Volume 135, Issue 17, 07 November 2011

The contribution of scalar coupling relaxation of the second kind on the relaxation behaviour of nuclear spin singlet states has been derived. The analytical equation found for the relaxation rate constant of singlet state has been compared to the equation for the relaxation of longitudinal magnetization in order to find the conditions for which the singlet state remains longlived even in the presence of this scalar relaxation mechanism. These results are relevant when the singlet state is formed in molecules with more than two interacting spins.
 ARTICLES

 Theoretical Methods and Algorithms

Identification of key residues for protein conformational transition using elastic network model
View Description Hide DescriptionProteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The largescale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in proteinconformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins,nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their openclosed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

Enhanced diffusion in conic channels by means of geometric stochastic resonance
View Description Hide DescriptionGeometric stochastic resonance of Brownian particles diffusing across a converging conic channel subject to oscillating forces is studied in this paper. Conic channel geometries have been previously considered as a model for transport of particles in biological membranes,zeolites, and nanostructures. For this system, a broad excess peak of the effective diffusion above the free diffusion limit is exhibited over a wide range of frequencies, suggesting a synchronization effect in the confining geometry as particles respond to the periodic modulation of the external force. This indicates that the geometric stochastic resonance effect with unbiased ac forces can be exploited for improving the transport of particles in complex geometries.

An offlattice, selflearning kinetic Monte Carlo method using local environments
View Description Hide DescriptionWe present a method called local environment kinetic Monte Carlo (LEKMC) method for efficiently performing offlattice, selflearning kinetic Monte Carlo(KMC) simulations of activated processes in material systems. Like other offlattice KMC schemes, new atomic processes can be found onthefly in LEKMC. However, a unique feature of LEKMC is that as long as the assumption that all processes and rates depend only on the local environment is satisfied, LEKMC provides a general algorithm for (i) unambiguously describing a process in terms of its local atomic environments, (ii) storing new processes and environments in a catalog for later use with standard KMC, and (iii) updating the system based on the local information once a process has been selected for a KMC move. Search, classification, storage and retrieval steps needed while employing local environments and processes in the LEKMC method are discussed. The advantages and computational cost of LEKMC are discussed. We assess the performance of the LEKMC algorithm by considering test systems involving diffusion in a submonolayerAg and AgCu alloy films on Ag(001) surface.

Anomalous kinetics in diffusion limited reactions linked to nonGaussian concentration probability distribution function
View Description Hide DescriptionWe investigate anomalous reaction kinetics related to segregation in the onedimensional reactiondiffusion systemA + B → C. It is well known that spatial fluctuations in the species concentrations cause a breakdown of the meanfield behavior at low concentration values. The scaling of the average concentration with time changes from the meanfieldt ^{−1} to the anomalous t ^{−1/4} behavior. Using a stochastic modeling approach, the reactiondiffusion system can be fully characterized by the multipoint probability distribution function (PDF) of the species concentrations. Its evolution is governed by a FokkerPlanck equation with moving boundaries, which are determined by the positivity of the species concentrations. The concentration PDF is in general nonGaussian. As long as the concentration fluctuations are small compared to the mean, the PDF can be approximated by a Gaussian distribution. This behavior breaks down in the fluctuation dominated regime, for which anomalous reaction kinetics are observed. We show that the transition from mean field to anomalous reaction kinetics is intimately linked to the evolution of the concentration PDF from a Gaussian to nonGaussian shape. This establishes a direct relationship between anomalous reaction kinetics, incomplete mixing and the nonGaussian nature of the concentration PDF.

Rapid calculation of partition functions and free energies of fluids
View Description Hide DescriptionThe 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 highenergy partition and half to a lowenergy partition. By recursively dividing the lowenergy 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.

Optimization of a genetic algorithm for searching molecular conformer space
View Description Hide DescriptionWe present two sets of tunings that are broadly applicable to conformer searches of isolated molecules using a genetic algorithm (GA). In order to find the most efficient tunings for the GA, a second GA – a metagenetic algorithm – was used to tune the first genetic algorithm to reliably find the already known a priori correct answer with minimum computational resources. It is shown that these tunings are appropriate for a variety of molecules with different characteristics, and most importantly that the tunings are independent of the underlying model chemistry but that the tunings for rigid and relaxed surfaces differ slightly. It is shown that for the problem of molecular conformational search, the most efficient GA actually reduces to an evolutionary algorithm.

Largescale symmetryadapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNAintercalator interactions
View Description Hide DescriptionSymmetryadapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Loworders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with densityfitted twoelectron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DFSAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplacetransformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DFSAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavineDNA interaction. Overall, the proflavineDNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (twothirds of the total), but contain important contributions from the intercalatorbackbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogenbonding type interactions. The longrange interactions between the intercalator and the nextnearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.

A combination of the treecode and IPS method to simulate large scale systems by molecular dynamics
View Description Hide DescriptionAn IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and treebased method was developed for largescale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The treebased method uses a hierarchical tree structure to reduce the calculation cost of longrange interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating largescale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with treebased method is well known, the accuracy for the combination of the IPS and treebased methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32 000 bulk water molecules, which contains around 10^{5} point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary treebased method. These facts show that the algorithm of the treebased method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The selfdiffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

Construction of a disorder variable from Steinhardt order parameters in binary mixtures at high densities in three dimensions
View Description Hide DescriptionUsing molecular dynamics simulation, we investigate the structural disorder in crystal, polycrystal, and glass in a LennardJones binary mixture composed of N _{1} + N _{2} = 4096 particles at a low temperature in three dimensions. The size ratio σ_{2}/σ_{1} between the large and small particles is either 1.2 or 1.4. The crossovers among these states occur, as the composition of the large particles c = N _{2}/(N _{1} + N _{2}) is varied. We define a disorder variable D _{ j } for each particle j in terms of local bond order parameters based on spherical harmonics (Steinhardt order parameters). Stacking faults and grain boundaries in fcc polycrystal and mesoscopic structural heterogeneity in glass are then visualized. At small c, disturbances of large particles is stronger for larger σ_{2}/σ_{1}. At large c, the transition between glass and polycrystal occurs nearly discontinuously at c = c _{ c } ∼ 0.8. At σ_{2}/σ_{1} = 1.4, microphase separation occurs in polycrystal states with c > c _{ c }, where fcc crystal grains comprising the large particles are enclosed by amorphous layers composed of the two particle species.

Efficient computation of adiabatic populations in multimode JahnTeller systems through the use of effective vibrational modes
View Description Hide DescriptionA highly efficient scheme for computing adiabatic electronic populations in multimode JahnTeller systems is presented. It relies on the transformation to an effectivemode vibrational basis in which the relevant quantities depend on the coordinates of a single mode only. In this way, the generally tedious numerical evaluation of highdimensional integrals is avoided and replaced by onedimensional integrations. The effectivemode scheme is applied to a variety of twomode and threemode JahnTeller systems and gives a typical speedup of about two to three orders of magnitude as compared to the direct evaluation of the adiabatic populations. The gain grows rapidly with the numbers of modes.

Stability analysis of multiple nonequilibrium fixed points in selfconsistent electron transport calculations
View Description Hide DescriptionWe present a method to perform stability analysis of nonequilibrium fixed points appearing in selfconsistent electron transport calculations. The nonequilibrium fixed points are given by the selfconsistent solution of stationary, nonlinear kinetic equation for singleparticle density matrix. We obtain the stability matrix by linearizing the kinetic equation around the fixed points and analyze the real part of its spectrum to assess the asymptotic time behavior of the fixed points. We derive expressions for the stability matrices within HartreeFock and linear response adiabatic timedependent density functional theory. The stability analysis of multiple fixed points is performed within the nonequilibrium HartreeFock approximation for the electron transport through a molecule with a spindegenerate single level with local Coulomb interaction.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Elastic scattering and rotational excitation of nitrogen molecules by sodium atoms
View Description Hide DescriptionA quantal study of the rotational excitation of nitrogen molecules by sodium atoms is carried out. We present the twodimensional potential energy surface of the NaN_{2} complex, with the N_{2} molecule treated as a rigid rotor. The interaction potential is computed using the spin unrestricted coupledcluster method with single, double, and perturbative triple excitations (UCCSD(T)). The longrange part of the potential is constructed from the dynamic electric dipole polarizabilities of Na and N_{2}. The total, differential, and momentum transfer cross sections for rotationally elastic and inelastic transitions are calculated using the closecoupling approach for energies between 5 cm^{−1} and 1500 cm^{−1}. The collisional and momentum transfer rate coefficients are calculated for temperatures between 100 K and 300 K, corresponding to the conditions under which Na–N_{2}collisions occur in the mesosphere.

Reactions between chlorine atom and acetylene in solid parahydrogen: Infrared spectrum of the 1chloroethyl radical
View Description Hide DescriptionWe applied infrared matrix isolation spectroscopy to investigate the reactions between Cl atom and acetylene (C_{2}H_{2}) in a parahydrogen (pH_{2}) matrix at 3.2 K; Cl was produced via photodissociation at 365 nm of matrixisolated Cl_{2} in situ. The 1chloroethyl radical (·CHClCH_{3}) and chloroethene (C_{2}H_{3}Cl) are identified as the main products of the reaction Cl + C_{2}H_{2} in solidpH_{2}. IR absorption lines at 738.2, 1027.6, 1283.4, 1377.1, 1426.6, 1442.6, and 2861.2 cm^{−1} are assigned to the 1chloroethyl radical. For the reaction of Cl + C_{2}D_{2}, lines due to the ·CDClCH_{2}D radical and transCHDCDCl are observed; the former likely has a synconformation. These assignments are based on comparison of observed vibrational wavenumbers and ^{13}C and Disotopic shifts with those predicted with the B3LYP/augccpVDZ and MP2/augccpVDZ methods. Our observation indicates that the primary addition product of Cl + C_{2}H_{2}, 2chlorovinyl (·CHCHCl) reacts readily with a neighboring pH_{2} molecule to form ·CHClCH_{3} and C_{2}H_{3}Cl. Observation of ·CDClCH_{2}D and transCHDCDCl from Cl + C_{2}D_{2} further supports this conclusion. Although the reactivity of pH_{2} appears to be a disadvantage for making highly reactive free radicals in solidpH_{2}, the formation of 1chloroethyl radical indicates that this secondary reaction might be advantageous in producing radicals that are difficult to prepare from simple photolysis or bimolecular reactionsin situ.

The X^{2}Σ^{+} state of LiCa studied by Fouriertransform spectroscopy
View Description Hide DescriptionThe paper reports on a successful observation of high resolution Fourier transform spectra of LiCa. The fine structure of the ground state was observed and attributed to effective spinrotation interaction. The experimental observations are described by two models using potential energy curves. One of them takes into account the fine structure splitting by means of effective constants, the other by means of a R dependent function γ(R), built in the radial Schrödinger equation. Ab initio calculations were performed for γ(R) which comes close to the experimental function.

The JahnTeller effect in the triply degenerate electronic state of methane radical cation
View Description Hide DescriptionA quantum dynamics study is performed to examine the complex nuclear motion underlying the first photoelectron band of methane. The broad and highly overlapping structures of the latter are found to originate from transitions to the ground electronic state,, of the methane radical cation. Ab initio calculations have also been carried out to establish the potential energy surfaces for the triply degenerate electronic manifold of . A suitable diabatic vibronic Hamiltonian has been devised and the nonadiabatic effects due to JahnTeller conical intersections on the vibronic dynamics investigated in detail. The theoretical results show fair accord with experiment.
 Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Hydrophobic interactions in presence of osmolytes urea and trimethylamineNoxide
View Description Hide DescriptionMolecular dynamics simulations were carried out to study the influences of two naturally occurring osmolytes, urea, and trimethylamineNoxide (TMAO) on the hydrophobic interactions between neopentane molecules. In this study, we used two different models of neopentane: One is of single united site (UA) and another contains fivesites. We observe that, these two neopentane models behave differently in pure water as well as solutions containing osmolytes. Presence of urea molecules increases the stability of solventseparated state for fivesite model, whereas osmolytes have negligible effect in regard to clustering of UA model of neopentane. For both models, dehydration of neopentane and preferential solvation of it by urea and TMAO over water molecules are also observed. We also find the collapse of the secondshell of water by urea and water structure enhancement by TMAO. The orientational distributions of water molecules around different layers of neopentane were also calculated and we find that orientation of water molecules near to hydrophobic moiety is anisotropic and osmolytes have negligible effect on it. We also observe osmolyteinduced waterwater hydrogen bond life time increase in the hydration shell of neopentane as well as in the subsequent water layers.

Singlet state relaxation via scalar coupling of the second kind
View Description Hide DescriptionThe contribution of scalar coupling relaxation of the second kind on the relaxation behaviour of nuclear spin singlet states has been derived. The analytical equation found for the relaxation rate constant of singlet state has been compared to the equation for the relaxation of longitudinal magnetization in order to find the conditions for which the singlet state remains longlived even in the presence of this scalar relaxation mechanism. These results are relevant when the singlet state is formed in molecules with more than two interacting spins.

Spectroscopic properties of alkali atoms embedded in Ar matrix
View Description Hide DescriptionWe present a theoretical investigation of visible absorption and related luminescence of alkali atoms (Li, Na, and K) embedded in Ar matrix. We used a model based on core polarization pseudopotentials, which allows us to determine accurately the gastomatrix shifts of various trapping sites. The remarkable agreement between our calculated results and the experimental spectra recorded by several authors allows us to establish a clear assignment of the observed spectra, which are made of contributions from crystalline sites on the one hand, and of grain boundary sites on the other hand. Our study reveals remarkably large Stokes shifts, up to 9000 cm^{−1}, which could be observed experimentally to identify definitely the trapping sites.

Electron interaction with nitromethane embedded in helium droplets: Attachment and ionization measurements
View Description Hide DescriptionResults of a detailed study on electron interactions with nitromethane (CH_{3}NO_{2}) embedded in heliumnanodroplets are reported. Anionic and cationic products formed are analysed by mass spectrometry. When the dopedheliumdroplets are irradiated with lowenergy electrons of about 2 eV kinetic energy, exclusively parent cluster anions (CH_{3}NO_{2})_{ n } ^{−} are formed. At 8.5 eV, three anion cluster series are observed, i.e., (CH_{3}NO_{2})_{ n } ^{−}, [(CH_{3}NO_{2})_{ n }–H]^{−}, and (CH_{3}NO_{2})_{ n }NO_{2} ^{−}, the latter being the most abundant. The results obtained for anions are compared with previous electron attachment studies with bare nitromethane and nitromethane condensed on a surface. The cation chemistry (induced by electron ionization of the helium matrix at 70 eV and subsequent charge transfer from He^{+} to the dopant cluster) is dominated by production of methylated and protonated nitromethane clusters, (CH_{3}NO_{2})_{ n }CH_{3} ^{+} and (CH_{3}NO_{2})_{ n }H^{+}.

Photoisomerization dynamics of 3,3′diethyloxadicarbocyanine iodide in ionic liquids: Breakdown of hydrodynamic Kramers model
View Description Hide DescriptionPhotoisomerization dynamics of 3,3^{′}diethyloxadicarbocyanine iodide (DODCI) has been examined in a series of 1alkyl3methylimidazolium (alkyl = methyl, ethyl, propyl, butyl, and hexyl) bis(trifluoromethylsulfonyl)imides by measuring its fluorescence lifetimes and quantum yields. This study has essentially been undertaken to find out whether the process of photoisomerization of DODCI in ionic liquids is different compared to that observed in conventional solvents such as alcohols. Activation energy of the reaction has been attained with the aid of isoviscosity plots and was found to be 22 ± 3 kJ mol^{−1}, which is a factor of two higher compared to that obtained in alcohols. The significantly higher activation energy obtained in bis(trifluoromethylsulfonyl)imides compared to alcohols is probably due to the highly ordered nature of the ionic liquids, which hinders the twisting process. Kramers theory has been applied to understand the reduced isomerizationrate constants in terms of solventfriction. As in case of alcohols, the isomerization data could not be explained by the Kramers model. However, a power law relation, which is a phenomenological functional form, could mimic the observed trend.