Biomedical subjects

Yoshihide Nakao

Publications and source records attributed to Yoshihide Nakao.

8 recordsLinked to original sources

PubMed2006

Silapropargyl/silaallenyl and silylene acetylide complexes of [Cp(CO)2W]+. Theoretical study of their interesting bonding nature and formation reaction.

The geometry and bonding nature of Cp(CO)(2)W(CCH)(SiH(2)) (1) and the reaction leading to the formation of 1 from Cp(CO)(2)W(SiH(2)C triple bond CH)(9) were theoretically investigated with DFT, MP2 to MP4(SDTQ), and CCSD(T) methods, where 9 and 1 were adopted as models of the interesting new complexes reported recently, Cp*(CO)(2)W(Si(Ph)(2)C triple bond C(t)Bu) and Cp*(CO)(2)W(C triple bond C(t)Bu)(SiPh(2)), respectively. Our computational results clearly indicate that 1 involves neither a pure silacyclopropenyl group nor pure silylene and acetylide groups and that the silylene group strongly interacts with both the W center and the acetylide group. Frontier orbitals of 1 resemble those observed in the formation of silacyclopropene from silylene and acetylene. The frontier orbitals, as well as the geometry, indicate that the (CCH)(SiH(2)) moiety of 1 can be understood in terms of an interesting intermediate species trapped by the W center in that formation reaction. Complex 1 is easily formed from 9 through Si-C sigma-bond activation with moderate activation barriers of 15.3, 18.8, and 15.8 kcal/mol, which are the DFT-, MP4(SDTQ)-, and CCSD(T)-calculated values, respectively. This reaction takes place without a change of the oxidation state of the W center. Intermediate 9 is easily formed from Cp(CO)(2)W(Me)(H(3)SiC triple bond CH) via Si-H oxidative addition, followed by C-H reductive elimination. The bonding nature of 9 is also very interesting; the nonbonding pi-orbital of the H(2)SiCCH moiety is essentially the same as that of the propargyl group, but the pi-conjugation between Si and C atoms is very weak in the pi-orbital, unlike that in the propargyl group.

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PubMed2006

Deep blue mixed-valent PtIIIPtIIIPtII complex [Pt3Br2(mu-pz)6] (pz=pyrazolate) showing valence-detrapping behavior in solution.

The oxidation of the pyrazolate bridged cyclic PtII trimer, [Pt3(mu-pz)6] (1), in the presence of bromide ion gave a deep blue mixed-valent Pt(II,III,III) complex, [Pt3Br2(mu-pz)6] (2). The structural analysis of 2 disclosed that the complex has localized Pt--Pt bond. Our theoretical calculations revealed that the HOMO and LUMO of Pt3 (II,III,III) species mainly consists of (dsigma-dsigma) and (dsigma-dsigma)* orbitals, respectively, and the origin of deep blue color of the bromo complex, 2, arises from the (dsigma-dsigma)-->(dsigma-dsigma)* transition. Unique fluxional behavior was observed due to valence-detrapping of 2 in solution. The activation parameters of the valence-detrapping of 2 obtained by Eyring analyses were DeltaH(not equal)=37(2) kJ mol(-1) and DeltaS(not equal)=-67(7) J mol(-1) K(-1).

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PubMed2006

Discrete sandwich compounds of monolayer palladium sheets.

Despite the abundance of "sandwich" complexes, in which two cyclic aromatic hydrocarbon ligands flank a metal center, this motif has not been extended to sheets of multiple metal atoms. We prepared and isolated two such compounds. In the first, three palladium centers form a planar triangular array, capped by chlorides, between two cycloheptatrienyl ligands. In the second, a pentapalladium sheet adopts an edge-sharing triangle-trapezoid skeleton between two naphthacene rings. The compounds were characterized by x-ray crystallography and nuclear magnetic resonance spectroscopy. The nature of bonding in the clusters was analyzed by quantum calculations.

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PubMed2006

Theoretical study of rhenium dinuclear complexes: Re-Re bonding nature and electronic structure.

Four dinuclear rhenium complexes, [Re2Cl8](2-) (1), [Re2(mu-Cl)3Cl6](2-) (2a), [Re2(mu-Cl)3Cl6](-) (2b), and [Re2(mu-Cl)2Cl8](2-) (3), were theoretically investigated by the CASSCF, MRMP2, SA-CASSCF, and MCQDPT methods. Interesting differences in electronic structure and Re-Re bonding nature among these complexes are clearly reported here, as follows: In 1, the ground state is the 1A1g state. The approximate stabilization energies by the sigma, pi, and delta bonding interactions are evaluated to be 4.36, 2.89, and 0.52 eV, respectively, by the MRMP2 method. In 2a, the ground state is the 2E" state. The approximate stabilization energy by two degenerate delta bonding interactions is estimated to be 0.36 eV by the MCQDPT method. One delta bonding interaction of 2a is much weaker than that of 1, which is discussed in terms of the Re-Re distance and the Re oxidation state. In 2b, the ground state is the 1A1' state, of which multiconfigurational nature is extremely large unlike that of the 2E" ground state of 2a despite similarities between 2a and 2b. In 3, the sigma, pi, and delta bonding interactions are not effectively formed between two Re centers. As a result, the 1Ag, 3B1u, 5Ag, and 7B1u states are in almost the same energy within 0.03 eV. This result is consistent with the paramagnetism of 3 experimentally reported.

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PubMed2006

A new analysis of molecular orbital wave functions based on resonance theory.

A new method to evaluate the weights of resonance structures from molecular orbital wave function is proposed, which is based on the second quantization of singlet-coupling. The present method is useful to analyze molecules of which the electronic structures are well localizable. The evaluation is carried out through localization of molecular orbitals followed by algebraic calculation of density matrices. This method is applied to H(2)O, H(3)O(+), and BH(3). The calculated weights of covalent and ionic structures are in excellent agreement with those of the previous works and our chemical intuition.

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PubMed2005

Theoretical study of M(PH3)2 complexes of C60, corannulene (C20H10), and sumanene (C21H12) (M = Pd or Pt). Unexpectedly large binding energy of M(PH3)2(C60).

DFT and MP2 to MP4(SDQ) methods were applied to M(PH3)2(C60), Pt(PH3)2(C20H10), and Pt(PH3)2(C21H12) (M = Pd or Pt, C20H10 = corannulene, and C21H12 = sumanene). The binding energy considerably fluctuates around MP2 and MP3 levels but much less upon going from MP3 to MP4(SDQ) in Pt(PH3)2(C2H4), Pt(PH3)2(C20H10), and Pt(PH3)2(C21H12). Also, the MP4(SDQ) method presents a binding energy similar to that of the CCSD(T) method in Pt(PH3)2(C2H4). Thus, it is likely that the MP4(SDQ) method is useful to evaluate binding energies of these complexes. The binding energies of Pt(PH3)2(C20H10) and Pt(PH3)2(C21H12) are evaluated to be 24.9 and 26.1 kcal/mol, respectively, by the MP4(SDQ) method and only +5.8 and -2.6 kcal/mol, respectively, by the DFT(B3LYP) method. These MP4(SDQ)-calculated binding energies of Pt(PH3)2(C20H10) and Pt(PH3)2(C21H12) are similar to that of Pt(PH3)2(C2H4), which strongly suggests that these complexes can be successfully synthesized. The binding energy of Pt(PH3)2(C60) is evaluated to be 44.8 and 45.5 kcal/mol with the ONIOM(MP4(SDQ):UFF) and ONIOM(MP4(SDQ):B3LYP) methods, respectively, and that of the Pd analogue is evaluated to be 39.9 kcal/mol with the ONIOM(MP4(SDQ):UFF) method, whereas the DFT(B3LYP), DFT(BVP86), and DFT(BPW91) methods provide much smaller binding energies. It is noted that these binding energies are much larger than those of the ethylene, corannulene, and sumanene analogues. This difference is reasonably interpreted in terms that the LUMO of C60 is at much lower energy than those of ethylene, corannulene, and sumanene. We investigated also how to separate the high level and the low level regions in the ONIOM calculation of M(PH3)2(C60) and proposed here the reasonable way to evaluate the binding energy of transition-metal complexes of C60.

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PubMed2005

Ruthenium(II)-catalyzed hydrogenation of carbon dioxide to formic acid. Theoretical study of real catalyst, ligand effects, and solvation effects.

Ruthenium-catalyzed hydrogenation of carbon dioxide to formic acid was theoretically investigated with DFT and MP4(SDQ) methods, where a real catalyst, cis-Ru(H)2(PMe3)3, was employed in calculations and compared with a model catalyst, cis-Ru(H)2(PH3)3. Significant differences between the real and model systems are observed in CO2 insertion into the Ru(II)-H bond, isomerization of a ruthenium(II) eta1-formate intermediate, and metathesis of the eta1-formate intermediate with a dihydrogen molecule. All these reactions more easily occur in the real system than in the model system. The differences are interpreted in terms that PMe3 is more donating than PH3 and the trans-influence of PMe3 is stronger than that of PH3. The rate-determining step is the CO2 insertion into the Ru(II)-H bond. Its deltaG(o++) value is 16.8 (6.8) kcal/mol, where the value without parentheses is calculated with the MP4(SDQ) method and that in parentheses is calculated with the DFT method. Because this insertion is considerably endothermic, the coordination of the dihydrogen molecule with the ruthenium(II)-eta1-formate intermediate must necessarily occur to suppress the deinsertion. This means that the reaction rate increases with increase in the pressure of dihydrogen molecule, which is consistent with the experimental results. Solvent effects were investigated with the DPCM method. The activation barrier and reaction energy of the CO2 insertion reaction moderately decrease in the order gas phase > n-heptane > THF, while the activation barrier of the metathesis considerably increases in the order gas phase < n-heptane < THF. Thus, a polar solvent should be used because the insertion reaction is the rate-determining step.

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PubMed2004

A local second-order Møller-Plesset method with localized orbitals: a parallelized efficient electron correlation method.

Using orthogonal localized occupied orbitals we have developed and implemented a parallelized local second-order Møller-Plesset (MP2) method based on the idea developed by Head-Gordon and co-workers. A subset of nonorthogonal correlation functions (the orbital domain) was assigned to each of the localized occupied orbitals using a distance criterion and excitations from localized occupied orbitals that were arranged into subsets. The correlation energy was estimated using a partial diagonalization and an iterative efficient method for solving large-scale linear equations. Some illustrative calculations are provided for molecules with up to 1484 Cartesian basis sets. The orbital domain sizes were found to be independent of the molecular size, and the present local MP2 method covered about 98%-99% of the correlation energy of the conventional canonical MP2 method.

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