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To establish the theory of soft crystals, computational chemistry must be applied to analyze the structural phase transitions of molecular crystals and develop new methodologies. The accuracy of first-principles calculations for molecular crystals has rapidly improved over the last decade with the contribution of the Cambridge Crystallographic Data Centre blind test, which predicts the crystal structure from the structural formula. However, it is often difficult to apply first-principles calculations to large molecular crystals, such as typical soft crystals, because of the computational cost. In this chapter, we review the applicability of crystal force field calculations as an alternative method for theoretically analyzing molecular crystals. We also introduce some examples of our previous collaborations and discuss the promising methodologies to elucidate the soft crystal phenomena.

Computational approach to elucidate the phase transitions in lanthanide complexes will support to understand their electronic structure changes by weak stimuli such as gas adsorptions. There are no...

Vapochromic crystals of Ni(II)-quinonoid complexes were theoretically investigated using density functional theory (DFT) calculations. Kato et al. previously reported that the purple crystals of a four-coordinate Ni(II)-quinonoid complex (

In this paper, selective formation of noncentrosymmetric (Cc; α-crystal) and centrosymmetric (P21/c; β-crystal) 1,1,2,2-tetramethyl-1-(4-(N,N-dimethylamino)phenyl)-2-(2′-cyanophenyl)disilane (1) wa...

The electronic and vibrational structures of 1,2-benzanthracene- h12 ( aBA- h12) and 1,2-benzanthracene- d12 ( aBA- d12) were elucidated by analyzing fluorescence excitation spectra and dispersed fluorescence spectra in a supersonic jet on the basis of DFT calculation. We also observed the high-resolution and high-precision fluorescence excitation spectrum of the [Formula: see text] band, and determined the accurate rotational constants in the zero-vibrational levels of the S0 and S1 states. In this high-resolution measurement, we used a single-mode UV laser whose frequencies were controlled with reference to an optical frequency comb. The inertial defect is negligibly small, the molecule is considered to be planar, and the obtained rotational constants were well reproduced by the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculation. Both a-type and b-type transitions are found to be included in the rotationally resolved spectrum, and the a-type contribution is dominant, that is, the transition moment is nearly parallel to the long axis of the aBA molecule. We concluded that the S1 state is mainly composed of the Φ(B) configuration. The observed fluorescence lifetime (106 ns) is considerably longer than that of the Φ(A) system, such as anthracene (18 ns). The transition moment for the lower state of mixed states becomes small, reflecting a near-cancelation of the contributions from the parts of the wavefunction corresponding to the two electronic configurations. The bandwidth of the S2 ← S0 transition is large, and the structure is complicated. It is attributed to vibronic coupling with the high vibrational levels of the S1 state.

Ionization energies of catechins were calculated by using B3LYP density functional method with 6-31G** basis set. Then, conformations of catechins were extensively explored. Geometry optimizations starting from the explored conformers were made not only for the neutral species but also for the radical cation. The ionization energy of each catechin was estimated as the energy difference between the most stable geometries obtained for the neutral species and radical cation. Tendency of experimental oxidation potential in catechins is well reproduced by this calculation, and the ionization energy correlates well with the singlet-oxygen quenching efficiency in case that stereochemistry of attachment at the 3-position is common. Electron transfer from catechins plays an important role in the singlet-oxygen quenching, free-radical scavenging and recycling from vitamin E radical to vitamin E. The reason for discrepancy among antioxidant efficiencies with regard to the ionization energy dependence is explained.

We describe here the preparation of soft crystals using disilanyl macrocycle C4 possessing four p-phenylenes circularly connected by four flexible disilane bonds. Single crystals of C4 exhibited a reversible thermal single-crystal-to-single-crystal (SCSC) phase transition behavior between two crystal phases accompanied by remarkable mechanical motion (thermosalient effect), as revealed by thermal analyses and X-ray diffraction measurements. Detailed structural analyses implied that flexibility of the parallelogram disilanyl architecture and molecular packing mode via weak intermolecular interactions facilitated a concerted structural transformation (parallel crank motion) of macrocycles in the crystal, thus resulting in the SCSC phase transition accompanied by anisotropic shrinking/elongation of the cells to induce the thermosalient effect. This work explores a new area of organosilicon chemistry and presents the potential utility of disilanyl macrocycles as soft crystals.

Corannulene is a nonplanar aromatic hydrocarbon also known as a buckybowl. Its electronic and vibrational structure has been investigated by analyzing its fluorescence excitation spectrum and dispersed fluorescence spectrum in a supersonic jet. Its spectral features are in keeping with the expectation, confirmed by some previous results, that it has fivefold or C

Formation of 15-membered azalactone by double reductive amination was analyzed using molecular mechanics and density functional theory calculations for simplified model compounds. As a result, the following aspects were clarified. When methylamine attacks a linear bis-aldehyde in the first step, there are possibilities that two regioisomers are formed. However, one of them exhibited remarkably stable energy level compared with the other. The stable isomer indicated a short distance between a methylamine moiety and an unreacted aldehyde. This short distance, about 2.3 Å, could be explained by hydrogen bonding, which implied relatively easy cyclization in the second step. Moreover, this cyclization process was supposed to be exothermic according to comparison of energy levels before and after cyclization.

Optically active spirocyclopropyloxindole derivatives were efficiently synthesized from diazooxindoles and olefins in the presence of a Ru(II)-Pheox catalyst. Among a series of Ru(II)-Pheox catalysts, Ru(II)-Pheox 6e was determined to be the best catalyst for spirocyclopropanation reactions of diazooxindoles with various olefins in high yields (up to 98%) with high diastereoselectivities (up to trans:cis = >99:1

Corannulene is a nonplanar aromatic hydrocarbon also known as a buckybowl. Its electronic and vibrational structure has been investigated by analyzing its fluorescence excitation spectrum and dispersed fluorescence spectrum in a supersonic jet. Its spectral features are in keeping with the expectation, confirmed by some previous results, that it has fivefold or C5v symmetry. The observed prominent vibronic bands in the S1 ← S0 transition have been assigned to e1 and e2 bands on the basis of theoretical calculations so that the S1 state was assigned to 1E2. The symmetry adapted cluster configuration interaction calculation supports this assignment of the S1 electronic state, although the time-dependent density functional theory calculation suggests that the S1 state is 1A2. It has also been shown that the normal coordinates for strong vibronic bands mainly include out-of-plane vibrational motion. The rotational envelopes are well explained by taking account of the Coriolis interaction between the degenerate vibrational and rotational levels. The mechanism of bowl-to-bowl inversion is also discussed with the results of theoretical calculations regarding the barrier to inversion and metastable conformation.

Computational chemical analysis of Ru(II)-Pheox-catalyzed highly enantioselective intramolecular cyclopropanation reactions was performed using density functional theory (DFT). In this study, cyclopropane ring-fused γ-lactones, which are 5.8 kcal/mol more stable than the corresponding minor enantiomer, are obtained as the major product. The results of the calculations suggest that the enantioselectivity of the Ru(II)-Pheox-catalyzed intramolecular cyclopropanation reaction is affected by the energy differences between the starting structures 5l and 5i. The reaction pathway was found to be a stepwise mechanism that proceeds through the formation of a metallacyclobutane intermediate. This is the first example of a computational chemical analysis of enantioselective control in an intramolecular carbene-transfer reaction using C1 -symmetric catalysts.

Fluorescence excitation spectra and fluorescence lifetimes at single vibronic levels in the S 1 state have been observed for jet-cooled pyrene. The fluorescence lifetimes at the zero-vibrational levels of the S 1 1 B 3 u states of pyrene- h 10 and pyrene- d 10 are 1480 and 1470 ns, respectively, and the relaxation is considered to be dominated by the radiative process. For some vibrational levels, however, the lifetimes are remarkably shorter such as 765 ns at the 221 vibronic level of pyrene- h 10 ( ν 22 ( b 1 g ); C–H bending and skeletal deforming mode), indicating that nonradiative transition occurs at a specific vibrational level. In this study, we demonstrate that the main process is internal conversion to the S 0 1 A g state caused by nonadiabatic vibronic interaction via b 3 u promoting modes.

We observed fluorescence excitation spectra and dispersed fluorescence spectra for single vibronic level excitation of jet-cooled perylene-h 12 and perylene-d 12, and carefully examined the vibrational structures of the S0[1] A g and S1[1] B 2u states. We performed vibronic assignments on the basis of the results of ab initio calculation, and found that the vibrational energies in the S1 state are very similar to those in the S0 state, indicating that the potential energy curves are not changed much upon electronic excitation. We conclude that the small structural change is the main cause of its slow radiationless transition and high fluorescence quantum yield at the zero-vibrational level in the S1 state. It has been already reported that the lifetime of perylene is remarkably short at specific vibrational levels in the S1 state. Here, we show that the mode-selective nonradiative process is internal conversion (IC) to the S0 state, and the ν16(a g ) in-plane ring deforming vibration is the promoting (doorway) mode in the S1 state which enhances vibronic coupling with the high-vibrational level (b 2u ) of the S0 state.

A rotationally resolved ultrahigh-resolution fluorescence excitation spectrum of the S1 ˆ S0 transition of perylene has been observed using a collimated supersonic jet technique in conjunction with a single-mode UV laser. We assigned 1568 rotational lines of the 0 0 band, and accurately determined the rotational constants. The obtained value of inertial defect was positive, accordingly, the perylene molecule is considered to be planar with D2h symmetry. We determined the geometrical structure in the S0 state by ab initio theoretical calculation at the RHF/6-311+G(d,p) level, which yielded rotational constant values approximately identical to those obtained experimentally. Zeeman broadening of each rotational line with the external magnetic field was negligibly small, and the mixing with the triplet state was shown to be very small. This evidence indicates that intersystem crossing (ISC) in ✩ Presented in part at the 64th International Symposium on Molecular Spectroscopy

The origin of P- or M-chirality of methyl substituted 1,3-cyclohexadienes are elucidated by time-dependent density functional theory (TD-DFT) calculation of 1,3-cyclohexadiene derivatives and acyclic 1,3-dienes. The sign-inversion of the rotatory strength of the lowest excited state between 1,3-cyclohexadiene and (5R)-axial-methyl-1,3-cyclohexadiene is caused by the conformation around the (C=)C-C(-Me) dihedral angle. The correlation between the sign of the rotatory strength and conformation has been found not only in methyl substituted derivatives but also fluoro substituted compounds.

Excitation energies of 123 polycyclic aromatic hydrocarbons were calculated by incorporating the improved method of new-γ for the two-center electron repulsion integral into two semiempirical molecular orbital methods (CNDO/S and INDO/S). This variable method well reproduced experimental excitation energies of them. The average error of the improvement is about 0.162 (CNDO/S) or 0.237 eV (INDO/S) though the average error without the improvement is about 0.541 (CNDO/S) or 0.536 eV (INDO/S). The improvement was useful for the calculations of other organic compounds including hetero atoms, such as organic dye.

The reaction mechanism of the one-way isomerization of 2‘-hydroxychalcone (2HC) was studied by calculating the potential energy surfaces of the twist of the CC double bond and the intramolecular hydrogen atom transfer in the excited triplet state by the UB3LYP/6-31G** level. The calculations reveal the following. The potential energy curve of the triplet state between the keto forms (trans-2HC and cis-2HC) is similar to that of stilbene, which exhibits mutual isomerization. On the other hand, the potential energy curve between the enol forms (trans-2HC‘ and cis-2HC‘) is similar to that of styrylanthracene, which exhibits one-way isomerization from the cis to trans isomer. Although the hydrogen atom transfer has an energy barrier (

An ab initio molecular orbital study of the radical cation of 1,5-dithiacyclooctane and its dimer dication is reported. The calculations performed range from HF/3-21G (∗) to MP2/6-31G ∗ . Nine energy-minimum structures were located for the monomer, of which a boat–chair (BC) form was calculated to be the most stable consistent with the liquid-phase ESR spectra reported. However, barriers to conformational interconversion are predicted to be less than 10 kcal mol −1 for the isolated radical cation, which is not consistent with the ESR results at various temperatures. Therefore, it is likely that the solvent and/or counter ion prevent conformational changes. The dimer is predicted to adopt structures which have a four-center six-electron bond consisting of linearly aligned sulfur atoms.

A variety of ab initio molecular orbital methods, RHF, MP2 and B3LYP, have been applied to N-methyl-N-nitrosourea (1), N-methyl-N-nitrosoacetamide (2) and N-methyl-N-nitrosomethylcarbamate (3) and the anti and syn structures and the transition state (TS) structures connecting them have been examined. In each of these compounds, the anti structure was predicted to be more stable than the syn structure and the relative energy of the TS structure was considerably higher than those of the anti and syn structures. The energy difference between anti and syn of 1 is slightly smaller than those of 2 and 3 owing to the existence of hydrogen bonding between O in the nitroso group and H in the NH2 group.

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.

Methylation reaction at ten nucleophilic sites in four DNA base molecules by methanediazonium ion (N(2)Me+) was examined by ab initio MO/GB calculation which includes the solvent effect with the continuum model using the generalized Born formula. The stabilization energy of the ion-dipole complex as well as the energy of the transition state are roughly consistent with the experimental fraction of methylation by N -methyl- N -nitrosourea. For the guanine N7 site, which is the principal site of methylation, the stabilization energy is the largest and the energy of the transition state is low. The reactions at the guanine O6 and N7 sites were analysed by drawing the potential energy surface with respect to two parameters, the O6-C(Me) distance and the N7-C(Me) distance. The methylation reactions of the guanine O6 and N7 sites begin from the common geometry, the global minimum in the two-dimensional potential energy surface.

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.