Hainam Do

Structure and bonding in ionized water clusters.

The structure and bonding in ionized water clusters, (H2O)(n)(+) (n = 3–9), has been studied using the basin hopping search algorithm in combination with quantum chemical calculations. Initially candidate low energy isomers were generated using basin hopping in conjunction with density functional theory. Subsequently, the structures and energies were refined using second order Møller–Plesset perturbation theory and coupled cluster theory, respectively. The lowest energy isomers are found to involve proton transfer to give H(3)O(+) and a OH radical, which are more stable than isomers containing the hemibonded hydrazine-like fragment (H(2)O–OH(2)), with the calculated infrared spectra consistent with experimental data. For (H(2)O)(9)(+) the observation of a new structural motif comprising proton transfer to form H(3)O(+) and OH, but with the OH radical involved in hemibonding to another water molecule is discussed.

Structural optimization of molecular clusters with density functional theory combined with basin hopping

Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol, and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H(+)(H(2)O)(7) is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H(+) prefers to combine with methanol rather than water in the lowest-energy structures.

Rapid calculation of partition functions and free energies of fluids

The partition function (Q) is a central quantity in statistical mechanics. All the thermodynamic properties can be derived from it. Here we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the Helmholtz free energy (F) via F = -k(B)T ln Q. In our approach, we divide the density of states, assigning half of the configurations found in a simulation to a high-energy partition and half to a low-energy partition. By recursively dividing the low-energy partition into halves, we map out the complete density of states for a continuous system. The result allows free energy to be calculated directly as a function of temperature. We illustrate our method in the context of the free energy of water.

Calculation of Partition Functions and Free Energies of a Binary Mixture Using the Energy Partitioning Method: Application to Carbon Dioxide and Methane

It is challenging to compute the partition function (Q) for systems with enormous configurational spaces, such as fluids. Recently, we developed a Monte Carlo technique (an energy partitioning method) for computing Q [ J. Chem. Phys. 2011 , 135 , 174105 ]. In this paper, we use this approach to compute the partition function of a binary fluid mixture (carbon dioxide + methane); this allows us to obtain the Helmholtz free energy (F) via F = -k(B)T ln Q and the Gibbs free energy (G) via G = F + pV. We then utilize G to obtain the coexisting mole fraction curves. The chemical potential of each species is also obtained. At the vapor-liquid equilibrium condition, the chemical potential of methane significantly increases, while that of carbon dioxide slightly decreases, as the pressure increases along an isotherm. Since Q is obtained from the density of states, which is independent of the temperature, equilibrium thermodynamic properties at any condition can be obtained by varying the total composition and volume of the system. Our methodology can be adapted to explore the free energies of other binary mixtures in general and of those containing CO(2) in particular. Since the method gives access to the free energy and chemical potentials, it will be useful in many other applications.

Gibbs ensemble Monte Carlo simulations of binary mixtures of methane, difluoromethane, and carbon dioxide.

Gibbs ensemble Monte Carlo simulations were used to study the vapor-liquid equilibrium of binary mixtures of carbon dioxide + methane and carbon dioxide + difluoromethane. The potential forcefields we employ are all atomistic models, and have not previously been mixed together to study the vapor-liquid equilibrium of the binary mixtures. In addition, we characterize the microscopic structure of these liquid mixtures. In carbon dioxide + methane at 230 K and 56 bar, the microscopic structure of carbon dioxide in the mixture is the same as that in the pure liquid. In carbon dioxide + difluoromethane at 283 K and 56 bar, the presence of carbon dioxide does not noticeably perturb the liquid structure of difluoromethane, but the structure of carbon dioxide is subtly changed, due to a strong interaction between it and difluoromethane. The simulations in the isobaric-isothermal (NPT) ensemble agree well with the experimental data, except at the two extreme regions of the pressure range. The good agreement of most simulated state points with experimental data encourages one to develop more accurate potentials for predicting the thermodynamic properties of these systems as well as other complicated systems, which are less amenable to measurement by experiment.

Microscopic structure of liquid 1-1-1-2-tetrafluoroethane (R134a) from Monte Carlo simulation

1-1-1-2-tetrafluoroethane (R134a) is one of the most commonly used refrigerants. Its thermophysical properties are important for evaluating the performance of refrigeration cycles. These can be obtained via computer simulation, with an insight into the microscopic structure of the liquid, which is not accessible to experiment. In this paper, vapour-liquid equilibrium properties of R134a and its liquid microscopic structure are investigated using coupled-decoupled configurational-bias Monte Carlo simulation in the Gibbs ensemble, with a recent potential [J. Phys. Chem. B 2009, 113, 178]. We find that the simulations agree well with the experimental data, except at the vicinity of the critical region. Liquid R134a packs like liquid argon, with a coordination number in the first solvation shell of 12 at 260 K. The nearest neighbours prefer to be localized in three different spaces around the central molecule, in such a manner that the dipole moments are in a parallel alignment. Analysis of the pair interaction energy shows clear association of R134a molecules, but no evidence for C-HF type hydrogen bonding is found. The above findings should be of relevance to a broad range of fluoroalkanes.

Density of States Partitioning Method for Calculating the Free Energy of Solids

We propose a new simulation method, which combines a cage model and a density of states partitioning technique, to compute the free energy of an arbitrary solid. The excess free energy is separated into two contributions, noninteracting and interacting. The excess free energy of the noninteracting solid is computed by partitioning its geometrical configuration space with respect to the ideal gas. This quantity depends on the lattice type and the number of molecules. The excess free energy of the interacting solid, with respect to the noninteracting solid, is calculated using density of states partitioning and a cage model. The cage model is better than the cell model in that it has a smaller configuration space and better represents the equilibrium distribution of solid configurations. Since the partition function (and hence free energy) is obtained from the density of states, which is independent of the temperature, equilibrium thermodynamic properties at any condition can be obtained by varying the density. We illustrate our method in the context of the free energy of dry ice.

First principles predictions of thermophysical properties of refrigerant mixtures

We present pair potentials for fluorinated methanes and their dimers with CO(2) based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO(2) without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH(3)F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH(2)F(2) and CO(2) is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.

Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins.

The calculation of the electronic circular dichroism (CD) spectra of the oxidized form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multireference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimized in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures, it is shown that the intensity of this band is sensitive to the nonplanarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

Calculation of high-order virial coefficients for the square-well potential

Accurate virial coefficients B_{N}(λ,ɛ) (where ɛ is the well depth) for the three-dimensional square-well and square-step potentials are calculated for orders N=5-9 and well widths λ=1.1-2.0 using a very fast recursive method. The efficiency of the algorithm is enhanced significantly by exploiting permutation symmetry and by storing integrands for reuse during the calculation. For N=9 the storage requirements become sufficiently large that a parallel algorithm is developed. The methodology is general and is applicable to other discrete potentials. The computed coefficients are precise even near the critical temperature, and thus open up possibilities for analysis of criticality of the system, which is currently not accessible by any other means.