Initio SCF Research Articles

Catalytic activity of the first solvation shell in the CO2 hydration reaction

The catalytic activity of the first solvation shell for the CO2 hydration reaction has been studied within the ab initio LCAO MO SCF supermolecular approach to determine the significance of the specific solvation sites in lowering the activation barrier. The role of OH- ion replacing some solvent molecules has also been investigated suggesting alternative mechanism of CO2 hydration in alkaline solutions. In addition, the basis set dependence of the activation barrier and basis set superposition effect on barrier lowerings were examined.

Conformational Preferences of Hypermodified Nucleoside Lysidine (k2C) Occurring at “Wobble” Position in Anticodon Loop of tRNAIle

Conformational preferences of hypermodified nucleoside, 4-amino-2-(N6-lysino)-1-(β-D-ribofuranosyl) pyrimidinium (Lysidine or 2-lysyl cytidine), usually designated as k2C, have been investigated theoretically by the quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The zwitterionic, non-zwitterionic, neutral, and tautomeric forms have been studied. Automated geometry optimization using molecular mechanics force field (MMFF), semi-empirical quantum chemical PM3, and ab initio molecular orbital Hartree-Fock SCF quantum mechanical calculations have also been made to compare the salient features. The predicted most stable conformations of zwitterionic, non-zwitterionic, neutral, and tautomeric form are such that in each of these molecules the orientation of lysidine moiety (R) is trans to the N(1) of cytidine. The preferred base orientation is anti (χ = 3°) and the lysine substituent folds back toward the ribose ring. This results in hydrogen bonding between the carboxyl oxygen O(12a) of lysine moiety and the 2′-hydroxyl group of ribose sugar. In all these four forms of lysidine O(12a)…H-C(9) and O(12b)…H-N(11) interactions provide stability to respective stable conformers. Watson-Crick base pairing of lysidine with A is feasible only with the tautomeric form of usual anti oriented lysidine. This can help in recognition of AUA codon besides in avoiding misrecognition of AUG.

Theoretical Modeling of the Stereoisomerization of Tetracoordinated Be(II) Bis(chelate) Complexes

Quantum-chemical (semiempirical MNDO and ab initio RHF SCF with an STO-3G basis set) calculations were performed for stereoisomerization of tetracoordinated Be(II) bis(chelate) complexes with BeN2O2 coordination unit. The most probable pathway for their monomolecular isomerization was found to involve, in agreement with experimental data, cleavage of a Be–N coordination bond to form a tricoordinated Be intermediate (dissociation–recombination mechanism) rather than a competitive polytopal rearrangement. The planar structure of the intermediate detected upon thermo- and photoexcitation of the complexes was predicted from our calculations.

Ab Initio Structure Investigation of the Enol Forms of β-Diketones RCOCH2COR (R = H, CH3, CF3)

The geometrical parameters, force field parameters, and vibrational frequencies of the enol forms of β-diketones RCOCH2COR (R = H, CH3, CF3) were calculated using the ab initio MO LCAO SCF method involving broad bases of Cartesian Gaussian functions. For acetylacetone (R = CH3), the potential surface of rotation of the two methyl groups was investigated in detail, and the minimal energy route of the transfer of the hydroxyl proton inside the chelate ring was calculated. For hexafluoroacetylacetone (R = CF3) and malonic dialdehyde (R = H), calculations were carried out only for stationary points on the potential energy surface. For all the geometrical configurations under study, the relative energies were refined with inclusion of electron correlation in terms of second-, third-, and fourth-order Moller–Plesset perturbation theory; for molecules with R = H, CH3, the configuration interaction procedure taking account of all single and double excitations was additionally employed. The experimental and theoretical data are compared with those available in the literature. The substituent effect on the geometrical and electronic structure of the chelate ring is studied.

Tetrafluoroberrylate(2) Ions as Hydrogen-Bond Proton Acceptors: Quantum Chemical Considerations

The experimentally observed lower proton acceptor ability of the tetrafluorober-rylate(2-) anion, compared to that of the sulphate(2-) and selenate(2-) anions, was explained on the basis of various quantum chemical approaches. The geometries of the above-mentioned XY4 2 anions were fully optimised at the ab initio HF SCF and MP2 levels of theory, as well as within the DFT (BLYP and B3LYP) approach, using the 6-311+G* and LANL2DZ basis sets. The 6-311++G(3df,3pd) basis set was also used within the DFT BLYP approach. The molecular charge distribution was partitioned among the atomic centers using the Mulliken as well as the natural population analysis. All levels of theory (both with and without inclusion of the electron correlation effects), regardless of the basis set employed, predict lower (by absolute value) atomic charge on the fluorine atom in the tetra-ftuoroberrylate(2-) anion than that on oxygen atoms in sulphate(2-) and selenate(2-) anions. The quantum chemical predictions are fully in line with the spec-troscopically observed order of the proton acceptor abilities in these anions.

Quantum chemistry of quantum size-effects in semiconductors: Small clusters electronic structure calculations

Ab initio RHF SCF calculations are used for some small clusters MxXy, where M=Cd, Ag; X=S, I; and x, y≤7. Variation of electronic structure with size for some clusters with the bulklike tetrahedral coordination and with the lower symmetry allows one to predict their possible geometries which are compared with experimental data on the existence of the clusters. The chemical-bonding factor (the chemical nature of bounded atoms, coordination number for metal and nonmetal atoms, hybridization, etc.) is of more importance for properties of the clusters than is the familiar quantum confinement effect of semiconductor clusters. The essential difference in regularities of small cluster formation is analyzed for CdS- and AgI-based structures. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 337–341, 1999

Structure and Bonding in Metal−Oxide Systems: The CuMgO and CuCaO Molecular Systems

The molecular structure of the different isomers arising from the interaction of Cu and both MgO and CaO molecules has been determined from all-electron ab initio self-consistent field, SCF, and complete active space self-consistent field, CASSCF, wave functions. Only linear stable structures are found as characterized through the vibrational analysis. The dissociation energy with respect to the isolated molecules was obtained by explicitly considering the electronic correlation effects through second-order perturbation theory, MP2, or multireference configuration interaction calculations. The role of electronic correlation is very important due to the near degeneracies existing in the isolated MgO and CaO molecules where the SCF description is not adequate enough. A set of theoretical techniques has been used to analyze the chemical bond in these molecular complexes. All the results indicate that the bonding in the O- and M-bonded complexes is very different. This fact may be interpreted from the differe...

Molecular electronegativity in density functional theory (I)——Direct calculation of atomic charges in a molecule via electronegativity equalization principle

On the basis of electronegativity expressed in density functional theory and electronegativity equalization principle, a new scheme for calculating the atomic charges in a molecule has been proposed and designed, which gives a new scale of the atomic electronegativity and hardness in a certain molecular environment and takes the harmonic mean electronegativity as a reference value of the molecular electronegativity so that the multiple-regression and nonuniform parameters in the original method are avoided. This approach can be easily and widely applied to the calculation of atomic charges for a big molecule and quite good results of atomic charges in some illustrated molecules are obtained as compared with those from the ab initio STO-3G SCF calculations.

Calibration of angular functions of the?-fluorine isotropic hyperfine interaction based on theab initio LCAO-MO UHF SCF calculations of?-fluorinated ethyl radicals

Ab initio LCAO-MO UHF SCF calculations have been carried out for the s-fluorinated ethyl radicals R-CH2, where R=CH3-nFn (n=0,1,2,3). Parameteres of the s-fluorine angular functions of the isotropic hyperfine interaction have been calculated for the ⇏-radical and radical anion fragments\(R - \mathop C\limits^. \begin{array}{*{20}c} / \\ \backslash \\ \end{array} \) and\(R - \overline {\mathop C\limits^. } \begin{array}{*{20}c} / \\ \backslash \\ \end{array} \)

Conformational preferences of XONO2 systems (X = H, F, Cl, CH3) from ab initio techniques

AbstractAb initio SCF and MP2 methods have been used to calculate the geometries and relative energies of both planar and nonplanar rotamers of several nitrates with a DZP basis set. The planar arrangement of atoms is found to be the lower energy configuration in all cases. The interconversion between rotamers is analyzed by partitioning the contributions to the total SCF energy in a variety of ways.

About the first solvation shell of protonated hydrates: H3O+(H2O)6

A b initio SCF and semiempirical calculations have been performed on some geometrical configurations of the system H3O+(H2O)6, with either three or four water molecules in the first solvation shell. The dispersion energy has been evaluated from perturbation theory. It is shown that the pair approximation overestimates the stability of the second category of structures. However, the present work confirms that geometries with either three or four water molecules in the first solvation shell are close in energy. Comparison is done with results obtained from several semiempirical expressions and parameters available in the literature.

Quantum-chemical investigation of mechanisms of reactions of nucleophilic addition to acetylene. 7. Evaluation of possible interactions in C2H2/MOH/DMSO system

Within the framework of the ab initio method SCF MO LCAO, using a model potential, the influence of alkali metal cations on the reactivity of the acetylene molecule has been investigated. Activation of acetylene with respect to a nucleophile is favored by a lowering of energy of the vacant π* orbital upon coordination, a change in its form as a consequence of sufficiently free motion of the cation along the triple bond, and stabilization of the transdistorted form of acetylene in the complex. In the acetylene/alkali/DMSO system, the activating capability of cations is related to the ease of replacement of a solvent molecule in the solvate complex of the acetylene molecule, this capability increasing in the series Li < Na< K.

Theoretical investigation of the hydration properties for the trans and gauche rotamers of succinonitrile

AbstractAb initio SCF were performed on the trans and gauche rotamers of succinonitrile (SN) and on the monohydrated rotamers to determine the most probable hydration site(s) of water with SN and the relative strengths of these interactions and to examine the effect of one water molecule on the relative stability of the rotamers. MOPAC was used to determine the location of water on the rotamers of SN; the geometries of the hydrated rotamers were then optimized at the HF/4–31G level followed by single‐point calculations at the HF/6–31G and HF/6–31G* levels. The results show that trans SN is more stable than is gauche SN by 1.2 kcal/mol (at the HF/4–31G level with zero‐point energy corrections) and 0.8 kcal/mol (at the HF/6–31G* level, excluding zero‐point energy corrections). The hydrogen bond formed between the methylene hydrogen of trans SN and the oxygen of water is more stable than is the hydrogen bond formed between the nitrogen of SNt and the hydrogen of water by 0.63 kcal/mol. The most stable hydrogen‐bonding interaction for the gauche rotamer occurs for the methylene—OH2 hydrogen‐bonding interaction, which also has the largest hydration energy (ΔE = −4.39 kcal/mol), but it is less stable than is the most stable trans hydrogen‐bonding interaction (SNt—OH2) by 0.63 kcal/mol. Our results suggest that the trans rotamer of SN should associate with more water molecules than should the gauche. The relative rotamer stability between the trans and gauche rotamers of SN decreases by 0.2 kcal/mol (at the HF/6–31G* level) when water is hydrogen bonded to the methylene group of SN. A mechanism is also proposed to explain the phase‐separation behavior of this system.

Vibrational spectra, lattice dynamics and chemical constitution of oxides

The relationships among lattice dynamics of oxides and their chemical constitution are discussed in terms of the concept of dynamic crystal chemistry. A new approach to the design of a dynamic model of an ionic-covalent crystal combining molecular force constants with explicit treatment of long-range electrostatic forces in a lattice is outlined and its applications exemplified. The conditions of introduction of scaled quantum chemical force constants of a suitable molecular system into the secular equation for lattice vibrations are determined rigorously. The importance of unified treatment of stability conditions and various dynamic properties of crystals including phonon spectra, macroscopic elastic and piezoelectric constants etc., is emphasized. Several results of ab initio quantum chemical SCF computations by the gradient method for molecular species containing silicon-oxygen bonds are presented and are used to explain some empirical regularities in silicate structures.

ChemInform Abstract: Ab initio Study of Structure and Stability of Beryllium Compounds

Abstract The ab initio closed-shell SCF method, combined with the energy gradient technique, is applied to study the structures of the monomers and heavy atom bridged dimers of the monosubstituted beryllium hydrides: HBeX (X = BH 2 , CH 3 , NH 2 , OH, F and Cl) and the BeX 2 (X = CH 3 , F and Cl). The nature of the bridging BeX bond in the electron deficient group (X = BH 2 and CH 3 ) and the strong donor—acceptor group (X = NH 2 , OH, F and Cl) differs from each other. The relationship between the dimerization energies and the type of bridging radicals is examined with and without electron correlation by using SDCI and MP3 methods. The electron correlation plays an important role in forming the electron deficient bridged dimers (X = H, BH 2 and CH 3 ) and Cl bridged dimer, but not so much in the other lone pair bridged dimers (X = NH 2 , OH and F). The dimerization energy of Be(CH 3 ) 2 is estimated to be 18 kcal mol −1 , which is compatible with the experimental value of ca. 24 kcal mol −1 . The vibrational frequencies of the monomers and dimers of BeX 2 are evaluated and compared with the experimental data if it exists.

Hole localization and broken symmetry: A theoretical study of core electron ionization in the Li2 molecule

AbstractAb initio SCF, CI, CEPA, and MCSCF techniques are compared and contrasted in a theoretical study of the 1s core ionized Li2 molecule from the point of view of core hole localization. In agreement with earlier studies of symmetric core ionized molecules, SCF theory is found to give a physically reasonable description of core ionization only when symmetry breaking is allowed. This results in a dramatic lowering of the energy of the core ionized state and hence of the ionization potential. By extension, CI wave functions that are developed in terms of a broken symmetry SCF reference plus its single and double excitations are found to perform significantly better than those constructed from symmetry adapted SCF orbitals. Alternatively, if the full point group symmetry is to be retained, a multiconfigurational treatment is called for and, in agreement with the conclusions of an analogous study on O2 [H. Ågren, P.S. Bagus, and B.O. Roos, Chem. Phys. Letters 82, 505(1981)], it is found that a modestly sized MCSCF wave function is capable of accounting for the energetic effects of symmetry breaking. Potential energy curves for Li2 and several states of core ionized Li2 have been calculated, allowing predictions of the adiabatic ionization potential and vibrational, satellite, and Auger structures in the photoelectron spectrum of Li2 to be made.

Ab initio, Xα and IEHT Mo calculations of Mössbauer spectroscopy parameters for iron carbonyls

Calculations of charge density and the electric field gradient tensor at the iron nucleus by means of ab initio LCAO SCF, MS-Xα, SCC-Xα and IEHT methods for iron carbonyls Fe(CO)n, n=1–5, are presented. The calculated EFG values for the closed-shell molecule Fe(CO)5 show reasonable agreement with experiment while the values obtained for the open-shell molecules Fe(CO)n, n=1–4, significantly depend on the calculational method. Ab initio results, though using a minimal basis set, are closer to experimental data than Xα and IEHT results.

Electronic states of CuO

A b initio SCF and CI calculations are reported for the ground state and low-lying excited electronic states of CuO (i.e., within ∼20×103 cm−1 of the X̃ 2Π ground state), employing an ab initio effective potential for the Cu atomic core (1s–3p), and including comparisons of several atomic orbital basis sets. The calculated bond lengths, energy separation, and population analyses for the lowest two electronic states, X̃ 2Π and Y 2Σ+ [corresponding roughly to Cu+ (3d10) and O− (2p5), where the 2p oxygen hole is, repectively, 2pπ and 2pσ], do not vary appreciably among the basis sets tested (minimal and split valence bases on Cu, and a split valence basis on oxygen, with and without d-polarization functions and diffuse p functions on oxygen) and are in reasonable agreement with previous experimental and theoretical estimates. Most of the remaining excited states of CuO below ∼20×103 cm−1 may be rationalized in terms of atomic-like excitations originating from the X̃ 2Π ground state: 3d(Cu) → 4s(Cu) and 3d(Cu) → 2 pπ (O) (the latter formally corresponds to Cu2+O2−, though covalent 2p‘gs–4s bonding reduces the charge to ∼Cu+O−). Close agreement (rms deviation of ∼103 cm−1) is obtained between calculated (CI) and observed adiabatic transition energies for ten Σ, Π, and Δ doublet excited states (relative to the X̃ 2Π state), after the calculated excitation energies are reduced by ∼5×103 cm−1, a term which corrects primarily for limitations in the Cu atom basis set, and whose magnitude can be obtained both in terms of calculated and observed atomic quantities and by direct least-squares fitting of calculated and observed CuO transition energies. The calculations yield the first comprehensive assignment of Kronig symmetry (±) for the observed 2Σ states (δ 2Σ−, A 2Σ−, A′ 2Σ+, and G 2Σ+) and one which is consistent with recent analyses of experimental data. The extent of specific molecular correlation effects is analyzed, and found to be important in the assignment of several of the observed transitions. The CI mixing of different principal configurations may be significant for states involving the ‘‘Cu2+O2−’’ configuration (as also suggested in previous studies), and the assignments based on the present CI results for these states are only tentative.

A b i n i t i o assignment of the UV spectra of the ethyl, isopropyl, and t-butyl radicals

A b initio SCF and CI calculations are used to assign the UV spectra of a series of alkyl radicals. Contrary to earlier speculation, the low-lying states are shown to be predominantly Rydberg in character. The spectra of the methyl, ethyl, isopropyl, and t-butyl radicals are found to be successively red shifted in accordance with the trend observed in their ionization potentials. The nature of the first valence transition in this series of radicals is also investigated and its transition energy placed relative to the Rydberg transitions.

ChemInform Abstract: INTERNAL ROTATIONS OF VINYLCYCLOPROPANE, CYCLOPROPANECARBOXALDEHYDE AND CYCLOPROPANECARBOXYLIC ACID STUDIED BY QUANTUM CHEMICAL CALCULATIONS

Abstract The internal rotations in vinylcyclopropane (1), cyclopropanecarboxaldehyde (2) and cyclopropanecarboxylic acid (3) were studied by using an effective two-step procedure: first, MNDO complete geometry optimization along the potential curves, then ab initio 4-31G SCF calculations on the MNDO optimized geometries to obtain the potential curves. This method was first qualified in the case of 1, for which there are plenty of available experimental and calculation results and it produced a curve for 1 which is compatible with a 3-21G potential curve. The potential curves of 2 and 3 are also in agreement with available experimental results. The effects of conjugation and steric interaction on the rotation curves are discussed in connection with the variations of important geo-metrical parameters with the rotation angles.