Biomedical subjects

Hirofumi Sato

Publications and source records attributed to Hirofumi Sato.

At least 19 recordsLinked to original sources

PubMed2006

Electron transfer in a radical ion pair: quantum calculations of the solvent reorganization energy.

Results are presented for an investigation of intermolecular electron transfer (ET) in solution by means of quantum calculations. The two molecules that are involved in the ET reaction form a solvent-separated radical ion pair. The solvent plays an important role in the ET between the two molecules. In particular, it can give rise to specific solute-solvent interactions with the solutes. An example of specific interactions is the formation of a hydrogen bond between a protic solvent and one of the molecules involved in the ET. We address the study of this system by means of quantum calculations on the solutes immersed in a continuum solvent. However, when the solvent can give rise to hydrogen bond formation with the negatively charged ion after ET, we explicitly consider solvent molecules in the solute cavity, determining the hydrogen bond energetic contribution to the overall interaction energy. Solute-solvent pair distribution functions, showing the different arrangement of solvent molecules before and after ET in the first solvation shell, are reported. We provide results of the solvent reorganization energy from quantum calculations for both the two isolated fragments and the ion pair in solution. Results are in agreement with available experimental data.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

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.

Letter↗

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.

Journal Article↗

PubMed2006

Ab initio theoretical study of temperature and density dependence of molecular and thermodynamic properties of water in the entire fluid region: autoionization processes.

The temperature and density dependence of the molecular and thermodynamic properties of water is investigated theoretically by means of the ab initio electronic structure theory combined with the reference interaction site model method, so-called RISM-SCF. We consider the autoionization process (H2O + H2O right harpoon over left harpoon H3O+ + OH-) by regarding H2O, H3O+, and OH- as "solute" molecules in an aqueous solution and evaluate molecular geometry, electronic structure, solvation structure, and the ionic product of water (pKw) of these species as functions of thermodynamic conditions. In our previous paper, we calculated these properties by using essentially the same method in a wide range of density values (0.6-1.4 g/cm3). However, the calculation was limited at rather higher density (>0.6 g/cm3) due to the difficulty of convergence, which is inherent to the hypernetted-chain (HNC) closure. The problem is overcome in this study by employing the Kovalenko-Hirata (KH) closure which hybridizes the HNC and the mean-spherical approximation (MSA). Here, we present the results for the thermodynamic range of densities from 0.025 to 1.0 g/cm3 and for temperatures from 300 to 800 K including the supercritical point.

Journal Article↗

PubMed2006

RNA recognition and recognition control of alpha-peptide ribonucleic acids containing arginine residue by external factors.

A novel nucleic acid model using alpha-peptide ribonucleic acid (alpha-PRNA) possessing alternative alpha-PRNA/lysine and alpha-PRNA/arginine sequences, where the lysine or arginine residue are expected to stabilize the complex not only by the conventional hydrogen-bonding interactions between the complementary nucleobase pairs but also through the electrostatic interactions between basic amino acid side-chain groups and DNA's phosphate anions on the backbone. These alpha-PRNAs form stable sequence-specific complex with the complementary DNA.

Arginine↗

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.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

PubMed2005

DNA recognition and recognition control of alpha-peptide ribonucleic acids by external factors.

Peptide ribonucleic acid (PRNA) is one of artificial nucleic acids, which enables us to control its nucleobase orientation and recognition behavior by external factors through the synergetic effects of reversible borate ester formation and intramolecular hydrogen bond formation. In this study, a series of novel alpha-PRNA oligomers, possessing alternative alpha-PRNA/basic amino acid sequences, were newly designed, synthesized, and evaluated as the second-generation PRNA. As expected, these alpha-PRNAs indeed formed highly stable sequence-specific complexes with the complementary DNAs, for which both the conventional hydrogen-bonding interactions between the complementary nucleobase pairs and the electrostatic interactions between the basic amino acid's ammonium cation and the DNA's phosphate anion on the backbone are jointly responsible.

Buffers↗

PubMed2004

External reversible control of recognition behavior of alpha-peptide ribonucleic acid (alpha-PRNA) through anti-syn orientational switching of the nucleobase induced by borate esterification of the cis-2',3'-diol.

A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orientational switching of the nucleobase induced by borate.

Borates↗

PubMed2004

Synthesis of peptide ribonucleic acid consisting of D- and L-gamma-glutamic acid as a backbone structure.

A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5-amino-5-deoxyribonucleoside as a recognition site for nucleic acids and consists D-glutamic acid (D-PRNA) instead of L-glutamic acid (L-PRNA) as a backbone structure, has been designed and synthesized. Difference between D-PRNA and L-PRNA oligomers was elucidated on the basis of the effects of chirality of gamma-glutamic acid backbone upon structure elucidated by CD spectra.

Buffers↗

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.

Journal Article↗

PubMed2003

The inhibitory effect of glycolic acid and lactic acid on melanin synthesis in melanoma cells.

Alpha-hydroxy acids (AHAs) such as glycolic acid (GA) and lactic acid (LA) have been reported to be effective in treating pigmentary lesions such as melasma, solar lentigines, and postinflammatory hyperpigmentation. The mechanism of this effect might be due to epidermal remodeling and accelerated desquamation, which would result in quick pigment dispersion. However, the direct effect of AHAs on melanin synthesis has not yet been well studied. To elucidate such a direct effect of AHAs on melanogenesis, we performed melanin assays, growth curve determinations, Northern and Western blotting for melanogenic proteins [tyrosinase, tyrosinase related protein (TRP)-1 and TRP-2], and tyrosinase and, 4-dihydroxyphenylalaninechrome tautomerase enzyme activity assays using mouse B16 and human melanoma cells. GA or LA (at doses of 300 or 500 microg/ml) inhibited melanin formation in similar dose-dependent manner, without affecting cell growth. Although the mRNA and protein expression or molecular size of tyrosinase, TRP-1 and TRP-2 were not affected, tyrosinase activity was inhibited. To see whether GA and/or LA directly inhibit tyrosinase catalytic function, the effect of GA and LA on human tyrosinase purified from the melanosome-rich large granule fraction of human melanoma cells was performed. GA or LA were shown to inhibit tyrosinase enzyme activity directly, but this effect was not due to the acidity of GA or LA, because adjusting the pH to 5.6 (the pH of GA and LA at concentrations of 2500 microg/ml), did not affect tyrosinase activity. Taken together, these results show that GA and LA suppress melanin formation by directly inhibiting tyrosinase activity, an effect independent of their acidic nature. GA and LA might work on pigmentary lesions not only by accelerating the turnover of the epidermis but also by directly inhibiting melanin formation in melanocytes.

Animals↗

PubMed2003

A novel strategy for reversible control of conformation and DNA/RNA recognition of peptide ribonucleic acid (PRNA) by external factors.

A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxyribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary oligomeric DNA through the orientational switching of the nucleobase induced by borates. In case of PRNA 12-mers, efficient orientational change of nucleobases was observed. Furthermore, these oligomeric PRNAs form a stable complex with complementary DNA's and the recognition behavior of oligomeric PRNAs with DNA's is controlled by the borate added as an external factor.

DNA↗

PubMed2002

The expression of corticotropin-releasing hormone in melanoma.

We previously demonstrated that advanced melanoma cells express high amounts of proopiomelanocortin (POMC) that correlate with tumor progression. We now investigated whether the high expression of POMC derives from increased expression of corticotropin-releasing hormone (CRH) and the possible role of CRH as a melanoma growth factor. Forty-five cases of melanoma [25 primary malignant melanoma; 20 metastatic melanoma (MetM)] were immunohistochemically analysed for coexpression of POMC and CRH peptides. The ability of CRH to induce POMC expression in cultured melanoma cells was examined using CRH and a CRH antagonist. In CRH positive melanomas, seven out of nine cases (78%) of primary melanoma, and 7 out of 12 cases (58%) of MetM showed colocalization of CRH and POMC peptides. CRH induced POMC mRNA expression, an effect that was inhibited by a CRH antagonist. These results provide evidence for the existence of the CRH/POMC axis in pigmented lesions.

Corticotropin-Releasing Hormone↗