Nobuaki Koga

Determination of the lowest energy point on the crossing seam between two potential surfaces using the energy gradient

Abstract A method is presented to search for the energy minimum crossing point between two potential surfaces with the aid of the energy gradient and the optimization method with a constraint. The method has been applied to two low-lying triplet excited states of chlorobenzene with the ab initio UHF wavefunction.

Ab initio MO study of the C60 anion radical: the Jahn—Teller distortion and electronic structure

Abstract The ab initio UHF structure determination for the C 60 anion radical shows that small Jahn—Teller distortions take place to give the D 5d , D 3d , and D 2h symmetric structures. They are almost degenerate and 2 kcal/mol more stable than the I h symmetric structure. Therefore, rearrangement among them could take place easily. The nodal properties of the singly occupied molecular orbital, localized mainly in the vicinity of the equator, make C − 60 ellipsoidally stretched along the principal axis.

Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods.

A comparison of the performance of various density functional methods including long‐range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D, B1B95, MPWB1K, M06‐2X, SVWN5, ωB97XD, long‐range correction (LC)‐ωPBE, and CAM‐B3LYP using 6‐31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A+) forms of alanine with benzene by taking the Møller–Plesset (MP2)/6‐31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine–benzene complexes were assessed at coupled cluster (CCSD)/6‐31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06‐2X, SVWN5, and the dispersion corrected B97‐D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97‐D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long‐range corrected methods, LC‐ωPBE and CAM‐B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values.

Intramolecular CH...M interaction: theoretical study of the structure of the six-coordinate ethyldiphosphinetitanium complex EtTi(PH3)2X2Y

Calcul de la geometrie de Ti(I 2 H 5 ) (PH 3 ) 2 Cl 2 H par une methode MO ab initio: presence du groupe C 2 H 5 deforme avec une distance Hβ..Ti courte

An ab initio molecular orbital study on adsorption at the MgO surface. I. H2 chemisorption on the (MgO)4 cluster

The hydrogen molecule chemisorption on the low coordination or corner site of the MgO surface has been studied with the ab initio method, adopting the (MgO)4 cluster as the surface site model. The effect of basis functions and correlation have been examined. Two physisorbed complexes have been found; one is an end‐on complex on the oxygen site and the other a side‐on complex on the Mg site. These complexes are led to a common transition state (TS) and then to a dissociative chemisorption product. A substantial polarization of charges in the hydrogen molecule takes place at the TS, from where the dissociative chemisorption proceeds ionically. The best estimates of energies of the physisorbed complexes, the TS and the product, relative to the isolated reactants are −2, +2, and −21 kcal/mol, respectively, for this cubic cluster model. When the effect of the Madelung potential is taken into account, the chemisorbed product is further stabilized by 4 kcal/mol.

Ab initio MO calculation of (η2-C60)Pt(PH3)2. Electronic structure and interaction between C60 and Pt

Abstract With an ab initio molecular orbital method, we have calculated the structure of (η 2 -C 60 )Pt(PH 3 ) 2 , a model of the experimentally studied (η 2 -C 60 )Pt(PPh 3 ) 2 . Compared with (C 2 H 4 )Pt(PH 3 ) 2 , much stronger back-donation from Pt(PH 3 ) 2 to C 60 takes place; the amount of charge transfer is about three times larger and the stabilization energy is about 15 kcal/mol larger. Analysis also shows that the PtC σ bonds are formed as a result of back-donation and the interacting PtCC moiety becomes a metallacy-clopropane. The electron affinity of the complex is only 0.44 eV smaller than that of C 60 , suggesting that several metals can simultaneously coordinate with C 60 .

A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation.

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER–GAUSSIAN interface (AG‐IF), which can be one of the simplest architectures. In the AG‐IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG‐IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG‐IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.

Photochromism of an organorhodium dithionite complex in the crystalline-state: molecular motion of pentamethylcyclopentadienyl ligands coupled to atom rearrangement in a dithionite ligand.

In the crystalline state, the rhodium dinuclear complex [(RhCp*)(2)(mu-CH(2))(2)(mu-O(2)SSO(2))] (1) with a photoresponsive dithionite group (mu-O(2)SSO(2)) and two pentamethylcyclopentadienyl ligands (Cp* = eta(5)-C(5)Me(5)) undergoes a 100% reversible unimolecular type T inverse photochromism upon interconversion to [(RhCp*)(2)(mu-CH(2))(2)(mu-O(2)SOSO)] (2). The photochromism can be followed directly by using stepwise crystal structure analysis (Angew. Chem., Int. Ed. 2006, 45, 6473). In this study, we found that the photoreaction of 1 was triggered by absorption of the 510 nm light (charge transfer band from sigma(S-S) to sigma*(S-S) and sigma*(Rh-Rh) orbitals assigned by DFT calculation) and included two important processes: kinetically controlled oxygen-atom transfer to produce four stereoisomers of 2 and thermodynamically controlled isomerization between the four stereoisomers of 2 to afford the most stable isomer. Although the formation rate of the four stereoisomer products was kinetically controlled and the population of the four stereoisomers produced in the system was thermodynamically controlled, both processes were regulated by the steric hindrance between the mu-O(2)SSO(2) or mu-O(2)SOSO ligand and the reaction cavity formed by the Cp* ligands. The cooperation of both processes achieved an intriguing stereospecific oxygen-atom rearrangement to produce only one stereoisomer of 2 at the final stage of the photoreaction at room temperature. We also determined the effect of the oxygen-atom rearrangement on the rotational motion of the two crystallographically independent Cp* ligands (parallel and perpendicular arrangement). Using variable-temperature (13)C CP/MAS NMR and quadrupolar echo solid-state (2)H NMR spectroscopies, before photoirradiation, the activation energies for the rotation of the parallel and perpendicular Cp* ligands in 1 were determined to be 33 +/- 3 and 7.8 +/- 1 kJ/mol, respectively, and after photoirradiation, in 2, they were much lower than those in 1 (21 +/- 2 and 4.7 +/- 0.5 kJ/mol, respectively). The large decrease in the activation energy for the parallel Cp* in 2 is attributed to the relaxation of molecular stress via a stereospecific oxygen-atom rearrangement, which suggests that the rotational motion of the Cp* ligands is coupled to the photochromism.

Role of structural water molecule in HIV protease‐inhibitor complexes: A QM/MM study

Structural water molecule 301 found at the interface of HIV protease‐inhibitor complexes function as a hydrogen bond (H‐bond) donor to carbonyl groups of the inhibitor as well as H‐bond acceptor to amide/amine groups of the flap region of the protease. In this study, six systems of HIV protease‐inhibitor complexes were analyzed, which have the presence of this “conserved” structural water molecule using a two‐layer QM/MM ONIOM method. The combination of QM/MM and QM method enabled the calculation of strain energies of the bound ligands as well as the determination of their binding energies in the ligand–water and ligand–water–protease complexes. Although the ligand experiences considerable strain in the protein bound structure, the H‐bond interactions through the structural water overcomes this strain effect to give a net stability in the range of 16–24 kcal/mol. For instance, in 1HIV system, the strain energy of the ligand was 12.2 kcal/mol, whereas the binding energy associated with the structural water molecule was 20.8 kcal/mol. In most of the cases, the calculated binding energy of structural water molecule showed the same trend as that of the experimental binding free energy values. Further, the classical MD simulations carried out on 1HVL system with and without structural water 301 showed that this conserved water molecule enhances the H‐bond dynamics occurring at the Asp‐bound active site region of the protease‐inhibitor system, and therefore it will have a direct influence on the mechanism of drug action.

Ab initio study on the structure and H2 dissociation reaction of a tetrahydride-bridged dinuclear Ru complex, (C5H5)Ru(μ-H)4Ru(C5H5)

Abstract The structure and bonding nature, and the H 2 dissociation reaction of (C 5 H 5 )Ru(μ-H) 4 Ru(C 5 H 5 ) have been studied using an ab initio molecular orbital (MO) method at the RHF and the MP2 level. Between the two Ru atoms there are four hydride-bridged, three-center two-electron bonds (RuHRu) with a bond energy of 74 kcal mol −1 , but no direct RuRu bonds. The four hydrides are almost equivalent and there is no HH bond. The H 2 dissociation reaction which gives coordinatively highly unsaturated CpRu(μ-H) 2 RuCp (Cp  C 5 H 5 ) is uphill and endothermic by 57 kcal mol −1 as a result of loss of the strong hydride-bridged bonds.