Yoshiyuki Koyano

A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation.

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER–GAUSSIAN interface (AG‐IF), which can be one of the simplest architectures. In the AG‐IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG‐IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG‐IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.

An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: Application to zwitterionic glycine in aqueous solution

An efficient methodology is presented to improve the QM description of solute-solvent interactions in condensed systems within the quantum mechanical/molecular mechanical (QM/MM) framework. It is based on the recently developed new treatment of the adaptive multiscale QM/MM-MD method, i.e., the number-adaptive multiscale method that includes the close solvent molecules around the solute into QM region and enables them to flow across the boundary between the QM and MM regions. We have applied it to zwitterionic (ZW) glycine molecule in aqueous solution, and investigated the hydration structures and charge distributions, which are compared with those by the standard (SD) method that only a solute glycine molecule is treated quantum mechanically. It is shown that the total energy and temperature are satisfactorily conserved, providing reasonable hydration numbers and induced polarization of ZW glycine molecule in aqueous solution. In contrast, the SD method is found overestimated the hydration numbers in comparison to the experimental ones due to the inappropriate expression of the electron distribution. In conclusion, the present method should become quite useful as the quantitative statistical sampling method to study various chemical phenomena in condensed systems.

Influence of Monomer Mixing Ratio on Membrane Nanostructure in Interfacial Polycondensation: Application of Hybrid MC/MD Reaction Method with Minimum Bond Convention.

FT-30, a typical aromatic polyamide membrane, is formed by interfacial polycondensation (IP) reaction between m-phenylenediamine (MPD) and benzene 1,3,5-tricarboxylic acid chloride (TMC) monomers. To investigate its microscopic characteristics, we performed an atomistic molecular simulation using the hybrid MC/MD reaction method modified to allow intercellular chemical bonds stretching over the periodic boundaries. Starting with appropriate monomer model systems, we succeeded in making membrane models by simulating a succession of condensation reactions. Through an analysis comparing our calculation results for the degrees of polymer cross-linking (DPC) and the composition ratios to the experimental results, we clarified the MPD/TMC mixing ratios in the near-surface active (NSA) and interior active (IA) regions associated with the reaction mechanism of IP. Further, we executed water diffusion simulations using the membrane model of the IA region and showed the calculated values of the total mass density of the hydrated membrane and the partition coefficient K to be in good agreement with the experimental ones. In conclusion, the present computationally modeled polyamide membrane has sufficient fidelity to the actual membrane and should be considered a stable spatial structure in the local equilibrium state under a nonequilibrium stationary state of permeation.

Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations

We present an alternative approach to determine “density‐dependent property”‐derived charges for molecules in the condensed phase. In the case of a solution, it is essential to take into consideration the electron polarization of molecules in the active site of this system. The solute and solvent molecules in this site have to be described by a quantum mechanical technique and the others are allowed to be treated by a molecular mechanical method (QM/MM scheme). For calculations based on this scheme, using the forces and interaction energy as density‐dependent property our charges from interaction energy and forces (CHIEF) approach can provide the atom‐centered charges on the solute atoms. These charges reproduce well the electrostatic potentials around the solvent molecules and present properly the picture of the electron density of the QM subsystem in the solution system. Thus, the CHIEF charges can be considered as the atomic charges under the conditions of the QM/MM simulation, and then enable one to analyze electrostatic interactions between atoms in the QM and MM regions. This approach would give a view of the QM nuclei and electrons different from the conventional methods.

An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution

For the purpose to execute direct dynamics calculation in solution chemistry, we propose an optimum strategy for solution chemistry using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRP), i.e., the NDDO‐SSRP method. In this strategy, the empirical parameters of the semi‐empirical MO method were optimized individually for target molecule or ion by reference to the ab initio MO calculation data for many configurations on the potential energy surface near the reaction path. For demonstration, the NDDO‐SSRP method was applied to two molecules and two ions (OH−, H2O, NH3, NH4+) at their equilibrium states in aqueous solution, respectively. Accordingly, it was verified that both the potential energy surface and the charge distribution of these solutes in aqueous solution are dramatically improved to reproduce themselves accurately at ab initio MO calculation level. In conclusion, it is expected that the NDDO‐SSRP method should become quite useful for dynamic and statistical applications to chemical reaction systems in solution.

Free Energy Gradient Method and Its Recent Related Developments: Free Energy Optimization and Vibrational Frequency Analysis in Solution

To obtain stable states (SS) and transition states (TS) of chemical reaction system in condensed state at a finite temperature, the free energy gradient (FEG) method was proposed in 1998 as an optimization method on a multidimensional free energy surface (FES) . This is analogous to the method for the Born Oppenheimer potential energy surface (PES) considered by ab initio molecular orbital (MO) calculation , and utilizes the force and Hessian on the FES with respect to the coordinates of a solute molecule, which can be adiabatically calculated by molecular dynamics (MD) method . In this chapter, we reviewed the FEG methodology that is the method for estimating molecular properties based on the free energy (FE) landscape in condensed state and also discussed a future perspective for the improvement and the extension of the theoretical methods. We believe that a family of the FEG methodologies should become more efficient as one promising strategic setting and will play important roles to survey condensed state chemistry on the basis of recent supercomputing technology.

An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework.

For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO‐SSRP method. It has been further extended to develop the NDDO‐MAIS‐SSRP method, which is the NDDO‐SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core–core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO‐MAIS‐SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH3H2O molecule pair and a MM solvent H2O molecule. The NDDO‐MAIS‐SSRP method can reproduce the electrostatic energy in the region R > 4.0 Å, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 Å in some cases. Both the NDDO‐SSRP and the NDDO‐MAIS‐SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press).