Direct Elucidation of the Vibrationally Averaged Structure of Benzene: A Path Integral Molecular Dynamics Study.

Path integral molecular dynamics (PIMD) simulations for C6H6, C6D6, and C6T6 have been carried out to directly estimate the distribution of projected C-H(D,T) bond lengths onto the principal axis plane. The average values of raw C-H(D,T) bond lengths obtained from PIMD simulations are in the order of ⟨RC-H⟩ > ⟨RC-D⟩ > ⟨RC-T⟩ due to the anharmonicity of the potential energy curve. However, the projected C-H(D,T) bond lengths are almost the same as those reported by Hirano et al. [J. Mol. Struct. 2021, 1243, 130537]. Our PIMD simulations directly and strongly support the explanation by Hirano et al. for the experimental observations that almost the same projected C-H(D) bond lengths are found for C6H6 and C6D6. The PIMD simulations also predicted the same projected bond lengths for C6T6 as those of C6H(D)6. In addition to the previous local mode analysis, the present PIMD simulations predicted, for benzene isotopologues, that the vibrationally averaged structure is planar but non-flat.

Molecular Dynamics Study on Dynamical Features of Reorganization Process for Nanocapsule Formed with Gear-Shaped Amphiphile Molecules.

We have analyzed the dynamical feature of a hexameric structure of nanocube (16) from a gear-shaped amphiphile molecule (1) upon addition of solvophobic spherical adamantane molecule (G), by means of molecular dynamics (MD) simulation, to elucidate the conversion mechanism from the hexameric nanocube G@16 to a tetrameric G@14 tetrahedron. The adamantane molecule (G) in the nanocube G@16 is located around the triple π stacking, although G in the G@14 tetrahedron is at the central position of the capsule. Our MD simulation shows that the nanocube G@16 is more fluctuated than the G@14 tetrahedron. We have also found that a demethylated nanocube G@26 is converted to a tetrameric G@23 tetrahedron due to the solvophobic effect for the adamantane molecule.

Importance of Molecular Meshing for the Stabilization of Solvophobic Assemblies.

The effect of the methyl groups in neutral gear-shaped amphiphiles (GSAs) on the stability of nanocubes was investigated using a novel C2 v-symmetric GSA, which was synthesized using selective alternate trilithiation of a pentabrominated hexaphenylbenzene derivative. The lack of only one methyl group in the GSA decreased the association constant for the assembly of the nanocube by 3 orders of magnitude. A surface analysis recently developed by the authors (SAVPR: surface analysis with varying probe radii) was carried out for characteristic isomers of the nanocube consisting of C2 v-symmetric GSAs. It was found that the methyl groups near the equator of the nanocube play a significant role in the stabilization of the nanocubes.

Semi-quantitative evaluation of molecular meshing via surface analysis with varying probe radii.

A novel method for the semi-quantitative evaluation of molecular meshing in molecular complexes and assemblies (SAVPR: surface analysis with varying probe radii) is proposed. SAVPR revealed that the extremely high stability of hexameric assemblies (nanocubes) is due to tight molecular meshing between the components in the assemblies, indicating the importance of van der Waals interactions in hydrophobic molecular assemblies.

Quantitative Analysis of Self-Assembly Process of a Pd2 L4 Cage Consisting of Rigid Ditopic Ligands.

The self-assembly process of a Pd2 L4 cage complex consisting of rigid ditopic ligands, in which two 3-pyridyl groups are connected to a benzene ring through acetylene bonds and PdII ions was revealed by a recently developed quantitative analysis of self-assembly process (QASAP), with which the self-assembly process of coordination assemblies can be investigated by monitoring the evolution with time of the average composition of all the intermediates. QASAP revealed that the rate-determining steps of the cage formation are the intramolecular ligand exchanges in the final stage of the self-assembly: [Pd2 L4 Py*2 ]4+ →[Pd2 L4 Py*1 ]4+ +Py* and [Pd2 L4 Py*1 ]4+ →[Pd2 L4 ]4+ +Py* (Py*: 3-chloropyridine, which was used as a leaving ligand on the metal source). The energy barriers for the two reactions were determined to be 22.3 and 21.9 kcal mol-1 , respectively. DFT calculations of the transition-state (TS) structures for the two steps indicated that the distortion of the trigonal-bipyramidal PdII center at the TS geometries increases the activation free energy of the two steps.

Correlation among Singlet-Oxygen Quenching, Free-Radical Scavenging, and Excited-State Intramolecular-Proton-Transfer Activities in Hydroxyflavones, Anthocyanidins, and 1-Hydroxyanthraquinones.

Singlet-oxygen (1O2) quenching, free-radical scavenging, and excited-state intramolecular proton-transfer (ESIPT) activities of hydroxyflavones, anthocyanidins, and 1-hydroxyanthraquinones were studied by means of laser, stopped-flow, and steady-state spectroscopies. In hydroxyflavones and anthocyanidins, the 1O2 quenching activity positively correlates to the free-radical scavenging activity. The reason for this correlation can be understood by considering that an early step of each reaction involves electron transfer from the unfused phenyl ring (B-ring), which is singly bonded to the bicyclic chromen or chromenylium moiety (A- and C-rings). Substitution of an electron-donating OH group at B-ring enhances the electron transfer leading to activation of the 1O2 quenching and free-radical scavenging. In 3-hydroxyflavones, the OH substitution at B-ring reduces the activity of ESIPT within C-ring, which can be explained in terms of the nodal-plane model. As a result, the 1O2 quenching and free-radical scavenging activities negatively correlate to the ESIPT activity. A catechol structure at B-ring is another factor that enhances the free-radical scavenging in hydroxyflavones. In contrast to these hydroxyflavones, 1-hydroxyanthraquinones having an electron-donating OH substituent adjacent to the O-H---O═C moiety susceptible to ESIPT do not show a simple correlation between their 1O2 quenching and ESIPT activities, because the OH substitution modulates these reactions.

Theoretical study of the H/D isotope effect on phase transition of hydrogen-bonded organic conductor κ-H3(Cat-EDT-TTF)2.

κ-H3(Cat-EDT-TTF)2 (H-TTF) is a hydrogen-bonded π-electron system which was found to reveal C2/c symmetry at 50-293 K, while its isotopologue, κ-D3(Cat-EDT-TTF)2 (D-TTF), showed the phase transition at 185 K from C2/c to P1[combining macron]. To elucidate the origin of such a difference, we calculated the potential energy curves (PECs) for the hydrogen transfer along the H-bonds in these conductors. We found that both the π-stacking and the hydrogen nuclear quantum effect drastically affected the hydrogen transfer energy. By taking account of both effects, we obtained a symmetric single-well effective PEC for H-TTF, which indicated that the hydrogen was always located at the center of the H-bond. By contrast, the effective PEC of D-TTF was a low-barrier double-well, indicating that the position of the H-bonded deuterium would change according to the temperature. We concluded that the π-stacking and the nuclear quantum effect were the key factors for the appearance of phase transition only in D-TTF.

Correlation between excited-state intramolecular proton-transfer and singlet-oxygen quenching activities in 1-(acylamino)anthraquinones.

Excited-state intramolecular proton-transfer (ESIPT) and singlet-oxygen ((1)O2) quenching activities of intramolecularly hydrogen-bonded 1-(acylamino)anthraquinones have been studied by means of static and laser spectroscopies. The ESIPT shows a substituent effect, which can be explained in terms of the nodal-plane model. The ESIPT activity positively and linearly correlates with their (1)O2 quenching activity. The reason for this correlation can be understood by considering ESIPT-induced distortion of their ground-state potential surface and their encounter complex formation with (1)O2. Intramolecularly hydrogen-bonded hydroxyanthraquinones found in aloe also show a similar positive and linear correlation, which can be understood in the same way.

Electronic structure and rovibrational properties of ZnOH in the X̃²A' electronic state: a computational molecular spectroscopy study.

The three-dimensional ground-state potential energy surface of ZnOH has been calculated ab initio at the MR-SDCI+Q_DK3/[QZP ANO-RCC (Zn, O, H)] level of theory and used as basis for a study of the rovibrational properties carried out by means of the program MORBID (Morse Oscillator Rigid Bender Internal Dynamics). The electronic ground state is (2)A' (correlating with (2)Σ(+) at the linear configuration). The equilibrium structure has r(e)(Zn-O) = 1.8028 Å, r(e)(O-H) = 0.9606 Å, and ∠e(Zn-O-H) = 114.9°. The Zn-O bond is essentially ionic, with appreciable covalency. The bonding character is compared with those of FeOH (quasi-linear) and CsOH (linear). The rovibrationally averaged structural parameters, determined as expectation values over MORBID wavefunctions, are ⟨r(Zn-O)⟩0 = 1.8078 Å, ⟨r(O-H)⟩0 = 0.9778 Å, and ⟨∠(Zn-O-H)⟩0 = 117°. The Yamada-Winnewisser quasi-linearity parameter is found to be γ0 = 0.84, which is close to 1.0 as expected for a bent molecule. Since no experimental rovibrational spectrum has been reported thus far, this spectrum has been simulated from the ab initio potential energy and dipole moment surfaces. The amphoteric character of ZnOH is also discussed.

Geometries and electronic structures of the ground and low-lying excited states of FeCO: an ab initio study.

FeCO is a molecule of astrophysical interest. We report here theoretical calculations of its geometrical parameters, electronic structures, and molecular constants (such as dipole moment and spin-orbit coupling constant) in the electronic ground state X(3)Σ(-) and the low-lying triplet and quintet excited states. The calculations were made at the MR-SDCI+Q_DK3/[5ZP ANO-RCC (Fe, C, O)] and MR-AQCC_DK3/[5ZP ANO-RCC (Fe, C, O)] levels of theory. A multi-reference calculation was required to describe correctly the wavefunctions of all states studied. For all triplet states, the σ-donation through the 10σ molecular orbital (MO) as well as the π-back-donation through the 4π MO are observed, and the dipole moment vector points from O toward Fe as expected. However, in the excited quintet states (5)Π, (5)Φ, and (5)Δ, the almost negligible contribution of Fe 4s to the 10σ MO makes the dipole moment vector point from Fe toward O, i.e., in the same direction as in CO. In the X(3)Σ(-) state, the electron provided by the σ-donation through the 10σ MO is shared between the Fe atom and the C end of the CO residue to form a coordinate-covalent Fe-C bond. In the ã(5)Σ(-) state (the high-spin counterpart of X(3)Σ(-)), the σ-donation through the 10σ MO is not significant and so the Fe-C bond is rather ionic. The π-back-donation through the 4π MO is found to be of comparable importance in the two electronic states; it has a slightly larger magnitude in the X(3)Σ(-) state. The difference in the molecular properties of the low-spin X(3)Σ(-) and the high-spin ã(5)Σ(-) states can be understood in terms of the dynamical electron correlation effects.

Geometrical structure of benzene and naphthalene: ultrahigh-resolution laser spectroscopy and ab initio calculation.

Geometrical structures of the isolated benzene and naphthalene molecules have been accurately determined by using ultrahigh-resolution laser spectroscopy and ab initio calculation in a complementary manner. The benzene molecule has been identified to be planar and hexagonal (D(6h)) and the structure has been determined with accuracies of 2 × 10(-14) m (0.2 mÅ; 1 Å = 1 × 10(-10) m) for the C-C bond length and 1.0 × 10(-13) m (1.0 mÅ) for the C-H bond length. The naphthalene molecule has been identified to be symmetric with respect to three coordinate axes (D(2h)) and the structure has been determined with comparable accuracies. We discuss the effect of vibrational averaging that is a consequence of zero-point motions on the uncertainty in determining the bond lengths.

Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method.

A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors.

Electronic structures and rovibronically averaged geometries of the X 6Ai' and A 6Ai" states of FeOH.

We have recently reported a theoretical prediction of the rovibronic spectra of the FeOH molecule. These spectra have not been observed experimentally. In the present work, we complement the previously published information by reporting the details of the electronic structure of FeOH together with rovibrationally averaged structural parameters. The electronic ground state is X (6)A(i)', which is Renner-degenerate with the A (6)A(i)" state; the two states correlate with a (6)Delta state at linearity. We have calculated the three-dimensional potential energy surfaces (PESs) of the X and A states, which are close in energy over the range of geometries studied, at the MR-SDCI+Q+E(rel)/[Roos ANO (Fe), aug-cc-pVQZ (O, H)] level of theory. The equilibrium structure of the X state is bent with r(e)(Fe-O)=1.806 A, r(e)(O-H)=0.952 A, and angle(e)(Fe-O-H)=134.2 degrees. The barrier to linearity is 273 (266) cm(-1) in the X (A) state so that FeOH is quasilinear in the X and A states. The Fe-O bonds in both states are ionic and the bending potentials are shallow, resulting in large amplitude bending motion. The rovibrationally averaged structures of the X (6)A' and A (6)A" electronic states have been calculated for the average of the X and A PESs by the variational MORBID method as expectation values in terms of rotation-vibration wave functions. FeOH is said to be quasilinear, but the rovibrationally averaged structure is bent with (0)=1.805 A, (0)=0.967 A, and (0)=141(14) degrees (where the quantity in parentheses is the quantum mechanical uncertainty), which is close to the equilibrium structure. We demonstrate that by means of the Yamada-Winnewisser quasilinearity parameter we can distinguish linear and quasilinear molecules.

Excited state intramolecular proton transfer (ESIPT) in six-coordinated zinc(ii)-quinoxaline complexes with ligand hydrogen bonds: their fluorescent properties sensitive to axial positions.

Zinc(ii)-quinoxaline complexes, [Zn(hqxc)(2)(py)(2)] and [Zn(hqxc)(2)(DMSO)(2)] (hqxc = 3-hydroxy-2-quinoxalinecarboxylate, py = pyridine, DMSO = dimethyl sulfoxide), were prepared and characterized by X-ray crystallography and fluorescence spectroscopy. In both complexes, the zinc ion is six-coordinated by two equatorial bidentate hqxc ligands with an intramolecular hydrogen bond and two axial monodentate ligands such as pyridine or DMSO. In spite of similar coordination geometries, there is a remarkable difference between their solid-state fluorescent properties. The pyridine complex is strongly fluorescent (fluorescence quantum yield Phi = 0.22), giving rise to a significantly Stokes-shifted spectrum. From its thin film photopumped by a nitrogen gas laser, amplified spontaneous emission was observed. These results suggest that the fluorescence occurs by way of excited-state intramolecular proton-transfer (ESIPT) in the hydrogen bond of hqxc. On the other hand, the DMSO complex shows fluorescent intensity (Phi = 0.08) lower than that of the pyridine complex, and shows normal emission in addition to ESIPT emission. From IR measurements for these complexes, it is concluded that axial ligands influence the hydrogen bond strength of the equatorial hqxc ligand via zinc and thus the ESIPT efficiency.

Ab initio calculation of the electronic structures of the (7)Sigma+ ground and A (7)Pi and a (5)Sigma+ excited states of MnH.

Electronic structures and molecular constants of the ground (7)Sigma(+) and low-lying A (7)Pi and a (5)Sigma(+) electronic excited states of the MnH molecule were studied by multireference single and double excitation configuration interaction (MR-SDCI) with Davidson's correction (+Q) calculations under exact C(infinity v) symmetry using Slater-type basis sets. To correctly describe the (7)Sigma(+) electronic ground state, X (7)Sigma(+), at the MR-SDCI+Q calculation, we employed a large number of reference configurations in terms of the state-averaged complete active space self-consistent field (CASSCF) orbitals, taking into account the contribution from the B (7)Sigma(+) excited state. The A (7)Pi and a (5)Sigma(+) states can well be described by the MR-SDCI wave functions based on the CASSCF orbitals obtained for the lowest state only. In the MR-SDCI+Q, calculations of the X (7)Sigma(+), A (7)Pi, and a (5)Sigma(+) states required 16, 7, and 17 reference configurations, respectively. Molecular constants, i.e., r(e) and omega(e) of these states and excitation energy from the X (7)Sigma(+) state, obtained at the MR-SDCI+Q level, showed a good agreement with experimental values. The small remaining differences may be accounted for by taking relativistic effects into account.

Structure and excited-state dynamics of anthracene: ultrahigh-resolution spectroscopy and theoretical calculation.

Rotationally resolved ultrahigh-resolution spectra of the S(1) (1)B(2u)<--S(0) (1)A(g) transition of anthracene-h(10) and anthracene-d(10) have been observed using a single-mode UV laser and a collimated supersonic jet. We have determined rotational constants of the zero-vibrational levels of the S(0) and S(1) states by analyzing the precisely calibrated transition wavenumbers of rotational lines. We measured Zeeman splitting of each rotational line in the external magnetic field, of which the magnitude was small and strongly dependent on the rotational quantum numbers. We have shown that the magnetic moment in the S(1) (1)B(2u) state arises from J-L coupling with the S(2) (1)B(3u) state and that mixing with the triplet state is negligibly small. We concluded that the main radiationless transition in the S(1) state of anthracene is not intersystem crossing to the triplet state but internal conversion to the ground state. We also examined methods of ab initio theoretical calculation to determine which method most closely yielded the same values of rotational constants as the experimentally obtained ones. Moller-Plesset second-order perturbation method with a 6-31G(d,p) basis set yielded approximately the same values for the S(0) (1)A(g) state with an error of less than 0.04%. Geometrical structure in the S(0) (1)A(g) state of the isolated anthracene molecule has been accurately determined by this calculation. However, configurational-interaction with single excitations, time-dependent Hartree-Fock, and time-dependent density-function-theory methods did not yield satisfactory results for the excitation energy of the S(1) (1)B(2u) state. Symmetry-adapted-cluster configuration-interaction calculation was sufficiently good for the excitation energy and rotational constants.

CH3 internal rotation in the S0 and S1 states of 9-methylanthracene.

Fluorescence excitation spectra and dispersed fluorescence spectra of jet-cooled 9-methylanthracene-h12 and -d12 (9MA-h12 and 9MA-d12) have been observed, and the energy levels of methyl internal rotation (CH3 torsion) in the S0 and S1 states have been analyzed. The molecular symmetry of 9MA is the same as that of toluene (G12). Because of two-fold symmetry in the pi system, the potential curve has six-fold barriers to CH3 rotation. In toluene, the barrier height to CH3 rotation V6 is very small, nearly free rotation. As for 9MA-h12, we could fit the level energies by potential curves with the barrier heights of V6(S0) = 118 cm(-1) and V6(S1) = 33 cm(-1). These barrier heights are remarkably larger than those of toluene and are attributed to hyperconjugation between the pi orbitals and methyl group. The dispersed fluorescence spectrum showed broad emission for the excitation of 0(0)(0) + 386 cm(-1) band, indicating that intramolecular vibrational redistribution efficiently occurs, even in the vibronic level of low excess energy of the isolated 9MA molecule.

Parallel Fock matrix construction program for molecular orbital calculation--specific computer with a hierarchical network.

A parallel Fock matrix construction program for a hierarchical network has been developed on the molecular orbital calculation-specific EHPC system. To obtain high parallelization efficiency on the hierarchical network system, a multilevel dynamic load-balancing scheme was adopted, which provides equal load balance and localization of communications on a tree-structured hierarchical network. The parallelized Fock matrix construction routine was implemented into a GAMESS program on the EHPC system, which has a tree-structured hierarchical network. Benchmark results on a 63-processor system showed high parallelization efficiency even on the tree-structured hierarchical network.

H/D isotope effect in methyl torsional interaction of acetone as calculated by a multicomponent molecular orbital method.

We analyzed the H/D isotope effect in the methyl torsional interactions accompanying two methyl internal rotations for acetone (CH(3)COCH(3)) and deuterated acetone (CD(3)COCD(3) and CH(3)COCD(3)) in the ground state by means of the multicomponent molecular orbital (MC_MO) method, which directly accounts for the quantum effects of protons and deuterons. Our estimated rotational constants and moments of inertia for CH(3)COCH(3) and CD(3)COCD(3) agreed well with the experimental results because of the adequate treatment of protonic and deuteronic quantum effects afforded by the MC_MO method. Because the C-D bond distance in the CD(3) group was shorter than the C-H distance in CH(3) owing to the anharmonicity of the potential, the difference in potential energy surfaces of CH(3)COCH(3), CD(3)COCD(3), and CH(3)COCD(3) was strongly related to the differences induced in geometrical parameters by the H/D isotope effect. The potential energy obtained by the MC_MO method was estimated as 290.88 cm(-1) for CH(3)COCH(3), which is in excellent agreement with the experimental results. For CH(3)COCD(3), two potential energies were obtained for CH(3) and CD(3) internal rotations. The MC_MO method successfully elucidated the H/D isotope effect for methyl-methyl repulsive interactions by allowing the adequate treatment of protonic and deuteronic wave functions. The potential energies and bond distances associated with methyl internal rotation induced by the H/D isotope effect were also controlled by the distribution of wave functions of protons and deuterons.

HD isotope effect of methyl internal rotation for acetaldehyde in ground state as calculated from a multicomponent molecular orbital method.

We have analyzed the differences in the methyl internal rotation induced by the HD isotope effect for acetaldehyde (CH(3)CHO) and deuterated acetaldehyde (CD(3)CDO) in ground state by means of the multicomponent molecular orbital (MC_MO) method, which directly accounts for the quantum effects of protons and deuterons. The rotational constant of CH(3)CHO was in reasonable agreement with experimental one due to the adequate treatment of the protonic quantum effect by the MC_MO method. The C-D bond distances were about 0.007 A shorter than the C-H distances because of the effect of anharmonicity of the potential. The Mulliken population for CD(3) in CD(3)CDO is larger than that for CH(3) in CH(3)CHO because the distribution of wavefunctions for the deuterons was more localized than that for the protons. The barrier height obtained by the MC_MO method for CH(3)CHO was estimated as 401.4 cm(-1), which was in excellent agreement with the experimentally determined barrier height. We predicted the barrier height of CD(3)CDO as 392.5 cm(-1). We suggest that the internal rotation of the CD(3) group was more facile than that of the CH(3) group because the C-D bond distance was observed to be shorter than the C-H distance. Additionally the localized electrons surrounding the CD(3) group in CD(3)CDO caused the extent of hyperconjugation between the CD(3) and CDO groups to be smaller than that in the case of CH(3)CHO, which may have also contributed to the observed differences in methyl internal rotation. The differences in bond distances and electronic populations induced by the H/D isotope effect were controlled by the difference in the distribution of wavefunctions between the protons and deuterons.