Soohaeng Yoo Willow

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We have designed various nanoslit systems, whose opposing surfaces can be either hydrophobic, hydrophilic, or simply a water-vapor interface, for the molecular dynamics simulation of confined water with three different protein denaturants, i.e., urea, guanidinium chloride (GdmCl), and methanol, respectively. Particular attention is placed on the(More)
The direct simulation of the solid-liquid water interface with the effective fragment potential (EFP) via the constant enthalpy and pressure (NPH) ensemble was used to estimate the melting temperature (T(m)) of ice-I(h). Initial configurations and velocities, taken from equilibrated constant pressure and temperature (NPT) simulations at P = 1 atm and T =(More)
Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of(More)
The effect of the Hofmeister anions on the precipitation of proteins is often discussed using liquid-vapor coexisting systems with the assumption that the liquid-vapor interface mimics the liquid-protein interface. Solvated proteins, however, have both hydrophobic and hydrophilic regions on their surfaces rather than just a pure hydrophobic one. Using a(More)
A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the(More)
Experimental vibrational predissociation spectra of the magic NH4(+)(H2O)20 clusters are close to those of the magic H3O(+)(H2O)20 clusters. It has been assumed that the geometric features of NH4(+)(H2O)20 clusters might be close to those of H3O(+)(H2O)20 clusters, in which H3O(+) resides on the surface. Car-Parrinello molecular dynamics simulations in(More)
Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple(More)
A stochastic algorithm is proposed that can compute the basis-set-incompleteness correction to the second-order many-body perturbation (MP2) energy of a polyatomic molecule. It evaluates the sum of two-, three-, and four-electron integrals over an explicit function of electron-electron distances by a Monte Carlo (MC) integration at an operation cost per MC(More)
Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its(More)
Second-order many-body perturbation theory [MBPT(2)] is the lowest-ranked member of a systematic series of approximations convergent at the exact solutions of the Schrödinger equations. It has served and continues to serve as the testing ground for new approximations, algorithms, and even theories. This article introduces this basic theory from a variety of(More)