Biomedical subjects

Hiroshi Nakatsuji

Publications and source records attributed to Hiroshi Nakatsuji.

17 recordsLinked to original sources

PubMed2006

C4Cl: bent or linear?

The ground state structure for the CCCCCl radical was computed by using symmetry-adapted cluster configuration-interaction (SAC-CI) theory along with density functional theory to overcome the differences raised in the recently published paper [Y. Sumiyoshi et al., Chem. Phys. Lett. 414, 82 (2005)] between the theory and the experiment. SAC-CI results clearly support the earlier experimental conclusion that the radical has the bent ground state structure corresponding to 2Pi symmetry. Contrarily, probably due to spin contamination, mixing of a bent doublet ground state with the quartet components of a linear structure, coupled-cluster singles and doubles (CCSD) calculations were unable to provide reliable results. Results obtained using density functional theory also show that the radical has a bent structure. Some low-lying doublet excited states were also studied using the SAC-CI theory. The energy difference between the ground Pi state and the nearby Sigma state is around 0.2 eV. The excitation energy for the transition with the largest oscillator strength agrees with the strongest absorption peak.

Journal Article↗

PubMed2006

SAC and SAC-CI calculations of excitation and circular dichroism spectra of straight-chain and cyclic dichalcogens.

Accurate quantum-chemical calculations of the excitation energies and the rotatory strengths of dichalcogens R-Ch-Ch-R (Ch = S, Se, Te) were carried out with the symmetry adapted cluster (SAC) and SAC-configuration interaction (CI) methods. A series of straight-chain molecules (dihydrogen dichalcogenide, dimethyl dichalcogenide, and (+)-bis(2-methylbutyl) dichalcogenide) and one cyclic molecule (2,3-(R,R)-dichalcogenadecalin) were adopted for comparative analysis. The calculated excitation and circular dichroism (CD) spectra were in good agreement with experimental ones (Laur, P. H. A. In Proceedings of the Third International Symposium on Organic Selenium and Tellurium Compounds; Cagniant, D., Kirsch, G., Eds.; Universite de Metz: Metz, 1979; pp 219-299) within 0.3 eV. The fitting CD spectra also reasonably reproduced the experimental ones. In all the molecules adopted, the first and second lowest bands were assigned to the n-sigma(Ch-Ch) transition and the third and fourth lowest bands to the n-sigma(Ch-R) transition. The first and second lowest bands apparently depended on the R-Ch-Ch-R dihedral angle, suggesting that the orbital energies of two sigma(Ch-Ch) change with the R-Ch-Ch-R dihedral angle. This calculated trend agrees with two empirical rules: the C(2) rule and the quadrant rule.

Chalcogens↗

PubMed2006

Singly and doubly excited states of butadiene, acrolein, and glyoxal: Geometries and electronic spectra.

Excited-state geometries and electronic spectra of butadiene, acrolein, and glyoxal have been investigated by the symmetry adapted cluster configuration interaction (SAC-CI) method in their s-trans conformation. Valence and Rydberg states below the ionization threshold have been precisely calculated with sufficiently flexible basis sets. Vertical and adiabatic excitation energies were well reproduced and the detailed assignments were given taking account of the second moments. The deviations of the vertical excitation energies from the experiment were less than 0.3 eV for all cases. The SAC-CI geometry optimization has been applied to some valence and Rydberg excited states of these molecules in the planar structure. The optimized ground- and excited-state geometries agree well with the available experimental values; deviations lie within 0.03 A and 0.7 degrees for the bond lengths and angles, respectively. The force acting on the nuclei caused by the excitations has been discussed in detail by calculating the SAC-CI electron density difference between the ground and excited states; the geometry relaxation was well interpreted with the electrostatic force theory. In Rydberg excitations, geometry changes were also noticed. Doubly excited states (so-called 2 (1)A(g) states) were investigated by the SAC-CI general-R method considering up to quadruple excitations. The characteristic geometrical changes and large energetic relaxations were predicted for these states.

Journal Article↗

PubMed2006

Inner-shell ionizations and satellites studied by the open-shell reference symmetry-adapted cluster/symmetry-adapted cluster configuration-interaction method.

Open-shell reference version of the symmetry-adapted cluster (SAC) and SAC-configuration-interaction (CI) methods, termed open-shell reference (OR)-SAC and OR-SAC-CI methods, are developed and applied to inner-shell ionizations of CH4, NH3, H2O, and HF. The inner-shell ionization potentials and spectra calculated by the OR-SAC and OR-SAC-CI methods are in excellent agreement with the experimental data. Including both of the electron correlation and orbital relaxation is important for quantitative agreements. Timing comparisons with the SAC-CI general-R calculations that give similar high accuracies show an efficiency of the present OR-SAC and OR-SAC-CI methods.

Journal Article↗

PubMed2006

Electronic spectra and photodissociation of vinyl chloride: a symmetry-adapted cluster configuration interaction study.

The vertical absorption spectrum and photodissociation mechanism of vinyl chloride (VC) were studied by using symmetry-adapted cluster configuration interaction theory. The important vertical pi --> pi* excitation was intensively examined with various basis sets up to aug-cc-pVTZ augmented with appropriate Rydberg functions. The excitation energy for pi --> pi* transition obtained in the present study, 6.96 eV, agrees well with the experimental value, 6.7-6.9 eV. Calculated excitation energies along with the oscillator strengths clarify that the main excitation in VC is the pi --> pi* excitation. Contrary to the earlier theoretical reports, the results obtained here support that the C-Cl bond dissociation takes place through the n(Cl-)sigma(C-Cl)* state.

Journal Article↗

PubMed2006

On the reversible O2 binding of the Fe-porphyrin complex.

Electronic mechanism of the reversible O(2) binding by heme was studied by using Density Functional Theory calculations. The ground state of oxyheme was calculated to be open singlet state [Fe(S =1/2) + O(2)(S = 1/2)]. The potential energy surface for singlet state is associative, while that for triplet state is dissociative. Because the ground state of the O(2)+ deoxyheme system is triplet in the dissociation limit [Fe(S = 2) + O(2)(S = 1)], the O(2) binding process requires relativistic spin-orbit interaction to accomplish the intersystem crossing from triplet to singlet states. Owing to the singlet-triplet crossing, the activation energies for both O(2) binding and dissociation become moderate, and hence reversible. We also found that the deviation of the Fe atom from the porphyrin plane is also important reaction coordinate for O(2) binding. The potential surface is associative/dissociative when the Fe atom locates in-plane/out-of-plane.

Binding, Competitive↗

PubMed2006

On the O2 binding of Fe-porphyrin, Fe-porphycene, and Fe-corrphycene complexes.

Based on our previous study for the O2 binding of the Fe-Por complex, this study investigates the O2 binding mechanism in the Fe-porphyrin isomers, Fe-porphycene (FePc), and Fe-corrphycene (FeCor) complexes. By calculating the potential energy surface of the O2 binding, the present study explains the reason for the dramatic increase of O2 affinities observed in the FePc complex. In the case of FeCor-O2, the O2 binding process includes the intersystem crossing from a triplet to singlet state, as in the FePor-O2 complex. However, FePc-O2 uses only a singlet surface. This is because the ground state of the FePc complex in the deoxy state is a triplet state, while those of FePor and FeCor are a quintet state. Such difference originates from character of the SOMO. We estimated an equilibrium constant for the O2 binding that reasonably reproduced the trend observed in the experiments.

Ferrous Compounds↗

PubMed2005

Analytically solving the relativistic Dirac-Coulomb equation for atoms and molecules.

A method of solving the Schrödinger equation in an analytically expanded form reported previously is extended to the relativistic case and a general method of exactly solving the Dirac-Coulomb equation has been proposed for atoms and molecules. Some problems characteristic of the relativistic case are discussed. Test applications to the hydrogen-like, helium-like atoms are satisfactory, implying a high potentiality of the proposed method also for the relativistic case.

Journal Article↗

PubMed2005

Quasirelativistic theory for the magnetic shielding constant. III. Quasirelativistic second-order Møller-Plesset perturbation theory and its application to tellurium compounds.

The quasirelativistic (QR) generalized unrestricted Hartree-Fock method for the magnetic shielding constant [R. Fukuda, M. Hada, and H. Nakatsuji, J. Chem. Phys. 118, 1015 (2003); R. Fukuda, M. Hada, and H. Nakatsuji, J. Chem. Phys.118, 1027 (2003)] has been extended to include the electron correlation effect in the level of the second-order Møller-Plesset perturbation theory (MP2). We have implemented the energy gradient and finite-perturbation methods to calculate the magnetic shielding constant at the QR MP2 level and applied to the magnetic shielding constants and the NMR chemical shifts of 125Te nucleus in various tellurium compounds. The calculated magnetic shielding constants and NMR chemical shifts well reproduced the experimental values. The relations of the chemical shifts with the natures of ligands, and the tellurium oxidation states were investigated. The chemical shifts in different valence states were explained by the paramagnetic shielding and spin-orbit terms. The tellurium 5p electrons are the dominant origin of the chemical shifts in the Te I and Te II compounds and the chemical shifts were explained by the p-hole mechanism. The tellurium d electrons also play an important role in the chemical shifts of the hypervalent compounds.

Journal Article↗

PubMed2005

Theoretical fine spectroscopy with symmetry-adapted-cluster configuration-interaction method: outer- and inner-valence ionization spectra of furan, pyrrole, and thiophene.

Theoretical fine spectroscopy has been performed for the valence ionization spectra of furan, pyrrole, and thiophene with the symmetry-adapted-cluster configuration-interaction general-R method. The present method described that the pi(1) state interacts with the pi(3) (-2)pi*, pi(2) (-2)pi*, and pi(2) (-1)pi(3) (-1)pi* shake-up states providing the split peaks and the outer-valence satellites, both of which are in agreement with the experiments. The intensity distributions were analyzed in detail for the inner-valence region. In particular, for furan, theoretical intensities were successfully compared with the intensity measured by the electron momentum spectroscopy. The interactions of the 3b(2) and 5a(1) states with the shake-up states were remarkable for furan and pyrrole, while the 4b(2) state of thiophene had relatively large intensity.

Algorithms↗

PubMed2005

Iterative Cl general singles and doubles (ICIGSD) method for calculating the exact wave functions of the ground and excited states of molecules.

The iterative configuration-interaction general singles and doubles (ICIGSD) method was applied to various closed- and open-shell electronic states of molecules within finite basis sets and was shown to give the exact results that are identical to the full CI ones. The structure of the ICIGSD is unique among the ICI formalisms, that is, the singularity problem intrinsic to atomic and molecular Hamiltonians can be avoided. The convergence of the ICIGSD method was fairly good regardless of the characters of the electronic states and the qualities of the basis sets; only several iterations were enough for obtaining microhartree accuracy. These favorable properties are attributed to the unique GSD structure. The present method was shown to be applicable to various spin states and to quasidegenerate states appearing in bond dissociation process. We have also applied the ICIGSD-CI method to calculate the excited states simultaneously. We have confirmed that the ICIGSD-CI method is accurate for calculating the excited states the symmetries of which are not only similar to but also different from that of the ground state.

Algorithms↗

PubMed2005

Excited states of porphyrin isomers and porphycene derivatives: a SAC-CI study.

Excited states of free-base porphyrin isomers, porphycene (Pc), corrphycene (Cor), and hemiporphycene (hPc), were studied by the Symmetry-Adapted Cluster (SAC)/SAC-Configuration Interaction (CI) method. The absorption peaks of the porphyrin isomers were assigned on the basis of the SAC-CI spectra. The X, Y, X', and Y' bands of the porphyrin isomers, which have weak intensities, are identified. The differences in the Q-band absorptions among the isomers were clearly explained by the four-orbital model. In Cor and hPc, the wave function of the B-band corresponds to the mixture of the four-orbital excitations and the optically forbidden excitation of free-base porphin (P), due to the molecular symmetry lowering in the isomers. The B-band character is described by the five-orbital model in Pc and the six-orbital model in Cor and hPc. Two tetrazaporphycenes and two ring-extended (dibenzo) porphycenes were designed, and the Q-band transition moment was successfully controlled. These examples show that the control of the four-orbital energy levels is the guiding principle for pigment design in porphyrin compounds.

Electrochemistry↗

PubMed2005

Theoretical fine spectroscopy with symmetry adapted cluster-configuration interaction general-R method: first-row K-shell ionizations and their satellites.

Molecular core ionization spectra and their satellites were studied by the symmetry adapted cluster-configuration interaction (SAC-CI) general-R method. The core-electron binding energies of C, N, O, and F atoms of 22 molecules were calculated with an average deviation of 0.11 eV from the experimental values. The energy splittings between K-shell gerade and ungerade states were calculated and discussed in relation to the bond length. The satellite spectra of the C 1s and N 1s core ionizations of methane and ammonia were investigated. The SAC-CI general-R method gave many shake-up states with moderate intensities, reproducing the general feature of the experimental spectra, and thus enabling the detailed understanding and assignments of the core-electron ionization spectra.

Computer Simulation↗

PubMed2004

Scaled Schrödinger equation and the exact wave function.

We propose the scaled Schrödinger equation and the related principles, and construct a general method of calculating the exact wave functions of atoms and molecules in analytical forms. The nuclear and electron singularity problems no longer occur. Test applications to hydrogen atom, helium atom, and hydrogen molecule are satisfactory, implying a high potentiality of the proposed method.

Journal Article↗

PubMed2004

Analytical energy gradient of the symmetry-adapted-cluster configuration-interaction general-R method for singlet to septet ground and excited states.

A method of calculating analytical energy gradients of the singlet and triplet excited states, ionized states, electron-attached states, and high-spin states from quartet to septet states by the symmetry-adapted-cluster configuration-interaction general-R method is developed and implemented. This method is a powerful tool in the studies of geometries, dynamics, and properties of the states of molecules in which not only one-electron processes but also two- and multielectron processes are involved. The performance of the present method was confirmed by calculating the geometries and the spectroscopic constants of the diatomic and polyatomic molecules in various electronic states involving the ground state and the one- to three-electron excited states. The accurate descriptions were obtained for the equilibrium geometries, vibrational frequencies, and adiabatic excitation energies, which show the potential usefulness of the present method. The particularly interesting applications were to the C' 1Ag state of acetylene, the A 2Deltau and B 2Sigmau+ states of CNC and the 4B1 and a 4Piu states of N3 radical.

Journal Article↗

PubMed2003

Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study.

Two ground-state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC-CI method with regard to the excitation energy, fluorescence energy, and ground-state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO-LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A- and B-forms, respectively. The present results support the previous experimental observations.

Animals↗

PubMed2002

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-). Theoretical evidence for a competitive charge transfer mechanism.

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-) complexes have been investigated using the B3LYP and the symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theoretical methods. All the dicarbonyl complexes have singlet ground electronic states with large singlet-triplet separations. Thermal dissociations of CO from the parent dicarbonyls are energetically unfavorable. CO thermal dissociation is an activation process for [Cl(2)Rh(CO)(2)](-) while it is a repulsive potential for CpM(CO)(2). The natures of the main excited states of CpM(CO)(2) and [Cl(2)Rh(CO)(2)](-) are found to be quite different. For [Cl(2)Rh(CO)(2)](-), all the strong transitions are identified to be metal to ligand CO charge transfer (MLCT) excitations. A significant feature of the excited states of CpM(CO)(2) is that both MLCT excitation and a ligand Cp to metal and CO charge transfer excitation are strongly mixed in the higher energy states with the latter having the largest oscillator strength. A competitive charge transfer excited state has therefore been identified theoretically for CpRh(CO)(2) and CpIr(CO)(2). The wavelength dependence of the quantum efficiencies for the photoreactions of CpM(CO)(2) reported by Lees et al. can be explained by the existence of two different types of excited states. The origin of the low quantum efficiencies for the C-H/S-H bond activations of CpM(CO)(2) can be attributed to the smaller proportion of the MLCT excitation in the higher energy states.

Journal Article↗