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28 May 2013

Volume 138, Issue 20 (partial)

Issue Cover Spotlight Figure

J. Chem. Phys. 138, 204901 (2013); http://dx.doi.org/10.1063/1.4804270 (16 pages)

Mattia Felice Palermo, Antonio Pizzirusso, Luca Muccioli, and Claudio Zannoni
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back to top Theoretical Methods and Algorithms

A combined DFT and restricted open-shell configuration interaction method including spin-orbit coupling: Application to transition metal L-edge X-ray absorption spectroscopy

Michael Roemelt, Dimitrios Maganas, Serena DeBeer, and Frank Neese

J. Chem. Phys. 138, 204101 (2013); http://dx.doi.org/10.1063/1.4804607 (22 pages)

Online Publication Date: 23 May 2013

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A novel restricted-open-shell configuration interaction with singles (ROCIS) approach for the calculation of transition metal L-edge X-ray absorption spectra is introduced. In this method, one first calculates the ground state and a number of excited states of the non-relativistic Hamiltonian. By construction, the total spin is a good quantum number in each of these states. For a ground state with total spin S excited states with spin S′ = S, S − 1, and S + 1 are constructed. Using Wigner-Eckart algebra, all magnetic sublevels with MS = S, …, −S for each multiplet of spin S are obtained. The spin-orbit operator is represented by a mean-field approximation to the full Breit-Pauli spin-orbit operator and is diagonalized over this N-particle basis. This is equivalent to a quasi-degenerate treatment of the spin-orbit interaction to all orders. Importantly, the excitation space spans all of the molecular multiplets that arise from the atomic Russell-Saunders terms. Hence, the method represents a rigorous first-principles approach to the complicated low-symmetry molecular multiplet problem met in L-edge X-ray absorption spectroscopy. In order to gain computational efficiency, as well as additional accuracy, the excitation space is restricted to single excitations and the configuration interaction matrix is slightly parameterized in order to account for dynamic correlation effects in an average way. To this end, it is advantageous to employ Kohn-Sham rather than Hartree-Fock orbitals thus defining the density functional theory/ROCIS method. However, the method can also be used in an entirely non-empirical fashion. Only three global empirical parameters are introduced and have been determined here for future application of the method to any system containing any transition metal. The three parameters were carefully calibrated using the L-edge X-ray absorption spectroscopy spectra of a test set of coordination complexes containing first row transition metals. These parameters are universal and transferable. Hence, there are no adjustable parameters that are used to fit experimental X-ray absorption spectra. Thus, the new approach classifies as a predictive first-principles method rather than an analysis tool. A series of calculations on transition metal compounds containing Cu, Ti, Fe, and Ni in various oxidation and spin states is investigated and a detailed comparison to experimental data is reported. In most cases, the approach yields good to excellent agreement with experiment. In addition, the origin of the observed spectral features is discussed in terms of the electronic structure of the investigated compounds.
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31.15.E- Density-functional theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.20.Rm X-ray spectra
31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.xr Self-consistent-field methods

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

Yue Zheng, Ping Li, Nanrong Zhao, and Zhonghuai Hou

J. Chem. Phys. 138, 204102 (2013); http://dx.doi.org/10.1063/1.4801331 (8 pages)

Online Publication Date: 23 May 2013

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Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers’ rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Uv Stochastic theories of rate constants
82.37.Np Single molecule reaction kinetics, dissociation, etc.
82.20.Db Transition state theory and statistical theories of rate constants

Nonlocal van der Waals functionals: The case of rare-gas dimers and solids

Fabien Tran and Jürg Hutter

J. Chem. Phys. 138, 204103 (2013); http://dx.doi.org/10.1063/1.4807332 (9 pages)

Online Publication Date: 24 May 2013

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Recently, the nonlocal van der Waals (vdW) density functionals [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)10.1103/PhysRevLett.92.246401] have attracted considerable attention due to their good performance for systems where weak interactions are important. Since the physics of dispersion is included in these functionals, they are usually more accurate and show less erratic behavior than the semilocal and hybrid methods. In this work, several variants of the vdW functionals have been tested on rare-gas dimers (from He2 to Kr2) and solids (Ne, Ar, and Kr) and their accuracy compared to standard semilocal approximations, supplemented or not by an atom-pairwise dispersion correction [S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010)10.1063/1.3382344]. An analysis of the results in terms of energy decomposition is also provided.
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31.15.em Corrections for core-spin polarization, surface effects, etc.

Localized orbitals from basis sets augmented with diffuse functions

Ida-Marie Høyvik and Poul Jørgensen

J. Chem. Phys. 138, 204104 (2013); http://dx.doi.org/10.1063/1.4803456 (7 pages)

Online Publication Date: 24 May 2013

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Orbital localization of occupied and virtual Hartree–Fock orbitals generated from basis sets augmented with diffuse functions is performed using the Pipek–Mezey, Boys, powers of the second central moment, and powers of the fourth central moment localizations. The locality of the obtained orbital sets are presented in terms of second and fourth moment orbital spreads. The results show that both local occupied and virtual orbitals may be obtained when using powers of the second central moment and powers of the fourth central moment localizations, while the Pipek–Mezey and Boys localizations fail to produce sets of local virtual orbitals. The locality of the fourth central moment virtual orbitals exhibits a locality similar to the locality of a Boys localization for non-augmented basis sets.
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31.15.xr Self-consistent-field methods
back to top Atoms, Molecules, and Clusters

Correlation between a photoelectron and a fragment ion in dissociative ionization of ethanol in intense near-infrared laser fields

Kouichi Hosaka, Atsushi Yokoyama, Kaoru Yamanouchi, and Ryuji Itakura

J. Chem. Phys. 138, 204301 (2013); http://dx.doi.org/10.1063/1.4805085 (9 pages)

Online Publication Date: 22 May 2013

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The two dissociative ionization channels of ethanol (C2H5OH) induced by an intense near-infrared laser pulse (λ ∼ 783 nm), C2H5OH → CH2OH+ + CH3 + e− and C2H5OH → C2H5+ + OH + e−, are investigated using photoelectron-photoion coincidence method. It is shown that both the electronic ground state and the first electronically excited state of C2H5OH+ are produced at the moment of photoelectron emission. From the observed correlation between the electronic states of C2H5OH+ prepared at the moment of photoelectron emission and the kinetic energy release of the fragment ions, it is revealed that C2H5OH+ prepared in the electronic ground state at the photoelectron emission gains larger internal energy in the end than that prepared in the electronically excited state. The averaged internal energy of C2H5OH+ just before the dissociation is found to increase when the laser field intensity increases from 9 to 23 TW/cm2 and when the laser pulse duration increases from 35 to 800 fs.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.60.+q Photoelectron spectra
33.70.Fd Absolute and relative line and band intensities

Flowing afterglow measurements of the density dependence of gas-phase ion-ion mutual neutralization reactions

Nicholas S. Shuman, Albert A. Viggiano, and Rainer Johnsen

J. Chem. Phys. 138, 204302 (2013); http://dx.doi.org/10.1063/1.4803159 (5 pages)

Online Publication Date: 23 May 2013

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We have studied the dependence of several ion-ion mutual neutralization (MN) reactions on helium density in the range from 1.6 × 1016 to 1.5 × 1017 cm−3 at 300 K, using the Variable Electron and Neutral Density Attachment Mass Spectrometry method. The rate coefficients of the reactions Ar+ + Br2−, Ar+ + SF6−, and Ar+ + C7F14− were found to be independent of gas density over the range studied, in disagreement with earlier observations that similar MN reactions are strongly enhanced at the same gas densities. The cause of the previous enhancement with density is traced to the use of “orbital-motion-limit” theory to infer ion densities from the currents collected by ion-attracting Langmuir probes in a region where it is not applicable.
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82.33.Xj Plasma reactions (including flowing afterglow and electric discharges)
52.25.-b Plasma properties
52.70.Ds Electric and magnetic measurements
52.80.Hc Glow; corona
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions

Theoretical insight into electronic spectra of carbon chain carbenes H2Cn (n = 3−10)

Yanxin Zhang, Li Wang, Yuanyuan Li, and Jinglai Zhang

J. Chem. Phys. 138, 204303 (2013); http://dx.doi.org/10.1063/1.4806186 (9 pages)

Online Publication Date: 23 May 2013

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Ground-state geometries of carbenes H2Cn (n = 3−10) have been fully optimized with the C2ν-symmetry constraint at the density functional theory and restricted-spin coupled-cluster single-double plus perturbative triple excitation levels of theory, respectively. Comparison of structures corresponding to the X1A1 and B1B1 electronic states has been made by the complete active space self-consistent field calculations. Parity alternation effect on various properties of the ground-state geometries has been discovered in the present study, which generally gives illustration for the relative stabilities of the titled carbon chains. Further calculations on their electronic spectra have been carried out by means of the complete active space second-order perturbation theory method along with the cc-pVTZ basis set. It is found that the vertical excitation energies of the dipole-allowed B1B1 ← X1A1 transition in the gas phase are 2.28, 4.75, 1.69, 3.66, 1.30, 2.94, 1.12, and 2.49 eV, respectively, which agree very well with the available experimental result for H2C3 (2.27 eV). In addition, the vertical excitation energies for both transitions B1B1 ← X1A1 and A1A2 ← X1A1 are found to obey a nonlinear ΔE-n relationship as a function of chain size by performing curves fitting.
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31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Obtaining the lattice energy of the anthracene crystal by modern yet affordable first-principles methods

J. C. Sancho-García, J. Aragó, E. Ortí, and Y. Olivier

J. Chem. Phys. 138, 204304 (2013); http://dx.doi.org/10.1063/1.4806436 (8 pages)

Online Publication Date: 23 May 2013

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The non-covalent interactions in organic molecules are known to drive their self-assembly to form molecular crystals. We compare, in the case of anthracene and against experimental (electronic-only) sublimation energy, how modern quantum-chemical methods are able to calculate this cohesive energy taking into account all the interactions between occurring dimers in both first-and second-shells. These include both O(N6)- and O(N5)-scaling methods, Local Pair Natural Orbital-parameterized Coupled-Cluster Single and Double, and Spin-Component-Scaled-Møller-Plesset perturbation theory at second-order, respectively, as well as the most modern family of conceived density functionals: double-hybrid expressions in several variants (B2-PLYP, mPW2-PLYP, PWPB95) with customized dispersion corrections (–D3 and –NL). All-in-all, it is shown that these methods behave very accurately producing errors in the 1–2 kJ/mol range with respect to the experimental value taken into account the experimental uncertainty. These methods are thus confirmed as excellent tools for studying all kinds of interactions in chemical systems.
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71.20.Rv Polymers and organic compounds
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
71.15.Nc Total energy and cohesive energy calculations
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
31.15.ae Electronic structure and bonding characteristics
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Pseudo Jahn-Teller coupling in trioxides XO3(0,1,−1) with 22 and 23 valence electrons

Friedrich Grein

J. Chem. Phys. 138, 204305 (2013); http://dx.doi.org/10.1063/1.4805064 (9 pages)

Online Publication Date: 24 May 2013

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D3h and C2v geometries and energies, vertical excitation energies, as well as minimal energy paths as function of the O1(z)-X-O2 angle α were obtained for XO3(0,1,−1) (X = B, Al, Ga; C, Si, Ge; N, P, As; S, Se) molecules and ions with 22 and 23 valence electrons (VE), using density functional theory (DFT), coupled cluster with single and double substitutions with noniterative triple excitations (CCSD(T)), equation of motion (EOM)-CCSD, time-dependent DFT, and multi-reference configuration interaction methods. It is shown that pseudo Jahn-Teller (PJT) coupling increases as the central atom X becomes heavier, due to decreases in excitation energies. As is well known for CO3, the excited 1E′ states of the 22 VE systems SiO3, GeO3; NO 3+, PO3+, AsO3+; BO3−, AlO3−, GaO3− have strong vibronic coupling with the 1A1′ ground state via the e′ vibrational modes, leading to a C2v minimum around α = 145°. For first and second row X atoms, there is an additional D3h minimum (α = 120°). Interacting excited states have minima around 135°. In the 23 VE systems CO3−, SiO3−; NO3, PO3; SO3+, coupling of the excited 2E′ with the 2A2′ ground state via the e′ mode does not generate a C2v state. Minima of interacting excited states are close to 120°. However, due to very strong PJT coupling, a double-well potential is predicted for GeO3−, AsO3, and SeO3+, with a saddle point at D3h symmetry. Interaction of the b2 highest occupied molecular orbital with the b2 lowest unoccupied molecular orbital, both oxygen lone pair molecular orbitals, is seen as the reason for the C2v stabilization of 22 VE molecules.
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31.30.-i Corrections to electronic structure
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
31.15.V- Electron correlation calculations for atoms, ions and molecules

Thermalization of rotational states of NO A 2Σ+(v = 0) in an atmospheric pressure plasma

A. F. H. van Gessel and P. J. Bruggeman

J. Chem. Phys. 138, 204306 (2013); http://dx.doi.org/10.1063/1.4802959 (9 pages)

Online Publication Date: 24 May 2013

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Laser induced fluorescence (LIF) measurements of nitric oxide (NO) are performed in an atmospheric pressure microwave plasma jet, operated with a mixture of He and 3% air. The fluorescence signal of NO A 2Σ+(v = 0) is measured time and fluorescence wavelength resolved. Based on the evolution of the rotational spectrum at different positions in the plasma, we determined the thermalization time of the rotational distribution of NO A after pumping a single transition, at temperatures in the range 300–1500 K. Also, a LIF-RET (rotational energy transfer) model is developed to simulate the RET and to calculate the thermalization time. The RET rate coefficients are calculated using the energy corrected sudden-exponential power scaling law. It was found that it is necessary to take the fine structure of the rotational states into account. At room temperature the results of the measurement and the simulation are consistent, and the thermalization occurs during the laser pulse (11 ± 1 ns). At elevated temperatures the measurements show a large increase in thermalization time, up to 35 ± 4 ns at 1474 K. This time is much longer than the laser pulse, and of the order of the NO A lifetime. This means that for spectroscopy measurements of the rotational states of NO A, the RET has to be taken into account to derive gas temperatures from the rotational distribution of NO A.
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33.20.Sn Rotational analysis
33.50.Dq Fluorescence and phosphorescence spectra
34.50.Ez Rotational and vibrational energy transfer
33.80.-b Photon interactions with molecules
33.15.Mt Rotation, vibration, and vibration-rotation constants
back to top Surfaces, Interfaces, and Materials

Thermionic current densities from first principles

Johannes Voss, Aleksandra Vojvodic, Sharon H. Chou, Roger T. Howe, Igor Bargatin, and Frank Abild-Pedersen

J. Chem. Phys. 138, 204701 (2013); http://dx.doi.org/10.1063/1.4805002 (5 pages)

Online Publication Date: 22 May 2013

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We present a density functional theory-based method for calculating thermionic emission currents from a cathode into vacuum using a non-equilibrium Green's function approach. It does not require semi-classical approximations or crude simplifications of the electronic structure used in previous methods and thus provides quantitative predictions of thermionic emission for adsorbate-coated surfaces. The obtained results match well with experimental measurements of temperature-dependent current densities. Our approach can thus enable computational design of composite electrode materials.
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79.40.+z Thermionic emission
68.43.Mn Adsorption kinetics

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet

Malay Kumar Rana and Amalendu Chandra

J. Chem. Phys. 138, 204702 (2013); http://dx.doi.org/10.1063/1.4804300 (9 pages)

Online Publication Date: 22 May 2013

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The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.
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61.20.Ja Computer simulation of liquid structure
68.08.Bc Wetting
66.10.C- Diffusion and thermal diffusion
82.30.Nr Association, addition, insertion, cluster formation
61.25.Em Molecular liquids

Dynamics of acetone photooxidation on TiO2(110): State-resolved measurements of methyl photoproducts

Matthew D. Kershis, Daniel P. Wilson, and Michael G. White

J. Chem. Phys. 138, 204703 (2013); http://dx.doi.org/10.1063/1.4805065 (7 pages)

Online Publication Date: 22 May 2013

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State-resolved laser techniques were used to study the internal state distributions of gas phase methyl radicals which are produced during the photooxidation of acetone on TiO2(110). This approach was used as a means of understanding the nature of the bimodal kinetic energy distributions for these radicals. Specifically, we investigated the population of the ν2 “umbrella mode” which has been shown to be important in similar photodissociation reactions where methyl radicals are liberated. We observed that for methyl radicals undergoing prompt dissociation (EK = 0.15 eV), the vibrational population in the umbrella mode is quite cold and can be characterized by a Tvib = 151 ± 15 K. Methyl radicals in this channel were also characterized by a rotational energy distribution of Trot = 325 ± 25 K which is comparable to the gas phase value obtained by acetone photolysis. State-resolved energy distributions also show that methyl radicals which are vibrationally excited have an overall kinetic energy distribution which is ∼35 meV less than those which are in their vibrational ground state. This value is comparable to, but not exactly in agreement with, the known vibrational spacing of the ν2 mode and suggests that vibrationally excited methyl radicals have less energy available for translation.
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82.50.Hp Processes caused by visible and UV light
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

On the thermoelectric transport properties of graphyne by the first-principles method

Xiao-Ming Wang, Dong-Chuan Mo, and Shu-Shen Lu

J. Chem. Phys. 138, 204704 (2013); http://dx.doi.org/10.1063/1.4806069 (8 pages)

Online Publication Date: 22 May 2013

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Graphyne, another two-dimensional carbon allotrope, has received increased attentions in recent years. By using the first-principles density functional calculations combined with the non-equilibrium Green's function formalism, we investigated the electronic, thermal, and thermoelectric transport properties of graphyne systematically and comparatively. It is found that the phonon thermal conductance of graphyne is greatly reduced compared to that of graphene in most temperature regions while larger than that of graphene at low temperatures, which is attributed to the different bond strengths and phonon spectra of graphyne and graphene. Due to the semiconductor property of graphyne, the thermoelectric power (TEP) is found to be one magnitude larger than that of graphene. Besides, distinct peak value regions of TEP in the contour of chemical potential and temperature are displayed for graphyne and graphene. Finally, the thermoelectric figure of merit (ZT) of graphyne is found to be much larger than that of graphene as a result of large TEP and greatly reduced thermal conductance in graphyne, which indicates preferred thermoelectric applications for graphyne.
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72.20.Pa Thermoelectric and thermomagnetic effects
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
72.80.Vp Electronic transport in graphene
73.22.Pr Electronic structure of graphene
65.80.Ck Thermal properties of graphene
71.20.Mq Elemental semiconductors

A microscopic picture of surface charge trapping in semiconductor nanocrystals

Jonathan Mooney, Michael M. Krause, Jonathan I. Saari, and Patanjali Kambhampati

J. Chem. Phys. 138, 204705 (2013); http://dx.doi.org/10.1063/1.4807054 (9 pages)

Online Publication Date: 22 May 2013

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Several different compositions of semiconductor nanocrystals are subjected to numerous spectroscopic techniques to elucidate the nature of surface trapping in these systems. We find a consistent temperature-dependent relationship between core and surface photoluminescence intensity and marked differences in electron-phonon coupling for core and surface states based on ultrafast measurements and Resonance Raman studies, respectively. These results support a minimal model of surface charge trapping applicable to a range of nanocrystal systems involving a single surface state in which the trapped charge polarization leads to strong phonon couplings, with transitions between the surface and band edge excitonic states being governed by semiclassical electron-transfer theory.
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78.55.Et II-VI semiconductors
78.67.Bf Nanocrystals, nanoparticles, and nanoclusters
78.30.Fs III-V and II-VI semiconductors
71.35.-y Excitons and related phenomena
73.20.Mf Collective excitations (including excitons, polarons, plasmons and other charge-density excitations)
63.20.kd Phonon-electron interactions

Absorption induced modulation of magnetism in two-dimensional metal-phthalocyanine porous sheets

Jian Zhou and Qiang Sun

J. Chem. Phys. 138, 204706 (2013); http://dx.doi.org/10.1063/1.4807016 (7 pages)

Online Publication Date: 23 May 2013

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Metal-phthalocyanine porous sheets have uniformly dispersed metal sites in Pc framework, making absorption happen naturally. Here, we explore the effects of absorption of chlorine atoms on magnetism in transition metal embedded phthalocyanine (poly-TMPc) sheets with TM = Cr, Mn, and Fe. We show that when one Cl is absorbed on the TM, the strong square planar crystal field becomes weak in a square pyramidal configuration and the TM is in the +3 oxidized state, resulting in the magnetic moment of 3, 4, and 5 μB for Cr, Mn, and Fe, respectively, with weak antiferromagnetic couplings. When another Cl is introduced to the TM on the other side, it extracts one electron from the Pc framework making the substrate p-doped. The magnetic coupling is antiferromagnetic for poly-CrPc-2Cl and the poly-FePc-2Cl, while it becomes ferromagnetic for poly-MnPc-2Cl, suggesting that absorption can effectively modulate the bonding environment and tune the magnetic properties of the systems, and the controlled absorption can be used to tailor materials.
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68.43.Mn Adsorption kinetics
75.50.Xx Molecular magnets
75.30.Cr Saturation moments and magnetic susceptibilities
75.50.Dd Nonmetallic ferromagnetic materials
75.50.Ee Antiferromagnetics
75.50.Pp Magnetic semiconductors

Stretching tethered polymer chains: Density functional approach

M. Borówko, W. Rżysko, S. Sokołowski, Z. Sokołowska, and Z. Usatenko

J. Chem. Phys. 138, 204707 (2013); http://dx.doi.org/10.1063/1.4807086 (7 pages)

Online Publication Date: 23 May 2013

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We propose application of density functional theory to calculate the force acting on a selected segment of a tethered polymer chain that leads to stretching the chain. The density functional allows one to determine the effects due to the presence of other chains and solvent molecules. For high and moderate solvent densities the plot of the force versus the distance of the segment from the surface exhibits oscillatory behavior that has not been predicted by other approaches.
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61.41.+e Polymers, elastomers, and plastics
back to top Polymers and Soft Matter
FREE

An atomistic description of the nematic and smectic phases of 4-n-octyl-4′ cyanobiphenyl (8CB)

Mattia Felice Palermo, Antonio Pizzirusso, Luca Muccioli, and Claudio Zannoni

J. Chem. Phys. 138, 204901 (2013); http://dx.doi.org/10.1063/1.4804270 (16 pages)

Online Publication Date: 22 May 2013

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We report the results of atomistic molecular dynamics simulations of 4-n-octyl-4′ cyanobiphenyl (8CB) on samples of 750 and 3000 molecules showing the spontaneous formation of the nematic phase and then of smectic layers by gradually cooling down from the isotropic phase. Orientational, positional, and mixed order parameters, layer spacing, translational diffusion tensor components and their temperature dependence are reported. A detailed comparison with available experimental data validates the model and force field employed and clarifies the molecular organization of this important liquid crystal often used as reference smectic material.
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61.30.Eb Experimental determinations of smectic, nematic, cholesteric, and other structures
66.10.C- Diffusion and thermal diffusion
61.20.Ja Computer simulation of liquid structure

Dynamics of discrete semiflexible chains under dihedral constraints: Analytic results

Maxim Dolgushev and Alexander Blumen

J. Chem. Phys. 138, 204902 (2013); http://dx.doi.org/10.1063/1.4807058 (6 pages)

Online Publication Date: 23 May 2013

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Here we consider the dynamics of semiflexible polymers subject both to angular and to dihedral constraints. We succeed in obtaining analytically the dynamical matrix of such systems by extending the formalism developed by Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)10.1063/1.3184797]. This leads to a set of Langevin equations whose eigenvalues determine many dynamical properties. Exemplarily, we display the mechanical relaxation loss moduli [G″(ω)] as a function of several, distinct sets of microscopic stiffness parameters; it turns out that such differences lead to macroscopically distinct patterns.
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36.20.Ey Conformation (statistics and dynamics)
36.20.Fz Constitution (chains and sequences)

Dynamics of polymer translocation through a nanopore induced by different sizes of crowding agents

Yuhao Chen and Kaifu Luo

J. Chem. Phys. 138, 204903 (2013); http://dx.doi.org/10.1063/1.4807088 (8 pages)

Online Publication Date: 23 May 2013

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Using both theoretical analysis and Langevin dynamics simulations in two dimensions, we investigate the dynamics of polymer translocation through a nanopore induced by different sizes of the mobile crowding agents, where the crowding agents have equal area fraction ϕ and their diameters are σ and σb ⩾ σ at cis and trans sides, respectively. The chain prefers moving to the side with bigger crowding agents as expected, however, we find the size difference between crowding agents plays a complicated role in the probability of polymer translocation from cis to trans side, the translocation time τ and its distribution, and the translocation exponent. In particular, with increasing σb, the translocation probability shows a maximum value and τ has a minimum value. These results can be interpreted by the effective driving force, which always increases with increasing ϕ but has a maximum value with increasing σb.
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87.10.-e General theory and mathematical aspects
02.50.-r Probability theory, stochastic processes, and statistics
36.20.Ey Conformation (statistics and dynamics)

Effect of ion pair formation on the structure of polymer micelles with ionic amphiphilic coronae

A. M. Rumyantsev and E. Yu. Kramarenko

J. Chem. Phys. 138, 204904 (2013); http://dx.doi.org/10.1063/1.4807005 (11 pages)

Online Publication Date: 24 May 2013

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We report a theoretical study of micelles from diblock copolymers with an insoluble core-forming block and an amphiphilic ionic corona-forming block. We calculate the micelle structural parameters depending on the composition of the coronal block (ratio between the non-polar and ion-containing groups) as well as solvent quality and polarity for the coronal block. We focus on the effect of ion pair formation in a low polar corona medium and predict the existence of novel micelles with ionomer-type coronae. In these micelles most part of counterions is bound with ions in polymer chains. Two consecutive jump-like first-order phase transitions between different-type micelles can take place in the solution upon change of hydrophobic/polyelectrolyte balance within the micelle corona: large micelles with polyelectrolyte collapsed coronae → large micelles with ionomer-type coronae → small micelles with polyelectrolyte swollen coronae. These transitions are accompanied by non-monotonous change in the micelle aggregation number. New insight into the role of counterions is important for design of stimuli responsive systems.
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61.41.+e Polymers, elastomers, and plastics
82.70.Dd Colloids
82.45.Gj Electrolytes
82.45.Wx Polymers and organic materials in electrochemistry
64.75.Bc Solubility
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder

The phase behavior of linear and partially flexible hard-sphere chain fluids and the solubility of hard spheres in hard-sphere chain fluids

Bernardo Oyarzún, Thijs van Westen, and Thijs J. H. Vlugt

J. Chem. Phys. 138, 204905 (2013); http://dx.doi.org/10.1063/1.4807056 (12 pages)

Online Publication Date: 24 May 2013

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The liquid crystal phase behavior of linear and partially flexible hard-sphere chain fluids and the solubility of hard spheres in hard-sphere chain fluids are studied by constant pressure Monte Carlo simulations. An extensive study on the phase behavior of linear fluids with a length of 7, 8, 9, 10, 11, 12, 13, 14, 15, and 20 beads is carried out. The phase behavior of partially flexible fluids with a total length of 8, 10, 14, and 15 beads and with different lengths for the linear part is also determined. A precise description of the reduced pressure and of the packing fraction change at the isotropic-nematic coexistence was achieved by performing long simulation runs. For linear fluids, a maximum in the isotropic to nematic packing fraction change is observed for a chain length of 15 beads. The infinite dilution solubility of hard spheres in linear and partially flexible hard-sphere chain fluids is calculated by the Widom test-particle insertion method. To identify the effect of chain connectivity and molecular anisotropy on free volume, solubility is expressed relative to that of hard spheres in a hard sphere fluid at same packing fraction as relative Henry's law constants. A linear relationship between relative Henry's law constants and packing fraction is observed for all linear fluids. Furthermore, this linearity is independent of liquid crystal ordering and seems to be independent of chain length for linear chains of 10 beads and longer. The same linear relationship was observed for the solubility of hard spheres in nematic forming partially flexible fluids for packing fractions up to a value slightly higher than the nematic packing fraction at the isotropic-nematic coexistence. At higher packing fractions, the small flexibility of these fluids seems to improve solubility in comparison with the linear fluids.
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61.30.-v Liquid crystals
61.20.Ja Computer simulation of liquid structure
64.75.Bc Solubility
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Dynamics simulation of the interaction between serine and water

Yang Liu, Peng Zhang, Ying-Bo Lu, Sheng-Hao Han, and Hui Yu

J. Chem. Phys. 138, 205101 (2013); http://dx.doi.org/10.1063/1.4807004 (5 pages)

Online Publication Date: 23 May 2013

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Using the first principles density functional theory (DFT), we simulated the neutron scattering spectra of the hydration dynamics of serine. Experimental data analyses have shown that dissociative H2O molecules were more likely to form hydrogen bonds (H-bonds) with an –OH group in monohydrated serine and easily shift to a – NH 3+ group at a higher hydration level [P. Zhang, Y. Zhang, S. H. Han, Q. W. Yan, R. C. Ford, and J. C. Li, J. Phys. Chem. A 110, 5000 (2006)10.1021/jp0569741]. We set the 1:1 ratio hydrated compounds at the two positions and found that the H2O could be optimized to form H-bonds with –OH and –NH3+ separately. When the simulated phonon signals of the –OH…H2O and –NH3+…H2O combinations were summed on a 3:1 scale, the calculating spectra were in good agreement with the experimental results, especially for the peak at 423 cm−1 of the –OH…H2O combination and the peak at 367 cm−1 of the –NH3+…H2O combination, which mutually complemented the real spectrum. We confirm that H2O may break the intermolecular H-bonds of the interlaced binding –OH to form a new structure, and that with the skeleton deformation of serine, H2O forms stronger H-bonds more often with the –NH3+ side indicating the flexible dynamic mechanism of the serine hydration process.
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87.15.hg Dynamics of intermolecular interactions
31.15.E- Density-functional theory
87.15.ap Molecular dynamics simulation
87.15.Fh Bonding; mechanisms of bond breakage
82.30.Rs Hydrogen bonding, hydrophilic effects
33.15.Fm Bond strengths, dissociation energies

Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water

Marwa H. Farag, José Zúñiga, Alberto Requena, and Adolfo Bastida

J. Chem. Phys. 138, 205102 (2013); http://dx.doi.org/10.1063/1.4805086 (13 pages)

Online Publication Date: 24 May 2013

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Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ∼85%–90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.20.Tp Vibrational analysis
34.20.Gj Intermolecular and atom-molecule potentials and forces
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Erratum: “Semilocal and hybrid density embedding calculations of ground-state charge-transfer complexes” [J. Chem. Phys. 138, 124112 (2013)]

S. Laricchia, E. Fabiano, and F. Della Sala

J. Chem. Phys. 138, 209901 (2013); http://dx.doi.org/10.1063/1.4807776 (1 page)

Online Publication Date: 22 May 2013

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Abstract Unavailable
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99.10.Cd Errata
31.15.eg Exchange-correlation functionals (in current density functional theory)
34.70.+e Charge transfer
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