We have reformulated the reference interaction site model self-consistent-field (RISM-SCF) method to calculate the molecular properties of solute in solutions. The key feature is to introduce the Helmholtz free energy given as a sum of the solute electronic energy estimated by ab initio molecular orbital (MO) methods and the hypernetted-chain (HNC) excess chemical potential of solvation for the extended reference interaction site model (XRISM) method. The variational conditions for the multiconfigurational self-consistent-field (MCSCF) wave functions were derived. It was also shown that, in the case of the Hartree–Fock (HF) method, the present expression gives the same Fock matrix defined previously. Moreover the expression for first derivatives of the free energy with respect to the solute nuclear coordinates were obtained. Sample calculations for the chemical equilibrium of cis- and trans-isomers of 1,2-difluoroethylene are presented. With the use of analytical energy gradients for the MCSCF and HF methods, the solute molecular geometries were determined in an aqueous solution.

In the previous study, Chem. Phys. Lett. 214, 391 (1993), we developed a new computational procedure for the solvation effect on the electronic structure of solute based upon the reference interaction site model (RISM) integral equation and the Hartree–Fock equation. The method enables us to calculate the solvent distribution and solute electronic wave functions simultaneously, which is free from such empirical parametrizations as appeared in the usual models based on the dielectric continuum picture. In the present article, we have applied the method to several carbonyl compounds in aqueous solution. The SPC model was used to describe the liquid water. The vertical n→π*, π→π*, and σ→π* transitions of formaldehyde are examined by the RISM-self-consistent field formalism coupled with the restricted Hartree–Fock approximation, and then the free energy calculation was performed for the excited state in order to estimate the contributions for the optical fluorescence spectra. The intramolecular energy turned out to give significant contribution to the bathochromic shift of fluorescence relative to the absorption in the liquid phase. Furthermore the importance of the structural effect of the functional group was discussed by the calculations of three more carbonyl compounds, acetaldehyde, acetone, and acrolein.

The reaction mechanism of serine proteases (trypsin), which catalyze peptide hydrolysis, is studied theoretically by ab initio QM/MM electronic structure calculations combined with Molecular Dynamics-Free Energy Perturbation calculations. We have calculated the entire reaction free energy profiles of the first reaction step of this enzyme (acylation process). The present calculations show that the rate-determining step of the acylation is the formation of the tetrahedral intermediate, and the breakdown of this intermediate has a small energy barrier. The calculated activation free energy for the acylation is approximately 17.8 kcal/mol at QM/MM MP2/(aug)-cc-pVDZ//HF/6-31(+)G/AMBER level, and this reaction is an exothermic process. MD simulations of the enzyme-substrate (ES) complex and the free enzyme in aqueous phase show that the substrate binding induces slight conformational changes around the active site, which favor the alignment of the reactive fragments (His57, Asp102, and Ser195) together in a reactive orientation. It is also shown that the proton transfer from Ser195 to His57 and the nucleophilic attack of Ser195 to the carbonyl carbon of the scissile bond of the substrate occur in a concerted manner. In this reaction, protein environment plays a crucial role to lowering the activation free energy by stabilizing the tetrahedral intermediate compared to the ES complex. The polarization energy calculations show that the enzyme active site is in a very polar environment because of the polar main chain contributions of protein. Also, the ground-state destabilization effect (steric strain) is not a major catalytic factor. The most important catalytic factor of stabilizing the tetrahedral intermediate is the electrostatic interaction between the active site and particular regions of protein: the main chain NH groups in Gly193 and Ser195 (so-called oxyanion hole region) stabilize negative charge generated on the carbonyl oxygen of the scissile bond, and the main chain carbonyl groups in Ile212 approximately Ser214 stabilize a positive charge generated on the imidazole ring of His57.

We performed ab initio molecular orbital (MO) calculations of the response kernel (∂Q a /∂V b ), which represents the response of the intramolecular charge polarization by external electrostatic field, on the basis of the coupled perturbed Hartree−Fock equation. The response kernels of some organic molecules including pyrazine, pyrazinyl radical, acetone, and 2-hydroxypropyl radical were calculated along the present formulation. The results revealed that the hydrogen abstraction of pyrazine causes the product radical to be remarkably deformable in the partial charge distribution, while the hydrogen abstraction of acetone does not induce such enhancement of the charge sensitivity. The augmented sensitivity does not appear in the usual polarizability for a uniform field but emerges for a local fluctuated field. To elucidate the remarkable difference, we performed the normal mode analysis and decomposition based on the intrinsic soft MO pairs or localized orbitals. As a result, the enhancement in the aromatic species is attributed to the softest normal mode due to the π−σ mixing that facilitates the deformation of the π-electron orbitals. In the nonaromatic species, on the other hand, this effect is not dominant and is canceled by the breakdown of hyperconjugation. We suggest that the particular sensitivity of aromatic radicals is the origin of anomalously slow diffusion in solution.

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