JCP Nameplate
  • Volume/Page
  • Keyword
  • DOI
  • Citation
  • Advanced
   
 
 
 

You Tube Flickr Twitter UniPHY Group iResearch App Facebook

BROWSE VOLUMES

Year Range: 
Search Issue | RSS Feeds RSS
Previous Issue Next Issue

7 Nov 2011

Volume 135, Issue 17, Articles (17xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 174502 (2011); http://dx.doi.org/10.1063/1.3651479 (6 pages)

G. Pileio
Enlarge Image | Read More
Page 1 of 2 Pages Next Page | Jump to Page
back to top
RSS Feeds
back to top Theoretical Methods and Algorithms

Identification of key residues for protein conformational transition using elastic network model

Ji Guo Su (苏计国), Xian Jin Xu (许先进), Chun Hua Li (李春华), Wei Zu Chen (陈慰祖), and Cun Xin Wang (王存新)

J. Chem. Phys. 135, 174101 (2011); http://dx.doi.org/10.1063/1.3651480 (10 pages)

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale 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 protein conformational 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 open-closed 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.
Show PACS
87.15.B- Structure of biomolecules
87.15.ad Analytical theories
87.14.gk DNA
87.14.E- Proteins
36.20.Hb Configuration (bonds, dimensions)
36.20.Ey Conformation (statistics and dynamics)

Enhanced diffusion in conic channels by means of geometric stochastic resonance

M. V. Vazquez, F. J. Valdes-Parada, L. Dagdug, and J. Alvarez-Ramirez

J. Chem. Phys. 135, 174102 (2011); http://dx.doi.org/10.1063/1.3657405 (5 pages)

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Geometric 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.
Show PACS
05.40.Jc Brownian motion
05.60.Cd Classical transport

An off-lattice, self-learning kinetic Monte Carlo method using local environments

Dhrubajit Konwar, Vijesh J. Bhute, and Abhijit Chatterjee

J. Chem. Phys. 135, 174103 (2011); http://dx.doi.org/10.1063/1.3657834 (14 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present a method called local environment kinetic Monte Carlo (LE-KMC) method for efficiently performing off-lattice, self-learning kinetic Monte Carlo (KMC) simulations of activated processes in material systems. Like other off-lattice KMC schemes, new atomic processes can be found on-the-fly in LE-KMC. However, a unique feature of LE-KMC is that as long as the assumption that all processes and rates depend only on the local environment is satisfied, LE-KMC 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 LE-KMC method are discussed. The advantages and computational cost of LE-KMC are discussed. We assess the performance of the LE-KMC algorithm by considering test systems involving diffusion in a submonolayer Ag and Ag-Cu alloy films on Ag(001) surface.
Show PACS
81.90.+c Other topics in materials science (restricted to new topics in section 81)
02.70.Uu Applications of Monte Carlo methods
07.05.Tp Computer modeling and simulation

Anomalous kinetics in diffusion limited reactions linked to non-Gaussian concentration probability distribution function

Pietro de Anna, Tanguy Le Borgne, Marco Dentz, Diogo Bolster, and Philippe Davy

J. Chem. Phys. 135, 174104 (2011); http://dx.doi.org/10.1063/1.3655895 (9 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We investigate anomalous reaction kinetics related to segregation in the one-dimensional reaction-diffusion system A + B → C. It is well known that spatial fluctuations in the species concentrations cause a breakdown of the mean-field behavior at low concentration values. The scaling of the average concentration with time changes from the mean-field t−1 to the anomalous t−1/4 behavior. Using a stochastic modeling approach, the reaction-diffusion system can be fully characterized by the multi-point probability distribution function (PDF) of the species concentrations. Its evolution is governed by a Fokker-Planck equation with moving boundaries, which are determined by the positivity of the species concentrations. The concentration PDF is in general non-Gaussian. 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 non-Gaussian shape. This establishes a direct relationship between anomalous reaction kinetics, incomplete mixing and the non-Gaussian nature of the concentration PDF.
Show PACS
82.30.Nr Association, addition, insertion, cluster formation
82.40.Ck Pattern formation in reactions with diffusion, flow and heat transfer
82.20.Fd Collision theories; trajectory models
82.20.Hf Product distribution
05.45.-a Nonlinear dynamics and chaos
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
FREE

Rapid calculation of partition functions and free energies of fluids

Hainam Do, Jonathan D. Hirst, and Richard J. Wheatley

J. Chem. Phys. 135, 174105 (2011); http://dx.doi.org/10.1063/1.3656296 (7 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The partition function (Q) is a central quantity in statistical mechanics. All the thermodynamic properties can be derived from it. Here we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the Helmholtz free energy (F) via F = −kBT ln Q. In our approach, we divide the density of states, assigning half of the configurations found in a simulation to a high-energy partition and half to a low-energy partition. By recursively dividing the low-energy partition into halves, we map out the complete density of states for a continuous system. The result allows free energy to be calculated directly as a function of temperature. We illustrate our method in the context of the free energy of water.
Show PACS
65.20.-w Thermal properties of liquids
05.20.-y Classical statistical mechanics
73.20.At Surface states, band structure, electron density of states

Optimization of a genetic algorithm for searching molecular conformer space

Zoe E. Brain and Matthew A. Addicoat

J. Chem. Phys. 135, 174106 (2011); http://dx.doi.org/10.1063/1.3656323 (10 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We 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 meta-genetic 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.
Show PACS
31.15.xr Self-consistent-field methods
33.15.Bh General molecular conformation and symmetry; stereochemistry

Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

Edward G. Hohenstein, Robert M. Parrish, C. David Sherrill, Justin M. Turney, and Henry F. Schaefer, III

J. Chem. Phys. 135, 174107 (2011); http://dx.doi.org/10.1063/1.3656681 (13 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders 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 density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone 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 hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.
Show PACS
87.15.R- Reactions and kinetics
02.30.Uu Integral transforms
36.20.Hb Configuration (bonds, dimensions)
87.14.gk DNA
87.15.A- Theory, modeling, and computer simulation
87.15.Fh Bonding; mechanisms of bond breakage

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

Kazuaki Z. Takahashi, Tetsu Narumi, and Kenji Yasuoka

J. Chem. Phys. 135, 174108 (2011); http://dx.doi.org/10.1063/1.3658640 (9 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale 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 tree-based method is well known, the accuracy for the combination of the IPS and tree-based 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 105 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 tree-based method. These facts show that the algorithm of the tree-based 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 self-diffusion 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.
Show PACS
87.15.ap Molecular dynamics simulation
87.15.Vv Diffusion
FREE

Construction of a disorder variable from Steinhardt order parameters in binary mixtures at high densities in three dimensions

Takeshi Kawasaki and Akira Onuki

J. Chem. Phys. 135, 174109 (2011); http://dx.doi.org/10.1063/1.3656762 (8 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Using molecular dynamics simulation, we investigate the structural disorder in crystal, polycrystal, and glass in a Lennard-Jones binary mixture composed of N1 + N2 = 4096 particles at a low temperature in three dimensions. The size ratio σ2/σ1 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 = N2/(N1 + N2) is varied. We define a disorder variable Dj 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 σ2/σ1. At large c, the transition between glass and polycrystal occurs nearly discontinuously at c = cc ∼ 0.8. At σ2/σ1 = 1.4, microphase separation occurs in polycrystal states with c > cc, where fcc crystal grains comprising the large particles are enclosed by amorphous layers composed of the two particle species.
Show PACS
61.43.Bn Structural modeling: serial-addition models, computer simulation
61.43.Fs Glasses
61.66.Fn Inorganic compounds
61.72.Mm Grain and twin boundaries
61.72.Nn Stacking faults and other planar or extended defects

Efficient computation of adiabatic populations in multi-mode Jahn-Teller systems through the use of effective vibrational modes

Behnam Nikoobakht, Horst Köppel, Etienne Gindensperger, and Lorenz S. Cederbaum

J. Chem. Phys. 135, 174110 (2011); http://dx.doi.org/10.1063/1.3656686 (10 pages)

Online Publication Date: 3 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A highly efficient scheme for computing adiabatic electronic populations in multi-mode Jahn-Teller systems is presented. It relies on the transformation to an effective-mode 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 high-dimensional integrals is avoided and replaced by one-dimensional integrations. The effective-mode scheme is applied to a variety of two-mode and three-mode Jahn-Teller 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.
Show PACS
31.30.-i Corrections to electronic structure
33.15.Mt Rotation, vibration, and vibration-rotation constants

Stability analysis of multiple nonequilibrium fixed points in self-consistent electron transport calculations

Alan A. Dzhioev and D. S. Kosov

J. Chem. Phys. 135, 174111 (2011); http://dx.doi.org/10.1063/1.3658736 (7 pages)

Online Publication Date: 4 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present a method to perform stability analysis of nonequilibrium fixed points appearing in self-consistent electron transport calculations. The nonequilibrium fixed points are given by the self-consistent solution of stationary, nonlinear kinetic equation for single-particle 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 Hartree-Fock and linear response adiabatic time-dependent density functional theory. The stability analysis of multiple fixed points is performed within the nonequilibrium Hartree-Fock approximation for the electron transport through a molecule with a spin-degenerate single level with local Coulomb interaction.
Show PACS
31.15.xr Self-consistent-field methods
31.15.ee Time-dependent density functional theory
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Elastic scattering and rotational excitation of nitrogen molecules by sodium atoms

Jérôme Loreau, Peng Zhang, and Alexander Dalgarno

J. Chem. Phys. 135, 174301 (2011); http://dx.doi.org/10.1063/1.3653983 (9 pages) | Cited 2 times

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A quantal study of the rotational excitation of nitrogen molecules by sodium atoms is carried out. We present the two-dimensional potential energy surface of the NaN2 complex, with the N2 molecule treated as a rigid rotor. The interaction potential is computed using the spin unrestricted coupled-cluster method with single, double, and perturbative triple excitations (UCCSD(T)). The long-range part of the potential is constructed from the dynamic electric dipole polarizabilities of Na and N2. The total, differential, and momentum transfer cross sections for rotationally elastic and inelastic transitions are calculated using the close-coupling 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–N2 collisions occur in the mesosphere.
Show PACS
34.50.Cx Elastic; ultracold collisions
31.50.Df Potential energy surfaces for excited electronic states
33.20.Sn Rotational analysis
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
34.50.Ez Rotational and vibrational energy transfer
31.15.bw Coupled-cluster theory

Reactions between chlorine atom and acetylene in solid para-hydrogen: Infrared spectrum of the 1-chloroethyl radical

Barbara Golec and Yuan-Pern Lee

J. Chem. Phys. 135, 174302 (2011); http://dx.doi.org/10.1063/1.3653988 (13 pages) | Cited 1 time

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We applied infrared matrix isolation spectroscopy to investigate the reactions between Cl atom and acetylene (C2H2) in a para-hydrogen (p-H2) matrix at 3.2 K; Cl was produced via photodissociation at 365 nm of matrix-isolated Cl2 in situ. The 1-chloroethyl radical (·CHClCH3) and chloroethene (C2H3Cl) are identified as the main products of the reaction Cl + C2H2 in solid p-H2. 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 1-chloroethyl radical. For the reaction of Cl + C2D2, lines due to the ·CDClCH2D radical and trans-CHDCDCl are observed; the former likely has a syn-conformation. These assignments are based on comparison of observed vibrational wavenumbers and 13C- and D-isotopic shifts with those predicted with the B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ methods. Our observation indicates that the primary addition product of Cl + C2H2, 2-chlorovinyl (·CHCHCl) reacts readily with a neighboring p-H2 molecule to form ·CHClCH3 and C2H3Cl. Observation of ·CDClCH2D and trans-CHDCDCl from Cl + C2D2 further supports this conclusion. Although the reactivity of p-H2 appears to be a disadvantage for making highly reactive free radicals in solid p-H2, the formation of 1-chloroethyl radical indicates that this secondary reaction might be advantageous in producing radicals that are difficult to prepare from simple photolysis or bimolecular reactions in situ.
Show PACS
82.50.Hp Processes caused by visible and UV light
31.15.E- Density-functional theory
33.20.Ea Infrared spectra
33.80.Gj Diffuse spectra; predissociation, photodissociation
82.20.Tr Kinetic isotope effects including muonium
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

The X2Σ+ state of LiCa studied by Fourier-transform spectroscopy

Milena Ivanova, Alexander Stein, Asen Pashov, Andrey V. Stolyarov, Horst Knöckel, and Eberhard Tiemann

J. Chem. Phys. 135, 174303 (2011); http://dx.doi.org/10.1063/1.3652755 (10 pages)

Online Publication Date: 3 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The 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 spin-rotation 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.
Show PACS
33.20.Kf Visible spectra
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.15.Pw Fine and hyperfine structure
31.50.Bc Potential energy surfaces for ground electronic states
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure

The Jahn-Teller effect in the triply degenerate electronic state of methane radical cation

T. Mondal and A. J. C. Varandas

J. Chem. Phys. 135, 174304 (2011); http://dx.doi.org/10.1063/1.3658641 (9 pages) | Cited 1 time

Online Publication Date: 4 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A 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, math2T2, 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 CH 4+. A suitable diabatic vibronic Hamiltonian has been devised and the nonadiabatic effects due to Jahn-Teller conical intersections on the vibronic dynamics investigated in detail. The theoretical results show fair accord with experiment.
Show PACS
31.30.jy Higher-order effective Hamiltonians
33.60.+q Photoelectron spectra
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.ae Electronic structure and bonding characteristics
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Hydrophobic interactions in presence of osmolytes urea and trimethylamine-N-oxide

Rahul Sarma and Sandip Paul

J. Chem. Phys. 135, 174501 (2011); http://dx.doi.org/10.1063/1.3655672 (13 pages)

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Molecular dynamics simulations were carried out to study the influences of two naturally occurring osmolytes, urea, and trimethylamine-N-oxide (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 five-sites. 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 solvent-separated state for five-site 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 second-shell 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 osmolyte-induced water-water hydrogen bond life time increase in the hydration shell of neopentane as well as in the subsequent water layers.
Show PACS
68.08.Bc Wetting
61.20.Ja Computer simulation of liquid structure

Singlet state relaxation via scalar coupling of the second kind

G. Pileio

J. Chem. Phys. 135, 174502 (2011); http://dx.doi.org/10.1063/1.3651479 (6 pages)

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
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 long-lived 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.
Show PACS
33.25.+k Nuclear resonance and relaxation
32.30.Dx Magnetic resonance spectra

Spectroscopic properties of alkali atoms embedded in Ar matrix

E. Jacquet, D. Zanuttini, J. Douady, E. Giglio, and B. Gervais

J. Chem. Phys. 135, 174503 (2011); http://dx.doi.org/10.1063/1.3655467 (18 pages)

Online Publication Date: 1 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We 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 gas-to-matrix 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.
Show PACS
32.30.Jc Visible and ultraviolet spectra
32.50.+d Fluorescence, phosphorescence (including quenching)
32.70.Jz Line shapes, widths, and shifts
31.15.X- Alternative approaches

Electron interaction with nitromethane embedded in helium droplets: Attachment and ionization measurements

F. Ferreira da Silva, S. Ptasińska, S. Denifl, D. Gschliesser, J. Postler, C. Matias, T. D. Märk, P. Limão-Vieira, and P. Scheier

J. Chem. Phys. 135, 174504 (2011); http://dx.doi.org/10.1063/1.3656680 (7 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Results of a detailed study on electron interactions with nitromethane (CH3NO2) embedded in helium nanodroplets are reported. Anionic and cationic products formed are analysed by mass spectrometry. When the doped helium droplets are irradiated with low-energy electrons of about 2 eV kinetic energy, exclusively parent cluster anions (CH3NO2)n− are formed. At 8.5 eV, three anion cluster series are observed, i.e., (CH3NO2)n−, [(CH3NO2)n–H]−, and (CH3NO2)nNO2−, 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, (CH3NO2)nCH3+ and (CH3NO2)nH+.
Show PACS
36.40.Jn Reactivity of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
33.15.Ta Mass spectra
34.80.Gs Molecular excitation and ionization
34.80.Ht Dissociation and dissociative attachment
34.70.+e Charge transfer

Photoisomerization dynamics of 3,3′-diethyloxadicarbocyanine iodide in ionic liquids: Breakdown of hydrodynamic Kramers model

V. Gangamallaiah and G. B. Dutt

J. Chem. Phys. 135, 174505 (2011); http://dx.doi.org/10.1063/1.3656694 (7 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Photoisomerization dynamics of 3,3′-diethyloxadicarbocyanine iodide (DODCI) has been examined in a series of 1-alkyl-3-methylimidazolium (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 isomerization rate constants in terms of solvent friction. 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.
Show PACS
82.30.Qt Isomerization and rearrangement
82.50.-m Photochemistry
78.55.Bq Liquids
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Yn Solvent effects on reactivity

Debye to non-Debye scaling of the Boson peak dynamics: Critical behavior and local disorder in vitreous germania

M. Zanatta, G. Baldi, S. Caponi, A. Fontana, C. Petrillo, F. Rossi, and F. Sacchetti

J. Chem. Phys. 135, 174506 (2011); http://dx.doi.org/10.1063/1.3656697 (6 pages)

Online Publication Date: 2 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We report on the observation of a significant softening of the Boson peak (BP) frequency of vitreous GeO2 above the glass transition temperature. The softening reminds a critical trend, with a transition temperature intermediate between the glass transition temperature, Tg, and the melting point. The softening of the BP frequency corresponds to a transition from a region dominated by Debye scaling to a non-Debye one. Below Tg the density of vibrational states varies according to the modification of the elastic continuum medium. Above Tg the relevant softening of the BP modes can be explained by a broadening of the distribution of elastic constants between neighboring atoms, induced by the structural rearrangement. These findings are discussed together with recent experimental and theoretical results on the low frequency vibrations in glasses.
Show PACS
64.70.P- Glass transitions of specific systems
63.70.+h Statistical mechanics of lattice vibrations and displacive phase transitions
67.10.Ba Boson degeneracy
61.43.Fs Glasses
64.70.dj Melting of specific substances
81.40.Jj Elasticity and anelasticity, stress-strain relations

“Stubborn” triaminotrinitrobenzene: Unusually high chemical stability of a molecular solid to 150 GPa

Alistair J. Davidson, Ranga P. Dias, Dana M. Dattelbaum, and Choong-Shik Yoo

J. Chem. Phys. 135, 174507 (2011); http://dx.doi.org/10.1063/1.3658385 (5 pages)

Online Publication Date: 4 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We report an unexpectedly high chemical stability of molecular solid 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under static high pressures. In contrast to the high-pressure behavior of the majority of molecular solids, TATB remains both chemically stable and an insulator to 150 GPa—well above the predicted metallization pressure of 120 GPa. Single crystal studies have shown that TATB exhibits pressure-induced Raman changes associated with two subtle structural phase transitions at 28 and 56 GPa. These phase transitions are accompanied by remarkable color changes, from yellow to orange and to dark red with increasing pressure. We suggest that the high-stability of TATB arises as a result of its hydrogen-bonded aromatic two-dimensional (2D) layered structure and highly repulsive interlayer interaction, hindering the formation of 3D networks or metallic states.
Show PACS
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
85.40.Ls Metallization, contacts, interconnects; device isolation
62.50.-p High-pressure effects in solids and liquids
64.70.K- Solid-solid transitions
61.50.Lt Crystal binding; cohesive energy

H2O and D2 mixtures under pressure: Spectroscopy and proton exchange kinetics

Gustav M. Borstad and Choong-Shik Yoo

J. Chem. Phys. 135, 174508 (2011); http://dx.doi.org/10.1063/1.3658485 (11 pages)

Online Publication Date: 4 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We have investigated the pressure-induced spectral changes and the proton exchange reactions of D2-H2O mixtures to 64 GPa using micro-Raman spectroscopy. The results show the profound difference in the rotational and vibrational Raman spectra of hydrogen isotopes from those of the pure samples, showing the vibrational modes at higher frequencies and continuing to increase with pressure without apparent turnover. This indicates the repulsive nature of D2-H2O interaction without hydrogen bonds between the two and, thus, interstitial fillings of D2 molecules into the bcc-like ice lattice. The spectral analysis using the Morse potential yields a hydrogen bond distance of 0.734 Å at 6 GPa—slightly shorter than that in pure—attributed to the repulsive interaction. The pressure-dependent spectral changes suggest that the proton-ordering transition in the ice lattice occurs over a large pressure range between 28 and 50 GPa, which is substantially lower than that of pure ice (40–80 GPa). This again indicates the presence of high internal pressure arising from the repulsive interaction. The Raman spectra show evidences that the proton exchange occurs in various phases including in solid D2 and H2O mixtures. Based on the time-dependent spectral changes, we obtained the proton exchange rates of k ∼ 0.085 h−1 at 0.2 GPa in fluid D2 and water mixtures, k ∼ 0.03 h−1 and 0.003 h−1 at 2 GPa and 4 GPa, respectively, in fluid D2-ice mixtures, and k ∼ 10−3 h−1 at 8 GPa in solid D2 and ice mixtures.
Show PACS
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
78.30.-j Infrared and Raman spectra
82.20.Tr Kinetic isotope effects including muonium
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

Interpreting single turnover catalysis measurements with constrained mean dwell times

Maicol A. Ochoa, Xiaochun Zhou, Peng Chen, and Roger F. Loring

J. Chem. Phys. 135, 174509 (2011); http://dx.doi.org/10.1063/1.3657855 (12 pages)

Online Publication Date: 7 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Observation of a chemical transformation at the single-molecule level yields a detailed view of kinetic pathways contributing to the averaged results obtained in a bulk measurement. Studies of a fluorogenic reaction catalyzed by gold nanoparticles have revealed heterogeneous reaction dynamics for these catalysts. Measurements on single nanoparticles yield binary trajectories with stochastic transitions between a dark state in which no product molecules are adsorbed and a fluorescent state in which one product molecule is present. The mean dwell time in either state gives information corresponding to a bulk measurement. Quantifying fluctuations from mean kinetics requires identifying properties of the fluorescence trajectory that are selective in emphasizing certain dynamic processes according to their time scales. We propose the use of constrained mean dwell times, defined as the mean dwell time in a state with the constraint that the immediately preceding dwell time in the other state is, for example, less than a variable time. Calculations of constrained mean dwell times for a kinetic model with dynamic disorder demonstrate that these quantities reveal correlations among dynamic fluctuations at different active sites on a multisite catalyst. Constrained mean dwell times are determined from measurements of single nanoparticle catalysis. The results indicate that dynamical fluctuations at different active sites are correlated, and that especially rapid reaction events produce particularly slowly desorbing product molecules.
Show PACS
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
82.20.Fd Collision theories; trajectory models
82.20.Hf Product distribution

Surface and confinement effects on the dielectric relaxation of a monohydroxy alcohol

Catalin Gainaru, Sebastian Schildmann, and Roland Böhmer

J. Chem. Phys. 135, 174510 (2011); http://dx.doi.org/10.1063/1.3655356 (5 pages)

Online Publication Date: 7 November 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
2-ethyl-1-hexanol (2E1H) was confined to the surface of a collagen matrix at various concentration levels c. Dielectric spectroscopy revealed that upon decreasing c, the alcohol's prominent hydrogen-bond mediated Debye-like relaxation broadens and turns nonexponential. This destabilization of the supramolecular association is accompanied by an increasing relative strength of the structural relaxation in 2E1H up to a point beyond which the two processes are merged when the solvent molecules are sufficiently diluted. These results demonstrate that the contribution of the Debye-like relaxation can be completely suppressed and concomitantly the limit of a simple, nonassociating liquid is reached. Confinement of the alcohol in a monolithic glass with nanoscopic pores subjected to different internal surface treatments is also demonstrated to bear a large impact on the relative strengths of the two processes.
Show PACS
77.22.Gm Dielectric loss and relaxation
77.22.Jp Dielectric breakdown and space-charge effects
77.84.Jd Polymers; organic compounds
77.84.Nh Liquids, emulsions, and suspensions; liquid crystals
61.20.Ne Structure of simple liquids
77.22.Ch Permittivity (dielectric function)
Page 1 of 2 Pages Next Page | Jump to Page
Close

Google Calendar

ADVERTISEMENT

Your Recent History Recent History Help

Recently Viewed

  1. Computer simulation of bottle-brush polymers with flexible backbone: Good solvent versus theta solvent conditions
  2. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. II. Photoionization
  3. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. I. Photoabsorption
  4. Erratum: “Towards an accurate description of anharmonic infrared spectra in solution within the polarizable continuum model: Reaction field, cavity field and nonequilibrium effects” [J. Chem. Phys. 135, 104505 (2011)]
  5. Multiple state transition interface sampling of alanine dipeptide in explicit solvent
Go to AIP Home
Copyright © American Institute of Physics
close