New Algorithms for Global Optimization and Reaction Path Determination.

We present new schemes to improve the convergence of an important global optimization problem and to determine reaction pathways (RPs) between identified minima. Those methods have been implemented into the CAST program (Conformational Analysis and Search Tool). The first part of this chapter shows how to improve convergence of the Monte Carlo with minimization (MCM, also known as Basin Hopping) method when applied to optimize water clusters or aqueous solvation shells using a simple model. Since the random movement on the potential energy surface (PES) is an integral part of MCM, we propose to employ a hydrogen bonding-based algorithm for its improvement. We show comparisons of the results obtained for random dihedral and for the proposed random, rigid-body water molecule movement, giving evidence that a specific adaption of the distortion process greatly improves the convergence of the method. The second part is about the determination of RPs in clusters between conformational arrangements and for reactions. Besides standard approaches like the nudged elastic band method, we want to focus on a new algorithm developed especially for global reaction path search called Pathopt. We started with argon clusters, a typical benchmark system, which possess a flat PES, then stepwise increase the magnitude and directionality of interactions. Therefore, we calculated pathways for a water cluster and characterize them by frequency calculations. Within our calculations, we were able to show that beneath local pathways also additional pathways can be found which possess additional features.

First principles transport coefficients and reaction rates of Ar2(+) ions in argon for cold plasma jet modeling.

Momentum-transfer collision cross-sections and integral collision cross-sections for the collision-induced dissociation are calculated for collisions of ionized argon dimers with argon atoms using a nonadiabatic semiclassical method with the electronic Hamiltonian calculated on the fly via a diatomics-in-molecules semiempirical model as well as inverse-method modeling based on simple isotropic rigid-core potential. The collision cross-sections are then used in an optimized Monte Carlo code for evaluations of the Ar 2 (+) mobility in argon gas, longitudinal diffusion coefficient, and collision-induced dissociation rates. A thorough comparison of various theoretical calculations as well as with available experimental data on the Ar 2 (+) mobility and collision cross-sections is performed. Good agreement is found between both theoretical approaches and the experiment. Analysis of the role of inelastic processes in Ar 2 (+)/Ar collisions is also provided.

Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties.

Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank the performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.

Innovative approach for benzene degradation using hybrid surface/packed-bed discharge plasmas.

An innovative plasma reactor, which generates hybrid surface/packed-bed discharge (HSPBD) plasmas, was employed for the degradation of benzene. The HSPBD reactor was found to display remarkably better benzene degradation, mineralization, and energy performance than surface or packed-bed discharge reactors alone. The degradation efficiency, CO2 selectivity, and energy yield in the HSPBD reactor were 21%, 11%, and 3.9 g kWh-1 higher, respectively, than in a surface discharge reactor and 30%, 21%, and 5.5 g kWh-1 higher, respectively, than in a packed-bed discharge reactor operated at 280 J L-1. Particularly, the benzene degradation in the HSPBD reactor exhibited an unambiguous synergistic enhancement rather than a simple additive effect using the surface discharge and packed-bed discharge reactors. Moreover, in the HSPBD reactor, the formation of byproducts, such as NO2, was suppressed, while O3 was promoted. The use of N2 as the carrier gas was found to be effective for benzene degradation because of the fast reaction rate of N2(A3∑u+) with benzene, and oxygen species derived from the dissociation of O2 were found to be significant in the mineralization process. Thus, the addition of O2 to N2 allows for efficient degradation of benzene, and the optimized amount of O2 was determined to be 3%.

Finite temperature path integral Monte Carlo simulations of structural and dynamical properties of Ar(N)-CO2 clusters.

We report finite temperature quantum mechanical simulations of structural and dynamical properties of Ar(N)-CO(2) clusters using a path integral Monte Carlo algorithm. The simulations are based on a newly developed analytical Ar-CO(2) interaction potential obtained by fitting ab initio results to an anisotropic two-dimensional Morse/Long-range function. The calculated distributions of argon atoms around the CO(2) molecule in Ar(N)-CO(2) clusters with different sizes are consistent to the previous studies of the configurations of the clusters. A first-order perturbation theory is used to quantitatively predict the CO(2) vibrational frequency shift in different clusters. The first-solvation shell is completed at N = 17. Interestingly, our simulations for larger Ar(N)-CO(2) clusters showed several different structures of the argon shell around the doped CO(2) molecule. The observed two distinct peaks (2338.8 and 2344.5 cm(-1)) in the υ(3) band of CO(2) may be due to the different arrangements of argon atoms around the dopant molecule.

Assessment of a chair-side argon-based non-thermal plasma treatment on the surface characteristics and integration of dental implants with textured surfaces.

The biomechanical effects of a non-thermal plasma (NTP) treatment, suitable for use in a dental office, on the surface character and integration of a textured dental implant surface in a beagle dog model were evaluated. The experiment compared a control treatment, which presented an alumina-blasted/acid-etched (AB/AE) surface, to two experimental treatments, in which the same AB/AE surface also received NTP treatment for a period of 20 or 60 s per implant quadrant (PLASMA 20' and PLASMA 60' groups, respectively). The surface of each specimen was characterized by electron microscopy and optical interferometry, and surface energy and surface chemistry were determined prior to and after plasma treatment. Two implants of each type were then placed at six bilateral locations in 6 dogs, and allowed to heal for 2 or 4 weeks. Following sacrifice, removal torque was evaluated as a function of animal, implant surface and time in vivo in a mixed model ANOVA. Compared to the CONTROL group, PLASMA 20' and 60' groups presented substantially higher surface energy levels, lower amounts of adsorbed C species and significantly higher torque levels (p=.001). Result indicated that the NTP treatment increased the surface energy and the biomechanical fixation of textured-surface dental implants at early times in vivo.

Development of equations for differential and integral enthalpy change of adsorption for simulation studies.

We present equations to calculate the differential and integral enthalpy changes of adsorption for their use in Monte Carlo simulation. Adsorption of a system of N molecules, subject to an external potential energy, is viewed as one of transferring these molecules from a reference gas phase (state 1) to the adsorption system (state 2) at the same temperature and equilibrium pressure (same chemical potential). The excess amount adsorbed is the difference between N and the hypothetical amount of gas occupying the accessible volume of the system at the same density as the reference gas. The enthalpy change is a state function, which is defined as the difference between the enthalpies of state 2 and state 1, and the isosteric heat is defined as the negative of the derivative of this enthalpy change with respect to the excess amount of adsorption. It is suitable to determine how the system behaves for a differential increment in the excess phase adsorbed under subcritical conditions. For supercritical conditions, use of the integral enthalpy of adsorption per particle is recommended since the isosteric heat becomes infinite at the maximum excess concentration. With these unambiguous definitions we derive equations which are applicable for a general case of adsorption and demonstrate how they can be used in a Monte Carlo simulation. We apply the new equations to argon adsorption at various temperatures on a graphite surface to illustrate the need to use the correct equation to describe isosteric heat of adsorption.

Monte-Carlo multiscale simulation study of argon adsorption/desorption hysteresis in mesoporous heterogeneous tubular pores like MCM-41 or oxidized porous silicon.

In a recent paper [J. Chem. Phys. 2007, 127, 154701] a multiscale approach was introduced which allowed calculation of adsorption/desorption hysteresis for fluid confined in a single mesoporous, heterogeneous tubular pore. The main interest in using such an approach is that it allows one to reconcile a molecular simulation approach generally limited to the nanometer scale (atomistic description of the confined fluid and pore roughness) with the much larger scale (micrometer) relevant to understand the complexity of adsorption/desorption hysteresis (the numerous metastable states in the hysteresis loop are a consequence of the large-scale disorder in the porous material). In this paper, this multiscale approach is used to study adsorption phenomena in mesoporous models made of a collection of disordered, noninterconnected tubular pores, as MCM-41 or porous silicon. A double distribution is introduced: one to characterize the disorder in a given pore, and the other to characterize the disorder between the pores. We consider two distribution shapes: Gaussian and uniform truncated and two cases of pores open at one or both ends. These models are expected to cover a wide variety of real materials made of independent pores, as MCM-41 and oxidized porous silicon. A large variety of hysteresis shapes is obtained, ranging from almost parallel adsorption/desorption branches typical of MCM-41 adsorption to triangular hysteresis typical of porous silicon. The structure of the metastable states inside the hysteresis (scanning adsorption/desorption curves) is also examined. The results are expected to be useful to experimentalists who want to infer pore structure and level of disorder from experimental adsorption/desorption experiments.

Validating a MCNPX model of Mg(Ar) and TE(TE) ionisation chambers exposed to 60CO gamma rays.

For an accurate determination of the absorbed doses in complex radiation fields (e.g. mixed neutron-gamma fields), a better interpretation of the response of ionisation chambers is required. This study investigates a model of the ionisation chambers using a different approach, analysing the collected charge per minute as a response of the detector instead of the dose. The MCNPX Monte Carlo code is used. In this paper, the model is validated using a well-known irradiation field only: a (60)Co source. The detailed MCNPX models of a Mg(Ar) and TE(TE) ionisation chamber is investigated comparing the measured charge per minute obtained free-in-air and in a water phantom with the simulated results. The difference between the calculations and the measurements for the TE(TE) chamber is within +/-2% whereas for the Mg(Ar) chamber is around +7%. The systematic discrepancy in the case of Mg(Ar) chamber is expected to be caused by an overestimation of the sensitive volume.

Theory for the solvation of nonpolar solutes in water.

We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water.

Photoneutron production of a Siemens Primus linear accelerator studied by Monte Carlo methods and a paired magnesium and boron coated magnesium ionization chamber system.

When radiotherapy with photon energies greater than 10 MV is performed neutrons contaminate the photon beam. In this paper the neutron contamination of the 15 MV photon mode of the Siemens Primus accelerator was studied. The Monte Carlo code MCNPX was used for the description of the treatment head and treatment room. The Monte Carlo results were verified by studying the photon depth dose curve and beam profiles in a water phantom. After these verifications the locations of neutron production were studied and the neutron source spectrum and strength were calculated. The neutron response of the paired Mg/Ar and MgB/Ar ionization chamber system was calculated and experimentally verified for two experimental set-ups. The paired chamber system allowed us to measure neutrons inside the field borders and allowed rapid and point wise measurement in contrast to other methods of neutron detection.

Adsorption of CO2 on oxidized, defected, hydrogen and oxygen covered rutile (1 x 1)-TiO2(110).

Presented are initial, S(0) and coverage, Theta, dependent S(Theta), adsorption probability measurements of CO(2) as a function of impact energy, E(i) = 0.12-1.3 eV, adsorption temperature, T(s) = 85-300 K, hydrogen and oxygen pre-exposure, as well as density of defects, Gamma, as varied by annealing (T = 600-900 K) and Ar(+) ion sputtering (dose chi(Ar) at 600 eV at 85 K) of a rutile (1 x 1) TiO(2)(110) surface. The defect densities were qualitatively characterized by thermal desorption spectroscopy (TDS) of CO(2). The CO(2) TDS curves consisted of two structures that can be assigned to adsorption on pristine and oxygen vacancy sites, in agreement with earlier studies. S(0) decreased linearly with E(i) and was independent of T(s). The adsorption dynamics were dominated by the effect of precursor states leading to Kisliuk-like shapes over the E(i) and T(s) range studied. Oxygen vacancy sites reduced S(0) of CO(2). Preadsorbed oxygen blocked preferentially defect sites, which led to an increase in S(0). Hydrogen preadsorption results in physical site blocking with decreased S(0) as H-preexposure increased, while the shape of S(Theta) curves was conserved. In contrast to oxygen, hydrogen does not adsorb preferentially on defect sites. The adsorption probability data were parameterized by analytic functions (Kisliuk model) and by Monte Carlo simulations (MCSs).

Phase changes in Lennard-Jones mixed clusters with composition Ar(n)Xe(6-n) (n=0,1,2).

We have carried out parallel tempering Monte Carlo calculations on the binary six-atom mixed Lennard-Jones clusters, Ar(n)Xe(6-n) (n=0,1,2). We have looked at the classical configurational heat capacity C(V)(T) as a probe of phase behavior. All three clusters show a feature in the heat capacity in the region of 15-20 K. The Ar(2)Xe(4) cluster exhibits a further peak in the heat capacity near 7 K. We have also investigated dynamical properties of the Ar(2)Xe(4) cluster as a function of temperature using molecular dynamics. We report the interbasin isomerization rate and the bond fluctuation parameter obtained from these calculations. At 7 K, the isomerization rate is on the order of 0.01 ns(-1); at 20 K, the isomerization rate is greater than 10 ns(-1). Furthermore, at 7 K, the bond fluctuation parameter is less than 3%; at 20 K, it is in the range of 10-15% (depending on the sampling time used). Using this information, together with Monte Carlo quenching data, we assign the 15-20 K feature in the heat capacity to a solid-liquid phase change and the 7-K peak to a solid-solid phase change. We believe this is the smallest Lennard-Jones cluster system yet shown to exhibit solid-solid phase change behavior.

An ab initio and cryospectroscopic study of the hydrogen chloride and boron trifluoride complexes of cyclopropene.

Mid-infrared spectra of cyclopropene (c-C3H4) mixtures with HCl or BF3, dissolved in liquefied argon and in liquefied nitrogen have been examined. Evidence was found for the formation of two different isomers of the 1:1 complexes: a pi-type complex in which the interaction occurs with the pi-bond of cyclopropene, and a sigma-type complex in which the electron acceptors interact with one of the CC single bonds. At lower temperatures, indications for the formation of a 1:2 chain-type complex were found. Using spectra recorded between 90 and 124 K in liquid argon, the complexation enthalpies for the pi- and sigma-complexes with HCl were determined to be -8.8(3) and -7.9(3) kJ mol-1, respectively. For the pi-complex with BF3 a value of -7.4(3)kJ mol-1 was found. Structural and spectral information on the 1:1 complexes was obtained from B3LYP/6-311++G(d,p) and MP2(FC)/6-31+G(d) calculations. Using Free Energy Perturbation Monte Carlo simulations to calculate the solvent influences, and statistical thermodynamics to account for zero-point vibrational and thermal contributions, the solution enthalpies were transformed into complexation energies with values of -15.5(6) and -13.8(8) kJ mol-1 for the pi- and sigma-isomers of c-C3H4.HCl, respectively, and of -12.7(8) kJ mol-1 for the pi-type BF3 complex.

A cryosolution infrared and ab initio study of the van der Waals complexes of cyclopentene with hydrogen chloride and boron trifluoride.

The formation of weak molecular complexes of cyclopentene with HCl and BF3, dissolved in liquid argon is investigated using infrared spectroscopy. Evidence is found for the formation of 1:1 complexes in which the Lewis acid under study binds to the CC double bond. At higher concentrations of HCl, weak absorption bands due to 1:2 species are also observed. From spectra recorded at different temperatures between 92 and 127 K, the complexation enthalpies for CP.HCl and CP.BF3 are determined to be -9.5(3) and -16.1(9) kJ mol-1, while for CP.(HCl)2 a value of -17.0(6) kJ mol-1 is obtained. For the 1:1 and 1:2 complexes, structural and spectral information is obtained from ab initio calculations at the MP2/6-31+G(d) level. Using free energy perturbation Monte Carlo simulations to calculate the solvation enthalpies and statistical thermodynamics to account for zero-point vibrational and thermal contributions, the complexation energies for CP.HCl and CP.(HCl)2 are estimated from the experimental complexation enthalpies to be -17.4(14) and -34.0(20) kJ mol-1, while the value for CP.BF3 was derived to be -23.4(22) kJ mol-1. The experimental complexation energies are compared with the theoretical values derived from the MP2/6-31+G(d) potential energy surfaces and with single point energies calculated at the MP2/6-311++G(3df,2pd) level.

Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy S and free energy F by analyzing Boltzmann samples obtained by Monte Carlo or molecular dynamics techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). At each step of the process the system is divided into two parts, the already treated molecules (the "past"), which are fixed, and the as yet unspecified (mobile) "future" molecules. Obtaining the TP exactly requires calculating partition functions over all positions of the future molecules in the presence of the frozen past, thus it is customary to invoke various approximations to best represent these quantities. In a recent publication [Proc. Natl. Acad. Sci. USA 101, 9235 (2004)] we developed a version of HS called complete HSMC, where each TP is calculated from an MC simulation involving all of the future molecules (the complete future); the method was applied very successfully to Lennard-Jones systems (liquid argon) and a box of TIP3P water molecules. In its basic implementation the method provides lower and upper bounds for F, where the latter can be evaluated only for relatively small systems. Here we introduce a new expression for an upper bound, which can be evaluated for larger systems. We also propose a new exact expression for F and verify its effectiveness. These free energy functionals lead to significantly improved accuracy (as applied to the liquid systems above) which is comparable to our thermodynamic integration results. We formalize and discuss theoretical aspects of HSMC that have not been addressed in previous studies. Additionally, several functionals are developed and shown to provide the free energy through the analysis of a single configuration.