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January 2012

Volume 6, Issue 1

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Clusters in a mixture of an “amphiphilic” ionic liquid and a nonionic liquid: Theoretical study

Artem A. Aerov, Alexei R. Khokhlov, and Igor I. Potemkin

J. Chem. Phys. 136, 014504 (2012); http://dx.doi.org/10.1063/1.3670016 (12 pages)

Online Publication Date: 4 January 2012

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A Flory-Huggins type lattice approach is used to describe theoretically a heterogeneous mixture composed of an ionic liquid (IL) and a nonionic liquid (nIL). It is analyzed, how the behavior of the system depends on the difference in the affinities of the cations and the anions to the neutral molecules (i.e., on the “amphiphilicity” of the IL with respect to the nIL). It is proved that if the difference in the affinities is not large, two macrophases coexist in the mixture; if the difference exceeds a certain threshold value, the mixture becomes microheterogeneous: depending on its composition, it can turn either into ion clusters dispersed over the phase having low concentration of ions, or into clusters of neutral molecules dispersed over the phase having high concentration of ions. If the system is not close to the critical point, the ion clusters can be only small: the maximal ratio of their diameter to an ion diameter is of the order of ten; however, the clusters of nonionic molecules can be large, if the difference in the affinities has a certain value. It is predicted also that cavities can nucleate inside an IL, and clusters of ions can appear in a saturated vapor of an IL.
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61.20.Gy Theory and models of liquid structure
81.30.Dz Phase diagrams of other materials

Solid effect dynamic nuclear polarization and polarization pathways

Albert A. Smith, Björn Corzilius, Alexander B. Barnes, Thorsten Maly, and Robert G. Griffin

J. Chem. Phys. 136, 015101 (2012); http://dx.doi.org/10.1063/1.3670019 (16 pages)

Online Publication Date: 4 January 2012

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Using dynamic nuclear polarization (DNP)∕nuclear magnetic resonance instrumentation that utilizes a microwave cavity and a balanced rf circuit, we observe a solid effect DNP enhancement of 94 at 5 T and 80 K using trityl radical as the polarizing agent. Because the buildup rate of the solid effect increases with microwave field strength, we obtain a sensitivity gain of 128. The data suggest that higher microwave field strengths would lead to further improvements in sensitivity. In addition, the observation of microwave field dependent enhancements permits us to draw conclusions about the path that polarization takes during the DNP process. By measuring the time constant for the polarization buildup and enhancement as a function of the microwave field strength, we are able to compare models of polarization transfer, and show that the major contribution to the bulk polarization arises via direct transfer from electrons, rather than transferring first to nearby nuclei and then transferring to bulk nuclei in a slow diffusion step. In addition, the model predicts that nuclei near the electron receive polarization that can relax, decrease the electron polarization, and attenuate the DNP enhancement. The magnitude of this effect depends on the number of near nuclei participating in the polarization transfer, hence the size of the diffusion barrier, their T1, and the transfer rate. Approaches to optimizing the DNP enhancement are discussed.
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76.70.Fz Double nuclear magnetic resonance (DNMR), dynamical nuclear polarization
07.57.Pt Submillimeter wave, microwave and radiowave spectrometers; magnetic resonance spectrometers, auxiliary equipment, and techniques

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: Theory and experiments

Christoph Gögelein, Dana Wagner, Frédéric Cardinaux, Gerhard Nägele, and Stefan U. Egelhaaf

J. Chem. Phys. 136, 015102 (2012); http://dx.doi.org/10.1063/1.3673442 (12 pages)

Online Publication Date: 4 January 2012

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Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluid–solid transition and the gas–liquid coexistence curve (binodal) shift to lower temperatures and the gap between them increases. The experimentally observed trends are consistent with our theoretical predictions based on the thermodynamic perturbation theory and the Derjaguin-Landau-Verwey-Overbeek model for the lysozyme-lysozyme pair interactions. The values of the parameters describing the interactions, namely the refractive indices, dielectric constants, Hamaker constant and cut-off length, are extracted from literature or are experimentally determined by independent experiments, including static light scattering, to determine the second virial coefficient. We observe that both, glycerol and DMSO, render the potential more repulsive, while sodium chloride reduces the repulsion.
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87.15.km Protein-protein interactions
87.15.R- Reactions and kinetics
87.15.Zg Phase transitions
05.70.Ce Thermodynamic functions and equations of state
87.14.ej Enzymes
87.15.B- Structure of biomolecules

Structure and dynamics of nano-sized raft-like domains on the plasma membrane

Fernando E. Herrera and Sergio Pantano

J. Chem. Phys. 136, 015103 (2012); http://dx.doi.org/10.1063/1.3672704 (11 pages)

Online Publication Date: 5 January 2012

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Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, membrane trafficking, etc. Atomic-detail information in the nanometer∕second scale is still elusive to experimental techniques. In this context, molecular simulations on membrane systems have provided useful insights contributing to bridge this gap. Here we present the results of a series of simulations of biomembranes representing non-raft and raft-like nano-sized domains in order to analyze the particular structural and dynamical properties of these domains. Our results indicate that the smallest (5 nm) raft domains are able to preserve their distinctive structural and dynamical features, such as an increased thickness, higher ordering, lower lateral diffusion, and specific lipid-ion interactions. The insertion of a transmembrane protein helix into non-raft, extended raft-like, and raft-like nanodomain environments result in markedly different protein orientations, highlighting the interplay between the lipid-lipid and lipid-protein interactions.
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87.16.dt Structure, static correlations, domains, and rafts
87.16.dj Dynamics and fluctuations
87.14.Cc Lipids
87.14.E- Proteins

Exploring the dynamics of dimer crossing over a Kramers type potential

Mesfin Asfaw and Yohannes Shiferaw

J. Chem. Phys. 136, 025101 (2012); http://dx.doi.org/10.1063/1.3675920 (9 pages)

Online Publication Date: 10 January 2012

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We explore the escape rate of a dimer crossing a potential barrier using both analytical and numerical approaches. We find that for small coupling strength k, the barrier hopping can be well approximated by a two step reaction scheme where one monomer hops over the barrier and is then followed by the other. In this regime the escape rate increases with k showing that the cooperativity between monomers enhances the crossing rate. However, in the limit of large coupling strength, applying the method of adiabatic elimination, we find that the escape rate is a decreasing function of k. Thus, we find that the escape rate is a non-monotonic function of the spring constant which is peaked at an optimal coupling strength. Furthermore, in the presence of a weak periodic signal, we show that the system response to the periodic signal is pronounced at a particular spring constant showing the dimer can be transported rapidly across the reaction coordinate in a half period.
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31.50.Gh Surface crossings, non-adiabatic couplings

On binding of DNA-bending proteins to DNA minicircles

Shlomi Medalion and Yitzhak Rabin

J. Chem. Phys. 136, 025102 (2012); http://dx.doi.org/10.1063/1.3674978 (9 pages)

Online Publication Date: 10 January 2012

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We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is identical on open and closed long DNA molecules, there is significant enhancement of binding on DNA minicircles, compared to their linear counterparts. We also find that the ratio of the radii of gyration of open and closed chains depends on protein concentration for short DNA molecules. Experimental tests of our predictions are proposed.
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87.15.A- Theory, modeling, and computer simulation
87.15.R- Reactions and kinetics
68.43.Mn Adsorption kinetics
87.15.La Mechanical properties
FREE

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

Zaixing Yang, Zhigang Wang, Xingling Tian, Peng Xiu, and Ruhong Zhou

J. Chem. Phys. 136, 025103 (2012); http://dx.doi.org/10.1063/1.3675486 (10 pages)

Online Publication Date: 10 January 2012

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Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.
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87.15.B- Structure of biomolecules
87.15.R- Reactions and kinetics
87.15.La Mechanical properties

Cross-linked biopolymer bundles: Cross-link reversibility leads to cooperative binding/unbinding phenomena

Richard L. C. Vink and Claus Heussinger

J. Chem. Phys. 136, 035102 (2012); http://dx.doi.org/10.1063/1.3675832 (11 pages)

Online Publication Date: 17 January 2012

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We consider a biopolymer bundle consisting of filaments that are cross-linked together. The cross-links are reversible: they can dynamically bind and unbind adjacent filament pairs as controlled by a binding enthalpy. The bundle is subjected to a bending deformation and the corresponding distribution of cross-links is measured. For a bundle consisting of two filaments, upon increasing the bending amplitude, a first-order transition is observed. The transition is from a state where the filaments are tightly coupled by many bound cross-links, to a state of nearly independent filaments with only a few bound cross-links. For a bundle consisting of more than two filaments, a series of first-order transitions is observed. The transitions are connected with the formation of an interface between regions of low and high cross-link densities. Combining umbrella sampling Monte Carlo simulations with analytical calculations, we present a detailed picture of how the competition between cross-link shearing and filament stretching drives the transitions. We also find that, when the cross-links become soft, collective behavior is not observed: the cross-links then unbind one after the other leading to a smooth decrease of the average cross-link density.
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87.85.jj Biocompatibility
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
81.40.Lm Deformation, plasticity, and creep
62.20.F- Deformation and plasticity
FREE

Understanding the EF-hand closing pathway using non-biased interatomic potentials

L. Dupuis and Normand Mousseau

J. Chem. Phys. 136, 035101 (2012); http://dx.doi.org/10.1063/1.3671986 (13 pages)

Online Publication Date: 17 January 2012

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The EF-hand superfamily of proteins is characterized by the presence of calcium binding helix-loop-helix structures. Many of these proteins undergo considerable motion responsible for a wide range of properties upon binding but the exact mechanism at the root of this motion is not fully understood. Here, we use an unbiased accelerated multiscale simulation scheme, coupled with two force fields — CHARMM-EEF1 and the extended OPEP — to explore in details the closing pathway, from the unbound holo state to the closed apo state, of two EF-hand proteins, the Calmodulin and Troponin C N-terminal nodules. Based on a number of closing simulations for these two sequences, we show that the EF-hand β-scaffold, identified as crucial by Grabarek for the EF-hand opening driven by calcium binding, is also important in closing the EF-hand. We also show the crucial importance of the phenylalanine situated at the end of first EF-hand helix, and identify an intermediate state modulating its behavior, providing a detailed picture of the closing mechanism for these two representatives of EF-hand proteins.
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87.15.B- Structure of biomolecules
87.15.A- Theory, modeling, and computer simulation
87.14.E- Proteins
36.20.Hb Configuration (bonds, dimensions)
36.20.Ey Conformation (statistics and dynamics)

Effective interactions in lysozyme aqueous solutions: A small-angle neutron scattering and computer simulation study

M. C. Abramo, C. Caccamo, D. Costa, G. Pellicane, R. Ruberto, and U. Wanderlingh

J. Chem. Phys. 136, 035103 (2012); http://dx.doi.org/10.1063/1.3677186 (9 pages)

Online Publication Date: 20 January 2012

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We report protein-protein structure factors of aqueous lysozyme solutions at different pH and ionic strengths, as determined by small-angle neutron scattering experiments. The observed upturn of the structure factor at small wavevectors, as the pH increases, marks a crossover between two different regimes, one dominated by repulsive forces, and another one where attractive interactions become prominent, with the ensuing development of enhanced density fluctuations. In order to rationalize such experimental outcome from a microscopic viewpoint, we have carried out extensive simulations of different coarse-grained models. We have first studied a model in which macromolecules are described as soft spheres interacting through an attractive r−6 potential, plus embedded pH-dependent discrete charges; we show that the uprise undergone by the structure factor is qualitatively predicted. We have then studied a Derjaguin-Landau-Verwey-Overbeek (DLVO) model, in which only central interactions are advocated; we demonstrate that this model leads to a protein-rich/protein-poor coexistence curve that agrees quite well with the experimental counterpart; experimental correlations are instead reproduced only at low pH and ionic strengths. We have finally investigated a third, “mixed” model in which the central attractive term of the DLVO potential is imported within the distributed-charge approach; it turns out that the different balance of interactions, with a much shorter-range attractive contribution, leads in this latter case to an improved agreement with the experimental crossover. We discuss the relationship between experimental correlations, phase coexistence, and features of effective interactions, as well as possible paths toward a quantitative prediction of structural properties of real lysozyme solutions.
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87.14.ej Enzymes
87.15.B- Structure of biomolecules

Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Jaeoh Shin and Wokyung Sung

J. Chem. Phys. 136, 045101 (2012); http://dx.doi.org/10.1063/1.3673439 (6 pages)

Online Publication Date: 23 January 2012

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Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible polymer looping in the presence of such tensions by using Brownian dynamics simulation combined with an analytical theory. We show a minute tension dramatically changes the looping time, especially for long chains. Considering a dichotomically flipping noise as a simple example of the nonequilibrium tension, we find the phenomenon of resonant activation, where the looping time can be the minimum at an optimal flipping time. We discuss our results in connection with recent experiments.
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87.15.hm Folding dynamics
87.16.dj Dynamics and fluctuations
83.10.Mj Molecular dynamics, Brownian dynamics
87.15.La Mechanical properties

Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment

Chao Lv, Lianqing Zheng, and Wei Yang

J. Chem. Phys. 136, 044103 (2012); http://dx.doi.org/10.1063/1.3678220 (10 pages)

Online Publication Date: 23 January 2012

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Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.
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02.70.Ns Molecular dynamics and particle methods
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.-r Probability theory, stochastic processes, and statistics

Prediction of reaction barriers and force-induced instabilities under mechanochemical conditions with an approximate model: A case study of the ring opening of 1,3-cyclohexadiene

Adrian Bailey and Nicholas J. Mosey

J. Chem. Phys. 136, 044102 (2012); http://dx.doi.org/10.1063/1.3678010 (11 pages)

Online Publication Date: 23 January 2012

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Mechanochemistry, the use of mechanical stresses to activate chemical reactions, has emerged as a topic of significant interest. The present study examines the use of an approximate model for the prediction of reaction barriers under mechanochemical conditions using the ring opening of 1,3-cyclohexadiene along conrotatory and disrotatory directions as a specific test case. To do this, reaction barriers are evaluated using quantum chemical methods with an external force applied between various pairs of atoms. The results show that the consequent effects on the barrier exhibit a significant dependence on the locations of the atoms used to apply the external force, and in some cases, force-induced instabilities occur that alter the fundamental nature of the reaction pathway. The ability of an approximate model based on a second-order expansion of the force-modified potential energy with respect to nuclear coordinates to reproduce this behavior is then assessed. Good agreement between the results obtained through the quantum chemical calculations and approximate model is attained when force-induced instabilities do not occur. In addition, a strategy for predicting when such instabilities occur is presented and found to yield results that are in qualitative agreement with the quantum chemical calculations. Finally, the response of the system to the external force is interpreted in terms of the parameters entering the model, which correspond to interatomic distances and stiffnesses, and possibly sheds lights on ways to design molecules that exhibit a desired chemical response to mechanochemical conditions.
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82.20.Kh Potential energy surfaces for chemical reactions

Model-free nuclear magnetic resonance study of intermolecular free energy landscapes in liquids with paramagnetic Ln3+ spotlights: Theory and application to Arg-Gly-Asp

Pascal H. Fries

J. Chem. Phys. 136, 044504 (2012); http://dx.doi.org/10.1063/1.3671990 (20 pages)

Online Publication Date: 23 January 2012

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We propose an easily applicable method for investigating the pair distribution function of a lanthanide Ln3+ complex LnL (L = ligand) with respect to any solvent or solute molecule A carrying observable nuclear spins. Let r be the distance of Ln3+ to the observed nuclear spin I. We derive a simple expression of the experimental value of the configurational average of 1∕r6 in terms of longitudinal paramagnetic relaxation (rate) enhancements (PREs) of the spin I measured on a standard high-resolution NMR spectrometer and due to well-chosen concentrations of LnL complexes in which Ln3+ is a fast-relaxing paramagnetic lanthanide or the slowly-relaxing gadolinium Gd3+. The derivation is justified in the general case of a molecule A which is by turns in a bound state where it follows the complex and a free state where it moves independently. It rests on the expression of the underlying PRE theory in terms of the angle-dependent pair distribution function of LnL and A. The simplifications of this theory in the high-field regime and under the condition of fast exchange between bound and free states are carefully discussed. We also show that original information on the angle dependence of the molecular pair distribution function can be gained from the measured paramagnetic dipolar shifts induced by complexed fast-relaxing Ln3+ ions. The method is illustrated by the case study of the anionic Lnttha3− = [Ln3+(ttha)]3− (ttha6− = triethylene tetraamine hexacetate) complex interacting with the biologically important tripeptide Arg-Gly-Asp (RGD) which carries peripheral ionic groups. The usefulness of an auxiliary reference outer sphere probe solute is emphasized.
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33.25.+k Nuclear resonance and relaxation
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Bh General molecular conformation and symmetry; stereochemistry

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

David A. Sivak and Phillip L. Geissler

J. Chem. Phys. 136, 045102 (2012); http://dx.doi.org/10.1063/1.3679654 (11 pages)

Online Publication Date: 31 January 2012

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The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1–10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of microscopic models which allow for disruption of base pairing (i.e., a “melt” or “kink”, generically an “excitation”) and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.gk DNA
87.15.ak Monte Carlo simulations

Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: A new ab initio dipole surface for high-temperature applications

Xiaoping Li, Anirban Mandal, Evangelos Miliordos, and Katharine L. C. Hunt

J. Chem. Phys. 136, 044320 (2012); http://dx.doi.org/10.1063/1.3676406 (17 pages)

Online Publication Date: 31 January 2012

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We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H2 bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H2 bond axis. The expansion coefficients depend on the H2 bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.bw Coupled-cluster theory
33.15.Dj Interatomic distances and angles
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.20.Tp Vibrational analysis
33.70.Jg Line and band widths, shapes, and shifts
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