformations of the two-center repulsion integrals characteristic for the neglect of diatomic differential overlap (NDDO) methods. We pass it by replacing the fictitious charge configurations usual for the NDDO scheme by atomic multipoles interacting through semiempirical potentials. It ensures invariance of these integrals and improves the computational efficiency of the whole method. We discuss possible schemes for evaluating the integrals as well as their numerical values. The method proposed is implemented for the most popular modified neglect of diatomic overlap (MNDO), Austin model 1 (AM1), and PM3 parametrization schemes of the NDDO family. Our calculations involving well-justified cutoff procedures for molecular interactions unequivocally show that the proposed scheme provides almost linear scaling of computational costs with the system's size. The numerical results on molecular properties certify that our method is superior with respect to its SCF-based ancestors.     

Calculated electron impact cross sections for the K-shell ionization of Fe,Co, Mn,Ti, Zn,Nb, and Mo atoms using the DM formalism

We used the Deutsch-Märk (DM) formalism to calculate atomic K-shell electron impact ionization cross sections for the elements Fe, Co, Mn, Ti, Zn, Nb, and Mo. The calculated K-shell ionization cross sections are compared with recently measured K-shell ionization cross sections. Good to satisfactory agreement was found for all atoms with the exception of Ti. Moreover, when compared to other available K-shell ionization cross sections for these atoms, calculated using other theoretical methods and semiempirical formulae, the predictions of the DM formalism achieve a level of agreement with experimental data that is as good or better than the predictions from the other methods.