Solvent Degrees Of Freedom Research Articles

Incorporating Electrolyte Correlation Effects into Variational Models of Electrochemical Interfaces.

We propose a way for obtaining a classical free energy density functional for electrolytes based on a first-principle many-body partition function. Via a one-loop expansion, we include coulombic correlations beyond the conventional mean-field approximation. To examine electrochemical interfaces, we integrate the electrolyte free energy functional into a hybrid quantum-classical model. This scheme self-consistently couples electronic, ionic, and solvent degrees of freedom and incorporates electrolyte correlation effects. The derived free energy functional causes a correlation-induced enhancement in interfacial counterion density and leads to an overall increase in capacitance. This effect is partially compensated by a reduction of the dielectric permittivity of interfacial water. At larger surface charge densities, ion crowding at the interface stifles these correlation effects. While scientifically intriguing already at planar interfaces, we anticipate these correlation effects to play an essential role for electrolytes in nanoconfinement.

Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments.

In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.

Structure ordering and glass transition in size-asymmetric ternary mixtures of hard spheres: Variation from fragile to strong glasses.

We investigate the structure and activated dynamics of a binary mixture of colloidal particles dispersed in a solvent of much smaller-sized particles. The solvent degrees of freedom are traced out from the grand partition function of the colloid-solvent mixture which reduces the system from ternary to effective binary mixture of colloidal particles. In the effective binary mixture colloidal particles interact via effective potential that consists of bare potential plus the solvent-induced interaction. Expressions for the effective potentials and pair correlation functions are derived. We used the result of pair correlation functions to determine the number of particles in a cooperatively reorganizing cluster (CRC) in which localized particles form "long-lived" nonchemical bonds with the central particle. For an event of relaxation to take place these bonds have to reorganize irreversibly, the energy involved in the processes is the effective activation energy of relaxation. Results are reported for hard sphere colloidal particles dispersed in a solvent of hard sphere particles. Our results show that the concentration of solvent can be used as a control parameter to fine-tune the microscopic structural ordering and the size of CRC that governs the glassy dynamics. We show that a small variation in the concentration of solvent creates a bigger change in the kinetic fragility which highlights a wide variation in behavior, ranging from fragile to strong glasses. We conclude that the CRC which is determined from the static pair correlation function and the fluctuations embedded in the system is probably the sole player in the physics of glass transition.

Coarse-grained Hamiltonian and effective one component theory of colloidal suspensions

We develop a theory to trace out the solvent degrees of freedom from the grand partition function of colloid-solvent mixtures. Our approach to coarse-graining is based on density functional formalism of density profile and the grand thermodynamic potential of solvent. The solvent-induced interaction which is many-body in character is expressed in terms of two functionals; one that couples the solvent to the colloidal density distribution and the second represents the density–density correlation function of the solvent. The nature, strength, and range of the potential depend on these functionals and therefore on the thermodynamic state of the solvent. The solvent-induced contribution to free energy functional is also derived. A self-consistent procedure is developed to calculate the effective potential between colloidal particles, colloid-solvent, and colloid-colloid correlation functions. The theory is used to investigate both additive and nonadditive binary hard-sphere mixtures. Results are reported for the two systems for several values of packing fractions ηb and ηs and particles diameter ratio q=σsσb where symbols b and s refer to colloid and solvent, respectively. Several interesting features are found: The short-range attractive part of the potential shows non-monotonic dependence on ηb; when ηb is increased from zero, initially the potential becomes more attractive but beyond a certain value of ηb that depends on q, the attraction starts weakening. The repulsive peaks formed at R∼(1+12nq) where R is a distance between centers of colloidal particles expressed in units of σb and n is an integer, become stronger on increasing ηb. These results show that many-body contribution to the effective potential depends in a subtle way on packing fractions ηb,ηs, size ratio q, and on nature of the interaction model and makes a non-negligible contribution to the coarse-grained Hamiltonian.

Salt Enrichment and Dynamics in the Interface of Supercooled Aqueous Droplets.

The interconversion reaction of NaCl between the contact-ion pair (CIP) and the solvent-separated ion pair (SSIP) as well as the free-ion state in cold droplets has not yet been investigated. We report direct computational evidence that the lower is the temperature, the closer to the surface the ion interconversion reaction takes place. In supercooled droplets the enrichment of the subsurface in salt becomes more evident. The stability of the SSIP relative to the CIP increases as the ion-pairing is transferred toward the droplet's outer layers. In the free-ion state, where the ions diffuse independently in the solution, the number density of Cl- shows a broad maximum in the interior in addition to the well-known maximum in the surface. In the study of the reaction dynamics, we find a weak coupling between the interionic NaCl distance reaction coordinate and the solvent degrees of freedom, which contrasts with the diffusive crossing of the free energy barrier found in bulk solution modeling. The H2O self-diffusion coefficient is found to be at least an order of magnitude larger than that in the bulk solution. We propose to exploit the enhanced surface ion concentration at low temperature to eliminate salts from droplets in native mass spectrometry ionization methods.

Solution and Interface Structure and Dynamics in Geochemistry: Gateway to Link Elementary Processes to Mineral Nucleation and Growth

Our understanding of the process of mineral nucleation is starting to evolve from the solely thermodynamical aspects in classical nucleation theory toward a mechanistic study of reactions influenced by solvation structures of ions and their dynamics. A knowledge of how these atomic and molecular interactions respond to changing solution composition and/or the nature of an interface will form a fundamental foundation to understand rate-limiting reactions and processes for nucleation and growth. Here, we review recent advances from multidisciplinary experimental and computational approaches of the structure and dynamics of aqueous solutions and mineral–liquid interfaces that will influence rates of nucleation (and growth behavior) both homogeneously in aqueous solutions and heterogeneously at mineral–liquid interfaces. These processes include structure (and extent) of solute clustering, solvent degrees of freedom, and the presence of noninnocent charge-balancing ions, all of which can drive the selectivity and exert control over nucleation mechanisms. Similar controlling reactions can also occur at interfaces with the added complexities of how solute ions interact with and assemble on surface sites and use different mechanisms from bulk solutes, such as lateral solvent exchanges between distinct surface sites. To gain a predictive understanding of nucleation chemistry, we emphasize several key knowledge gaps that will need to be addressed in this field and highlight the importance of combining computations and experiments.

Implicit-solvent coarse-grained modeling for polymer solutionsviaMori-Zwanzig formalism

We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system. In particular, tens to hundreds of bonded polymer atoms (or Lennard-Jones beads) are coarse-grained as one CG particle, and the solvent degrees of freedom are eliminated. The dynamics of the CG system is governed by the generalized Langevin equation (GLE) derived via the Mori-Zwanzig formalism, by which the CG variables can be directly and rigorously linked to the microscopic dynamics generated by molecular dynamics (MD) simulations. The solvent-mediated dynamics of polymers is modeled by the non-Markovian stochastic dynamics in GLE, where the memory kernel can be computed from the MD trajectories. To circumvent the difficulty in direct evaluation of the memory term and generation of colored noise, we exploit the equivalence between the non-Markovian dynamics and Markovian dynamics in an extended space. To this end, the CG system is supplemented with auxiliary variables that are coupled linearly to the momentum and among themselves, subject to uncorrelated Gaussian white noise. A high-order time-integration scheme is used to solve the extended dynamics to further accelerate the CG simulations. To assess, validate, and demonstrate the established implicit-solvent CG modeling, we have applied it to study four different types of polymers in solution. The dynamic properties of polymers characterized by the velocity autocorrelation function, diffusion coefficient, and mean square displacement as functions of time are evaluated in both CG and MD simulations. Results show that the extended dynamics with auxiliary variables can construct arbitrarily high-order CG models to reproduce dynamic properties of the reference microscopic system and to characterize long-time dynamics of polymers in solution.

Efficient Implicit Solvation Method for Full Potential DFT.

With the advent of efficient electronic structure methods, effective continuum solvation methods have emerged as a way to, at least partially, include solvent effects into simulations without the need for expensive sampling over solvent degrees of freedom. The multipole moment expansion (MPE) model, while based on ideas initially put forward almost 100 years ago, has recently been updated for the needs of modern electronic structure calculations. Indeed, for an all-electron code relying on localized basis sets and-more importantly-a multipole moment expansion of the electrostatic potential, the MPE method presents a particularly cheap way of solving the macroscopic Poisson equation to determine the electrostatic response of a medium surrounding a solute. In addition to our implementation of the MPE model in the FHI-aims electronic structure theory code [ Blum , V. ; Comput. Phys. Commun. 2009 , 180 , 2175 - 2196 , DOI: 10.1016/j.cpc.2009.06.022 ], we describe novel algorithms for determining equidistributed points on the solvation cavity-defined as a charge density isosurface-and the determination of cavity surface and volume from just this collection of points and their local density gradients. We demonstrate the efficacy of our model on an analytically solvable test case, against high-accuracy finite-element calculations for a set of ≈140000 2D test cases, and finally against experimental solvation free energies of a number of neutral and singly charged molecular test sets [ Andreussi , O. ; J. Chem. Phys. 2012 , 136 , 064102 , DOI: 10.1063/1.3676407 ; Marenich , A. V. ; Minnesota Solvation Database , Version 2012; University of Minnesota : Minneapolis, MN, USA , 2012 . ]. In all test cases we find that our MPE approach compares very well with given references at computational overheads < 20% and sometimes much smaller compared to a plain self-consistency cycle.

McMillan-Mayer theory of solutions revisited: simplifications and extensions.

McMillan and Mayer (MM) proved two remarkable theorems in their paper on the equilibrium statistical mechanics of liquid solutions. They first showed that the grand canonical partition function for a solution can be reduced to one with an effectively solute-only form, by integrating out the solvent degrees of freedom. The total effective solute potential in the effective solute grand partition function can be decomposed into components which are potentials of mean force for isolated groups of one, two, three, etc., solute molecules. Second, from the first result, now assuming low solute concentration, MM derived an expansion for the osmotic pressure in powers of the solute concentration, in complete analogy with the virial expansion of gas pressure in powers of the density at low density. The molecular expressions found for the osmotic virial coefficients have exactly the same form as the corresponding gas virial coefficients, with potentials of mean force replacing vacuum potentials. In this paper, we restrict ourselves to binary liquid solutions with solute species A and solvent species B and do three things: (a) By working with a semi-grand canonical ensemble (grand with respect to solvent only) instead of the grand canonical ensemble used by MM, and avoiding graphical methods, we have greatly simplified the derivation of the first MM result, (b) by using a simple nongraphical method developed by van Kampen for gases, we have greatly simplified the derivation of the second MM result, i.e., the osmotic pressure virial expansion; as a by-product, we show the precise relation between MM theory and Widom potential distribution theory, and (c) we have extended MM theory by deriving virial expansions for other solution properties such as the enthalpy of mixing. The latter expansion is proving useful in analyzing ongoing isothermal titration calorimetry experiments with which we are involved. For the enthalpy virial expansion, we have also changed independent variables from semi-grand canonical, i.e., fixed {N(A), μ(B), V, T}, to those relevant to the experiment, i.e., fixed {N(A), N(B), p, T}, where μ denotes chemical potential, N the number of molecules, V the volume, p the pressure, and T the temperature.

Cluster formation in fluids with competing short-range and long-range interactions

We investigate the low density behaviour of fluids that interact through a short-ranged attraction together with a long-ranged repulsion (SALR potential) by developing a molecular thermodynamic model. The SALR potential is a model of effective solute interactions where the solvent degrees of freedom are integrated-out. For this system, we find that clusters form for a range of interaction parameters where attractive and repulsive interactions nearly balance, similar to micelle formation in aqueous surfactant solutions. We focus on systems for which equilibrium behaviour and liquid-like clusters (i.e., droplets) are expected, and find in addition a novel coexistence between a low density cluster phase and a high density cluster phase within a very narrow range of parameters. Moreover, a simple formula for the average cluster size is developed. Based on this formula, we propose a non-classical crystal nucleation pathway whereby macroscopic crystals are formed via crystal nucleation within microscopic precursor droplets. We also perform large-scale Monte Carlo simulations, which demonstrate that the cluster fluid phase is thermodynamically stable for this system.

Entropy in specificity and thermodynamics of binding.

Entropy is an elusive and somehow non-intuitive concept. Nevertheless, entropy governs spontaneous thermodynamic processes as important contribution to Gibbs Free Energy. Information theory defines Shannon entropy as a measure for uncertainty. In the context of protein binding the inherent link between flexibility, thus conformational entropy, and substrate specificity is discussed. Substrate promiscuity of proteases is quantified as cleavage entropy correlating local binding site flexibility directly with substrate readout. Caspases are examined as example protease family, where active site dynamics play a major role in mediating substrate specificity. Direct comparison of entropy in substrate data allows highlighting previously unexpected similarities in substrate recognition in proteases. Promiscuous binding to several protease targets demonstrates the emerging importance of quantitative studies on binding specificity. Shannon entropy applied to probability densities is used to rationalize ordering or disordering by binding processes. We have developed a data-driven method to reconstruct probability densities from discrete sampling by computer simulations. Application to solvent degrees of freedom leads to excellent correlation with experimental data.

On the coupling of solvent characteristics to the electronic structure of solute molecules

We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.

Building Markov state models with solvent dynamics

BackgroundMarkov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dynamics. However, the solvent information in molecular simulations are often ignored in current methods, because of the large number of solvent molecules in a system and the indistinguishability of solvent molecules upon their exchange.MethodsWe present a solvent signature that compactly summarizes the solvent distribution in the high-dimensional data, and then define a distance metric between different configurations using this signature. We next incorporate the solvent information into the construction of Markov state models and present a fast geometric clustering algorithm which combines both the solute-based and solvent-based distances.ResultsWe have tested our method on several different molecular dynamical systems, including alanine dipeptide, carbon nanotube, and benzene rings. With the new solvent-based signatures, we are able to identify different solvent distributions near the solute. Furthermore, when the solute has a concave shape, we can also capture the water number inside the solute structure. Finally we have compared the performances of different Markov state models. The experiment results show that our approach improves the existing methods both in the computational running time and the metastability.ConclusionsIn this paper we have initiated an study to build Markov state models for molecular dynamical systems with solvent degrees of freedom. The methods we described should also be broadly applicable to a wide range of biomolecular simulation analyses.

Non-continuum solvation using the EC-RISM method applied to predict tautomer ratios, pKa and enantiomeric excess of alkylation reactions

The three-dimensional “reference interaction site model” (3D-RISM) integral equation theory is a statistical-mechanical approach to predict liquid state structural and thermodynamic features. It is based on approximate solute-solvent correlation functions to be computed on a 3D grid as a function of the interaction potential between the solute and the solvent sites, circumventing the need of costly sampling of explicit solvent degrees of freedom. In combination with quantum-chemical calculations within the embedded cluster (EC-)RISM framework [1] the theory allows for studying chemical reactions in solution with an accuracy not reached by traditional continuum solvation methods. In particular, it improves upon dielectric continuum solvation by taking solvent granularity into account and also provides a means towards physically cavity formation and dispersion free Energies without introducing artificial boundaries and empirically fitted radii. We outline the general framework and show application examples from pKa and tautomeric ratio estimation [2] as well as enantiomeric excess prediction for stereoselective alkylation reactions in organic solvent.

Dynamics of Methionine Ligand Rebinding in Cytochrome c

Geminate recombination of the methionine ligand to the heme iron in ferrous cytochrome c protein following photodissociation displays rich kinetics. It is of particular interest to develop an understanding of fast and slow rebinding time scales, observed in experimental studies, in terms of features of the underlying complex energy landscape. The classical empirical force field in the heme pocket has been extended by incorporating ab initio potential energy surface calculations representing the ground singlet state and quintet state associated with methionine bond breaking and rebinding. An algorithm based on the Landau-Zener nonadiabatic transition theory has been employed to model the electronic surface hopping between two spin states during the process of ligand dissociation and recombination. Multiple conformational substates of the dissociated methionine ligand are found to participate in the reaction dynamics. Varying time scales for interconversion between substates lead to a mechanism elucidating the fast and slow rebinding time scales. The reaction system may be understood in terms of a two-dimensional reaction coordinate distinctly separated from the coupled bath of surrounding protein and solvent degrees of freedom. Insights into the reaction dynamics provided by this study lead to suggestions for future experiments to further probe the role of dynamic heterogeneity in the kinetics of ligand-protein binding.

Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride

The entropic driving forces of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride (BmimCl) are investigated via molecular dynamics simulations and the two-phase thermodynamic model. An atomistic model of cellulose was simulated at a dissociated state and a microfibril state to represent dissolution. The calculated values of entropy and internal energy changes between the two states inform the interplay of energetic and entropic driving forces in cellulose dissolution. In both water and BmimCl, we found that the entropy associated with the solvent degrees of freedom (DOF) decreases upon cellulose dissolution. However, solvent entropy reduction in BmimCl is much smaller than that in water and counteracts the entropy gain from the solute DOF to a much lesser extent. Solvent entropy reduction in water also plays a major role in making the free energy change of cellulose dissolution unfavorable at room temperature. In BmimCl, the interaction energies between solvent molecules and glucan chains and the total entropy change both contribute favorably to the dissolution free energy of cellulose. Calculations at different temperatures in the two solvents indicate that changes in total internal energy are a good indicator of the sign of the free energy change of cellulose dissolution.

Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

The elucidation of the chemical mechanisms whereby biological molecules control, regulate and catalyze phosphoryl transfer reactions has profound implications for processes such as transcription, energy storage and transfer, cell signalling and gene regulation.[1, 2] The catalytic properties of RNA, in particular, have application in the design of new biotechnology and implications into the evolutionary origins of life itself.[3] Of primary importance to the understanding of mechanism is the characterization of the transition state for these reactions. Kinetic isotope effects (KIEs) offer one of the most powerful and sensitive experimental probes to interrogate the chemical environment of the transition state.[4-6] However, for complex reactions, theoretical methods are required to interpret the experimental measurements in terms of a detailed mechanistic model that traces the pathway from the reactant state through the transition state and into the product state.[7, 8] This paper presents experimental and computational results to characterize the mechanism of model phosphoryl transfer reactions that mimic RNA cleavage transesterification catalyzed by enzymes such as RNase A[1] as well as endonucleolytic ribozymes such as the hammerhead, hairpin, hepatitis delta virus (HDV), VS and glmS ribozymes.[9-11] Herein, secondary kinetic isotope effects are reported for the cleavage transesterification of a dinucleotide system, which, together with previously reported primary isotope effect measurements,[12, 13] represent a comprehensive characterization of isotope effects for a native (unmodified) RNA system. Scheme 1 illustrates the general mechanism for the reverse dianionic in-line methanolysis of ethylene phosphate, a model for base-catalysed RNA phosphate transesterification, with phosphoryl oxygen positions labelled in accord with their RNA counterparts. In this study, the free energy profiles for Scheme 1 were determined with density-functional quantum mechanical/molecular mechanical (QM/MM) simulations in explicit solvent.[14-17] These simulations are state-of-the-art, and take into account the dynamical fluctuations of the solute and solvent degrees of freedom in determination of the free energy profiles. In addition, adiabatic reaction energy profiles were determined with solvation effects treated implicitly with a polarizable continuum model (PCM)[18] specifically calibrated for the native and 3′ and 5′ thio-substituted compounds (Figure 1). The 3′ and 5′ thio-substituted compounds model the corresponding chemically modified RNAs that serve as valuable experimental probes of phosphoryl transfer mechanisms catalyzed by ribozymes.[19] The S5′ substitution, for example, in the HDV ribozyme serves as an enhanced leaving group that suppresses the deleterious effect of mutation of a critical cytosine residue, which has been interpreted to support its role as a general acid catalyst.[20] The energy values for stationary points of the native and thio-substituted reactions are in Table 1. Using our recently developed ab initio path-integral method based on Kleinert’s variational perturbation theory,[7, 21-23] we also calculated kinetic isotope effects, which are shown along with the most relevant experimental values for comparison in Table 2. The agreement that is achieved between the theoretical and experimental results allows a detailed mechanistic interpretation based on the theoretical models.[7, 8] Figure 1 (Color online) Comparison of density-functional QM/MM free-energy and adiabatic PCM profiles for the native reaction (top), and density-functional adiabatic PCM profiles for native and thio-substituted reactions (bottom) as a function of the difference ... Scheme 1 General reaction scheme for the (associative) reverse of dianionic in-line methanolysis of ethylene phosphate: a model for RNA phosphate transesterification under alkaline conditions. In the present work, the native reaction shown in the scheme is studied ... Table 1 Relative free energy (kcal/mol) and reaction coordinate (Δbond) values (A) computed for stationary points along the coordinate of the native and thio-substituted RNA phosphate transesterification reaction models shown in Scheme 1.[[a] ... Table 2 Primary kinetic isotope effects (KIEs) on 2′ nucleophile (18kNu) and 5′ leaving (18kLg) oxygens, and secondary KIEs on O1P (18kO1P) and O2P (18kO2P) oxygens in aqueous solution for the TS1 and TS2 transition states, along with the most ... All of the profiles calculated in this work correspond to associative (or concerted) mechanisms characterized by initial nucleophilic attack, as is typical of phosphate diesters.[6] The departure of the leaving group can be concerted with nucleophilic attack (as in the S5′ substituted reaction) or can occur in a stepwise fashion resulting in the formation of a stable pentavalent phosphorane intermediate. In the stepwise mechanism, two transition states occur: one in which nucleophilic attack occurs (TS1) and another one in which leaving group departure takes place (TS2) as indicated in Scheme 1. These transition states themselves can be characterized as either “early” or “late”, depending on the degree of P-O2′ and P-O5′ bond formation/cleavage.

Solvent Fluctuations Drive the Hole Transfer in DNA: A Mixed Quantum−Classical Study

We studied the hole transfer across adenine bridges in double-stranded DNA by means of a multiscale approach, propagating the hole in the framework of time-dependent DFT coupled to classical molecular dynamics simulation using a QM/MM scheme. The hole transfer in DNA is codetermined by the large fluctuations of site energies on the order of 0.4 eV, induced by the solvent degrees of freedom. These fluctuations lead to charge-transfer active conformations with large transfer efficiency, which are characterized by a favorable alignment of site energies along the DNA strand. This reduces the barrier for the hole transfer dramatically. Consequently, we find that a charge hopping mechanism is operative already for short bridges with fewer than four adenines, in contrast to the charge-transfer models assuming static DNA structures, where only tunneling occurs. The solvent fluctuations introduce a significant correlation between neighboring sites, enhancing the charge-transfer rate, while the fluctuation of electronic couplings has only a minor impact on the charge-transfer characteristics. Our results emphasize the importance of an accurate description of solvent effects as well as proper sampling, and it is suggested that charge transfer in DNA is gated by the dynamics of solvent.

The Role of Solvent Fluctuations in Hydrophobic Assembly

We use a coarse-grained solvent model to study the self-assembly of two nanoscale hydrophobic particles in water. We show how solvent degrees of freedom are involved in the process. By using tools of transition path sampling, we elucidate the reaction coordinates describing the assembly. In accord with earlier expectations, we find that fluctuations of the liquid-vapor-like interface surrounding the solutes are significant, in this case leading to the formation of a vapor tunnel between the two solute particles. This tunnel accelerates assembly. While considering this specific model system, the approach we use illustrates a methodology that is broadly applicable.

Mode-specific energy absorption by solvent molecules during CO2 vibrational cooling

Non-equilibrium molecular dynamics (NEMD) simulations of energy transfer from vibrationally excited CO(2) to CCl(4) and CH(2)Cl(2) solvent molecules are performed to identify the efficiency of different energy pathways into the solvent bath. Studying in detail the work performed by the vibrationally excited solute on the different solvent degrees of freedom, it is shown that vibration-to-vibration (V-V) processes are strongly dominant and controlled by those accepting modes which are close in frequency to the CO(2) bend and symmetric stretch vibration.