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Volume 129, Issue 9

7 September 2008

All Issues

ISSN 0021-9606

EISSN 1089-7690

In this Issue

COMMUNICATIONS
ARTICLES
LETTERS TO THE EDITOR
- Errata

COMMUNICATIONS

On the Crooks fluctuation theorem and the Jarzynski equality

L. Y. Chen

J. Chem. Phys. 129, 091101 (2008) https://doi.org/10.1063/1.2978949

Abstract

View articletitled, On the Crooks fluctuation theorem and the Jarzynski equality

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Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins

A. L. Burin; J. A. Dickman; D. B. Uskov; C. F. F. Hebbard; G. C. Schatz

J. Chem. Phys. 129, 091102 (2008) https://doi.org/10.1063/1.2977727

Abstract

View articletitled, Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins

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ARTICLES

Theoretical Methods and Algorithms

Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints

Ming Lin; Hsiao-Mei Lu; Rong Chen; Jie Liang

J. Chem. Phys. 129, 094101 (2008) https://doi.org/10.1063/1.2968605

Abstract

View articletitled, Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints

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Electronic stress tensor description of chemical bonds using nonclassical bond order concept

Paweł Szarek; Yutaka Sueda; Akitomo Tachibana

J. Chem. Phys. 129, 094102 (2008) https://doi.org/10.1063/1.2973634

Abstract

View articletitled, Electronic stress tensor description of chemical bonds using nonclassical bond order concept

Supplementary Material

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Spectral and entropic characterizations of Wigner functions: Applications to model vibrational systems

A. V. Luzanov

J. Chem. Phys. 129, 094103 (2008) https://doi.org/10.1063/1.2968607

Abstract

View articletitled, Spectral and entropic characterizations of Wigner functions: Applications to model vibrational systems

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Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle

Shubin Liu; Niranjan Govind; Lee G. Pedersen

J. Chem. Phys. 129, 094104 (2008) https://doi.org/10.1063/1.2976767

Abstract

View articletitled, Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle

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Two-component relativistic hybrid density functional computations of nuclear spin-spin coupling tensors using Slater-type basis sets and density-fitting techniques

Jochen Autschbach

J. Chem. Phys. 129, 094105 (2008) https://doi.org/10.1063/1.2969100

Abstract

View articletitled, Two-component relativistic hybrid density functional computations of nuclear spin-spin coupling tensors using Slater-type basis sets and density-fitting techniques

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Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

The geometric, optical, and magnetic properties of the endohedral stannaspherenes $M @ {Sn}_{12}$ (⁠ $M = Ti$ ⁠, V, Cr, Mn, Fe, Co, Ni)

Xuan Chen; Kaiming Deng; Yuzhen Liu; Chunmei Tang; Yongbo Yuan; Weishi Tan; Xin Wang

J. Chem. Phys. 129, 094301 (2008) https://doi.org/10.1063/1.2969111

Abstract

View articletitled, The geometric, optical, and magnetic properties of the endohedral stannaspherenes <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><mtext>M</mtext><mo>@</mo><msub><mrow><mtext>Sn</mtext></mrow><mrow><mn>12</mn></mrow></msub></mrow></math> (⁠<math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><mtext>M</mtext><mo>=</mo><mtext>Ti</mtext></mrow></math>⁠, V, Cr, Mn, Fe, Co, Ni)

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Exploring remnants of invariants buried in a deep potential well in chemical reactions

Hiroshi Teramoto; Tamiki Komatsuzaki

J. Chem. Phys. 129, 094302 (2008) https://doi.org/10.1063/1.2973639

Abstract

View articletitled, Exploring remnants of invariants buried in a deep potential well in chemical reactions

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Isolating the spectra of cluster ion isomers using Ar-“tag” -mediated IR-IR double resonance within the vibrational manifolds: Application to $N O_{2}^{-} \cdot H_{2} O$

Ben M. Elliott; Rachael A. Relph; Joseph R. Roscioli; Joseph C. Bopp; George H. Gardenier; Timothy L. Guasco; Mark A. Johnson

J. Chem. Phys. 129, 094303 (2008) https://doi.org/10.1063/1.2966002

Abstract

View articletitled, Isolating the spectra of cluster ion isomers using Ar-“tag” -mediated IR-IR double resonance within the vibrational manifolds: Application to <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><mi mathvariant="normal">N</mi><msubsup><mi mathvariant="normal">O</mi><mn>2</mn><mo>−</mo></msubsup><mo>⋅</mo><msub><mi mathvariant="normal">H</mi><mn>2</mn></msub><mi mathvariant="normal">O</mi></mrow></math>

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Potential energy surface for interactions between two hydrogen molecules

Konrad Patkowski; Wojciech Cencek; Piotr Jankowski; Krzysztof Szalewicz; James B. Mehl; Giovanni Garberoglio; Allan H. Harvey

J. Chem. Phys. 129, 094304 (2008) https://doi.org/10.1063/1.2975220

Abstract

View articletitled, Potential energy surface for interactions between two hydrogen molecules

Supplementary Material

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A comparison of quantum and quasiclassical statistical models for reactions of electronically excited atoms with molecular hydrogen

F. J. Aoiz; T. González-Lezana; V. Sáez Rábanos

J. Chem. Phys. 129, 094305 (2008) https://doi.org/10.1063/1.2969812

Abstract

View articletitled, A comparison of quantum and quasiclassical statistical models for reactions of electronically excited atoms with molecular hydrogen

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Infrared predissociation spectroscopy of cluster cations of protic molecules, ${(N H_{3})}_{n}^{+}$ ⁠, $n = 2 - 4$ and ${(C H_{3} O H)}_{n}^{+}$ ⁠, $n = 2, 3$

Masaki Hachiya; Yoshiyuki Matsuda; Ken-ichiro Suhara; Naohiko Mikami; Asuka Fujii

J. Chem. Phys. 129, 094306 (2008) https://doi.org/10.1063/1.2971186

Abstract

View articletitled, Infrared predissociation spectroscopy of cluster cations of protic molecules, <math xmlns="http://www.w3.org/1998/Math/MathML"><mmultiscripts xmlns=""><mrow><mo>(</mo><mi mathvariant="normal">N</mi><msub><mi mathvariant="normal">H</mi><mn>3</mn></msub><mo>)</mo></mrow><mi>n</mi><mtext></mtext><mtext></mtext><mo>+</mo></mmultiscripts></math>⁠, <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><mi>n</mi><mo>=</mo><mn>2</mn><mo>–</mo><mn>4</mn></mrow></math> and <math xmlns="http://www.w3.org/1998/Math/MathML"><mmultiscripts xmlns=""><mrow><mo>(</mo><mi mathvariant="normal">C</mi><msub><mi mathvariant="normal">H</mi><mn>3</mn></msub><mi mathvariant="normal">O</mi><mi mathvariant="normal">H</mi><mo>)</mo></mrow><mi>n</mi><mtext></mtext><mtext></mtext><mo>+</mo></mmultiscripts></math>⁠, <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><mi>n</mi><mo>=</mo><mn>2</mn><mo>,</mo><mn>3</mn></mrow></math>

Supplementary Material

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Highly delocalized orbiting resonances

A. García-Vela

J. Chem. Phys. 129, 094307 (2008) https://doi.org/10.1063/1.2974097

Abstract

View articletitled, Highly delocalized orbiting resonances

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Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Study of secondary relaxation in disordered plastic crystals of isocyanocyclohexane, cyanocyclohexane, and 1-cyanoadamantane

L. P. Singh; S. S. N. Murthy

J. Chem. Phys. 129, 094501 (2008) https://doi.org/10.1063/1.2961036

Abstract

View articletitled, Study of secondary relaxation in disordered plastic crystals of isocyanocyclohexane, cyanocyclohexane, and 1-cyanoadamantane

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Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport

Byung Chan Eu

J. Chem. Phys. 129, 094502 (2008) https://doi.org/10.1063/1.2971039

Abstract

View articletitled, Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport

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Force autocorrelation function in linear response theory and the origin of friction

Janka Petravic

J. Chem. Phys. 129, 094503 (2008) https://doi.org/10.1063/1.2972977

Abstract

View articletitled, Force autocorrelation function in linear response theory and the origin of friction

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Femtosecond midinfrared study of the photoinduced Wolff rearrangement of diazonaphthoquinone

Daniel Wolpert; Marco Schade; Tobias Brixner

J. Chem. Phys. 129, 094504 (2008) https://doi.org/10.1063/1.2971037

Abstract

View articletitled, Femtosecond midinfrared study of the photoinduced Wolff rearrangement of diazonaphthoquinone

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Columnar mesophases of hexabenzocoronene derivatives. I. Phase transitions

Valentina Marcon; Thorsten Vehoff; James Kirkpatrick; Cheol Jeong; Do Y. Yoon; Kurt Kremer; Denis Andrienko

J. Chem. Phys. 129, 094505 (2008) https://doi.org/10.1063/1.2969763

Abstract

View articletitled, Columnar mesophases of hexabenzocoronene derivatives. I. Phase transitions

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Columnar mesophases of hexabenzocoronene derivatives. II. Charge carrier mobility

James Kirkpatrick; Valentina Marcon; Kurt Kremer; Jenny Nelson; Denis Andrienko

J. Chem. Phys. 129, 094506 (2008) https://doi.org/10.1063/1.2969764

Abstract

View articletitled, Columnar mesophases of hexabenzocoronene derivatives. II. Charge carrier mobility

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Femtosecond spectral interferometry of optical activity: Theory

Hanju Rhee; Jeong-Hyon Ha; Seung-Joon Jeon; Minhaeng Cho

J. Chem. Phys. 129, 094507 (2008) https://doi.org/10.1063/1.2968130

Abstract

View articletitled, Femtosecond spectral interferometry of optical activity: Theory

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Water uptake coefficients and deliquescence of NaCl nanoparticles at atmospheric relative humidities from molecular dynamics simulations

Ranjit Bahadur; Lynn M. Russell

J. Chem. Phys. 129, 094508 (2008) https://doi.org/10.1063/1.2971040

Abstract

View articletitled, Water uptake coefficients and deliquescence of NaCl nanoparticles at atmospheric relative humidities from molecular dynamics simulations

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Solvent smectic order parameters from solute nematic order parameters

Giorgio Celebre; Giorgio Cinacchi; Giuseppina De Luca

J. Chem. Phys. 129, 094509 (2008) https://doi.org/10.1063/1.2970074

Abstract

View articletitled, Solvent smectic order parameters from solute nematic order parameters

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Surfaces, Interfaces, and Materials

Potential energy surface and unimolecular dynamics of stretched $n$ -butane

Upakarasamy Lourderaj; Jason L. McAfee; William L. Hase

J. Chem. Phys. 129, 094701 (2008) https://doi.org/10.1063/1.2969898

Abstract

View articletitled, Potential energy surface and unimolecular dynamics of stretched <math xmlns="http://www.w3.org/1998/Math/MathML"><mi xmlns="">n</mi></math>-butane

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First-principles investigation on electronics characteristics of benzene derivatives with different side groups

Z. H. Zhang; Z. Yang; J. H. Yuan; H. Zhang; X. Q. Ding; M. Qiu

J. Chem. Phys. 129, 094702 (2008) https://doi.org/10.1063/1.2970073

Abstract

View articletitled, First-principles investigation on electronics characteristics of benzene derivatives with different side groups

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Three-dimensional orientation determination of the emission dipoles of single molecules: The shot-noise limit

Johannes Hohlbein; Christian G. Hübner

J. Chem. Phys. 129, 094703 (2008) https://doi.org/10.1063/1.2971183

Abstract

View articletitled, Three-dimensional orientation determination of the emission dipoles of single molecules: The shot-noise limit

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Exciton transfer in quantum dot arrays: Comparison of eigenbasis and site basis representations

Yoji Kubota; Katsuyuki Nobusada

J. Chem. Phys. 129, 094704 (2008) https://doi.org/10.1063/1.2975328

Abstract

View articletitled, Exciton transfer in quantum dot arrays: Comparison of eigenbasis and site basis representations

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A first-principles study of linear and nonlinear optical properties of 4-nitro- $4^{'}$ -methylbenzylidene aniline

S. J. Luo; W. F. Du; H. Z. Wang

J. Chem. Phys. 129, 094705 (2008) https://doi.org/10.1063/1.2971191

Abstract

View articletitled, A first-principles study of linear and nonlinear optical properties of 4-nitro-<math xmlns="http://www.w3.org/1998/Math/MathML"><msup xmlns=""><mn>4</mn><mo>′</mo></msup></math>-methylbenzylidene aniline

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Coverage-dependent quantum versus classical scattering of thermal neon atoms from Li/Cu(100)

D. A. MacLaren; C. Huang; A. C. Levi; W. Allison

J. Chem. Phys. 129, 094706 (2008) https://doi.org/10.1063/1.2976766

Abstract

View articletitled, Coverage-dependent quantum versus classical scattering of thermal neon atoms from Li/Cu(100)

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Temperature-programed time-of-flight secondary ion mass spectrometry study of 1-butyl-3-methylimidazolium trifluoromethanesulfonate during glass-liquid transition, crystallization, melting, and solvation

Ryutaro Souda; Jens Günster

J. Chem. Phys. 129, 094707 (2008) https://doi.org/10.1063/1.2965526

Abstract

View articletitled, Temperature-programed time-of-flight secondary ion mass spectrometry study of 1-butyl-3-methylimidazolium trifluoromethanesulfonate during glass-liquid transition, crystallization, melting, and solvation

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Polarizability evolution on natural and artificial low dimensional binary semiconductor systems: A case study of stoichiometric aluminum phosphide semiconductor clusters

Panaghiotis Karamanis; Demetrios Xenides; Jerzy Leszczynski

J. Chem. Phys. 129, 094708 (2008) https://doi.org/10.1063/1.2976771

Abstract

View articletitled, Polarizability evolution on natural and artificial low dimensional binary semiconductor systems: A case study of stoichiometric aluminum phosphide semiconductor clusters

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Polymers and Complex Systems

Multistep relaxation in equilibrium polymer solutions: A minimal model of relaxation in “complex” fluids

Evgeny B. Stukalin; Jack F. Douglas; Karl F. Freed

J. Chem. Phys. 129, 094901 (2008) https://doi.org/10.1063/1.2976341

Abstract

View articletitled, Multistep relaxation in equilibrium polymer solutions: A minimal model of relaxation in “complex” fluids

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Biological Molecules, Biopolymers, and Biological Systems

Relaxation and fluctuations of the number of particles in a membrane channel at arbitrary particle-channel interaction

Vladimir Yu. Zitserman; Alexander M. Berezhkovskii; Mark A. Pustovoit; Sergey M. Bezrukov

J. Chem. Phys. 129, 095101 (2008) https://doi.org/10.1063/1.2972981

Abstract

View articletitled, Relaxation and fluctuations of the number of particles in a membrane channel at arbitrary particle-channel interaction

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Polarization-dependent fluorescence of proteins bound to nanopore-confined lipid bilayers

R.-Q. Li; A. Marek; Alex I. Smirnov; H. Grebel

J. Chem. Phys. 129, 095102 (2008) https://doi.org/10.1063/1.2972143

Abstract

View articletitled, Polarization-dependent fluorescence of proteins bound to nanopore-confined lipid bilayers

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Characterization of nanofibers formed by self-assembly of $β$ -peptide oligomers using small angle x-ray scattering

Claire L. Pizzey; William C. Pomerantz; Bong-June Sung; Virany M. Yuwono; Samuel H. Gellman; Jeffery D. Hartgerink; Arun Yethiraj; Nicholas L. Abbott

J. Chem. Phys. 129, 095103 (2008) https://doi.org/10.1063/1.2955745

Abstract

View articletitled, Characterization of nanofibers formed by self-assembly of <math xmlns="http://www.w3.org/1998/Math/MathML"><mi xmlns="">β</mi></math>-peptide oligomers using small angle x-ray scattering

Supplementary Material

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Ab initio determination of the electron affinities of DNA and RNA nucleobases

Daniel Roca-Sanjuán; Manuela Merchán; Luis Serrano-Andrés; Mercedes Rubio

J. Chem. Phys. 129, 095104 (2008) https://doi.org/10.1063/1.2958286

Abstract

View articletitled, Ab initio determination of the electron affinities of DNA and RNA nucleobases

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Stochastic chemical kinetics and the total quasi-steady-state assumption: Application to the stochastic simulation algorithm and chemical master equation

Shev MacNamara; Alberto M. Bersani; Kevin Burrage; Roger B. Sidje

J. Chem. Phys. 129, 095105 (2008) https://doi.org/10.1063/1.2971036

Abstract

View articletitled, Stochastic chemical kinetics and the total quasi-steady-state assumption: Application to the stochastic simulation algorithm and chemical master equation

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Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of $α$ -helical peptides?

Vincent Pouthier; Yury O. Tsybin

J. Chem. Phys. 129, 095106 (2008) https://doi.org/10.1063/1.2965525

Abstract

View articletitled, Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of <math xmlns="http://www.w3.org/1998/Math/MathML"><mi xmlns="">α</mi></math>-helical peptides?

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Predicting conformational entropy of bond vectors in proteins by networks of coupled rotators

Anne Dhulesia; Geoffrey Bodenhausen; Daniel Abergel

J. Chem. Phys. 129, 095107 (2008) https://doi.org/10.1063/1.2969809

Abstract

View articletitled, Predicting conformational entropy of bond vectors in proteins by networks of coupled rotators

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Identifying critical residues in protein folding: Insights from $ϕ$ -value and $P_{fold}$ analysis

P. F. N. Faísca; R. D. M. Travasso; R. C. Ball; E. I. Shakhnovich

J. Chem. Phys. 129, 095108 (2008) https://doi.org/10.1063/1.2973624

Abstract

View articletitled, Identifying critical residues in protein folding: Insights from <math xmlns="http://www.w3.org/1998/Math/MathML"><mi xmlns="">ϕ</mi></math>-value and <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow xmlns=""><msub><mi>P</mi><mrow><mtext>fold</mtext></mrow></msub></mrow></math> analysis

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LETTERS TO THE EDITOR

Errata

Erratum: “Binding energies of hydrogen-bonded complexes from extrapolation with localized basis sets” [J. Chem Phys. 127, 085104 (2007)]

Jae Shin Lee

J. Chem. Phys. 129, 099901 (2008) https://doi.org/10.1063/1.2973191

Extract

View articletitled, Erratum: “Binding energies of hydrogen-bonded complexes from extrapolation with localized basis sets” [J. Chem Phys. 127, 085104 (2007)]

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COMMUNICATIONS

ARTICLES

Theoretical Methods and Algorithms

Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Surfaces, Interfaces, and Materials

Polymers and Complex Systems

Biological Molecules, Biopolymers, and Biological Systems

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