Diffusion in linear porous media with periodic entropy barriers: A tube formed by contacting spheres

The problem of transport in quasi-one-dimensional periodic structures has been studied recently by several groups [D. Reguera et al., Phys. Rev. Lett.96, 130603 (2006); P. S. Burada et al., Phys. Rev. E75, 051111 (2007); B. Q. Ai and L. G. Liu, ibid.74, 051114 (2006); B. Q. Ai et al., ibid.75, 061126 (2007); B. Q. Ai and L. G. Liu, J. Chem. Phys.126, 204706 (2007); 128, 024706 (2008); E. Yariv and K. D. Dorfman, Phys. Fluids19, 037101 (2007); N. Laachi et al., Europhys. Lett.80, 50009 (2007); A. M. Berezhkovskii et al., J. Chem. Phys.118, 7146 (2003); 119, 6991 (2003)]. Using the concept of "entropy barrier" [R. Zwanzig, J. Phys. Chem.96, 3926 (1992)] one can classify such structures based on the height of the entropy barrier. Structures with high barriers are formed by chambers, which are weakly connected with each other because they are connected by small apertures. To escape from such a chamber a diffusing particle has to climb a high entropy barrier to find an exit that takes a lot of time [I. V. Grigoriev et al., J. Chem. Phys.116, 9574 (2002)]. As a consequence, the particle intrachamber lifetime tau(esc) is much larger than its intrachamber equilibration time, tau(rel), tau(esc)>tau(rel). When the aperture is not small enough, the intrachamber escape and relaxation times are of the same order and the hierarchy fails. This is the case of low entropy barriers. Transport in this case is analyzed in the works of Schmid and co-workers, Liu and co-workers, and Dorfman and co-workers, while the work of Berezhkovskii et al. is devoted to diffusion in the case of high entropy barriers.     

Stochastic Liouville equation treatment of the electron paramagnetic resonance line shape of an S-state ion in solution

The current approaches used for the analysis of electron paramagnetic resonance spectra of Gd3+ complexes suffer from a number of drawbacks. Even the elaborate model of [Rast et al., J. Chem. Phys. 113, 8724 (2000)] where the electron spin relaxation is explained by the modulation of the zero-field splitting (ZFS), by molecular tumbling (the so called static contribution), and deformations (transient contribution), is only readily applicable within the validity range of the Redfield theory [Advances in Magnetic Resonance, edited by J.-S. Waugh (Academic, New York, 1965), Vol. 1, p. 1], that is, when the ZFS is small compared to the Zeeman energy and the rotational and vibrational modulations are fast compared to the relaxation time. Spin labels (nitroxides and transition metal complexes) have been studied for years in systems that violate these conditions. The theoretical framework commonly used in such studies is the stochastic Liouville equation (SLE). The authors shall show how the physical model of Rast et al. can be cast into the SLE formalism, paying special attention to the specific problems introduced by the [Uhlenbeck and Ornstein, Phys. Rev. 36, 823 (1930)] process used to model the transient ZFS. The resulting equations are very general and valid for arbitrary correlation times, magnetic field strength, electron spin S, or symmetry. The authors demonstrate the equivalence of the SLE approach with the Redfield approximation for two well-known Gd3+ complexes.     

Relative energy of the high-(5T2g) and low-(1A1g) spin states of the ferrous complexes [Fe(L)(NHS4)]: CASPT2 versus density functional theory

High-level ab initio calculations using multiconfigurational perturbation theory [complete active space with second-order perturbation theory (CASPT2)] were performed on the transition energy between the lowest high-spin (corresponding to (5T2g) in Oh) and low-spin (corresponding to 1A1g in Oh) states in the series of six-coordinated Fe(II) molecules [Fe(L)(NHS4)], where NHS4 is 2,2'-bis(2-mercaptophenylthio)diethylamine dianion and L=NH3, N2H4, PMe3, CO, and NO+. The results are compared to (previous and presently obtained) results from density functional theory (DFT) calculations with four functionals, which were already shown previously by Casida and co-workers [Fouqueau et al., J. Chem. Phys. 120, 9473 (2004); Ganzenmuller et al., ibid. 122, 234321 (2005); Fouqueau et al., ibid. 122, 044110 (2005); Lawson Daku et al., ChemPhysChem 6, 1393 (2005)] to perform well for the spin-pairing problem in these and other Fe(II) complexes, i.e., OLYP, PBE0, B3LYP, and B3LYP*. Very extended basis sets were used both for the DFT and CASPT2 calculations and were shown to be necessary to obtain quantitative results with both types of method. This work presents a sequel to a previous DFT/CASPT2 study of the same property in the complexes [Fe(H2O)6]2+, [Fe(NH3)6]2+, and [Fe(bpy)3]2+ [Pierloot et al., J. Chem. Phys. 125, 124303 (2006)]. The latter work was extended with new results obtained with larger basis sets and including the OLYP functional. For all considered complexes, the CASPT2 method predicts the correct ground state spin multiplicity. Since experimental data for the actual quintet-singlet (free) energy differences are not available, the performance of the different DFT functionals was judged based on the comparison between the DFT and CASPT2 results. From this, it was concluded that the generalized gradient OLYP functional performs remarkably well for the present series of ferrous compounds, whereas the success of the three hybrid functionals varies from case to case.     

Accuracy of recent potential energy surfaces for the He-N2 interaction. II. Molecular beam scattering and bulk gas relaxation phenomena

A new semiempirical exchange-Coulomb model potential energy surface for the N(2)-He interaction was reported recently [A. K. Dham et al., J. Chem. Phys. 127, 054302 (2007)] and, using it, the temperature dependence of bulk gas properties of N(2)-He mixtures, such as the second virial coefficient and traditional transport phenomena, most of which depend primarily on the isotropic component of the interaction potential energy surface, was determined. Values of these properties, along with values calculated using two high-quality ab initio potential energy surfaces [C.-H. Hu and A. J. Thakkar, J. Chem. Phys. 104, 2541 (1996); K. Patel et al., ibid 119, 909 (2003)] were compared critically to available experimental data. The present paper reports on the ability of the same three potential energy surfaces to predict state-to-state and total differential cross sections, total integral cross sections, and the temperature dependence of bulk gas relaxation phenomena (including magnetic field effects on transport coefficients). While all three potential energy surfaces give total differential and higher speed integral scattering results that fall within the experimental uncertainties, integral scattering results and state-to-state differential cross section measurements consistently exceed the calculated values. All three surfaces give similar agreement with the relaxation properties of N(2)-He binary mixtures, with the semiempirical exchange-Coulomb model potential energy surface giving slightly better overall agreement with experiment than the two ab initio potential energy surfaces.     

Molecular simulation of polymer assisted protein refolding

Protein refolding in vitro, the formation of the tertiary structure that enables the protein to display its biological function, can be significantly enhanced by adding a polymer of an appropriate hydrophobicity and concentration into the refolding buffer. A molecular simulation of the refolding of a two-dimensional simple lattice protein was presented. A protein folding map recording the occurrence frequency of specified conformations was derived, from which the refolding thermodynamics and kinetics were interpreted. It is shown that, in the absence of polymer, the protein falls into the "energy trapped" conformations characterized by a high intramolecular hydrophobic interaction, denoted as HH contact, and a high magnitude of the structure overlap function, chi. This makes it difficult for the protein to fold to the native state. The polymer with a suitable chain length, concentration, and hydrophobicity has formed complex with partially folded protein and created diversified intermediates with low chi. This gives more pathways for the protein to fold to the native state. At a given hydrophobicity, the short chain polymer has a broader concentration range where it assists protein folding than those of long chains. The above simulation agrees well with the experimental results reported elsewhere [Cleland et al., J. Biol. Chem. 267, 13327 (1992); ibid., Bio/Technology 10, 1013 (1992); Chen et al., Enzyme Microb. Technol. 32, 120 (2003); Lu et al., Biochem. Eng. J. 24, 55 (2005); ibid., J. Chem. Phys. 122, 134902 (2005); ibid., Biochem. Eng. J. (to be published)] and is of fundamental importance for the design and application of polymers for protein refolding.     

Modeling of HeN+ clusters. II. Calculation of He3+ vibrational spectrum

We have computed the vibrational spectrum of the helium ionized trimer He(3)(+) using three different potential energy surfaces [D. T. Chang and G. L. Gellene, J. Chem. Phys. 119, 4694 (2003); E. Scifoni et al., ibid. 125, 164304 (2006); I. Paidarova et al., Chem. Phys. 342, 64 (2007)]. Differences in the details of these potential energy surfaces induce discrepancies between bound state energies of the order of 0.01 eV. The effects of the geometric phase induced by the conical intersection between the ground electronic potential energy surface and the first excited one are studied by computing vibrational spectra with and without this phase. The six lowest vibrational bound states are negligibly affected by the geometric phase. Indeed, they correspond to wavefunctions localized in the vicinity of the linear symmetric configurations and can be assigned well defined vibrational quantum numbers. On the other hand, higher excited states are delocalized, cannot be assigned definite vibrational quantum numbers, and the geometric phase shifts their energies by approximately 0.005 eV.     

Prevalence for the universal distribution of relaxation times near the glass transitions in experimental model systems: rodlike liquid crystals and orientationally disordered crystals

Recently, Nielsen et al. [J. Chem. Phys. 130, 154508 (2009); Philos. Mag. 88, 4101 (2008)] demonstrated a universal pattern for the high frequency wing of the loss curve for primary relaxation time on approaching the glass transition for organic liquids. In this contribution it is presented that a similar universality occurs for glass-forming liquid crystals and orientationally disordered crystals (plastic crystals). Empirical correlations of the found behavior are also briefly discussed.     

Calculation of the charge-carrier mobility of polyguanylic acid: the simultaneous effect of stretching and twisting

Charge-carrier (electron and hole) mobilities of polyguanylic acid have been computed using the deformation-potential approximation from ab initio Hartree-Fock band structure. Mobilities resulting from electron scattering on torsional acoustic phonons are calculated and compared to those obtained from a previous calculation [F. B. Beleznay et al., J. Chem. Phys. 119, 5690 (2003)] considering interaction with compressional phonons. The simultaneous effect of the two independent scatterings is also calculated.     

Pulsed ENDOR study of Cu(I)-NO adsorption complexes in Cu-L zeolite

The local environments of Cu(I)-NO adsorption complexes formed in zeolites Cu-L and Cu-ZSM-5 were studied by electron spin resonance (ESR), pulsed electron nuclear double resonance (ENDOR), and hyperfine sublevel correlation spectroscopy (HYSCORE). Cu(I)-NO complexes have attracted special interest because they are important intermediates in the catalytic decomposition of nitric oxide over copper exchanged zeolites. Recently, detailed structures of the complexes in Cu-ZSM-5 zeolites, O2-Al-O2-Cu(I)-NO, have been proposed on the basis of quantum chemical calculations (Pietrzyk, et al. J. Phys. Chem. B 2003, 107, 6105. Dedecek, et al. Phys. Chem. Chem. Phys. 2002, 4, 5406). 27Al pulsed ENDOR and HYSCORE experiments allowed the hyperfine coupling parameters of an aluminum nuclei found in the vicinity of the Cu(I)-NO complex formed in zeolite Cu-L to be estimated. The data indicate that the aluminum atom is located in the third coordination sphere of the adsorbed NO molecule in agreement with the suggested geometry of the adsorption sites. Broad distributions of aluminum nuclear quadrupole and hyperfine coupling parameters and short electron spin relaxation times of the Cu(I)-NO species prevented the determination of the 27Al hyperfine couplings for zeolite Cu-ZSM-5.     

Quantum Monte Carlo calculations of the dissociation energy of the water dimer

We report diffusion quantum Monte Carlo (DMC) calculations of the equilibrium dissociation energy D(e) of the water dimer. The dissociation energy measured experimentally, D(0), can be estimated from D(e) by adding a correction for vibrational effects. Using the measured dissociation energy and the modern value of the vibrational energy Mas et al., [J. Chem. Phys. 113, 6687 (2000)] leads to D(e)=5.00+/-0.7 kcal mol(-1), although the result Curtiss et al., [J. Chem. Phys. 71, 2703 (1979)] D(e)=5.44+/-0.7 kcal mol(-1), which uses an earlier estimate of the vibrational energy, has been widely quoted. High-level coupled cluster calculations Klopper et al., [Phys. Chem. Chem. Phys. 2, 2227 (2000)] have yielded D(e)=5.02+/-0.05 kcal mol(-1). In an attempt to shed new light on this old problem, we have performed all-electron DMC calculations on the water monomer and dimer using Slater-Jastrow wave functions with both Hartree-Fock approximation (HF) and B3LYP density functional theory single-particle orbitals. We obtain equilibrium dissociation energies for the dimer of 5.02+/-0.18 kcal mol(-1) (HF orbitals) and 5.21+/-0.18 kcal mol(-1) (B3LYP orbitals), in good agreement with the coupled cluster results.     

High resolution NMR study of T(1) magnetic relaxation dispersion. III. Influence of spin 1∕2 hetero-nuclei on spin relaxation and polarization transfer among strongly coupled protons

Effects of spin-spin interactions on the nuclear magnetic relaxation dispersion (NMRD) of protons were studied in a situation where spin [fraction one-half] hetero-nuclei are present in the molecule. As in earlier works [K. L. Ivanov, A. V. Yurkovskaya, and H.-M. Vieth, J. Chem. Phys. 129, 234513 (2008); S. E. Korchak, K. L. Ivanov, A. V. Yurkovskaya, and H.-M. Vieth, ibid. 133, 194502 (2010)], spin-spin interactions have a pronounced effect on the relaxivity tending to equalize the longitudinal relaxation times once the spins become strongly coupled at a sufficiently low magnetic field. In addition, we have found influence of (19)F nuclei on the proton NMRD, although in the whole field range, studied protons and fluorine spins were only weakly coupled. In particular, pronounced features in the proton NMRD were found; but each feature was predominantly observed only for particular spin states of the hetero-nuclei. The features are explained theoretically; it is shown that hetero-nuclei can affect the proton NMRD even in the limit of weak coupling when (i) protons are coupled strongly and (ii) have spin-spin interactions of different strengths with the hetero-nuclei. We also show that by choosing the proper magnetic field strength, one can selectively transfer proton spin magnetization between spectral components of choice.     

Adding salt to an aqueous solution of t-butanol: is hydrophobic association enhanced or reduced?

Recent neutron scattering experiments on aqueous salt solutions of amphiphilic t-butanol by Bowron and Finney [Phys. Rev. Lett. 89, 215508 (2002); J. Chem. Phys. 118, 8357 (2003)] suggest the formation of t-butanol pairs, bridged by a chloride ion via O-H...Cl- hydrogen bonds, leading to a reduced number of intermolecular hydrophobic butanol-butanol contacts. Here we present a joint experimental/theoretical study on the same system, using a combination of molecular dynamics (MD) simulations and nuclear magnetic relaxation measurements. Both MD simulation and experiment clearly support the more classical scenario of an enhanced number of hydrophobic contacts in the presence of salt, as it would be expected for purely hydrophobic solutes. [T. Ghosh et al., J. Phys. Chem. B 107, 612 (2003)]. Although our conclusions arrive at a structurally completely distinct scenario, the molecular dynamics simulation results are within the experimental error bars of the Bowron and Finney data.     

Study of the molecular structure, ionization spectrum, and electronic wave function of 1,3-butadiene using electron momentum spectroscopy and benchmark Dyson orbital theories

The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within approximately 0.2 eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense pi(-2) pi(*+1) satellite at approximately 13.1 eV in the ionization spectrum of the s-trans conformer.     

The use of atomic intrinsic polarizabilities in the evaluation of the dispersion energy

The recent approach presented by Becke and Johnson [J. Chem. Phys. 122, 154104 (2005); 123, 024101 (2005); 123, 154101 (2005); 124, 174104 (2006); 124, 014104 (2006)] for the evaluation of dispersion interactions based on the properties of the exchange-hole dipole moment is combined with a Hirshfeld-type partitioning for the molecular polarizabilities into atomic contributions, recently presented by some of the present authors [A. Krishtal et al., J. Chem. Phys. 125, 034312 (2006)]. The results on a series of nine dimers, involving neon, methane, ethene, acetylene, benzene, and CO(2), taken at their equilibrium geometry, indicate that when the C(6), C(8), and C(10) terms are taken into account, the resulting dispersion energies can be obtained deviating 3% or 8% from high level literature data [E. R. Johnson and A. D. Becke, J. Chem. Phys. 124, 174104 (2006)], without the use of a damping function, the only outlier being the parallel face-to-face benzene dimer.     

Three-dimensional potential energy surface of the Ar-OH(2Pi i) complex

Pure rotational transitions in the ground state for Ar-OH and Ar-OD [Y. Ohshima et al., J. Chem. Phys. 95, 7001 (1991) and Y. Endo et al., Faraday Discuss. 97, 341 (1994)], those in the excited states of the OH vibration, nu(s)=1 and 2, observed by Fourier-transform microwave spectroscopy in the present study, rotation-vibration transitions observed by infrared-ultraviolet double-resonance spectroscopy [K. M. Beck et al., Chem. Phys. Lett. 162, 203 (1989) and R. T. Bonn et al., J. Chem. Phys. 112, 4942 (2000)], and the P-level structure observed by stimulated emission pumping spectroscopy [M. T. Berry et al., Chem. Phys. Lett. 178, 301 (1991)] have been simultaneously analyzed to determine the potential energy surface of Ar-OH in the ground state. A Schrodinger equation, considering all the freedom of motions for an atom-diatom system in the Jacobi coordinate, R, theta, and r, was numerically solved to obtain energies of the rovibrational energy levels using the discrete variable representation method. A three-dimensional potential energy surface is determined by a least-squares fitting. In the analysis the potential parameters, obtained by ab initio calculations at the RCCSD(T) level of theory with a set of basis functions of aug-cc-pVTZ and midbond functions, are used as initial values. The determined intermolecular potential energy surface and its dependence on the OH monomer bond length are compared with those of an isovalent radical complex, Ar-SH.     

A global 12-dimensional ab initio potential energy surface and dynamical studies for the SiH4+H-->SiH3+H2 reaction

A global 12-dimensional ab initio interpolated potential energy surface (PES) for the SiH(4)+H-->SiH(3)+H(2) reaction is presented. The ab initio calculations are based on the unrestricted quadratic configuration interaction treatment with all single and double excitations together with the cc-pVTZ basis set, and the modified Shepard interpolation method of Collins and co-workers [K. C. Thompson et al., J. Chem. Phys. 108, 8302 (1998); M. A. Collins, Theor. Chem. Acc. 108, 313 (2002); R. P. A. Bettens and M. A. Collins, J. Chem. Phys. 111, 816 (1999)] is applied. Using this PES, classical trajectory and variational transition state theory calculations have been carried out, and the computed rate constants are in good agreement with the available experimental data.     

Reactivity enhancement of ultracold O(3P)+H2 collisions by van der Waals interactions

The role of van der Waals forces in O((3)P)+H(2)(upsilon=1,j=0) collisions is investigated theoretically at low and ultralow temperatures. Quantum scattering calculations have been performed for zero total angular momentum using the lowest London-Eyring-Polanyi-Sato double-polynomial (3)A(") potential-energy surface reported by [Rogers et al., J. Phys. Chem. A 104, 2308 (2000)] and its recent BMS1 and BMS2 extensions developed by [Brandao et al., J. Chem. Phys. 121, 8861 (2004)] which provide a more accurate treatment of the van der Waals interaction. Our calculations show that van der Waals forces strongly influence chemical reactivity at ultracold translational energies. The presence of a zero-energy resonance for the BMS1 surface is found to enhance reactivity in the ultracold regime and shift the Wigner threshold to lower temperatures.     

The new insight into dynamic crossover in glass forming liquids from the apparent enthalpy analysis

One of the most intriguing phenomena in glass forming systems is the dynamic crossover (T(B)), occurring well above the glass temperature (T(g)). So far, it was estimated mainly from the linearized derivative analysis of the primary relaxation time τ(T) or viscosity η(T) experimental data, originally proposed by Stickel et al. [J. Chem. Phys. 104, 2043 (1996); J. Chem. Phys. 107, 1086 (1997)]. However, this formal procedure is based on the general validity of the Vogel-Fulcher-Tammann equation, which has been strongly questioned recently [T. Hecksher et al. Nature Phys. 4, 737 (2008); P. Lunkenheimer et al. Phys. Rev. E 81, 051504 (2010); J. C. Martinez-Garcia et al. J. Chem. Phys. 134, 024512 (2011)]. We present a qualitatively new way to identify the dynamic crossover based on the apparent enthalpy space (H(a) (')=dlnτ/d(1/T)) analysis via a new plot lnH(a) (') vs. 1∕T supported by the Savitzky-Golay filtering procedure for getting an insight into the noise-distorted high order derivatives. It is shown that depending on the ratio between the "virtual" fragility in the high temperature dynamic domain (m(high)) and the "real" fragility at T(g) (the low temperature dynamic domain, m = m(low)) glass formers can be splitted into two groups related to f < 1 and f > 1, (f = m(high)∕m(low)). The link of this phenomenon to the ratio between the apparent enthalpy and activation energy as well as the behavior of the configurational entropy is indicated.