Masataka Nagaoka

Unveiling thermal transitions of polymers in subnanometre pores.

The thermal transitions of confined polymers are important for the application of polymers in molecular scale devices and advanced nanotechnology. However, thermal transitions of ultrathin polymer assemblies confined in subnanometre spaces are poorly understood. In this study, we show that incorporation of polyethylene glycol (PEG) into nanochannels of porous coordination polymers (PCPs) enabled observation of thermal transitions of the chain assemblies by differential scanning calorimetry. The pore size and surface functionality of PCPs can be tailored to study the transition behaviour of confined polymers. The transition temperature of PEG in PCPs was determined by manipulating the pore size and the pore–polymer interactions. It is also striking that the transition temperature of the confined PEG decreased as the molecular weight of PEG increased.

Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace

Molecules confined in nanospaces will have distinctly different properties to those in the bulk state because of the formation of specific molecular assemblies and conformations. We studied the chain conformation and dynamics of single polystyrene (PSt) chains confined in highly regular one-dimensional nanochannels of a porous coordination polymer [Zn 2(bdc) 2ted] n ( 1; bdc = 1,4-benzenedicarboxylate, ted = triethylenediamine). Characterization by two-dimensional (2D) heteronuclear (1)H- (13)C NMR gave a direct demonstration of the nanocomposite formation and the intimacy between the PSt and the pore surfaces of 1. Calorimetric analysis of the composite did not reveal any glass transition of PSt, which illustrates the different nature of the PSt encapsulated in the nanochannels compared with that of bulk PSt. From N 2 adsorption measurements, the apparent density of PSt in the nanochannel was estimated to be 0.55 g cm (-3), which is much lower than that of bulk PSt. Results of a solid-state (2)H NMR study of the composite showed the homogeneous mobility of phenyl flipping with significantly low activation energy, as a result of the encapsulation of single PSt chains in one-dimensional regular crystalline nanochannels. This is also supported by molecular dynamics (MD) simulations.

Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution

The free energy gradient method was applied to the multidimensional geometry optimization of glycine zwitterion (ZW) in aqueous solution in order not only to demonstrate its applicability, but also to examine its efficiency. The method utilizes force on the free energy surface that can be directly calculated by the molecular dynamics method and the free energy perturbation theory. Then, the most stable ZW structure in aqueous solution was obtained within the tolerance assumed, and it was found that the free energy (FE) and enthalpy changes of stabilization from the initial geometry optimized in the gas phase are −0.9 and −3.5 kcal/mol, respectively, and the amino and carboxyl groups are spatially separated by each other due to their solvating with water molecules. Comparing the contributions of enthalpy and entropy to FE, the former is attributed to the main origin of FE stabilization during the optimization procedure, and it was found that solvation entropy prevents water molecules from solvating the ZW ...

Slippage of initial conditions for the Redfield master equation

For a slow open quantum subsystem weakly coupled to a fast thermal bath, we derive the general form of the slippage to be applied to the initial conditions of the Redfield master equation. This slippage is given by a superoperator which describes the non-Markovian dynamics of the subsystem during the short-time relaxation of the thermal bath. We verify in an example that the Redfield equation preserves positivity after the slippage superoperator has been applied to the initial density matrix of the subsystem. For δ-correlated baths, the Redfield master equation reduces to the Lindblad master equation and the slippage of initial conditions vanishes consistently.

Transition-state optimization by the free energy gradient method: Application to aqueous-phase Menshutkin reaction between ammonia and methyl chloride

The transition state (TS) for the Menshutkin reaction H3N+CH3Cl→H3NCH3++Cl− in aqueous solution was located on the free energy surface (FES) by the free energy gradient (FEG) method. The solute–solvent system was described by a hybrid quantum mechanical and molecular mechanical (QM/MM) method. The reaction path in water was found to deviate largely from that in the gas phase. It was concluded that, in such a reaction including charge separation, TS structure optimization on an FES is inevitable for obtaining valid information about a TS in solution.

PRODUCT ENERGY DISTRIBUTION OF MOLECULAR HYDROGEN FORMED ON ICY MANTLES OF INTERSTELLAR DUST

The formation pumping mechanism of H2 molecules formed on icy mantles of interstellar dust was investigated theoretically based on a classical molecular dynamics (MD) computational simulation. The slab-shaped amorphous water ice was prepared at 10 and 70 K, as a realistic model surface for icy mantles of dust, and the formation process of molecular hydrogen, H + H → H2, was simulated on the ice surface at 10 and 70 K, where two MD procedures were employed. Method A: H2O molecules were treated as rigid (hard ice model). Method B: intramolecular vibrational modes of H2O were taken into account (soft ice model). A numerical energy analysis was performed, and the product energy distribution was obtained for H2. It has become clear that H2 molecules formed on the amorphous water ice are in highly excited states not only vibrationally, but also rotationally and translationally. The vibrational energy levels with large populations are, respectively, v = 6-10 and 6-10 for 10 and 70 K hard ice systems and v = 6-9 and 5-9 for 10 and 70 K soft ice systems. The average vibrational energies correspond to v = 8-9 and v = 7-8 for the hard ice and the soft ice, respectively. The evaluated rotational and translational temperatures were 5500-6000 and 4000-5000 K, respectively, for the hard ice, whereas they were 6500-8000 and 5500-6500 K, respectively, for the soft ice. The largest portion of the H2 formation energy resided in the vibrational energy of H2 (70%-79%), and the second and third largest portions were the rotational (10%-15%) and translational energies (7%-12%), respectively. The energy absorbed by the ice was evaluated to be only about 4-5 kcal mol-1 (3%-5% of the H2 formation energy, 109.5 kcal mol-1). The present results suggest that the H2 vibrational emission might be detectable in regions without a source of UV pumping or dynamical excitation.

Non-Markovian stochastic Schrödinger equation

We report a study of a stochastic Schrodinger equation corresponding to the Redfield master equation with slipped initial conditions, which describes the dynamics of a slow subsystem weakly coupled to a fast thermal bath. Using the projection-operator method of Feshbach, we derive a non-Markovian stochastic Schrodinger equation of the generalized Langevin type, which simulates the time evolution of the quantum wave functions of the subsystem driven by the fluctuating bath. For δ-correlated baths, the non-Markovian stochastic Schrodinger equation reduces to the previously derived Markovian one. Numerical methods are proposed to simulate the time evolution under our non-Markovian stochastic Schrodinger equation. These methods are illustrated with the spin-boson model.

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.

Theoretical prediction of proton chemical shift in supercritical water using gas-phase approximation

Abstract Chemical shifts of the OH proton in supercritical water referenced to the benzene proton have been estimated theoretically using the ab initio molecular orbital (MO) method. The degree of dissociation from hydrogen-bonded water clusters to monomers calculated using the CCSD (T)/6-31+G(d)//MP2 (frozen core)/6-31+G(d) level of theory indicates that supercritical water is comprised of 80% monomer and 20% dimer at the critical point ( T c =647.1 K, P c =22.06 MPa). On the basis of this supercritical water composition, the chemical shift of the OH proton is determined to be −6.19 ppm at the MP2 (frozen core)/6-31+G(d)// MP2 (frozen core)/6-31+G(d) level of theory, which reproduces the recent NMR experimental results well.

On vibrational cooling upon photodissociation of carbonmonoxymyoglobin and its microscopic mechanism from the viewpoint of vibrational modes of heme

Abstract We report some results via molecular dynamics simulations for the photodissociation process of carbonmonoxymyoglobin in vacuo. The vibrational temperature of heme shows a biphasic decay (time constants, 0.84 ps (66%) and 18.7 ps (34%), are in good agreement with the experimental ones). The vibrational frequencies of the active center were obtained by time-resolved Fourier transform of velocity autocorrelation functions. Then, the vibrational modes of propionate groups of heme would couple with those of a water molecule. Since these groups are exposed to the water solvent, they should play an important role for the channel of fast energy transfer from the heme protein to the solvents.