Ab Initio MO Method Research Articles

Theoretical studies on magnetic interactions in many types of organic donor salts: BEDT-TTF, BETS, TMTTF and TMTSF

Intermolecular magnetic interaction of some donors, i.e. BEDT-TTF, BETS, TMTTF and TMTSF, in some organic superconductive crystals were studied theoretically by using ab initio MO and DFT methods. In addition, donor arrangements in both κ- and λ-phases crystals are also focused. For this purpose we employed κ-BETS2FeCl4 and λ-BETS2FeCl4 crystals for BETS salts; κ-(BEDT-TTF)2Cu[N(CN)2]X (X=Cl, Br and I) and κ-(BEDT-TTF)2Cu(NCS)2 crystals for BEDT-TTF salts; TMTTF2PF6 and TMTSF2PF6 crystals for TMTTF and TMTSF salts. For these systems all the effective exchange integral (Jab) values between two donors and between donor and counter anions were successfully evaluated. In addition the other effective parameters (tab, Ueff) were also obtained. Finally relationship between integral pair (J, J′) and transition temperature (TSC) was discussed. The two- and one-dimensional magnetic networks are essential for these crystals.

Computational Procedure of Lattice Energy Using the Ab Initio MO Method

Recently, we have proposed a computational procedure for calculations of lattice energies of molecular crystals using the ab initio MO method. This procedure does not use potential functions and is applicable to a variety of molecular crystals. The procedure has been successfully applied to calculation of packing structure of electron donor-acceptor complex, H3N–BF3, and hydrogen bonding crystal, CH3OH. In this work, we present a full account of the computational procedure. This method is applied to the packing structure calculations of hydrocarbon crystals, C2H2, C2H4 and C6H6. The lattice parameters optimized at the MP2/6-311++G** level are in good agreement with the experimental values. The basis set dependence of the lattice constants is also discussed for several crystals.

The Absolute Configuration of (+)‐Oxopropaline D by Theoretical Calculation of Specific Rotation and Asymmetric Synthesis.

The specific optical rotations of (R)-oxopropaline D calculated by two ab initio MO methods were +52+/-31 degrees and +61+/-29 degrees, respectively, and (+)-oxopropaline D (3) was presumed to have an R-configuration. On the basis of this theoretical result, the reaction of 1-litio-beta-carboline with (R)-glyceraldehyde acetonide followed by oxidation with MnO(2) gave (R)-oxopropaline D acetonide (4a), which was consistent with the previously synthesized (+)-oxopropaline D acetonide (4) in all respects. From the results of theoretical calculations and the experimental synthesis, we determined that natural (+)-oxopropaline D (3) has an R-configuration.

Ab initio MO approach to the magnetic interactions in chain structure of A2MnF5

We studied the magnetic interactions in the chain structures of A 2 Mn III F 5 by an ab initio MO method using cluster model molecules. The effective exchange integral (J) in the chain structures has been estimated from the total energy difference between the highest and lowest spin states in the alternant MO method. We calculated also a dependence of angle (Mn-F-Mn) of the J value in the cluster model. The calculated values are in agreement with the experimental ones. We also discuss a change of the overlap integral between d orbital of Mn and p orbital of F atom to confirm the dependence of angle for the exchange interaction.

Theoretical analysis of magnetic parameters between donors in BEDT-TTF, BETS, TMTTF and TMTSF crystals

Intermolecular magnetic interaction of BEDT-TTF, BETS, TMTTF and TMTSF donors in some crystals are studied theoretical calculations by using ab initio MO and DFT methods. The two and one dimensional magnetic networks are essential for BEDT-TTF, BETS and TMTTF, TMTSF donors, respectively. The J ab values succesfully evaluated and discussed relationship between J, J' and T SC .

Ab initio MO based lattice energy for molecular crystals: packing structure of electron donor–acceptor (EDA) complex H 3N–BF 3

A computational procedure is proposed for calculating the lattice energy of molecular crystals using the ab initio MO method. Our method does not require any adjustable parameters and provides a general description for various molecular crystals including electron donor–acceptor (EDA) complexes. Using the method, the packing structure of H 3N–BF 3 crystal was optimized at the HF/3-21 + G level and the lattice energy was calculated at the MP2/6-311 + G * level. The calculation reproduced the experimental lattice constants with reasonable accuracy. Moreover, the structural feature of the H 3N–BF 3 crystal was discussed based on the molecular interactions in the crystal.

Electron Delocalization in Isocyanates, Formamides, and Ureas: Importance of Orbital Interactions

The electron delocalization in isocyanates, amides, and ureas has been studied using ab initio MO and density functional methods. The observed trends in the CN rotational barriers and N-inversion barriers in these systems have been explained in terms of orbital interactions. NBO analysis indicates that there is nN → π*[C-X] electron delocalization in amides, which increases with a decrease in the energy difference (ΔE) between the two interacting orbitals. This phenomenon, rather than electronegativity, is responsible for the observed increase in the CN rotational barrier in amides XC(R)NH2 (R = H, NH2) in the order X = O < S < Se.

Electronic structure of N‐sulfenylimines

AbstractThe electronic structure of N‐sulfenylimines was studied in detail using ab initio MO and density functional methods. The S—N rotational barriers and N‐inversion barriers in HS—NCH2 at the G2MP2 level were found to be 5.60 and 21.76 kcal mol−1, respectively. There is a partial pπ–pπ bond and a relatively weak nN → σ*S—R anomeric π bond between sulfur and nitrogen in N‐sulfenylimines. NBO analysis was carried out to estimate quantitatively the above delocalizations in RS—NCH2 (R = H, Me, Cl, F, BH2) systems. Copyright © 2003 John Wiley &amp; Sons, Ltd.

The structure, energy and stability of components formed in the preparation of fac-[99mTc(CO)3(H2O)3

The geometry and total molecular energy of ten species in the system [Tc(CO)i(H2O)6−i]+ (i = 0–6) are calculated by using ab initio MO method at the MP2/CEP-121G level. Their formation free energies are estimated in the sequence [Tc(H2O)6]+ > trans-[Tc(CO)2(H2O)4]+ > [Tc(CO)(H2O)5]+ > trans-[Tc(CO)4(H2O)2]+ > mer-[Tc(CO)3(H2O)3]+ > cis-[Tc(CO)2(H2O)4]+ > cis-[Tc(CO)4(H2O)2]+ > [Tc(CO)5(H2O)]+ > fac-[Tc(CO)3(H2O)3]+ > [Tc(CO)6]+. The computation results of relative composition for various CO-to-H2O concentration ratios indicate that fac-[Tc(CO)3(H2O)3]+ is the dominant species when the pressure of CO is 0.1 MPa as experimentally observed, and preparation of some of the other species is also possible in controlled conditions.

The Absolute Configuration of (+)-Oxopropaline D by Theoretical Calculation of Specific Rotation and Asymmetric Synthesis.

The specific optical rotations of (R)-oxopropaline D calculated by two ab initio MO methods were +52+/-31 degrees and +61+/-29 degrees, respectively, and (+)-oxopropaline D (3) was presumed to have an R-configuration. On the basis of this theoretical result, the reaction of 1-litio-beta-carboline with (R)-glyceraldehyde acetonide followed by oxidation with MnO(2) gave (R)-oxopropaline D acetonide (4a), which was consistent with the previously synthesized (+)-oxopropaline D acetonide (4) in all respects. From the results of theoretical calculations and the experimental synthesis, we determined that natural (+)-oxopropaline D (3) has an R-configuration.

Ab initio MO法によるペプチド鎖の分子力場の解析

Ab initio MO法によるペプチド鎖の分子力場の解析

Electronic structure of N-sulfonylimines

The electronic structure of N-sulfonylimines has been studied in detail using ab initio MO and density functional methods. The S–N rotational barriers in HS(O)2NCH2 at G2MP2 and CBS-Q levels have been found to be 3.25 and 3.43kcal/mol respectively. Complete optimization at HF/6-31+G∗, MP2(full)/6-31+G∗ and B3LYP/6-31+G∗ levels have shown that synperiplanar arrangement of S–O with respect to CN is more stable. NBO analysis has been carried out to quantitatively estimate these delocalisations and charge polarization in RS(O)2NCH2 (R=H, Me, Cl, F). The Lewis basic character in N-sulfonylimines is less compared to N-alkylimines due to anomeric interactions that reduce the lone pair electron density on nitrogen in 1.

Theoretical studies of intra- and inter-molecular magnetic interaction of organic polyradicals with [formula omitted] and 2 spin sites

Intra- and inter-molecular effective exchange integrals ( J ab) in the crystals of BIP-TENO and PNN-BNO are calculated by ab initio MO method based on DFT. It is found that the USVWN method evaluates them close to the experimental data obtained by Hosokoshi et al.

Kinetics and Mechanism of the OH + C6H6 Reaction: A Detailed Analysis with First-Principles Calculations

The capability of various high-level DFT and ab initio MO methods to predict molecular and energetic parameters has been critically tested for the OH radical reaction with benzene. G3 theory proved to be the most accurate in estimating reaction barriers and enthalpies. For the first time, the molecular structure, stabilization energy and nature of the bonding interactions of the [C6H6···OH] prereaction complex have been characterized. Accurate thermochemistry for major reaction channels was established by making combined use of experimental and theoretical parameters. A multistep kinetic model for the OH-addition channel was proposed, and the effects of T, P, and reaction time on the apparent rate constants were evaluated by weak collision master equation/RRKM analysis. Available experimental kinetic data for all relevant reactions are critically analyzed and correlated with modeled effective rate constants.

A theoretical study of conformational properties of N-methyl azapeptide derivatives.

The conformational properties of azapeptide derivatives, Ac-azaGly-NHMe (1), Ac-azaAla-NHMe (2), Ac-NMe-azaGly-NHMe (3), Ac-NMe-azaAla-NHMe (4), Ac-azaGly-NMe(2) (5), Ac-azaAla-NMe(2) (6), Ac-NMe-azaGly-NMe(2) (7), and Ac-NMe-azaAla-NMe(2) (8), were systematically examined by using ab initio MO and DFT methods. Structural perturbations in azapeptides resulting from cyclic substitution of a methyl group at three N-positions of an azaamino acid were studied on the basis of the structure of the simplest model azapeptide, 1. Potential energy surfaces were generated at the HF/6-31G level for 1-4 and at the HF/6-31G//HF/3-21G level for 5-8 by rotating two key dihedral angles (phi, psi) in increments of 30 degrees. The backbone (phi, psi) angles of the minima for 1-4 are observed at the i + 2 position to form the betaI(I')-, betaII(II')-, betaVI-turns or the polyproline II structure according to the orientation of the acetyl group and the positions of the N-methyl groups. Compounds 5-8 coupled to a secondary amine were found to preferentially adopt polyproline II, betaI(III)-turn, or alpha-helical structure or even extended conformations depending on the orientation of the acetyl group and the positions of the N-methyl groups. Furthermore, N-methyl groups, depending on their positions, were found to affect the orientation of the amide group in the lowest energy conformations, the pyramidality of the N2 atom, and the bond length in azapeptide derivatives. These unique theoretical conformations of N-methyl azapeptide derivatives could be utilized in the definite design of secondary structure for peptides and proteins, and in the development of new drugs and molecular machines.

Proton NMR Chemical Shift Behavior of Hydrogen-Bonded Amide Proton of Glycine-Containing Peptides and Polypeptides as Studied by ab initio MO Calculation

NMR chemical shifts of the amide proton of a supermolecule, an Nmethylacetamide hydrogen-bonded with a formamide, were calculated as functions of hydrogen-bond length RN…O and hydrogen-bond angles by FPT-GIAO method within the framework of HF/STO 6-31++G(d,p) ab initio MO method. The calculations explained reasonably the experimental data reported previously that the isotropic proton chemical shifts move downfield with a decrease in RN…O. Further, the behavior of proton chemical shift tensor components depending on the hydrogen-bond length and hydrogen-bond angle was discussed.

Electronic state of small and large cavities for methane hydrate.

It is well known that methane hydrate is aggregates of small and large hydrogen bonded water cavities (composed of 12 pentagonal faces of 20 water molecules, and 12 pentagonal and two hexagonal faces of 24 water molecules, respectively) where one methane molecule is encaged. We calculated the methane molecule in vacuum, the small and large cavities by ab initio MO method to clarify the electronic state. The proton of methane in the cavities is shown to form the weak hydrogen bond (O...H[bond]C) between methane and four water molecules, and the H-bond lengths and energies in the small and large cavities were estimated as (0.293 nm, 6.8 kJ/mol) and (0.309 nm, 5.2 kJ/mol), respectively. The calculated values of symmetric C[bond]H stretching frequencies and (13)C-NMR chemical shieldings of the methane in the two cluster cavities show good agreement with the experimental ones observed by Sum et al. and Ripmeester and coworker, respectively.

Role of initial complexes in 1,2-addition reactions of disilene derivatives

Mechanisms of four 1,2-addition reactions, H2Si=SiHMe + H2O, H2Si=SiHF + H2O, H2Si=SiH(C≡CH) + H2O, H2Si=SiH(NH2) + HF, were investigated in detail by the ab initio MO method using a recent approach combined with frontier MO theory. Twelve reaction pathways were found. The initial step of each reaction is the formation of a weakly bonded complex. According to the structure and the charge distribution of the complexes, the reactions are categorized into two types. Reactions starting from electrophilic interaction between the LUMO of water (or hydrogen fluoride) and the HOMO of disilene always result in syn-adducts. On the other hand, nucleophilic interaction between the HOMO of the water and the LUMO of disilene leads both syn and anti adducts. Depending on the acidity of the reagent and the charge on the silicon to be attacked, the reactions proceed in simple one-step mechanisms or in two-step ones via a Lewis-type complex. The paired interacting orbitals of the initial complexes were examined in order to predict the reaction pathways.

C232 熱物性シミュレーションのための非経験的分子間ポテンシャルの構築

A 2-body intermolecular potential between N_2 molecules was determined with the ab initio MO method. At first, effects of basis sets and approximation level of electron correlation were examined quantitatively and MO calculation with MP4SDQ/6-311++G (3df) was conducted to construct a database of N_2 intermolecular potential. Furthermore, the database obtained was expressed as a function of 4 parameters defining the configuration of two N_2 molecules and the accuracy in expressing as the function was investigated. As the result, in the vicinity of the potential well, the difference between the database and the approximate function was kept in less than 7% that seemed to be enough accuracy for MD simulation.

The thermal decomposition of thiirane: a mechanistic study by ab initio MO theory.

Using high-level ab initio MO methods, we have identified two reaction pathways with different thermodynamic and kinetic properties for the thermal decomposition of the three-membered heterocycle thiirane (C2H4S) and related derivatives. A homolytic ring opening, followed by attack of the generated diradical on another thiirane molecule, and subsequent elimination of ethene in a fast radical chain reaction results in the formation of disulfur molecules in their triplet ground state (3S2) and requires activation enthalpies of deltaH#(298) = 222 kJ mol(-1) and deltaG#(298) = 212 kJ mol(-1). This reaction mechanism would result in a first-order rate law in agreement with one reported gas-phase experiment but does neither match the experimental activation energy nor does it explain the observed retention of the stereochemical configuration in the thermal decomposition of certain substituted thiiranes. Alternatively, sulfur atoms can be transferred from one thiirane moleculeto another with the intermediate formation of thiirane 1-sulfide (C2H4S2). This molecule can either decompose unimolecularly to ethene and disulfur in its excited singlet state (1S2) or, by means of spin crossover, S2 in its triplet ground state may be formed. On the other hand, the thiirane 1-sulfide may react with itself and transfer one sulfur atom from one molecule to another with formation of thiirane 1,1-disulfide (C2H4S3), which is an analogue of thiirane sulfone; thiirane is formed as the second product. The 1,1-disulfide may then decompose to ethene and S3. In still another bimolecular reaction, the thiirane 1-sulfide may react with itself in a strongly exothermic reaction to give S4 and two equivalents of ethene. This series of reactions results in a second-order rate law and requires activation enthalpies of deltaH#(298) = 109 kJ mol(-1) and deltaG#(298) = 144 kJ mol(-1) for the formation of thiirane 1-sulfide, while the consecutive reactions require less activation enthalpy. Elemental sulfur (S8) is eventually formed by oligomerization of either S2, S3, or S4 in spin-allowed reactions. These findings are in agreement with most experimental data on the thermal desulfurization of thiirane and its substituted derivatives. Thiirane 1-persulfide (C2H4S3) with a linear arrangement of the three sulfur atoms as well as zwitterions and radicals derived from thiirane are not likely to be intermediates in the thermal decomposition of episulfides.