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

21 Sep 2011

Volume 135, Issue 11, Articles (11xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 114301 (2011); http://dx.doi.org/10.1063/1.3625957 (7 pages)

Lidia Chomicz, Janusz Rak, Piotr Paneth, Michael Sevilla, Yeon Jae Ko, Haopeng Wang, and Kit H. Bowen
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

Periodic force induced stabilization or destabilization of the denatured state of a protein

Pulak Kumar Ghosh, Mai Suan Li, and Bidhan Chandra Bag

J. Chem. Phys. 135, 114101 (2011); http://dx.doi.org/10.1063/1.3635774 (6 pages)

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both stabilization or destabilization of the denatured state of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field.
Show PACS
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
36.20.Fz Constitution (chains and sequences)
36.20.Ey Conformation (statistics and dynamics)
87.15.R- Reactions and kinetics
87.15.Fh Bonding; mechanisms of bond breakage
87.14.E- Proteins

Quantum and semiclassical theories for nonadiabatic transitions based on overlap integrals related to fast degrees of freedom

Mikiya Fujii

J. Chem. Phys. 135, 114102 (2011); http://dx.doi.org/10.1063/1.3634025 (14 pages)

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Alternative treatments of quantum and semiclassical theories for nonadiabatic dynamics are presented. These treatments require no derivative couplings and instead are based on overlap integrals between eigenstates corresponding to fast degrees of freedom, such as electronic states. Derived from mathematical transformations of the Schrmathdinger equation, the theories describe nonlocal characteristics of nonadiabatic transitions. The idea that overlap integrals can be used for nonadiabatic transitions stems from an article by Johnson and Levine [Chem. Phys. Lett. 13, 168 (1972)]10.1016/0009-2614(72)80069-1. Furthermore, overlap integrals in path-integral form have been recently made available by Schmidt and Tully [J. Chem. Phys. 127, 094103 (2007)]10.1063/1.2757170 to analyze nonadiabatic effects in thermal equilibrium systems. The present paper expands this idea to dynamic problems presented in path-integral form that involve nonadiabatic semiclassical propagators. Applications to one-dimensional nonadiabatic transitions have provided excellent results, thereby verifying the procedure. In principle these theories that are presented can be applied to multidimensional systems, although numerical costs could be quite expensive.
Show PACS
82.20.Ln Semiclassical theory of reactions and/or energy transfer
82.20.Gk Electronically non-adiabatic reactions
82.60.Hc Chemical equilibria and equilibrium constants
82.20.Ej Quantum theory of reaction cross section

Coarse-graining Brownian motion: From particles to a discrete diffusion equation

J. A. de la Torre and Pep Español

J. Chem. Phys. 135, 114103 (2011); http://dx.doi.org/10.1063/1.3625556 (9 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We study the process of coarse-graining in a simple model of diffusion of Brownian particles. At a detailed level of description, the system is governed by a Brownian dynamics of non-interacting particles. The coarse-level is described by discrete concentration variables defined in terms of Delaunay cells. These coarse variables obey a stochastic differential equation that can be understood as a discrete version of a diffusion equation. We study different models for the two basic building blocks of this equation which are the free energy function and the diffusion matrix. The free energy function is shown to be non-additive due to the overlapping of cells in the Delaunay construction. The diffusion matrix is state dependent in principle, but for near-equilibrium situations it is shown that it may be safely evaluated at the equilibrium value of the concentration field.
Show PACS
05.40.Jc Brownian motion
05.60.-k Transport processes
05.70.Ce Thermodynamic functions and equations of state
02.30.Hq Ordinary differential equations

Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise

B. Uma, T. N. Swaminathan, P. S. Ayyaswamy, D. M. Eckmann, and R. Radhakrishnan

J. Chem. Phys. 135, 114104 (2011); http://dx.doi.org/10.1063/1.3635776 (13 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF


See Also: Erratum

Show Abstract
A direct numerical simulation (DNS) procedure is employed to study the thermal motion of a nanoparticle in an incompressible Newtonian stationary fluid medium with the generalized Langevin approach. We consider both the Markovian (white noise) and non-Markovian (Ornstein-Uhlenbeck noise and Mittag-Leffler noise) processes. Initial locations of the particle are at various distances from the bounding wall to delineate wall effects. At thermal equilibrium, the numerical results are validated by comparing the calculated translational and rotational temperatures of the particle with those obtained from the equipartition theorem. The nature of the hydrodynamic interactions is verified by comparing the velocity autocorrelation functions and mean square displacements with analytical results. Numerical predictions of wall interactions with the particle in terms of mean square displacements are compared with analytical results. In the non-Markovian Langevin approach, an appropriate choice of colored noise is required to satisfy the power-law decay in the velocity autocorrelation function at long times. The results obtained by using non-Markovian Mittag-Leffler noise simultaneously satisfy the equipartition theorem and the long-time behavior of the hydrodynamic correlations for a range of memory correlation times. The Ornstein-Uhlenbeck process does not provide the appropriate hydrodynamic correlations. Comparing our DNS results to the solution of an one-dimensional generalized Langevin equation, it is observed that where the thermostat adheres to the equipartition theorem, the characteristic memory time in the noise is consistent with the inherent time scale of the memory kernel. The performance of the thermostat with respect to equilibrium and dynamic properties for various noise schemes is discussed.
Show PACS
47.11.Fg Finite element methods
02.70.Dh Finite-element and Galerkin methods
02.30.Hq Ordinary differential equations
02.50.Ga Markov processes

A semiclassical study of the thermal conductivity of low temperature liquids

Jian Liu, Berni J. Alder, and William H. Miller

J. Chem. Phys. 135, 114105 (2011); http://dx.doi.org/10.1063/1.3639107 (10 pages) | Cited 1 time

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The conventional classical energy current auto-correlation function has been extended into a quantum mechanical version and then approximated by the linearized semiclassical initial value representation approach. Comparison of the thermal conductivity to simulation results shows that about 15% quantum correction to the classical molecular dynamics results for liquid neon are quantitatively predicted. For liquid para-hydrogen the quantum effects are sufficiently large that the linearized semiclassical approach is only 20% accurate, while for both liquid He4 and He3 the thermal conductivity disagrees by a factor of 2, although exchange effects appear to play a minor role.
Show PACS
66.25.+g Thermal conduction in nonmetallic liquids
67.25.B- Normal phase of 4He
67.30.E- Normal phase of 3He

Zero field splitting of the chalcogen diatomics using relativistic correlated wave-function methods

J.-B. Rota, S. Knecht, T. Fleig, D. Ganyushin, T. Saue, F. Neese, and H. Bolvin

J. Chem. Phys. 135, 114106 (2011); http://dx.doi.org/10.1063/1.3636084 (13 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The spectrum arising from the (π*)2 configuration of the chalcogen dimers, namely, the X21, a2, and b0+ states, is calculated using wave-function theory based methods. Two-component (2c) and four-component (4c) multireference configuration interaction (MRCI) and Fock-space coupled cluster (FSCC) methods are used as well as two-step methods spin-orbit complete active space perturbation theory at 2nd order (SO-CASPT2) and spin-orbit difference dedicated configuration interaction (SO-DDCI). The energy of the X21 state corresponds to the zero-field splitting of the ground state spin triplet. It is described with high accuracy by the 2- and 4-component methods in comparison with experiment, whereas the two-step methods give about 80% of the experimental values. The b0+ state is well described by 4c-MRCI, SO-CASPT2, and SO-DDCI, but FSCC fails to describe this state and an intermediate Hamiltonian FSCC ansatz is required. The results are readily rationalized by a two-parameter model; Δε, the π* spinor splitting by spin-orbit coupling and K, the exchange integral between the π1* and the π−1* spinors with, respectively, angular momenta 1 and −1. This model holds for all systems under study with the exception of Po2.
Show PACS
33.15.Pw Fine and hyperfine structure
31.15.bw Coupled-cluster theory
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.xp Perturbation theory
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

Comparing different protocols of temperature selection in the parallel tempering method

Carlos E. Fiore

J. Chem. Phys. 135, 114107 (2011); http://dx.doi.org/10.1063/1.3636382 (7 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Parallel tempering Monte Carlo simulations have been applied to a variety of systems presenting rugged free-energy landscapes. Despite this, its efficiency depends strongly on the temperature set. With this query in mind, we present a comparative study among different temperature selection schemes in three lattice-gas models. We focus our attention in the constant entropy method (CEM), proposed by Sabo et al. In the CEM, the temperature is chosen by the fixed difference of entropy between adjacent replicas. We consider a method to determine the entropy which avoids numerical integrations of the specific heat and other thermodynamic quantities. Different analyses for first- and second-order phase transitions have been undertaken, revealing that the CEM may be an useful criterion for selecting the temperatures in the parallel tempering.
Show PACS
81.40.Gh Other heat and thermomechanical treatments
02.50.Ng Distribution theory and Monte Carlo studies
05.10.Ln Monte Carlo methods
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
05.70.Ce Thermodynamic functions and equations of state
05.70.Fh Phase transitions: general studies

Distribution-function approach to free energy computation

Shun Sakuraba and Nobuyuki Matubayasi

J. Chem. Phys. 135, 114108 (2011); http://dx.doi.org/10.1063/1.3637036 (11 pages) | Cited 2 times

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Connections are explored between the free energy difference of two systems and the microscopic distribution functions of the energy difference. On the basis of a rigorous relationship between the energy distribution functions and the free energy, the scheme of error minimization is introduced to derive accurate and simple methods of free energy computation. A set of distribution-function approaches are then examined against model systems, and the newly derived methods exhibit state-of-art performance. It is shown that the notion of error minimization is powerful to improve the free energy calculation using distribution functions.
Show PACS
05.70.Ce Thermodynamic functions and equations of state

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

Gareth A. Tribello, Jérôme Cuny, Hagai Eshet, and Michele Parrinello

J. Chem. Phys. 135, 114109 (2011); http://dx.doi.org/10.1063/1.3628676 (8 pages)

Online Publication Date: 20 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010)10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface.
Show PACS
36.40.Cg Electronic and magnetic properties of clusters
31.50.-x Potential energy surfaces
34.20.Gj Intermolecular and atom-molecule potentials and forces

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. I. Microcanonical ensemble

Igor P. Omelyan and Andriy Kovalenko

J. Chem. Phys. 135, 114110 (2011); http://dx.doi.org/10.1063/1.3637035 (9 pages) | Cited 1 time

Online Publication Date: 20 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We propose a new approach to eliminate the resonance instabilities inherent in multiple time step molecular dynamics simulations. The approach is developed within the microcanonical ensemble on the basis of an energy-constrained technique in the presence of orientational degrees of freedom. While the single and standard multiscale methods are restricted to small time steps of 5 and 8 fs, respectively, it is shown in simulations of water that the algorithms we have derived postpone the appearance of the instabilities to larger steps of about 16 fs. Such steps are close to the upper theoretical limit of 20 fs peculiar to the microcanonical ensemble and can be used without affecting static and dynamical properties.
Show PACS
61.20.Ja Computer simulation of liquid structure

Comparing ab initio density-functional and wave function theories: The impact of correlation on the electronic density and the role of the correlation potential

Ireneusz Grabowski, Andrew M. Teale, Szymon Śmiga, and Rodney J. Bartlett

J. Chem. Phys. 135, 114111 (2011); http://dx.doi.org/10.1063/1.3636114 (12 pages) | Cited 1 time

Online Publication Date: 21 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn–Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)10.1063/1.1809605]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)10.1063/1.3116157], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.
Show PACS
31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
back to top Advanced Experimental Techniques

Producing translationally cold, ground-state CO molecules

Janneke H. Blokland, Jens Riedel, Stephan Putzke, Boris G. Sartakov, Gerrit C. Groenenboom, and Gerard Meijer

J. Chem. Phys. 135, 114201 (2011); http://dx.doi.org/10.1063/1.3637037 (6 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Carbon monoxide molecules in their electronic, vibrational, and rotational ground state are highly attractive for trapping experiments. The optical or ac electric traps that can be envisioned for these molecules will be very shallow, however, with depths in the sub-milliKelvin range. Here, we outline that the required samples of translationally cold CO (X1Σ+, v′′ = 0, N′′ = 0) molecules can be produced after Stark deceleration of a beam of laser-prepared metastable CO (a3Π1) molecules followed by optical transfer of the metastable species to the ground state via perturbed levels in the A1Π state. The optical transfer scheme is experimentally demonstrated and the radiative lifetimes and the electric dipole moments of the intermediate levels are determined.
Show PACS
37.10.Pq Trapping of molecules
37.10.Mn Slowing and cooling of molecules
33.57.+c Magneto-optical and electro-optical spectra and effects
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
FREE

Valence anions of N-acetylproline in the gas phase: Computational and anion photoelectron spectroscopic studies

Lidia Chomicz, Janusz Rak, Piotr Paneth, Michael Sevilla, Yeon Jae Ko, Haopeng Wang, and Kit H. Bowen

J. Chem. Phys. 135, 114301 (2011); http://dx.doi.org/10.1063/1.3625957 (7 pages)

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)−, measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP/6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.
Show PACS
31.15.E- Density-functional theory
33.60.+q Photoelectron spectra
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
34.80.Lx Recombination, attachment, and positronium formation
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)

Efficient long-range collisional energy transfer between the E0g+(3P2) and D0u+(3P2) ion-pair states of I2, induced by H2O, observed using high-resolution Fourier transform emission spectroscopy

Trevor Ridley, Kenneth P. Lawley, Robert J. Donovan, and Amanda J. Ross

J. Chem. Phys. 135, 114302 (2011); http://dx.doi.org/10.1063/1.3638267 (8 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Using high-resolution Fourier transform emission techniques, we have resolved rotational structure in the D0u+(3P2) → X0g+ emission following collisional transfer from the E0g+(3P2) state in I2. The P:R branch ratios in the E0g+(3P2) → D0u+(3P2) transfer are found to vary enormously with vE and vD. We show that the observed intensities are all consistent with the transfer being dominated by long-range, near-resonant collisions with residual H2O. Unequal P:R branch ratios in the E0g+(3P2) → A1u emission have been shown to result from mixing of the E0g+(3P2) and β1g(3P2) states via Ω-uncoupling.
Show PACS
34.50.Ez Rotational and vibrational energy transfer
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Lg Ultraviolet spectra
33.70.Fd Absolute and relative line and band intensities

Spectral characterization in a supersonic beam of neutral chlorophyll a evaporated from spinach leaves

N. Shafizadeh, M. H. Ha-Thi, B. Soep, M. A. Gaveau, F. Piuzzi, and C. Pothier

J. Chem. Phys. 135, 114303 (2011); http://dx.doi.org/10.1063/1.3637048 (6 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The observation of the light absorption of neutral biomolecules has been made possible by a method implemented for their preparation in the gas phase, in supersonically cooled molecular beams, based upon the work of Focsa et al. [C. Mihesan, M. Ziskind, B. Chazallon, E. Therssen, P. Desgroux, S. Gurlui, and C. Focsa, Appl. Surf. Sci. 253, 1090 (2006)]10.1016/j.apsusc.2006.01.082. The biomolecules diluted in frozen water solutions are entrained in the gas plume of evaporated ice generated by an infrared optical parametric oscillators (OPO) laser tuned close to its maximum of absorption, at ∼3 μm. The biomolecules are then picked up in the flux of a supersonic expansion of argon. The method was tested with indole dissolved in water. The excitation spectrum of indole was found cold and large clusters of indole with water were observed up to n = 75. Frozen spinach leaves were examined with the same method to observe the chlorophyll pigments. The Qy band of chlorophyll a has been observed in a pump probe experiment. The Qy bands of chlorophyll a is centred at 647 nm, shifted by 18 nm from its position in toluene solutions. The ionization threshold could also be determined as 6.1 ± 0.05 eV.
Show PACS
87.15.R- Reactions and kinetics

Resonant two-photon ionization spectroscopy of jet-cooled OsN: 520–418 nm

Maria A. Garcia and Michael D. Morse

J. Chem. Phys. 135, 114304 (2011); http://dx.doi.org/10.1063/1.3633694 (12 pages)

Online Publication Date: 16 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The optical transitions of supersonically cooled OsN have been investigated in the range from 19 200 to 23 900 cm−1 using resonant two-photon ionization spectroscopy. More than 20 vibronic bands were observed, 17 of which were rotationally resolved and analyzed. The ground state is confirmed to be 2Δ5/2, deriving from the 1σ2 2σ2 1π4 1δ3 3σ2 electronic configuration. The X 2Δ5/2 ground state rotational constant for 192Os14N was found to be B0 = 0.491921(34) cm−1, giving r0 = 1.62042(6) Å (1σ error limits). The observed bands were grouped into three band systems with Ω′ = 7/2 and four with Ω′ = 3/2, corresponding to the three 2Φ7/2 and four 2Π3/2 states expected from the 1σ2 2σ2 1π4 1δ3 3σ1 2π1 and 1σ2 2σ2 1π4 1δ2 3σ2 2π1 electronic configurations. In addition, two interacting upper states with Ω′ = 5/2 were observed, one of which is thought to correspond to a 1σ2 2σ2 1π3 1δ3 3σ2 2π1, 2Δ5/2 state. Spectroscopic constants are reported for all of the observed states, and comparisons to related molecules are made. The ionization energy of OsN is estimated as IE(OsN) = 8.80 ± 0.06 eV.
Show PACS
33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Mt Rotation, vibration, and vibration-rotation constants
37.10.Mn Slowing and cooling of molecules
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)

Consistent assignment of the vibrations of monosubstituted benzenes

Adrian M. Gardner and Timothy G. Wright

J. Chem. Phys. 135, 114305 (2011); http://dx.doi.org/10.1063/1.3638266 (17 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We investigate the consistency of the labeling and assignments of the vibrations of the monosubstituted benzenes in the electronic ground state. In doing so, we also identify some inconsistencies in the labeling of the benzene modes. We commence by investigating the behavior of the benzene vibrations as one hydrogen is replaced by an artificial atomic substituent of increasing mass via quantum chemical calculations; the wavenumber variations with mass give insight into the assignments. We also examine how well the monohalobenzene vibrations can be described in terms of the benzene ones: consistent with some recent studies, we conclude that this is futile in a significant number of cases. We then show that “isotopic wavenumbers” obtained by artificially changing the mass of the fluorine atom in fluorobenzene are in very good agreement with the wavenumbers obtained via explicit calculation for the relevant monohalobenzene (chlorobenzene, bromobenzene, and iodobenzene) vibrations. As a consequence, we propose that the vibrations of monofluorobenzene be used as the basis for labelling the vibrational assignments of monosubstituted benzenes. As well as the four monohalobenzenes, we also apply this approach to the vibrations of aniline, toluene, benzonitrile, phenylacetylene, phenylphosphine, and nitrobenzene. This has allowed a much more consistent picture of the vibrational assignments to be obtained across ten monosubstituted benzenes.
Show PACS
31.15.E- Density-functional theory
33.20.Tp Vibrational analysis

Shattering dissociation in high-energy molecular collisions between nitrate esters

Igor V. Schweigert and Brett I. Dunlap

J. Chem. Phys. 135, 114306 (2011); http://dx.doi.org/10.1063/1.3640000 (6 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present ab initio molecular dynamics simulations of head-on collisions between ethyl nitrate molecules at collisional energies from 200 to 1200 kJ/mol. Above a threshold energy, an increasing fraction of the collisions led to rapid dissociation on impact—“shattering.” The probability of the shattering dissociation was derived from the quasiclassical trajectories sampling the initial vibrational motion at Tvib = 300 K. Even for the zero impact parameter and a fixed orientation considered, the observed dissociation probability exhibited a wide spread (much larger than kTvib) as a function of the collision energy. This is attributed to variations in the initial vibrational phase. We propose a closed-form expression for the energy-dependent dissociation probability that captures the dependence on the phase and use it to analyze the probability of the shattering dissociation of a larger nitrate ester, pentaerythritol tetranitrate.
Show PACS
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Fd Collision theories; trajectory models
82.20.Wt Computational modeling; simulation
34.50.Lf Chemical reactions
34.50.Ez Rotational and vibrational energy transfer
33.20.Tp Vibrational analysis

A quantum reaction dynamics study of the translational, vibrational, and rotational motion effects on the HD + H3+ reaction

Fanbin Meng, Tingting Wang, and Dunyou Wang

J. Chem. Phys. 135, 114307 (2011); http://dx.doi.org/10.1063/1.3636388 (7 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Time-dependent, quantum reaction dynamics wavepacket approach is employed to investigate the impacts of the translational, vibrational, and rotational motion on the HD +H3+ → H2D+ + H2 reaction using the Xie-Braams-Bowman potential energy surface [Z. Xie, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 122, 224307 (2005)]10.1063/1.1927529. We treat this five atom reaction with a seven-degree-of-freedom model by fixing one Jacobi and one torsion angle related to H3+ at the lowest saddle point geometry of the potential energy surface. The initial state selected reaction probabilities show that the rotational excitations of H+-H2 greatly enhance the reactivity with the reaction probabilities increased double at high rotational states compared to the ground state. However, the vibrational excitations of H3+ hinder the reactivity. The ground state reaction probability shows no reaction threshold for this exoergic reaction, and as the translational energy increases, the reaction probability decreases. Furthermore, reactive resonances and zero point energy play very important roles on the reaction dynamics. The obtained integral cross section has the character of an exoergic reaction without a threshold: it decreases with the translational energy increasing. The calculated thermal rate constants using this seven-degree-of-freedom model are in agreement with a later experiment measurement.
Show PACS
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Bc State selected dynamics and product distribution
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Wt Computational modeling; simulation

Nonadiabatic quantum dynamics of C(1D)+H2→CH+H: Coupled-channel calculations including Renner-Teller and Coriolis terms

Paolo Defazio, Béatrice Bussery-Honvault, Pascal Honvault, and Carlo Petrongolo

J. Chem. Phys. 135, 114308 (2011); http://dx.doi.org/10.1063/1.3636083 (9 pages) | Cited 1 time

Online Publication Date: 20 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The Renner-Teller (RT) coupled-channel dynamics for the C(1D)+H2(X1Σg+)→ CH (X2Π)+H(2S) reaction has been investigated for the first time, considering the first two singlet states math1A′ and math1A′′ of CH2 dissociating into the products and RT couplings, evaluated through the ab initio matrix elements of the electronic angular momentum. We have obtained initial-state-resolved probabilities, cross sections and thermal rate constants via the real wavepacket method for both coupled electronic states. In contrast to the N(2D)+H2(X1Σg+) system, RT effects tend to reduce probabilities, cross sections, and rate constants in the low energy range compared to Born-Oppenheimer (BO) ones, due to the presence of a repulsive RT barrier in the effective potentials and to long-lived resonances. Furthermore, contrary to BO results, the rate constants have a positive temperature dependence in the 100–400 K range. The two-state RT rate constant at 300 K, lower than the BO one, remains inside the error bars of the experimental value.
Show PACS
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
31.15.A- Ab initio calculations
33.20.Vq Vibration-rotation analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
82.20.Fd Collision theories; trajectory models
82.20.Pm Rate constants, reaction cross sections, and activation energies

Fragmentation of singly charged adenine induced by neutral fluorine beam impact at 3 keV

L. Chen, R. Brédy, J. Bernard, G. Montagne, A. R. Allouche, and S. Martin

J. Chem. Phys. 135, 114309 (2011); http://dx.doi.org/10.1063/1.3621713 (10 pages)

Online Publication Date: 21 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The fragmentation scheme of singly charged adenine molecule (H5C5N5+) has been studied via neutral fluorine impact at 3 keV. By analyzing in correlation the kinetic energy loss of the scattered projectile F− produced in single charge transfer process and the mass of the charged fragments, the excitation energy distribution of the parent adenine molecular ions has been determined for each of the main dissociation channels. Several fragmentation pathways unrevealed in standard mass spectra or in appearance energy measurements are investigated. Regarding the well-known hydrogen cyanide (HCN) loss sequence, we demonstrate that although the loss of a HCN is the dominant decay channel for the parent H5C5N5+ (m = 135), the decay of the first daughter ion H4C4N4+ (m = 108) involves not only the HNC (m = 27) loss but also the symmetric breakdown into two dimers of HCN.
Show PACS
34.70.+e Charge transfer
34.50.Bw Energy loss and stopping power
33.15.Ta Mass spectra
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Consistent treatment of coherent and incoherent energy transfer dynamics using a variational master equation

Dara P. S. McCutcheon and Ahsan Nazir

J. Chem. Phys. 135, 114501 (2011); http://dx.doi.org/10.1063/1.3636081 (12 pages) | Cited 1 time

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We investigate the energy transfer dynamics in a donor-acceptor model by developing a time-local master equation technique based on a variational transformation of the underlying Hamiltonian. The variational transformation allows a minimisation of the Hamiltonian perturbation term dependent on the system parameters, and consequently results in a versatile master equation valid over a range of system-bath coupling strengths, temperatures, and environmental spectral densities. While our formalism reduces to the well-known Redfield, Förster and polaron forms in the appropriate limits, in general it is not equivalent to perturbing in either the system-environment or donor-acceptor coupling strengths, and hence can provide reliable results between these limits as well. Moreover, we show how to include the effects of both environmental correlations and non-equilibrium preparations within the formalism.
Show PACS
31.15.xt Variational techniques
31.15.xp Perturbation theory

Proton transport in a binary biomimetic solution revealed by molecular dynamics simulation

Chungwen Liang and Thomas L. C. Jansen

J. Chem. Phys. 135, 114502 (2011); http://dx.doi.org/10.1063/1.3636381 (8 pages)

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration. The overall picture is more complicated than a recent suggestion that the presence of amphiphilic molecules suppresses the proton mobility by slowing down the reorientation of the surrounding water molecules. It has also been suggested that the hydronium ion induces local water orientational order, which results in an ordered region that has to move along with the proton potentially slowing down the proton transport as suggested by experiment. We find that water-wire like structures formed at low amphiphile concentrations facilitate proton transfer, and reduction of the hydrogen bond connectivity induced at high concentrations retards it.
Show PACS
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.39.Jn Charge (electron, proton) transfer in biological systems
87.15.R- Reactions and kinetics
82.20.Wt Computational modeling; simulation

Formation and relaxation dynamics of iso-CH2Cl–I in cryogenic matrices

Thomas J. Preston, Maitreya Dutta, Brian J. Esselman, Aimable Kalume, Lisa George, Robert J. McMahon, Scott A. Reid, and F. Fleming Crim

J. Chem. Phys. 135, 114503 (2011); http://dx.doi.org/10.1063/1.3633697 (10 pages)

Online Publication Date: 15 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Photolysis of chloroiodomethane (CH2ClI) in cryogenic matrices followed by recombination of the nascent radical pair produces an isomer (CH2Cl–I) that features a halogen-halogen (Cl–I) bond. Using ultrafast laser pulses, it is possible to follow the formation of this isomer by transient electronic absorption in low-temperature matrices of N2, CH4, and Ar. Frequency-domain measurements provide vibrational and electronic spectra, and electronic structure calculations give the structures of the isomers and the minimum energy path that connects them. The ultrafast experiments cleave the C–I bond with a 267-nm photolysis pulse and probe the formation of the isomer at wavelengths between 435 nm and 510 nm. The longest wavelengths preferentially interrogate vibrationally excited molecules, and their transient absorption shows that the highly vibrationally excited isomer appears within 1 to 2 ps, depending on the matrix, likely reflecting the loss of 2000 cm−1 or more of energy in a strong, inelastic collision of the fragments with the matrix. The subsequent relaxation of the vibrationally excited isomer occurs in 20 to 40 ps, a time that is comparable to those observed for halomethane molecules and their isomers in liquids and in supercritical CO2. These observations suggest that the formation and initial relaxation of the isomer in dense media do not depend strongly on the identity of the surroundings.
Show PACS
33.80.Wz Other multiphoton processes
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Fm Bond strengths, dissociation energies

Higher order diffusion Monte Carlo propagators for linear rotors as diffusion on a sphere: Development and application to O2@Hen

Massimo Mella

J. Chem. Phys. 135, 114504 (2011); http://dx.doi.org/10.1063/1.3639190 (9 pages)

Online Publication Date: 19 September 2011

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Exploiting the theoretical treatment of particles diffusing on corrugated surfaces and the isomorphism between the “particle on a sphere” and a linear molecule rotation, a new diffusion kernel is introduced to increase the order of diffusion Monte Carlo (DMC) simulations involving linear rotors. Tests carried out on model systems indicate the superior performances of the new rotational diffusion kernel with respect to the simpler alternatives previously employed. In particular, it is evidenced a second order convergence toward exact results with respect to the time step of dynamical correlation functions, a fact that guarantees an identical order for the diffusion part of the DMC projector. The algorithmic advantages afforded by the latter are discussed, especially with respect to the “a posteriori” and “on the fly” extrapolation schemes. As a first application to the new algorithm, the structure and energetics of O2@Hen (n = 1–40) clusters have been studied. This was done to investigate the possible cause of the quenching of the reaction between O2 and Mg witnessed upon increasing the size of superfluid He droplets used as a solvent. With the simulations on O2 indicating a strong localization in the cluster core, the behaviour as a function of n is ascribed to the extremely fluxional comportment of Mg@Hen, which dwells far from the droplet center, albeit being solvated, when n is large.
Show PACS
68.35.Fx Diffusion; interface formation
81.40.Gh Other heat and thermomechanical treatments
66.10.-x Diffusion and ionic conduction in liquids
Page 1 of 2 Pages Next Page | Jump to Page
Close

Google Calendar

ADVERTISEMENT

Your Recent History Recent History Help

Recently Viewed

  1. Erratum: Response to “Comment on ‘On the role of dissipation on the Casimir-Polder potential between molecules in dielectric media’” [J. Chem. Phys. 135, 047102 (2011)]
  2. Polymerization of actin filaments coupled with adenosine triphosphate hydrolysis: Brownian dynamics and theoretical analysis
  3. Franck–Condon simulation of the A 1B2 → X 1A1 dispersed fluorescence spectrum of fluorobenzene and its rate of the internal conversion
  4. Novel pentagonal silicon rings and nanowheels stabilized by flat pentacoordinate carbon(s)
  5. Ultrafast vibrational dynamics and spectroscopy of a siloxane self-assembled monolayer
Go to AIP Home
Copyright © American Institute of Physics
close