Soohaeng Yoo

On the phase diagram of water with density functional theory potentials: The melting temperature of ice Ih with the Perdew–Burke–Ernzerhof and Becke–Lee–Yang–Parr functionals

The melting temperature (T(m)) of ice I(h) was determined from constant enthalpy and pressure (NPH) Born-Oppenheimer molecular dynamics simulations to be 417+/-3 K for the Perdew-Burke-Ernzerhof and 411+/-4 K for the Becke-Lee-Yang-Parr density functionals using a coexisting ice (I(h))-liquid phase at constant pressures of P=2500 and 10,000 bar and a density rho=1 g/cm(3), respectively. This suggests that ambient condition simulations at rho=1 g/cm(3) will rather describe a supercooled state that is overstructured when compared to liquid water.

Communication: The effect of dispersion corrections on the melting temperature of liquid water

The melting temperature (T(m)) of liquid water with the Becke-Lee-Yang-Parr (BLYP) density functional including dispersion corrections (BLYP-D) and the Thole-type, version 3 (TTM3-F) ab-initio based flexible, polarizable classical potential is reported via constant pressure and constant enthalpy (NPH) molecular dynamics simulations of an ice I(h)-liquid coexisting system. Dispersion corrections to BLYP lower T(m) to about 360 K, a large improvement over the value of T(m) > 400 K previously obtained with the original BLYP functional under the same simulation conditions. For TTM3-F, T(m) = 248 K from classical molecular dynamics simulations.

Solvent Effects on Optical Properties of Molecules: A Combined Time-Dependent Density Functional Theory/Effective Fragment Potential Approach

A quantum mechanics/molecular mechanics (QM/MM) type of scheme is employed to calculate the solvent-induced shifts of molecular electronic excitations. The effective fragment potential (EFP) method was used for the classical potential. Since EFP has a density dependent functional form, in contrast with most other MM potentials, time-dependent density functional theory (TDDFT) has been modified to combine TDDFT with EFP. This new method is then used to perform a hybrid QM/MM molecular dynamics simulation to generate a simulated spectrum of the n-->pi(*) vertical excitation energy of acetone in vacuum and with 100 water molecules. The calculated water solvent effect on the vertical excitation energy exhibits a blueshift of the n-->pi(*) vertical excitation energy in acetone (Delta omega(1)=0.211 eV), which is in good agreement with the experimental blueshift.

Melting temperature of ice Ih calculated from coexisting solid-liquid phases

We carried out molecular-dynamics simulations by using the two-phase coexistence method with the constant pressure, particle number, and enthalpy ensemble to compute the melting temperature of proton-disordered hexagonal ice I(h) at 1-bar pressure. Four models of water were considered, including the widely used TIP4P [W. L. Jorgensen, J. Chandrasekha, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys.79, 926 (1983)] and TIP5P [M. W. Mahoney and W. L. Jorgensen J. Chem. Phys.112, 8910 (2000)] models, as well as recently improved TIP4P and TIP5P models for use with Ewald techniques-the TIP4P-Ew [W. Horn, W. C. Swope, J. W. Pitera, J. C. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, J. Chem. Phys.120, 9665 (2004)] and TIP5P-Ew [S. W. Rick, J. Chem. Phys.120, 6085 (2004)] models. The calculated melting temperature at 1 bar is T(m) = 229 +/- 1 K for the TIP4P and T(m) = 272.0 +/- 0.6 K for the TIP5P ice I(h), both are consistent with previous simulations based on free-energy methods. For the TIP4P-Ew and TIP5P-Ew models, the calculated melting temperature is T(m) = 257.0 +/- 1.1 K and T(m) = 253.9 +/- 1.1 K, respectively.

Global geometry optimization of silicon clusters described by three empirical potentials

The “basic-hopping” global optimization technique developed by Wales and Doye is employed to study the global minima of silicon clusters Sin(3⩽n⩽30) with three empirical potentials: the Stillinger–Weber (SW), the modified Stillinger–Weber (MSW), and the Gong potentials. For the small-sized SW and Gong clusters (3⩽n⩽15), it is found that the global minima obtained based on the basin-hopping method are identical to those reported by using the genetic algorithm [Iwamatsu, J. Chem. Phys. 112, 10976 (2000)], as well as with those by using molecular dynamics and the steepest-descent quench (SDQ) method [Feuston, Kalia, and Vashishta, Phys. Rev. B 37, 6297 (1988)]. However, for the mid-sized SW clusters (16⩽n⩽20), the global minima obtained differ from those based on the SDQ method, e.g., the appearance of the endohedral atom with fivefold coordination starting at n=17, as opposed to n=19. For larger SW clusters (20⩽n⩽30), it is found that the “bulklike” endohedral atom with tetrahedral coordination starts at n=...

The melting lines of model silicon calculated from coexisting solid–liquid phases

The molecular-dynamics simulation approach [Morris and Song, J. Chem. Phys. 116, 9352 (2002)] is employed to calculate the melting lines for two model systems of silicon: the Stillinger–Weber (SW) model and the Tersoff-89 model. To address the anisotropic stress problem indicated in the previous paper, a slightly improved simulation procedure is used to prepare the coexisting solid and liquid phases at the thermodynamic equilibrium. For the SW silicon, the calculated melting temperature Tm at zero pressure agrees with that based on the free-energy calculation [Broughton and Li, Phys. Rev. B 35, 9120 (1987)]. The dependence of Tm at zero pressure on the selected solid surface orientation is also examined. The relative difference between Tm calculated based on the sharp Si (111)/liquid interface and the faceted Si (100)/liquid interface is less than 1%. Both models predict that the melting line exhibits a negative slope, which is consistent with the fact that the molar volume of the solid is larger than tha...

Structures and stability of medium-sized silicon clusters. III. Reexamination of motif transition in growth pattern from Si15 to Si20.

It has been established from experiments that stable medium-sized ionic clusters Si15-Si20 are prolate in shape. Density-functional theories (DFTs) also predict that nearly all low-lying neutral clusters in this size range are prolate in shape. Moreover, most of them are built onto two generic structural motifs, either the tricapped-trigonal-prism (TTP) Si9 motif or the six/six Si6Si6 (sixfold-puckered hexagonal ring Si6 plus six-atom tetragonal bipyramid Si6) motif. However, it appears that the exact location of the TTP-to-six/six motif transition is dependent on the functional (e.g., PBE or BLYP) used in the DFT calculations. Here, we present total-energy calculations for two series of clusters (one series containing six/six motif and the other containing the TTP motif) in the size range of Si16-Si20. The calculations were based on all-electron DFT methods with a medium [6-311G (2d)] and a large (cc-pVTZ) basis sets, as well as coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] method with a modest (cc-pVDZ) basis set. In the DFT calculations, two popular hybrid density functionals, the B3LYP and PBE1PBE, were selected. It is found that the B3LYP total-energy calculations slightly favor the six/six motif, whereas the PBE1PBE calculations slightly favor the TTP motif. The CCSD(T) total-energy calculations, however, show that isomers based on the six/six motif are energetically slightly favorable in the size range of Si16-Si20. Hence, the TTP-to-six/six motif transition is more likely to occur at Si16.

Effect of polarizability of halide anions on the ionic solvation in water clusters

Molecular dynamics simulation has been performed to study the effect of the polarizabilities of model anions on the ionic solvation in water clusters. The primary focus is given to the surface versus interior solvation behavior of the anions. To this end, various combinations of polarizable/nonpolarizable water and anion models were considered. Using the nonpolarizable TIP4P water with polarizable Cl− and Br− models, the Cl− is fully solvated inside the (H2O)60 cluster, whereas the Br− is partially solvated at the surface of the cluster. However, when the polarizability of the Br− is turned off, the “Br−” anion is fully solvated. Using the polarizable Dang–Chang water, both Cl− and Br− reside at the surface of (H2O)60 as well as (H2O)500 clusters, consistent with the finding of Stuart and Berne [J. Phys. Chem. 100, 11934 (1996)] based on the polarizable TIP4P-FQ water with the polarizable Drude halide model. When the polarizabilities of the halide anions are turned off, the smaller size “Cl−” anion is ful...

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.

Search for global minimum geometries for medium sized germanium clusters: Ge12–Ge20

We have performed an unbiased search for the global minimum geometries of small-to-medium sized germanium clusters Gen(12< or =n< or =18) as well as a biased search (using seeding method) for Gen(17< or =n< or =20). We employed the basin-hopping algorithm coupled with the plane-wave pseudopotential density functional calculations. For each size, we started the unbiased search with using several structurally very different initial clusters, or we started the biased search with three different seeds. Irrespective of the initial structures of clusters we found that the obtained lowest-energy clusters of the size n=12-16 and 18 are the same. Among them, the predicted global minima of Gen(12< or =n< or =16) are identical to those reported previously [Shvartsburg et al., Phys. Rev. Lett. 83, 167 (1999)]. For n=17-20, we have identified two or three nearly isoenergetic low-lying isomers (for each size) that compete for the global minimum. Nearly all the low-lying clusters in the size range of 12< or =n< or =20 contain the tri-caped trigonal prism motif and are all prolate in geometry, in agreement with the experiment.