Biomedical subjects

Shigeyoshi Sakaki

Publications and source records attributed to Shigeyoshi Sakaki.

15 recordsLinked to original sources

PubMed2006

New evaluation of reconstructed spatial distribution function from radial distribution functions.

Although three dimensional (3D) solvation structure is much more informative than one dimensional structure, its evaluation is difficult experimentally and theoretically. In our previous Communication [Yokogawa et al., J. Chem. Phys. 123, 211102 (2005)], we proposed a new method to present reconstructed spatial distribution function (RC-SDF) from a set of radial distribution functions (RDFs). In this article, we successfully extended the method more accurately with new basis sets. This new method was applied to two liquid solvation structures, methanol and dimethyl sulfoxide, as examples. Their RC-SDFs evaluated here clearly show that the former solvation structure is well defined while the latter one is broad, which agrees well with the SDFs calculated directly from molecular dynamics simulations. These results indicate that the method can reproduce well these 3D solvation structures in reasonable computational cost.

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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

Phosphorus-containing hybrid calixphyrins: promising mixed-donor ligands for visible and efficient palladium catalysts.

Phosphorus-sulfur-containing hybrid calixphyrins were prepared by the BF3-promoted dehydrative condensation between sigma4-2,5-bis[(pyrrol-2-yl)methyl]phosphole and 2,5-bis[hydroxy(phenyl)methyl]thiophene. X-ray crystallographic analysis of the Pd-P,N2,S-hybrid calixphyrin complex revealed that the Pd center was coordinated by the four heteroatoms to adopt a distorted square planar geometry. The Pd complex, displaying a characteristic reddish purple color in solution, catalyzed the Heck reaction of bromoarenes with n-butyl acrylate with high efficiency at elevated temperatures.

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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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PubMed2006

Analysis on solvated molecules with a new energy partitioning scheme for intra- and intermolecular interactions.

A new partitioning scheme for the total energy of molecules is presented. In the scheme, the Hartree-Fock total energy of a molecular system is represented as the sum of one- and two-center terms exactly. The present method provides physically reasonable behavior for a wide range of interactions, and intermolecular interaction is treated equivalently with intramolecular interaction. The method is applied to analysis on the inter- and intramolecular interactions of molecular complexes both in gas phase and in aqueous solution. The results strongly indicate that the present method is a powerful tool to understand not only the bonding nature of molecules but also interaction between molecules.

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PubMed2005

A new method to reconstruct three-dimensional spatial distribution function from radial distribution function in solvation structure.

Three-dimensional spatial distribution function (SDF) of solvent is a fundamental quantity for analysis of solvation. However, its calculation has been very limited because long computational time is required. We here developed a novel and robust method to construct approximated SDFs of solvent sites from radial distribution functions. In this method, the expansion of SDFs in real solid harmonics around atoms of solute leads to a linear equation, from which SDFs are evaluated with reasonable computational time. This method is applied to the analysis of the solvation structure of liquid water, as an example. The successful results clearly show that this method is very powerful to investigate solvation structure.

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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

Theoretical study of trans-metalation process in palladium-catalyzed borylation of iodobenzene with diboron.

Trans-metalation process in the palladium-catalyzed borylation of iodobenzene with diboron was theoretically investigated with the DFT method. Palladium(II) hydroxo phenyl complex, Pd(OH)(Ph)(PH(3))(2), and the fluoro analogue easily undergo the trans-metalation with diboron, B(2)(eg)(2) (eg = -OCH(2)CH(2)O-), to afford Pd(Ph)(Beg)(PH(3))(HO-Beg) and Pd(Ph)(Beg)(PH(3))(F-Beg), respectively, where B(2)(eg)(2) is adopted as a model of bis(pinacolato)diboron used experimentally. The electron re-distribution in the trans-metalation clearly indicates that the B-B bond scission occurs in a heterolytic manner. In the chloro analogue, PdCl(Ph)(PH(3))(2), however, the trans-metalation occurs in a homolytic manner with much difficulty, which is consistent with the experimental result. The significant differences between the chloro complex and the other hydroxo and fluoro complexes are easily interpreted in terms that hydroxo and fluoro ligands can form strongly bonding interaction with B(2)(eg)(2) but the chloro ligand cannot.

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PubMed2004

Theoretical study of the Cp2Zr-catalyzed hydrosilylation of ethylene. Reaction mechanism including new sigma-bond activation.

The Cp(2)Zr-catalyzed hydrosilylation of ethylene was theoretically investigated with DFT and MP2-MP4(SDQ) methods, to clarify the reaction mechanism and the characteristic features of this reaction. Although ethylene insertion into the Zr-SiH(3) bond of Cp(2)Zr(H)(SiH(3)) needs a very large activation barrier of 41.0 (42.3) kcal/mol, ethylene is easily inserted into the Zr-H bond with a very small activation barrier of 2.1 (2.8) kcal/mol, where the activation barrier and the energy of reaction calculated with the DFT(B3LYP) method are given and in parentheses are those values which have been corrected for the zero-point energy, hereafter. Not only this ethylene insertion reaction but also the coupling reaction between Cp(2)Zr(C(2)H(4)) and SiH(4) easily takes place to afford Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with activation barriers of 0.3 (0.7) and 5.0 (5.4) kcal/mol, respectively. This coupling reaction involves a new type of Si-H sigma-bond activation which is similar to metathesis. The important interaction in the coupling reaction is the bonding overlap between the d(pi)-pi bonding orbital of Cp(2)Zr(C(2)H(4)) and the Si-H sigma orbital. The final step is neither direct C-H nor Si-C reductive elimination, because both reductive eliminations occur with a very large activation barrier and significantly large endothermicity. This is because the d orbital of Cp(2)Zr is at a high energy. On the other hand, ethylene-assisted C-H reductive elimination easily occurs with a small activation barrier, 5.0 (7.5) kcal/mol, and considerably large exothermicity, -10.6 (-7.1) kcal/mol. Also, ethylene-assisted Si-C reductive elimination and metatheses of Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with SiH(4) take place with moderate activation barriers, 26.5 (30.7), 18.4 (20.5), and 28.3 (31.5) kcal/mol, respectively. From these results, it is clearly concluded that the most favorable catalytic cycle of the Cp(2)Zr-catalyzed hydrosilylation of ethylene consists of the coupling reaction of Cp(2)Zr(C(2)H(4)) with SiH(4) followed by the ethylene-assisted C-H reductive elimination.

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PubMed2003

Iridium-catalyzed borylation of benzene with diboron. Theoretical elucidation of catalytic cycle including unusual iridium(v) intermediate.

Iridium-catalyzed borylation of benzene with diboron was theoretically investigated with the DFT method, where an iridium(I) boryl complex, Ir(Beg)(NN) 1, and an iridium(III) tris(boryl) complex, Ir(Beg)(3)(NN) 14, (eg (ethyleneglycolato) = -OCH(2)CH(2)O-, NN = HN=CHCH=NH (diim) or 2,2'-bipyridine (bpy)) were adopted as models of active species and B(2)(eg)(2) was adopted as a model of bis(pinacolato)diboron (pinacolato = -OCMe(2)CMe(2)O-). Oxidative addition of a benzene C-H sigma-bond to 1 takes place with an activation barrier (E(a)) of 11.2 kcal/mol, followed by reductive elimination of phenylborane, Ph-Beg, from Ir(Beg)(H)(Ph)(diim) with an activation barrier of 15.6 kcal/mol. Though the oxidative addition and the reductive elimination occur with moderate activation barriers, B(2)(eg)(2) much more easily reacts with 1 to afford 14 than does benzene, of which the activation barrier is very small (2.9 kcal/mol). Oxidative addition of the benzene C-H sigma-bond to 14 occurs with a moderate activation barrier of 24.2 kcal/mol to afford an unusual seven-coordinate iridium(V) complex, Ir(H)(Ph)(Beg)(3)(bpy) 16. From this complex, phenylborane Ph-Beg is produced through the reductive elimination with concomitant formation of IrH(Beg)(2)(bpy) 17, where the activation barrier is 4.9 kcal/mol. Complex 17 further reacts with diboron to form Ir(H)(Beg)(4)(bpy) (E(a) = 8.0 kcal/mol), followed by the reductive elimination of borane H-Beg (E(a) = 2.6 kcal/mol) to regenerate Ir(Beg)(3)(bpy), when diboron exists in excess in the reaction solution. After consumption of diboron, IrH(Beg)(2)(bpy) reacts with borane, H-Beg, to form Ir(H)(2)(Beg)(3) (E(a) = 21.3 kcal/mol) followed by the reductive elimination of H(2), to regenerate Ir(Beg)(3)(bpy) with concomitant formation of H(2). Formation of the iridium(III) tris(boryl) complex 14 from IrCl(diim) and diboron was also theoretically investigated; IrCl(diim) undergoes two steps of oxidative addition of diboron to afford a seven-coordinate iridium(V) complex, IrCl(Beg)(4)(NN), from which the reductive elimination of Cl-Beg takes place easily to afford 14. From these results, it should be clearly concluded that the iridium(III) tris(boryl) complex is an active species and an unusual iridium(V) species is involved as a key intermediate in the reaction. Detailed discussion is presented on the full catalytic cycle and the importance of a seven-coordinate iridium(V) intermediate.

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PubMed2002

Theoretical study of rhodium(III)-catalyzed hydrogenation of carbon dioxide into formic acid. Significant differences in reactivity among rhodium(III), rhodium(I), and ruthenium(II) complexes.

The title reaction was theoretically investigated, where cis-[RhH(2)(PH(3))(3)](+) and cis-[RhH(2)(PH(3))(2)(H(2)O)](+) were adopted as models of the catalyst. The first step of the catalytic cycle is the CO(2) insertion into the Rh(III)-H bond, of which the activation barrier (E(a)) is 47.2 and 28.4 kcal/mol in cis-[RhH(2)(PH(3))(3)](+) and cis-[RhH(2)(PH(3))(2)(H(2)O)](+), respectively, where DFT(B3LYP)-calculated E(a) values (kcal/mol unit) are given hereafter. These results indicate that an active species is not cis-[RhH(2)(PH(3))(3)](+) but cis-[RhH(2)(PH(3))(2)(H(2)O)](+). After the CO(2) insertion, two reaction courses are possible. In one course, the reaction proceeds through isomerization (E(a) = 2.8) of [RhH(eta(1)- OCOH)(PH(3))(2)(H(2)O)(2)](+), five-centered H-OCOH reductive elimination (E(a) = 2.7), and oxidative addition of H(2) to [Rh(PH(3))(2)(H(2)O)(2)](+) (E(a) = 5.8). In the other one, the reaction proceeds through isomerization of [RhH(eta(1)-OCOH)(PH(3))(2)(H(2)O)(H(2))](+) (E(a) = 5.9) and six-centered sigma-bond metathesis of [RhH(eta(1)-OCOH)(PH(3))(2)(H(2)O)](+) with H(2) (no barrier). RhH(PH(3))(2)-catalyzed hydrogenation of CO(2) proceeds through CO(2) insertion (E(a) = 1.6) and either the isomerization of Rh(eta(1)-OCOH)(PH(3))(2)(H(2)) (E(a) = 6.1) followed by the six-centered sigma-bond metathesis (E(a) = 0.3) or H(2) oxidative addition to Rh(eta(1)-OCOH)(PH(3))(2) (E(a) = 7.3) followed by isomerization of RhH(2)(eta(1)-OCOH)(PH(3))(2) (E(a) = 6.2) and the five-centered H-OCOH reductive elimination (E(a) = 1.9). From these results and our previous results of RuH(2)(PH(3))(4)-catalyzed hydrogenation of CO(2) (J. Am. Chem. Soc. 2000, 122, 3867), detailed discussion is presented concerning differences among Rh(III), Rh(I), and Ru(II) complexes.

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