We report a quantum wavepacket study on the characteristic bimodal translational energy distribution of photostimulated desorbed Xe from an oxidized silicon (001) surface observed by Watanabe and Matsumoto, Faraday Discuss. 117 (2000) 203. We have simulated the theoretical translational energy distributions based on wavepacket calculations with a sudden transition and averaging model to reproduce the experiment. We discuss the desorption mechanism and suggest a very strong position dependence of the deexcitation processes for Xe/oxidized Si(001).

Recent experimental and theoretical advances on the aromatic alcohol-water clusters are reviewed, focusing on the structure of the hydrogen bonding between the alcoholic OH group and the binding water molecules. The interplay of experimental observations and theoretical calculations for the elucidation of the structure is demonstrated for phenol-water, benzyl alcohol-water, substituted phenol-water, naphthol-water and tropolone -water clusters. Discussion is made on assigning the role (either proton-donating or -accepting) of the hydroxyl group by measuring the shifts of infrared frequency of the OH stretching mode in the cluster from that of bare aromatic alcohol for the experimental determination of the cluster structure.

We have theoretically studied the nonadiabatic transitions among the five lower states with the Ω=$1_u$ symmetry ($1_u^{(1)} to 1_u^{(5)}$) in the photodissociation of Cl₂, Br₂, and I₂by using the spin-orbit configuration interaction (SOCI) method and the semiclassical time-dependent coupled Schrodinger equations. From the configuration analyses of the SOCI wavefunctions, we found that the nonadiabatic transition between $1_u^{(2)}$ and $1_u^{(1)}$ is a noncrossing type, while that between $1_u^{(3)}$ and $1_u^{(4)}$ is a crossing type for all the molecules. The behavior of the radial derivative coupling element between $1_u^{(1)}$ and $1_u^{(2)}$ and that between $1_u^{(3)}$ and $1_u^{(4)}$ is analyzed in detail. In Cl₂, nonadiabatic transitions can take place even between the states correlating to different dissociation limits, while in Br₂ and I₂, with the usual photon energies e.g. less than 20 eV, nonadiabatic transitions occur only between the states correlating to the same dissociation limits, reflecting the different magnitudes of the spin-orbit interactions.

The semi-diabatic potential energy surfaces (PESs) of the excited states of polyatomic molecules can be constructed for use in ab initio molecular dynamics (AIMD) studies by relying on the continuity of the electronic energy, oscillator strength, and spherical extent of an excited state along with first derivatives of these quantities as computed by using the equation-of-motion coupled-cluster (EOM-CC) method. The semidiabatic PESs of both the π → $π^*$ valence excited state and the 3s-type Rydberg state of ethylene are presented and discussed in this paper, in conjunction with some of the AIMD results we obtained for these states.

The structure, force field and vibrational spectra of triphenylene are studied by $B3LYP/6-31G^*$(5d) level of theory. The results are compared to those of the related system, phenanthrene. The scale factors in nonredundant local coordinates obtained after fitting the DFT frequencies to the experimental numbers of phenanthrene-$d_0 and -d_{10}$ are transferred to predict the spectra and assignment of triphenylene for in-plane modes. The frequencies based on scaling methodology due to Lee et al. are also obtained. These frequencies are compared with the predicted numbers based on scale factors from phenanthrene. Probable assignment for out-of-plane modes is proposed based on simple scaling of Scott and Radom (scale factor 0.9614) as well as by scaling methodology by Lee et al.

Recently the ab initio effective valence shell Hamiltonian method $H^v$ has been extended to treat spin-orbit coupling in atoms or molecules. The quasidegenerate many-body perturbation theory based $H^v$ method has an advantage of determining the spin-orbit coupling energies of all valence states for both the neutral species and its ions with a similar accuracy from a single computation of the effective spin-orbit coupling operator. The new spin-orbit $H^v$ method is applied to calculating the fine structure splittings of the valence states of SiH, $SiH^+$, and $SiH^{2+}$ not only to assess the accuracy of the method but also to investigate the spin-orbit interaction of highly excited states of SiH species. The computed spin-orbit splittings for ground states are in good agreement with experiment and the few available ab initio computations. The ordering of fine structure levels of the bound and quasi-bound spin-orbit coupled valence states of SiH and its ions, for which neither experiment nor theory is available, is predicted.

Bond lengths, harmonic vibrational frequencies and dissociation energies of TlAt are calculated at ab initio molecular orbital and density functional theory using effective spin-orbit operator and relativistic effective core potentials. Spin-orbit effects estimated from density functional theory are in good agreement with those from ab initio calculations, implying that density functional theory with effective core potentials can be an efficient and reliable methods for spin-orbit interactions. The estimated $R_e$, $ω_e$ and $D_e$ values are 2.937 ${\AA}$, 120 $cm^{-1}$, 1.96 eV for TlAt. Spin-orbit effects generally cause the bond contraction in Group 13 elements and the bond elongation in the Group 17 elements, and spin-orbit effects on Re of TlAt are almost cancelled out. The spinorbit effects on $D_e$ of TlAt are roughly the sum of spin-orbit effects on $D_e$ of the corresponding element hydrides. Electron correlations and spin-orbit effects are almost additive in the TlAt molecule.

Mutagen X (MX), 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone is one of the most potent directing acting mutagen ever tested in SAL TA100 assay. Although MX analogues have been synthesized, tested for mutagenicity and modeled by structure-activity relationship (SAR) methods, the mechanism of interaction of these compounds with DNA to produce their remarkable mutagenic potency remains unresolved. MX exists as an equilibrium mixture of both ring and open form in water. This equilibrium is very fast for Ames test. Because the mixture is not separable by experimental methods, it is not clear which one is really responsible for the observed mutagenicity. There have been many debates that which one is really responsible for the observed mutagenicity. We used ab initio methods for the MX analogues. It seems both ring and open form could react with DNA bases as electrophiles. However, every open form has consistently lower LUMO energy than corresponding ring form. It is reasonable to assume that the major reaction will go through via open form for MX analogues. This suggest that the open form is more likely really mutagenic.

Linear scaling quantum theories are reviewed especially focusing on the method adopted in GAMESS. The three key translation equations of the fast multipole method (FMM) are deduced from the general polypolar expansions given earlier by Steinborn and Ruedenberg. Simplifications are introduced for the rotation-based FMM that lead to a very compact FMM formalism. The OPS (optimum parameter searching) procedure, a stable and efficient way of obtaining the optimum set of FMM parameters, is established with complete control over the tolerable error ε. In addition, a new parallel FMM algorithm, requiring virtually no inter-node communication, is suggested which is suitable for the parallel construction of Fock matrices in electronic structure calculations.

New quaternary compounds $ANb_2PS_{10}$ (A = Na, Ag) and $AuNb_4P_2S_{20}$ were synthesized and characterized. The structures of three compounds consist of one-dimensional infinite chains built by [$Nb_2S_{12}$] and [$PS_4$] units. Cation atoms are occupied within the van der Waals gap of sulfur atoms between infinite chains to make -S…$M^+$…S- contacts. There is only one Au atom site and so crystallographically a unit cell contains four equivalent Au atoms in $AuNb_4P_2S_{20}$. This is only the half of the numbers of Na or Ag atoms in $NaNb_2PS_{10}$ or $AgNb_2PS_{10}$. The ratio between $Nb_2PS_{10}$ matrix vs the cation is, therefore, 1 : 1 for Ag and Na, but it is 2 : 1 for Au. Mixed valency in Au or Nb was expected to balance the charge in the latter compound. The electronic structures calculated based on the extended Huckel tight-binding method show that $ANb_2PS_{10}$ (A = Ag, Na) are semiconducting, while $AuNb_4P_2S_{20}$ is metallic, which is not consistent with the experimental results of these three compounds that all exhibit semiconducting property. The result of calculation suggests that $AuNb_4P_2S_{20}$ might be a magnetic insulator. Magnetic measurement experiment exactly proved that the compound is a Slater antiferromagnetic material with the Neels' temperature of 45 K. It is recognized, therefore, that electronic structure analysis is very useful to understand the properties of compounds.

In quantum dynamics of many-body systems, to identify the Hamiltonian becomes more difficult very rapidly as the number of degrees of freedom increases. In order to simplify the dynamics and to deduce dynamically relevant Hamiltonian information, it is desirable to control the dynamics to lie within a reduced space. With a judicious choice for the cost functional, the closed loop optimal control experiments can be manipulated efficiently to steer the dynamics to lie within a subspace of the system eigenstates without requiring any prior detailed knowledge about the system Hamiltonian. The procedure is simulated for optimally controlled population transfer experiments in the system of two degrees of freedom. To show the feasibility of steering the dynamics to lie in a specified subspace, the learning algorithms guiding the dynamics are presented along with frequency filtering. The results demonstrate that the optimal control fields derive the system to the desired target state through the desired subspace.

We have investigated the solvent effects on Δlog $K_s$ (the difference of stability constant of binding) and the relative free energies of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 by a Monte Carlo simulation of statistical perturbation theory (SPT) in diverse solvents. We compared relative binding Gibbs free energies and the differences in stability constant (Δlog $K_s$) of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 in $CH_3OH$ in this study with the experimental. There is a good agreement between our study and the experimental. We noted that Borns function of the solvents, the electron pair donor properties of the solvent, the radii of host and guest and the differences in solvation dominate the differences in the stability constant (Δlog $K_s$) as well as the relative free energies of binding of TEX>$La^{3+} to Nd^{3+}$ ions to 18-crown-6. The results of this study appear promising for providing the association properties of crown ethers with alkaline earth metals among polar solvents and the less polar or non-polar solvents.

Since theoretical investigations of gas phase clusters enable the evaluation of intrinsic molecular properties and intermolecular interactions, one can predict the macroscopic properties of bulk matter, from a microscopic determination of the properties of individual atoms, molecules, or clusters. Based on the insights obtained from theoretical investigations of the properties of a large number of cluster systems (ranging from simple water clusters to large π-systems), we have investigated the properties of various novel molecular systems including endo/exohedral fullerenes, nanotori, nonlinear optical materials, ionophores/receptors, polypeptides, enzymes, organic nanotubes, nanowires, and electronic and nano-mechanical molecular devices. The present minireview highlights some of the interesting results obtained in the course of our extensive theoretical investigations of clusters and nanomaterials.

The $BH_5$ molecule, which is suggested as an intermediate of the acidolysis of $BH_4^-$, contains a weak two-electron-three-center bond and it requires extremely high-level of theories to calculate the energy and structure correctly. The structures and energies of $BH_5$ and the transition state for the hydrogen scrambling have been studied using recently developed multi-coefficient correlated quantum mechanical methods (MCCMs). The dissociation energies and the barrier heights agree very well with the previous results at the CCSD(T)/ TZ(3d1f1g, 2p1d) level. We have also calculated the potential energy curves for the dissociation of $BH_5$ to $BH_3$ and $H_2$. The lower levels of theory were unable to plot correct potential curves, whereas the MCCM methods give very good potential energy curves and requires much less computing resources than the CCSD(T)/ TZ(3d1f1g,2p1d) level. The potential energy of the $BH_5$ scrambling has been obtained by the multiconfiguration molecular mechanics algorithm (MCMM), and the rates are calculated using the variational transition state theory including multidimensional tunneling approximation. The rate constant at 300 K is 2.1 × $10^9s^{-1}$, and tunneling is very important.

The structural and dynamic properties of small n-alkane clusters embedded in a mesoscopic solvent are investigated. The solvent interactions are taken into account through a multi-particle collision operator that conserves mass, momentum and energy and the solvent dynamics is updated at discrete time intervals. The cluster molecules interact among themselves and with the solvent molecules through intermolecular forces. The properties of n-heptane and n-decane clusters interacting with the mesoscopic solvent molecules through repulsive Lennard-Jones interactions are studied as a function of the number of the mesoscopic solvent molecules. Modifications of both the cluster and solvent structure as a result of cluster-solvent interactions are considered. The cluster-solvent interactions also affect the dynamics of the small n-alkane clusters.

Density functional calculations and ab initio calculations have been carried out to study the lowest energy structure of the water ($H_2O)_{11}$. Among five structures suggested by four different groups, the lowest energy structure is found to have the skeletal structure of Prism56 (Pr56-24) that a cyclic pentamer and a cyclic hexamer are fused into a prism-shape with 16 hydrogen-bonds (HBs).

The collective electronic oscillator (CEO) method was developed by Mukamel and collaborators.[Phys. Rev. Lett. 1992, 69, 65; Science 1997, 277, 781] Recently Ⅰ have extended the CEO method to obtain the frequency dependent optical properties with all the contributing components. The brief introduction of the CEO fomalism and its recent applications to linear absorption and two-photon absorption (TPA) of conjugated organic molecules will be discussed. The size scaling of optical properties of polyenes and polyynes have studied by ab initio calculations, and this result is consistent with the coherence length of the time dependent densities to first ($ρ^(1)$) and second order ($ρ^(2)$) in the electric field obtained from the CEO method.

We have studied the folding mechanism of β-hairpins from proteins of 1GB1, 3AIT and 1A2P by unfolding simulations at high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the three β-hairpin structures follow different mechanism of folding. The results of unfolding simulations showed that the positions of the hydrophobic core residues influence the folding dynamics. We discussed the characteristics of different mechanisms of β-hairpin folding based on the hydrogen-bond-centric and the hydrophobic-centric models.

Polychlorinated dibenzo-p-dioxins (PCDDs) are extremely toxic and persistent environmental pollutants. Their chemical reactivities and other physicochemical/biological properties show a strong dependence on the chlorination pattern. With increasing the number of chlorines, dioxin congeners become more electronegative and gain higher electron affinities. The vertical electron affinities (VEA) are related with the LUMO energies of neutral molecules. LUMO energies of all PCDD congeners were calculated at the B3LYP/6-31G** level and those of some selected congeners at the level of B3LYP/6-311G**//B3LYP/6-31G** and B3LYP/cc-pvtz/ /B3LYP/6-31G**. The total energies of neutral and anionic species for dibenzo-p-dioxins (DD), 1469-TCDD, 2378-TCDD, and OCDD were calculated at the level of B3LYP/6-31G**, B3LYP/aug-cc-pvdz, and B3LYP/ aug-cc-pvtz//B3LYP/6-31G**. By using the four congeners with D2h symmetry as reference molecules, we could estimate VEA (B3LYP/aug-cc-pvdz) of 75 PCDD congeners based on the linear correlations between LUMO energy and VEA (B3LYP/6-31G**) and between VEA (B3LYP/6-31G**) and VEA (B3LYP/aug-ccpvtz// B3LYP/6-31G**). Results show that all PCDDs with the number of Cl ≥ 3 have positive electron affinities. The PCDD electron affinity values provided in this work can be a useful data set in understanding the congener-specific reactivities of dioxins in various environmental media.

One of the largest challenges for quantum chemistry today is to obtain accurate results for large complex molecular systems, and a variety of approaches have been proposed recently toward this goal. We have developed the ONIOM method, an onion skin-like multi-level method, combining different levels of quantum chemical methods as well as molecular mechanics method. We have been applying the method to many different large systems, including thermochemistry, homogeneous catalysis, stereoselectivity in organic synthesis, solution chemistry, fullerenes and nanochemistry, and biomolecular systems. The method has recently been combined with the polarizable continuum model (ONIOM-PCM), and was also extended for molecular dynamics simulation of solution (ONIOM-XS). In the present article the recent progress in various applications of ONIOM and other electronic structure methods to problems of homogeneous catalyses and nanochemistry is reviewed. Topics include 1. bond energies in large molecular systems, 2. organometallic reactions and homogeneous catalysis, 3. structure, reactivity and bond energies of large organic molecules including fullerenes and nanotubes, and 4. biomolecular structure and enzymatic reaction mechanisms.

The relative stabilities of weak binding clusters are sensitive to temperature due to the entropy effect. Thus, here we report significant changes in relative stabilities between two low-energy electron-water trimer structures and those between three low-energy electron-water pentamer structures, as the temperature increases. The trimer and pentamer show structural changes around 200 K.

Fundamental ideas of the free energy gradient method are briefly reviewed with three applications: the stable structures of glycine and ammonia-water molecule pair in aqueous solution and the transition state (TS) structure of a Menshutkin reaction $NH_3 + CH_3Cl → CH_3NH_3^+ + Cl^-$ in aqueous solution, which is the first example of full TS optimization of all internal degrees of freedom.

This brief review contains surveys of both four-component and two-component relativistic molecular theories. First the four-component relativistic approach is reviewed. Emphasis is placed on efficient computational schemes for the four-component Dirac-Hartree-Fock and Dirac-Kohn-Sham methods. Next, in the twocomponent relativistic framework, two relativistic Hamiltonians, RESC and higher-order Douglas-Kroll (DK), are introduced. An illustrative application is shown for the relativistic study on valence photoelectron spectrum of OsO₄. The developing four-component relativistic and approximate quasi-relativistic methods have been packed in a program suite named REL4D.

Accurate ab initio computational chemistry has evolved dramatically. In particular, the development of multireference-based approaches has opened up a completely new area, and has had a profound impact on the potential of theoretical chemistry. Multireference-based perturbation theory (MRPT) is an extension of the closed-shell single reference Møller-Plesset method, and has been successfully applied to many chemical and spectroscopic problems. MRPT has established itself as an efficient technique for treating nondynamical and dynamical correlations. Usually, a complete active space self-consistent field (CASSCF) wave function is chosen as a reference function of MRPT. However, CASSCF often generates too many configurations, and the size of the active space can outgrow the capacity of the present technology. Many attempts have been proposed to reduce the dimension of CASSCF and to widen the range of applications of MRPT. This review focuses on our recent development in MRPT.

We have performed ab initio calculation on the active site of HIV-1 protease. The FEP method was used to determine the binding free energy of four different of protonated states of HIV-1 protease with inhibitor. The structure of the active site and hole structure was taken from the X-ray crystallographic coordinates of the C₂ symmetric inhibitor A74704 protease bound. The active site was modeled with the fragment molecules of binding pocket, acetic acid/ acetate anion (Asp25, Asp125), formamide (amide bond of Thr26/Gly27, Thr126/ Gly127), and methanol as inhibitor fragment. All possibly protonated states of the active site were considered, which were diprotonated state (0, 0), monoprotonated (-1, 0),(0, -1) and diunprotonated state (-1, -1). Once the binding energy Debind, of each model was calculated, more probabilistic protonated states can be proposed from binding energy. From ab-initio results, the FEP simulations were performed for the three following mutations: Ⅰ) Asp25 … Asp125 → AspH25 … Asp125, ⅱ) Asp25 … Asp125 → Asp25 … AspH125, ⅲ) AspH25 … Asp125 → AspH25 … AspH125. The free energy difference between the four states gives the information of the more realistic protonated state of active site aspartic acid. These results provide a theoretical prediction of the protonation state of the catalytic aspartic residues for A74707 complex, and may be useful for the evaluation of potential therapeutic targets.

Our previous quantum mechanical calculations using polyalanine model systems showed that the monodipolemacrodipoleinteractions selectively stabilize α-helices and make it possible for α-helices to be formed inhydrophobic environment where the solvent effect is not available. The monodipole-macrodipole interactionsin α-helices were studied molecular mechanically using various point-charge systems available. The resultsshow that all the point-charge systems used in the calculations produce the monodipole-macrodipoleinteractions up to about 60% compared to the results of the quantum mechanical calculations. The results ofmolecular mechanical calculations are explained and discussed compared to the results of the quantummechanical calculations.

Various theoretical studies of σ-bond activation of organic molecules by transition metal complexes arereviewed. In the homolytic σ-bond activation, the d orbital energy level of the central metal is an importantfactor, as well known. At the same time, the electron-withdrawing substituent which stabilizes the sp3 orbitalaccelerates the homolytic σ-bond activation. In the heterolytic C-H σ-bond activation of RH by $MXL_n$, the XHbond formation is an important driving force, where $MRL_n$ and HX are formed as products. The heterolytic σ-bond activation is also understood in terms of the electrophilic attack of the metal center to the substrate.

To extend the knowledge of triple bonding between group 6 transition metal and heavier group 14 elements, the structural and bonding aspects of ($η^5-C_5H_5$)$(CO)_2$M≡ER (M = Cr, Mo, W; E = Si, Ge, Sn, Pb) are investigated by hybrid density functional calculations at the B3PW91 level. Substituent effects are also investigated with R = H, Me, $SiH_3$, Ph, $C_6H_3-2,6-Ph_2$, $C_6H_3-2,6-(C_6H_2-2,4,6-Me_3)_2$, and $C_6H_3-2,6-(C_6H_2-2,4,6- iPr_3)_2$.

In ab initio molecular dynamics, whenever information about the potential energy surface is needed for integrating the equations of motion, it is computed “on the fly” using electronic structure calculations. For Born-Oppenheimer methods, the electronic structure calculations are converged, whereas in the extended Lagrangian approach the electronic structure is propagated along with the nuclei. Some recent advances for both approaches are discussed.

We present a brief account of the theory of diffusion-influenced kinetics of reactions involving polymers. The review will be based on the recent contributions from the authors. Both intrapolymer and interpolymer reactions are considered, and the effects of various physical factors, such as the chain length, chain stiffness, and hydrodynamic interactions, are described within a unified theoretical framework.

The reaction mechanism of the pyrolysis of sulphonyl oximes ($CH_3-C_6H_4-S(O)_2O-N=C(H)-C_6H_4Y$), in the gas phase is studied theoretically at HF/3-21G, ONIOM (B3LYP/6-31G**:HF/3-21G) and ONIOM (MP2/6- 31G**:HF/3-21G) levels. All the calculations show that the thermal decomposition of sulphonyl oximes is a concerted asynchronous process via a six-membered cyclic transition state. The activation energies (Ea) predicted by ONIOM (B3LYP/6-31G**: HF/3-21G) method are in good agreement with the experimental results for a series of tosyl arenecarboxaldoximes. Five para substituents, Y = $OCH_3$, $CH_3$, H, Cl, and $NO_2$, are employed to investigate the substituent effect on the elimination reaction. Linear Hammett correlations are obtained in all calculations in contrast to the experimental finding.

We report on the theoretical positron affinities of closed-shell atomic anions. The second-order many-body perturbation theory is applied taking the positron-electron interaction as a perturbation. The corrections for the complete basis set effects to the second order affinity are calculated based on the variational and nonvariational energy functionals of explicitly correlated geminals. It is shown that the explicitly correlated methods accelerate the convergence of the expansion significantly giving the account of the cusp behavior outside the orbital space.

A unified picture for magnetism, superconductivity, quantum optics and other properties of molecule-based materials has been presented on the basis of effective model Hamiltonians, where necessary parameter values have been determined by the first principle calculations of cluster models and/or band models. These properties of the matetials are qualitatively discussed on the basis of the spin and pseudo-spin Hamiltonian models, where several quantum operators are expressed by spin variables under the two level approximation. As an example, ab initio broken-symmetry DFT calculations are performed for cyclic magnetic ring constructed of 34 hydrogen atoms in order to obtain effective exchange integrals in the spin Hamiltonian model. The natural orbital analysis of the DFT solution was performed to obtain symmetry-adapted molecular orbitals and their occupation numbers. Several chemical indices such as information entropy and unpaired electron density were calculated on the basis of the occupation numbers to elucidate the spin and pair correlations, and bonding characteristic (kinetic correlation) of this mesoscopic magnetic ring. Both classical and quantum effects for spin alignments and singlet spin-pair formations are discussed on the basis of the true spin Hamiltonian model in detail. Quantum effects are also discussed in the case of superconductivity, atom optics and quantum optics based on the pseudo spin Hamiltonian models. The coherent and squeezed states of spins, atoms and quantum field are discussed to obtain a unified picture for correlation, coherence and decoherence in future materials. Implications of theoretical results are examined in relation to recent experiments on molecule-based materials and molecular design of future molecular soft materials in the intersection area between molecular and biomolecular materials.