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102. A tribute to Alan Soper – foreword by the editors
- Author
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Felix Fernandez-Alonso, George Jackson, and Daniel T. Bowron
- Subjects
Honour ,Philosophy ,media_common.quotation_subject ,Biophysics ,Tribute ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Molecular Biology ,Classics ,media_common - Abstract
This special issue of Molecular Physics is a collection of papers to mark the retirement and honour the remarkable scientific contributions of Dr. Alan Kenneth Soper FRS. Over an active research ca...
- Published
- 2019
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103. Molecular dynamics calculation of the dielectric constant
- Author
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G. Bossis and C. Brot
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Physics ,Chemical polarity ,Biophysics ,Thermodynamics ,Dielectric ,Condensed Matter Physics ,Molecular dynamics ,Dipole ,Quadrupole ,Molecule ,Correlation factor ,Physical and Theoretical Chemistry ,Molecular Biology ,Transverse direction - Abstract
In the previous papers of this series it was shown, by molecular dynamics simulations, that 2D fluid systems of pure Stockmayer molecules have a higher dielectric constant than predicted by the Onsager model or, equivalently, that their Kirkwood orientational correlation factor g k is greater than unity. In this paper this observation is further considered; it is shown that it is due to the fact that the longitudinal positive correlations are enhanced, while the negative correlations in the transverse direction are diminished, compared with those induced in a continuum by a polar molecule. Modified Stockmayer model molecules are then studied. The adopted modifications are of two kinds: (i) the molecular point dipole is excentred and (ii) a central quadrupole is added to the central dipole. In both cases g k is found to be closer to unity than for the pure Stockmayer systems. However, this is not due to a better local validity of the Onsager picture: rather, the map of the local polarization around a refer...
- Published
- 1981
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104. Evaluation of structural integrals in the perturbation of hard sphere mixture properties by intermolecular attraction in mixtures
- Author
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Thomas W. Leland, Robert K.A. Tan, and Karl-Heinz Naumann
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Physics ,Computational chemistry ,Intermolecular force ,Biophysics ,Thermodynamics ,Perturbation (astronomy) ,Pair distribution function ,Hard spheres ,First order perturbation ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Molecular Biology ,Attraction - Abstract
This paper discusses the evaluation of the structural integrals which weight the contribution of various attraction pair potentials to mixture properties. These integrals are generated when pairwise attraction in a mixture is considered to be a first order perturbation on a mixture of nonattracting hard spheres. For pure components these integrals have the form ∫∞ 0 y 2-n g HS(y, ϱd 3) dy, where g HS is the pair distribution function for pure hard spheres of diameter d and y is the ratio r/d. This paper shows that the corresponding integral for the first order perturbation contribution of an i-j pair in a mixture can be evaluated to within about 3 per cent of its computer simulation value by means of an approximation given by ∫∞ 0 y 2-n g HS(y, ϱ ) dy. In this approximation, the term is a composition dependent average of the diameters of all constituents of the mixture, g HS is the pair distribution function for pure hard spheres with the pair interaction diameter dij , and y is the ratio r/dij ...
- Published
- 1986
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105. Evaluation of the CPY and PYX approximations for short ranged anisotropic potentials
- Author
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M. S. Wertheim, J. Ram, Peter T. Cummings, and C.G. Gray
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Series (mathematics) ,Chemistry ,Quantum mechanics ,Yield (chemistry) ,Biophysics ,Molecule ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Anisotropy ,Molecular Biology ,Integral equation ,Homonuclear molecule - Abstract
In the first paper in this series, a new integral equation approximation-the Percus-Yevick excess (PYX) approximation-was introduced and contrasted with the corrected Percus-Yevick (CPY) approximation. In the present paper, these two approximations are evaluated for a molecular fluid, the molecules of which interact via a short ranged anisotropic potential prototypical of the overlap interactions encountered between homonuclear diatomic molecules. We conclude that the CPY and PYX approximations are quite accurate; interestingly, however, they unexpectedly yield very similar results leading us to conclude that, on balance, both approximations are equally good.
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- 1983
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106. New aspects of the semiempirical theory of27Al-chemical shift and its application to glasses
- Author
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Ernst Hallas and Ulrich Sternberg
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Coordination sphere ,Chemistry ,Bond ,Chemical polarity ,Substitution (logic) ,Biophysics ,Parabola ,Condensed Matter Physics ,Interpretation (model theory) ,Electronegativity ,Computational chemistry ,Physical and Theoretical Chemistry ,Atomic physics ,Polarization (electrochemistry) ,Molecular Biology - Abstract
In the first part of the paper the semiempirical theory of nuclear shielding is extended to the case of the 27Al-chemical shift. The central point is a more precise interpretation of the formula for the dependence of the bond polarity on the electronegativity of the bond partners. The theory gives only a general guideline for the change of the chemical shift with substitution in the first coordination sphere. Using the form of the parabola obtained for the dependence of the chemical shift on the electronegativity of the bond partner it is possible to give an explanation for the large span of shifts in the case of neighbours with high electronegativity like oxygen. In the second part of the paper the recently developed bond polarization theory is applied to explain the influence of substituents in the second coordination sphere on the 27Alchemical shift. This theory establishes a linear correlation between the bond polarization energy and the chemical shift. The bond polarization energy can be calculated o...
- Published
- 1989
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107. The fluctuation hypothesis of hydrogen bonding
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Yu. Ya. Efimov and Yu. I. Naberukhin
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Coupling ,Hydrogen bond ,Chemistry ,Overtone ,Isotropy ,Biophysics ,Condensed Matter Physics ,Molecular physics ,Spectral line ,symbols.namesake ,Computational chemistry ,symbols ,Molecule ,Physical and Theoretical Chemistry ,Anisotropy ,Raman spectroscopy ,Molecular Biology - Abstract
The paper is devoted to calculations of the contour shapes in the infra-red and Raman spectra of the 1 : 1 and 1 : 2 type complexes of ordinary and heavy water with two organic bases, dioxane and dimethyl sulphoxide, by means of a computer. The calculations have been made using the mathematical formalism developed in the previous papers of this series which takes into account the coupling between two stretching vibrations of the water molecule and the overtone of its bending vibration for a set of the liquid molecules variously perturbed by non-equal H-bonds. The basic parameters of the model are obtained from the spectra of HOD molecules involved in the same complex as the one considered, and from empirical correlations discussed in the previous papers. Starting from a set of parameters determined in this manner we calculate three spectra simultaneously for each of the above-mentioned complexes, namely the infra-red spectrum and the isotropic and anisotropic components of the Raman spectrum. Every spectr...
- Published
- 1977
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108. A scattering theory of diatomic molecules
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F.H. Mies
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Continuum (measurement) ,Orthogonal transformation ,Chemistry ,Scattering ,Biophysics ,Condensed Matter Physics ,Diatomic molecule ,Quantum mechanics ,Physics::Atomic and Molecular Clusters ,Complete theory ,Scattering theory ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Adiabatic process ,Wave function ,Molecular Biology - Abstract
An exact theory of diatomic molecules must be consistent with atomic scattering theory. In general scattering wavefunctions can not be factored into electronic-rotational and radial terms. Yet the starting point of most diatomic analysis is the Born-Oppenheimer approximation (BOA) which factors the total molecule wavefunction into an electronic-rotational function and a radial or vibrational function which yields the Franck-Condon principle. This is a severe approximation which is at best valid for small amplitude vibrations, may be expected to fail near dissociation limits and is completely invalid in the dissociation continuum. In the preceding paper we presented a complete theory of the total molecular wavefunction in terms of atomic channel states which gives a unified description of diatomic states throughout the entire spectrum. In this paper we perform an orthogonal transformation on the channel states and expand the total wavefunction in a complete set of adiabatic electronic-rotational states. Th...
- Published
- 1980
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109. Robust solutions of the Yvon-Born-Green equation at very high densities
- Author
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Kraemer D. Luks, K.A. Green, and A. Jangkamolkulchai
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Mathematical analysis ,Biophysics ,Close-packing of equal spheres ,Closure (topology) ,Multiplicity (mathematics) ,Hard spheres ,Condensed Matter Physics ,Radial distribution function ,Interpretation (model theory) ,Superposition principle ,Computational chemistry ,Range (statistics) ,Physical and Theoretical Chemistry ,Molecular Biology ,Mathematics - Abstract
The Yvon-Born-Green equation under the Kirkwood superposition closure is solved for a system of hard spheres at very high densities, using a robust (second-order) convergence routine. In this paper, the range of the pair correlation function solutions is extended to 100 and 200 diameters. The several solution branches found in an earlier paper (Jangkamolkulchai, A., Green, K. A., and Luks, K. D., 1989, Molec. Phys., 68, 791) were incompletely mapped. These branches are completed for 50 and 100 diameters up to values of λ0 = 4πnσ3 = 20, where the ‘close packing’ value of λ0 is 17·77, and yield multiple results for values of the density parameter λ = λ0 g (2) (1 +) on each branch. The interpretation of our results is presented in light of the analysis of solution multiplicity put forth by Lovett for approximate density functional theories.
- Published
- 1989
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110. Spectra of rare gas hydrides
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G. Herzberg, D.-C. Wang, B.P. Hurley, I. Dabrowski, M. Vervloet, and R.H. Lipson
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Chemistry ,Near-infrared spectroscopy ,Diagram ,Biophysics ,Condensed Matter Physics ,medicine.disease_cause ,Spectral line ,symbols.namesake ,Atomic orbital ,Atomic electron transition ,Atom ,Rydberg formula ,symbols ,medicine ,Physical and Theoretical Chemistry ,Atomic physics ,Molecular Biology ,Ultraviolet - Abstract
Extensive emission bands of KrH and KrD have been observed in the near infrared, visible and ultraviolet regions. Most of them can readily be arranged in Rydberg series with nsσ, npσ, npπ, nd and nf upper states and a 5sσ 2Σ lower state. There is a strong resemblance of the diagram of electronic states of KrH to that of the electronic states of the united atom Rb. The present paper deals with the electronic transitions of KrH and KrD corresponding to the 2 S and 2 P states of Rb. Difficulties (not yet entirely overcome) arise with the nd and nf complexes which will be discussed in later papers of this series. The present paper deals only with the 2Σ and 2Π states arising from ns and np orbitals. The conventional molecular constants have been determined. For most electronic states only v = 0 levels have been observed but in a few cases also v = 1 and v = 2 have been observed from hot bands. No bands with v′ ≠ v″ have been found and thus no reliable vibrational frequencies are obtained. The rotational const...
- Published
- 1988
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111. Molecular dynamics studies of the condensed phases of n-butane and their transitions
- Author
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G. Stuart Pawley and Keith Refson
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Chemistry ,Neutron diffraction ,Biophysics ,Butane ,Condensed Matter Physics ,Molecular physics ,Molecular dynamics ,chemistry.chemical_compound ,Crystallography ,Phase (matter) ,Metastability ,Libration ,Molecule ,Physical and Theoretical Chemistry ,Molecular Biology ,Monoclinic crystal system - Abstract
Molecular dynamics (MD) simulations of solid n-butane have been performed with the model described in paper I. All calculations were done on the massively parallel ICL DAP computer which made possible the large number of molecules (2048) and the long simulation runs. The structures of all three experimental phases as observed by neutron diffraction have been closely reproduced by the simulation. The plastic phase structure was not input into the simulation; instead the transition from the metastable phase II was simulated, yielding phase I after transition in very satisfactory agreement with experiment. The experimental phase III is metastable in our model since its energy is 1 per cent higher than the monoclinic structure of paper I. Analysis of the statics and dynamics of the plastic phase show that molecules are disordered about the long molecular axis, and re-orient about that axis between one major and three subsidiary sites. Large-amplitude libration means that the distribution about these sites is ...
- Published
- 1987
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112. On the dielectric theory of fluids
- Author
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David E. Logan
- Subjects
Physics ,Static dielectric constant ,Direct method ,Biophysics ,Dielectric ,Optical field ,Condensed Matter Physics ,Integral equation ,Dipole ,Classical mechanics ,Quadrupole ,Physical and Theoretical Chemistry ,Molecular Biology ,Local field - Abstract
In this, the third paper of a series, we develop a rigorous theory of the static dielectric constant, e, of non-polar fluids within the Quadrupole Approximation, whereby the effects of induced molecular quadrupoles are incorporated into the theory. The molecular quadrupoles are induced in response to the gradients of both the externally applied field and the fields due to the molecular dipoles and quadrupoles. Two hitherto distinct approaches to the problem of the electrostatic constitutive relationship are considered. The first is a grand canonical fluctuation formalism, formulated in terms of the local field and field gradient introduced in paper I of the series. The second, or direct approach to the problem is based on treating the externally applied field (field gradient) as the driving field (field gradient) in the microscopic linear response equations. By starting from non-local integral equations relating the macroscopic dipole (quadrupole) polarization, P(Q), to the external field and field gradie...
- Published
- 1982
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113. Sur les variations azimutales de l'énergie superficielle d'un nématique
- Author
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M. Warenghem
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Surface tension ,Physics ,Optics ,Condensed matter physics ,Liquid crystal ,business.industry ,Biophysics ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,business ,Molecular Biology - Abstract
In the literature, two different values exist for the azimuthal variation of nematic surface tension. In this paper, we try to explain this discrepancy by distinguishing two typical experiments and thus are led to propose a somewhat more generalized expression for the nematic surface tension. The consequences of this new expression on the nematic orientation in a cell will be described in a forthcoming paper.
- Published
- 1983
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114. Rotational self-correlation functions of N2O dissolved in liquid SF6
- Author
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C. Dreyfus, Yves Guissani, and C. Breuillard
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Chemistry ,Mathematical analysis ,Biophysics ,Rotation around a fixed axis ,Theoretical models ,Function (mathematics) ,Condensed Matter Physics ,Theoretical physics ,Self correlation ,Simple (abstract algebra) ,Physics::Atomic and Molecular Clusters ,Range (statistics) ,Torque ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
In a recent paper (1986, Molec. Phys., 59, 985), it was shown that rotational correlation functions of N2O dissolved in SF6 may be reproduced using a simulated two Lennard-Jones centre liquid model. Our simulations provided an explanation of why simple theoretical models fail to describe the rotational motion. Following the same method, we investigate, in this paper, the models based on the memory function formulation. The main conclusions are that one of the models is particularly well adapted for the low reduced torque cases (≃16) while another is good for the high reduced torque cases (≃74). The simulated reduced torque range (20–50) corresponding to our experimental data lies precisely between these limits. This explains why the system N2O/SF6 was not correctly approximated by usual memory function models.
- Published
- 1987
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115. Ab initiomodelling of the interaction of H interstitials with grain boundaries in bcc Fe
- Author
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Alexander Mirzoev, A.V. Verkhovykh, K. Yu. Okishev, and D. A. Mirzaev
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Materials science ,Condensed matter physics ,Hydrogen ,Biophysics ,Ab initio ,chemistry.chemical_element ,02 engineering and technology ,Trapping ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,WIEN2k ,Crystallography ,Ferromagnetism ,chemistry ,0103 physical sciences ,Atom ,Density functional theory ,Grain boundary ,Physical and Theoretical Chemistry ,010306 general physics ,0210 nano-technology ,Molecular Biology - Abstract
Hydrogen that is accumulated within the grain boundaries can lead to a decrease of the critical strain required to fracture the material. The paper presents results of ab initio modelling of hydrogen–grain boundary interaction in ferromagnetic bcc iron. Modelling was performed using density functional theory with generalised gradient approximation (GGA’96), as implemented in WIEN2k package. Three fully relaxed tilt grain boundaries, Σ5(310), Σ5(210) and Σ3(111), were studied. The supercells contained 40–48 atoms, i.e. 20–24 atoms in each of the two ‘grains’. Calculated formation energies of grain boundaries is 1.44, 1.83 and 1.46 J/m2 and the maximum binding (trapping) energies of hydrogen to the boundaries are 0.43, 0.83 and 0.39 eV, respectively. These values are close to other researchers’ data. The higher value of trapping energy of the Σ5(210) boundary is probably due to the asymmetrical atom configurations resulting from mutual rigid shift of the two grains that was necessary to be introduce...
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- 2016
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116. Nuclear magnetic relaxation in liquid ammonia and conditional inertial rotation in liquids
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Y. Margalit, P.W. Atkins, and A. Loewenstein
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Nuclear magnetic relaxation ,Inertial frame of reference ,Condensed matter physics ,Anisotropic diffusion ,Chemistry ,Biophysics ,Condensed Matter Physics ,Nuclear magnetic resonance ,Reaction rate constant ,Lattice (order) ,Liquid ammonia ,Polar ,Molecule ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
A theory of nuclear magnetic relaxation induced by inertial rotation in polar liquids is described. It is proposed that such rotation occurs only when the neighbourhood of a molecule attains an expanded lattice configuration. The non-markovian processes involved in the relaxation are expressed in terms of rate constants that occur in a formulation due to Anderson, and these are interpreted in terms of the unconditioned inertial rotation theory described in the preceding paper. The theory is used to interpret the values of T 1 obtained for 14N and D in liquid ammonia. The paper concludes with an outline of a general theory of anisotropic diffusion in liquids.
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- 1969
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117. A quantum mechanical study of the He, H-, He-He and He-H systems
- Author
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Howard S. Taylor and Frank E. Harris
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Condensed Matter::Quantum Gases ,Helium atom ,Hydrogen ,Biophysics ,chemistry.chemical_element ,Hydrogen atom ,Condensed Matter Physics ,Diatomic molecule ,Molecular physics ,Ion ,chemistry.chemical_compound ,chemistry ,Physics::Atomic and Molecular Clusters ,Molecule ,Physics::Atomic Physics ,Physical and Theoretical Chemistry ,Atomic physics ,Molecular Biology ,Quantum ,Helium - Abstract
This paper applies the methods for treating diatomic molecules described in papers I and II of this series, to the interation of two normal helium atoms and the interaction of a normal helium atom and a hydrogen atom. The results are compared to the experimental results of Amdur and referred to other theoretical results where they exist. The results on the He-H interaction are in fair agreement with Amdur's experimental work. The repulsive potential of two normal helium atoms disagrees with Amdur's experimental results at the distances between 1 and 2 angstroms. The helium atom and negative hydrogen ion are also discussed.
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- 1964
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118. Finite temperature scaling in density functional theory
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James W. Dufty and S. B. Trickey
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Physics ,Statistical Mechanics (cond-mat.stat-mech) ,010304 chemical physics ,Temperature scaling ,Biophysics ,FOS: Physical sciences ,Extension (predicate logic) ,Statistical mechanics ,Condensed Matter Physics ,01 natural sciences ,0103 physical sciences ,Thermal ,Density functional theory ,Statistical physics ,Physical and Theoretical Chemistry ,010306 general physics ,Molecular Biology ,Scaling ,Condensed Matter - Statistical Mechanics - Abstract
A previous analysis of scaling, bounds, and inequalities for the non-interacting functionals of thermal density functional theory is extended to the full interacting functionals. The results are obtained from analysis of the related functionals from the equilibrium statistical mechanics of thermodynamics for an inhomogeneous system. Their extension to the functionals of density functional theory is described., Comment: invited paper in honor of Andreas Savin
- Published
- 2015
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119. The evaluation of some integrals that arise in the perturbation theory of liquids
- Author
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Douglas Henderson
- Subjects
Alternative methods ,Equation of state ,Laplace transform ,Biophysics ,Condensed Matter Physics ,Numerical integration ,Order of integration (calculus) ,Quantum mechanics ,Numerical differentiation ,Applied mathematics ,Physical and Theoretical Chemistry ,Perturbation theory ,Molecular Biology ,Mathematics - Abstract
The venerable, but still very useful, perturbation theory of liquids of Barker and Henderson involves some integrals that must be obtained numerically. There is no avoiding this for potentials such as the Lennard–Jones potential. However, to obtain the pressure, Barker and Henderson also obtained the necessary density derivatives numerically. This is cumbersome and care must be used to avoid excessive error. In this paper, it is noted that the earlier and less successful perturbation theory of Frisch et al. employed an alternative method, all but forgotten, for the evaluation of similar integrals. Their method still requires numerical integration. However, it allows an investigator to obtain the integrals for the pressure by analytical differentiation. The resultant integrals must still be evaluated numerically, but the extra step and annoyance of numerical differentiation is avoided. It is noted here that this method of using density derivatives can be incorporated into the Barker–Henderson theory.
- Published
- 2015
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120. Bonding description of the Harpoon mechanism
- Author
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Miquel Solà, Eloy Ramos-Cordoba, Pedro Salvador, Mauricio Rodríguez-Mayorga, Eduard Matito, and Ministerio de Economía y Competitividad (Espanya)
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Electron density ,Materials science ,Biophysics ,FOS: Physical sciences ,Química de l'estat excitat ,Electron ,010402 general chemistry ,01 natural sciences ,Physics - Chemical Physics ,0103 physical sciences ,Atom ,Physical and Theoretical Chemistry ,Molecular Biology ,Chemical Physics (physics.chem-ph) ,010304 chemical physics ,Enllaços químics ,Avoided crossing ,Chemical bonds ,Harpoon ,Condensed Matter Physics ,Diatomic molecule ,Electron localization function ,0104 chemical sciences ,Excited state chemistry ,Chemical bond ,Chemical physics - Abstract
The lowest-lying states of LiH have been widely used to develop and calibrate many different methods in quantum mechanics. In this paper we show that the electron-transfer processes occurring in these two states are a difficult test for chemical bonding descriptors and can be used to assess new bonding descriptors on its ability to recognize the harpoon mechanism. To this aim, we study the bond formation mechanism in a series of diatomic molecules. In all studied electron-reorganization mechanisms, the maximal electron-transfer variation point along the bond formation path occurs when about half electron has been transferred from one atom to another. If the process takes places through a harpoon mechanism, this point of the reaction path coincides with the avoided crossing. The electron sharing indices and one-dimensional plots of the electron localization function and the Laplacian of the electron density along the molecular axis can be used to monitor the bond formation in diatomics and provide a distinction between the harpoon mechanism and a regular electron-reorganization process., Comment: 21 pages, 9 figures
- Published
- 2015
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121. Atomic decomposition of Kohn–Sham molecular energies: the kinetic energy component
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Leonid Patrikeev, Laurent Joubert, Vincent Tognetti, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Kohn–Sham DFT ,Orbital-free density functional theory ,Biophysics ,Kohn–Sham equations ,Context (language use) ,010402 general chemistry ,Kinetic energy ,01 natural sciences ,Approximate density functionals ,Correlation energy ,0103 physical sciences ,[CHIM]Chemical Sciences ,Statistical physics ,Physical and Theoretical Chemistry ,Wave function ,Molecular Biology ,Bader's atoms-in-molecules theory ,010304 chemical physics ,Component (thermodynamics) ,Chemistry ,Condensed Matter Physics ,0104 chemical sciences ,Chemical species ,Density functional theory ,Atomic physics - Abstract
International audience; The decomposition of molecular energies into atomic contributions within Bader's atoms-in-molecules theory is instrumental in rationalising and accounting for not only the stability but also the reactivity of chemical species. Regardless of how it is achieved, it requires the partitioning of the electronic kinetic energy. While this is ‘natural’ (but computationally expensive) in the context of wavefunction approaches, it is not more practically straightforward in the framework of Kohn–Sham density functional theory, since the corresponding atomic fictitious (related to the non-interacting system) and correlation components must be calculated. In this paper, we discuss the ability of various approaches, based on either exact formal relationships or previously proposed functional approximations, to estimate them in an efficient way for a wide variety of molecular systems. Such results might pave the way toward the realistic modelling of larger systems of chemical interest and may provide new atomic descriptors to characterise atom types.
- Published
- 2015
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122. Identification of micellar stability zones and structural inversion process of thermoresponsive polymeric micelles by dissipative particle dynamics simulations
- Author
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María del Rosario Rodríguez-Hidalgo, César Soto-Figueroa, and Luis Vicente
- Subjects
Aqueous solution ,Nanostructure ,Polymeric micelles ,Dissipative particle dynamics ,Biophysics ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Micelle ,0104 chemical sciences ,Chemical physics ,Copolymer ,Organic chemistry ,Physical and Theoretical Chemistry ,0210 nano-technology ,Molecular Biology - Abstract
The stimuli-sensitive polymeric micelles have huge applications to industrial and technological level, know their behaviour under the influence of a pure stimulus, such as the temperature is an important aspect to control and amplify its application field. In this paper, we investigate the micellar stability zones together with the structural inversion process of thermoresponsive polymeric micelles formed by a diblock copolymer (poly(N-isopropylacrylamide-b-3-[N-(3-methacrylamidopropyl)-N,N-dimethyl]ammoniopropane sulphonate (PNIPA-b-PSPP)) in an aqueous environment employing dissipative particle dynamics simulations. Our outcomes show that the PNIPA-b-PSPP copolymer has the ability to form thermodynamically stable micelles with different core-shell structure (PSPP-core/PNIPA-shell and PNIPA-core/PSPP-shell) depending on the direction of the applied stimulus (low or high temperature), the duality of this micellar behaviour is controlled by temperature effect and by the double hydrophilic character...
- Published
- 2015
- Full Text
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123. Intermolecular correlations of racemic mixtures – comparison between liquid S2Cl2 and Se2Br2
- Author
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S. Takeda, Hironori Shimakura, K. Ohara, Satoshi Ohmura, Yukinobu Kawakita, and Satoru Ohno
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Number density ,Chemistry ,Stereochemistry ,Monte Carlo method ,Intermolecular force ,Biophysics ,02 engineering and technology ,Reverse Monte Carlo ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Crystallography ,0103 physical sciences ,Atom ,Racemic mixture ,Physical and Theoretical Chemistry ,Enantiomer ,010306 general physics ,0210 nano-technology ,Structure factor ,Molecular Biology - Abstract
Liquid chalcogen-halogen A2X2 (A: S, Se, X: Cl, Br) is a racemic mixture of enantiomers between left-handed (L) and right-handed (D) chiral molecules. The lone-pair orbital of the chalcogen atom significantly affects the molecular conformation and intermolecular interaction. The latter depends on the size of the orbital and number density. High-energy X-ray diffraction measurements and reverse Monte Carlo (RMC) structural modelling were performed for liquid S2Cl2 in addition to the previous structural analysis for liquid Se2Br2. By comparing the structures of the RMC model and hard-sphere Monte Carlo (HSMC) model, the effect of refinement on the experimental structure factor can be analysed. In this paper, nearest-neighbour intermolecular pairs are classified in terms of enantiomer pairs such as like-pair (L-L and D-D) and unlike-pair (L-D). As a result, the effect of a strong intermolecular attractive interaction is detected in Se2Br2 as increasing the number of like-pairs with geometrical advant...
- Published
- 2015
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124. Oriented O(3P2), Ne(3P2), and He(3S1) atoms emerging from a bent magnetic guide
- Author
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Kevin S. Reisyan, Justin Jankunas, Andreas Osterwalder, and T. Peter Rakitzis
- Subjects
Angular momentum ,010304 chemical physics ,Chemistry ,Bent molecular geometry ,Isotropy ,Biophysics ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Magnetic field ,Ionization ,0103 physical sciences ,Physical and Theoretical Chemistry ,Atomic physics ,Multipole expansion ,Spectroscopy ,Molecular Biology ,Molecular beam - Abstract
We describe our observation of strongly oriented total electronic angular momentum J in O(3P2), Ne(3P2), and He(3S1) atoms emerging from a bent magnetic multipole guide, as measured by resonant multiphoton ionisation. This was contrary to our expectation because no additional (uniform) magnetic fields were applied to orient the atoms behind the exit of the guide. Two- and three-photon ionisation techniques were employed to determine the degree of J polarisation, from which we infer that atoms become oriented as a result of a combination of weak fringe fields, possible stray fields, and the fact that molecular beam packets do not oscillate around the geometric center of the bent multipole guide. We conclude that similar effects may exist in other, related experiments and that a detailed characterisation of the degree of orientation is required prior to any study of chemical dynamics or spectroscopy. This paper should serve as a warning for anybody using similar devices not to assume isotropic angul...
- Published
- 2015
- Full Text
- View/download PDF
125. Quantum polyhedra in LCAO MO theory
- Author
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Ramon Carbó-Dorca
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Biophysics ,010402 general chemistry ,01 natural sciences ,Polyhedron ,Computational chemistry ,Quantum mechanics ,0103 physical sciences ,Molecule ,Molecular orbital ,Physical and Theoretical Chemistry ,Molecular Biology ,Quantum ,Quantum molecular polyhedra ,Physics ,MO density functions ,010304 chemical physics ,condensed MO indices ,collective MO distances ,Molecular orbital theory ,Condensed Matter Physics ,0104 chemical sciences ,Formalism (philosophy of mathematics) ,LCAO MO theory ,Linear combination of atomic orbitals ,statistical-like functions ,Mathematical structure - Abstract
This paper presents the definition and characterisation of quantum molecular polyhedra. They are taken here within the description of a single molecule, using quantum molecular orbital (MO) density functions as vertices. The formalism and parameters associated to these mathematical structures are analysed. Picture Drawn by Pep Camps, Girona (2015). © 2015 Taylor & Francis
- Published
- 2015
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126. Bucky-corn: van der Waals composite of carbon nanotube coated by fullerenes
- Author
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Eugene A. Katz, Leonid A. Chernozatonskii, V. G. Demin, and A. A. Artyukh
- Subjects
Fullerene ,Materials science ,Biophysics ,Shell (structure) ,FOS: Physical sciences ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,01 natural sciences ,law.invention ,Condensed Matter::Materials Science ,Molecular dynamics ,symbols.namesake ,law ,Mesoscale and Nanoscale Physics (cond-mat.mes-hall) ,Physics::Atomic and Molecular Clusters ,Molecule ,Physical and Theoretical Chemistry ,Molecular Biology ,Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics ,Materials Science (cond-mat.mtrl-sci) ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,0104 chemical sciences ,Chemical physics ,symbols ,Density functional theory ,van der Waals force ,0210 nano-technology ,Layer (electronics) - Abstract
Can a C60 layer cover a surface of single-wall carbon nanotube (SWCNT) forming an exohedral pure-carbon hybrid with only van der Waals interactions? The aim of the present paper is to address this question and to demonstrate that the fullerene shell layer in such a bucky-corn structure can be stable. Theoretical study of the structure, stability and electronic properties of bucky-corn hybrids is reported for the shell of C60 and C70 molecules on an individual SWCNT, C60 dimers on an individual SWCNT as well as C60 molecules on SWNT bundles. The geometry and total energies of the bucky-corn hybrids were calculated by the molecular dynamics method, while the density functional theory method was used to simulate the electronic band structures.
- Published
- 2015
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127. Electron scattering studies of DMS, DMDS and DMSO homologous series
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Jaspreet Kaur, Bobby Antony, and Suvam Singh
- Subjects
Scattering ,Biophysics ,Condensed Matter Physics ,Optical potential ,Formalism (philosophy of mathematics) ,Homologous series ,chemistry.chemical_compound ,chemistry ,Ionization ,Dimethyl disulphide ,Molecule ,Physical and Theoretical Chemistry ,Atomic physics ,Molecular Biology ,Electron scattering ,Astrophysics::Galaxy Astrophysics - Abstract
The present paper reports ionisation, elastic and total cross section for the first three members of dimethyl sulphide, dimethyl disulphide and dimethyl sulphoxide family of molecules. The multi-scattering centre spherical complex optical potential formalism is applied for integral elastic and inelastic cross section calculations. From the inelastic part, ionisation cross section is derived using complex scattering potential-ionisation contribution method. The total cross section is then obtained from the sum of elastic and inelastic contributions. A reasonably good agreement is obtained for elastic cross section, wherever comparison is available. The ionisation and total cross section calculation for the complete set of molecules has been performed for the first time.
- Published
- 2015
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128. Vibronic coupling in the first four electronic states of CH2F+2
- Author
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Susanta Mahapatra and Rudraditya Sarkar
- Subjects
Chemistry ,Wave packet ,Biophysics ,Ab initio ,Diabatic ,Conical intersection ,Condensed Matter Physics ,symbols.namesake ,Vibronic coupling ,symbols ,Vibronic spectroscopy ,Normal coordinates ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Atomic physics ,Hamiltonian (quantum mechanics) ,Molecular Biology - Abstract
Vibronic coupling in the energetically lowest first four electronic states of CH2F+2 is studied in this paper. A model 4×4 Hamiltonian is constructed in a diabatic electronic representation employing normal coordinates of vibrational modes and standard vibronic coupling theory. Extensive ab initio quantum chemistry calculations are carried out to determine the parameters of the Hamiltonian and energetic ordering of the electronic states. The topographical features of the latter are examined at length and several conical intersections are established. Nuclear dynamics calculations on coupled electronic states are carried out from first principles by propagating wave packet. Theoretically calculated broad band vibronic structure of the four states are found to be in good accord with the experimental results.
- Published
- 2015
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129. QM/MM study of hydrolysis of arginine catalysed by arginase
- Author
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Takashi Kawakami, Mitsutaka Okumura, Toru Saito, and Shusuke Yamanaka
- Subjects
Reaction mechanism ,Hydrogen bond ,Stereochemistry ,Biophysics ,Condensed Matter Physics ,Catalysis ,Arginase ,QM/MM ,chemistry.chemical_compound ,Hydrolysis ,chemistry ,Nucleophile ,Hydroxide ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.
- Published
- 2015
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130. The rise and fall of lattice theories of the liquid state
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John S. Rowlinson
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Physics ,Theoretical physics ,Classical mechanics ,Liquid state ,Lattice (order) ,Mathematics::History and Overview ,Biophysics ,Statistical mechanics ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Molecular Biology ,Physics::History of Physics - Abstract
In this paper, the rise and fall of lattice theories of the liquid state in middle of the twentieth century is discussed in the context of contemporary developments in statistical mechanics.
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- 2015
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131. A posteriori corrections to the configuration interaction method: a single-reference and multi-reference study
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M. Erturk and Leszek Meissner
- Subjects
Scheme (programming language) ,Electronic correlation ,Computer science ,media_common.quotation_subject ,Biophysics ,Configuration interaction ,Condensed Matter Physics ,Computational chemistry ,A priori and a posteriori ,Simplicity ,Physical and Theoretical Chemistry ,Molecular Biology ,computer ,Algorithm ,media_common ,computer.programming_language - Abstract
The single-reference (SR) configuration interaction (CI) method is nowadays rather rarely used in quantum-chemical calculations. The reason is that the method is not competitive with the coupled-cluster (CC) approach that uses the same number of parameters but is size-extensive and more accurate. The accuracy of the CI method can be increased by applying size-extensivity a posteriori corrections but even that does not make the SR-CI method much more attractive. The CI scheme has, however, one important advantage over the CC one. Due to its formal simplicity, the SR-CI approach can be easily generalised to the multi-reference (MR) case while such a generalisation for the CC method turned out nontrivial. Two basic MR-CC formulations are formally complicated, numerically demanding, vulnerable to intruder states, and sensitive to the problem of multiple solutions. Contrary to that the MR-type CI schemes are among very few methods that are used in routine calculations for systems requiring a MR description. The problem of improving the MR-type CI results by applying an a-posteriori correction is in this context very appealing. In the paper, we discuss different types of corrections trying to show that the one based on the SR cluster expansion is both well theoretically justified and reliable in numerical applications. That is illustrated on model CI calculations of SR and MR type.
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- 2015
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132. Elastic constants and dynamics in nematic liquid crystals
- Author
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Michael P. Allen and Anja Humpert
- Subjects
Work (thermodynamics) ,Condensed matter physics ,Chemistry ,Biophysics ,Condensed Matter Physics ,Space (mathematics) ,Condensed Matter::Soft Condensed Matter ,Molecular dynamics ,Classical mechanics ,Liquid crystal ,Vector field ,Tensor ,Physical and Theoretical Chemistry ,Twist ,Exponential decay ,Molecular Biology ,QC - Abstract
In this paper we present molecular dynamics calculations of the Frank elastic constants, and associated time correlation functions, in nematic liquid crystals. We study two variants of the Gay-Berne potential, and use system sizes of half a million molecules, significantly larger than in previous studies of elastic behaviour. Equilibrium orientational fluctuations in reciprocal (k-) space were calculated, to determine the elastic constants by fitting at low k; our results indicate that small system size may be a source of inaccuracy in previous work. Furthermore the dynamics of the Gay-Berne nematic were studied by calculating time correlation functions of components of the order tensor, together with associated components of the velocity field, for a set of wave vectors k. Confirming our earlier work, we found exponential decay for splay and twist correlations, and oscillatory exponential decay for the bend correlation. In the present work, we confirm similar behaviour for the corresponding velocity components. In all cases the decay rates, and oscillation frequencies, were found to be accurately proportional to k-squared for small k, as predicted by the equations of nematodynamics. However, the observation of oscillatory bend fluctuations, and corresponding oscillatory shear flow decay, is in contradiction to the usual assumptions appearing in the literature, and in standard texts. We discuss the advantages and drawbacks of using large systems in these calculations.
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- 2015
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133. Effects of wettability and interfacial nanobubbles on flow through structured nanochannels: an investigation of molecular dynamics
- Author
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Tsu-Hsu Yen
- Subjects
Materials science ,Isotropy ,Biophysics ,Nanotechnology ,Slip (materials science) ,Condensed Matter Physics ,Contact angle ,Molecular dynamics ,Chemical physics ,Surface roughness ,Wetting ,Graphite ,Boundary value problem ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
Solid–fluid boundary conditions are strongly influenced by a number of factors, including the intrinsic properties of the solid/fluid materials, surface roughness, wettability, and the presence of interfacial nanobubbles (INBs). The interconnected nature of these factors means that they should be considered jointly. This paper employs molecular dynamics (MD) simulation in a series of studies aimed at elucidating the influence of wettability in boundary behaviour and the accumulation of interfacial gas. Specifically, we examined the relationship between effective slip length, the morphology of nanobubbles, and wettability. Two methods were employed for the promotion of hydrophobicity between two structured substrates with similar intrinsic contact angles. We also compared anisotropic and isotropic atomic arrangements in the form of graphite and Si(100), respectively. A physical method was employed to deal with variations in surface roughness, whereas a chemical method was used to adjust the wall–fluid inte...
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- 2015
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134. Mobility of carbon ions andC+(4P)in helium computed from quantum-mechanical transport cross sections
- Author
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K. Alioua, Lamia Aïssaoui, and Moncef Bouledroua
- Subjects
Work (thermodynamics) ,Buffer gas ,Biophysics ,chemistry.chemical_element ,Condensed Matter Physics ,Ion ,Boltzmann kinetic equation ,chemistry ,Physical and Theoretical Chemistry ,Atomic physics ,Molecular Biology ,Carbon ,Quantum ,Helium - Abstract
On the light of a previous work and its recommendations by Matoba et al. [J. Phys. B 41, 145205 (2008)], this paper proposes to look at the mobility of ground and metastable-excited states of C+ ions moving into a helium buffer gas. The calculations, based on the three-temperature theory for solving the Boltzmann kinetic equation, are accomplished with quantum-mechanical transport cross sections at the low temperatures 4.3 and 77 K. The obtained mobility results are contrasted with the available theoretical data and experimental measurements, which show acceptable agreements.
- Published
- 2015
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135. Dissipative particle dynamics simulation on the rheological properties of heavy crude oil
- Author
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Sibo Wang, Junbo Xu, and Hao Wen
- Subjects
Chromatography ,Light crude oil ,Shear thinning ,Chemistry ,Dissipative particle dynamics ,Biophysics ,Condensed Matter Physics ,Chemical engineering ,Rheology ,Emulsion ,Heavy crude oil ,Physical and Theoretical Chemistry ,Molecular Biology ,Mass fraction ,Asphaltene - Abstract
The rheological properties of heavy crude oil have a significant impact on the production, refining and transportation. In this paper, dissipative particle dynamics (DPD) simulations were performed to study the effects of the addition of light crude oil and emulsification on the rheological properties of heavy crude oil. The simulation results reflected that the additionof light crude oil reduced the viscosity effectively. The shear thinning behaviour of crude oil mixtures were becoming less distinct as the increase of the mass fraction of light crude oil. According to the statistics, the shear had an influence on the aggregation and spatial orientation of asphaltene molecules. In addition, the relationship between the viscosity and the oil mass fraction was investigated in the simulations of emulsion systems. The viscosity increased with the oil mass fraction slowly in oil-in-water emulsions. When the oil mass fraction was higher than 50%, the increase became much faster since systems had been converted into water-in-oil emulsions. The equilibrated morphologies of emulsion systems were shown to illustrate the phase inversion. The surfactant-like feature of asphaltenes was also studied in the simulations.
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- 2015
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136. Aspects of structural order in 209 Bi-containing particles for potential MRI contrast agents based on quadrupole enhanced relaxation
- Author
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Carina Sampl, Stefan Spirk, Rupert Kargl, Karin Stana-Kleinschek, Roland Fischer, Martin Thonhofer, Paul Josef Krassnig, Evrim Umut, Danuta Kruk, Christian Gösweiner, and Hermann Scharfetter
- Subjects
Materials science ,010304 chemical physics ,medicine.diagnostic_test ,Relaxation (NMR) ,Biophysics ,Magnetic resonance imaging ,Contrast (music) ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Order (biology) ,Nuclear magnetic resonance ,0103 physical sciences ,Quadrupole ,medicine ,Physical and Theoretical Chemistry ,Nuclear quadrupole resonance ,Molecular Biology - Abstract
Quadrupole relaxation enhancement (QRE) has been suggested as the key mechanism for a novel class of field-selective, potentially responsive magnetic resonance imaging contrast agents. In previous publications, QRE has been confirmed for solid compounds containing Bi-209 as the quadrupolar nucleus (QN). For QRE to be effective in aqueous dispersions, several conditions must be met, i.e. high transition probability of the QN at the H-1 Larmor frequency, water exchange with the bulk and comparatively slow motion of the Bi-carrying particles. In this paper, the potential influence of structural order within the compounds (crystallinity') on QRE was studied by nuclear quadrupole resonance (NQR) spectroscopy in one crystalline and two amorphous preparations of Triphenylbismuth (BiPh3). The amorphous preparations comprised (1) a shock-frozen melt and (2) a granulate of polystyrene which contained homogeneously distributed BiPh3 after common dissolution in THF and subsequent evaporation of the solvent. In contrast to the crystalline powder which exhibits strong, narrow NQR peaks the amorphous preparations did not reveal any NQR signals above the noise floor. From these findings, we conclude that the amorphous state leads to a significant spectral peak broadening and that for efficient QRE in potential contrast agents structures with a high degree of order (near crystalline) are required.
- Published
- 2018
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137. Calculations of the optical and EPR spectral data for Cr3+ion in Y3Ga5O12crystal from the complete diagonalisation method
- Author
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Yang Mei, Ren-Ming Peng, Wen-Chen Zheng, and Cheng-Fu Wei
- Subjects
Chemistry ,Ligand ,Biophysics ,Lattice distortion ,Analytical chemistry ,Condensed Matter Physics ,Molecular physics ,law.invention ,Ion ,Crystal ,law ,Crystal field theory ,Condensed Matter::Strongly Correlated Electrons ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Spectral data ,Molecular Biology ,Energy matrix - Abstract
The complete diagonalisation (of energy matrix) method is applied in this paper to calculate together the optical and electron paramagnetic resonance (EPR) spectral data for Cr3+ ion at the trigonal Ga3+ site of Y3Ga5O12 crystal. The method is founded on the two-spin-orbit-parameter model where in addition to the contributions from the spin-orbit parameter of central dn ion (i.e., one-spin-orbit-parameter model) in the traditional crystal field theory, those from the spin-orbit parameter of ligand ion via covalence effect is also considered. The calculated results propose that by using only four adjustable parameters, the 12 observed spectral data (nine optical band positions and three EPR parameters g//, g⊥ and D) in Y3Ga5O12: Cr3+ are reasonably explained. The impurity-induced local lattice distortion of Cr3+ in Y3Ga5O12 crystal is also estimated through the calculations. The results are discussed.
- Published
- 2015
- Full Text
- View/download PDF
138. Proposing an efficient algorithm for designing universal nanoelectronic molecular logic gates
- Author
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Keyhan Khamforoosh
- Subjects
Structure (mathematical logic) ,Coupling ,Computer science ,Efficient algorithm ,Biophysics ,Nanotechnology ,Hardware_PERFORMANCEANDRELIABILITY ,Type (model theory) ,Condensed Matter Physics ,Simple (abstract algebra) ,Logic gate ,Hardware_INTEGRATEDCIRCUITS ,Electronic engineering ,Point (geometry) ,Physical and Theoretical Chemistry ,Molecular Biology ,Hardware_LOGICDESIGN ,Electronic circuit - Abstract
In today's world, there are still demands for minimising the dimensions of electronic circuits, the result of which is designing nanoelectronic circuits and very small molecular gates and switches. The point which causes trouble in this design is high impact of different parameters on the performance of circuit. Despite the suggestion of simple electronic circuits and different gates, impact of parameters like length of molecule, angle between different atoms, coupling situation of electrodes to molecule, the type of atoms used in a molecule's structure and other cases has made their development almost impossible. In this paper, there was an attempt to study previous works in order to, first, mention the effects of different conditions on circuit performance and, second, present an algorithm for designing gates so as to minimise the effects of these parameters on circuit performance.
- Published
- 2014
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139. Monte Carlo molecular simulation of the Na-, Mg-, and mixtures of Na/Mg-montmorillonites systems, in function of the pressure
- Author
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M.G. Miranda-Pascual and M.L. Chávez-García
- Subjects
Coordination number ,Monte Carlo method ,Biophysics ,Analytical chemistry ,Mineralogy ,Condensed Matter Physics ,chemistry.chemical_compound ,Adsorption ,Montmorillonite ,chemistry ,Volume (thermodynamics) ,medicine ,Physical and Theoretical Chemistry ,Swelling ,medicine.symptom ,Molecular Biology ,Bar (unit) ,Monte Carlo molecular modeling - Abstract
In this paper, Monte Carlo (MC) simulation has been used to study the swelling pattern of Na-montmorillonite (Na-Mnt), Mg-montmorillonite (Mg-Mnt), and Na/Mg-mixture montmorillonite (4NaMg-Mnt; 2Na2Mg-Mnt). The molecular simulation was performed in the NVT (number of molecules, volume and temperature are constant) ensemble at normal temperature (300 K) and 225, 300, and 340 bar over an H2O content 147, 196, and 294 mg g−1 of clay. The simulations reproduce the swelling pattern of Na-Mnt and Mg-Mnt. The predicted spacing of the Na/Mg-Mnt mixtures is closely related to that of Mg-Mnt and confirms the results reported in the literature for Na-rich/Mg-poor Mnt. The results of the water adsorption and the swelling properties on the system Na-Mnt, Mg-Mnt, and the Na/Mg-Mnt mixtures are reflected with a transformation to two-hydrate stages. The probability of the coordination number of Na+, Mg2+, and mixtures tends to increase with an increasing amount of H2O molecules, but decreases with increasing pressure. Th...
- Published
- 2014
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140. Computational prediction of a new class of tri-coordinate cyclic heavier carbene analogues RM(μ-R)2AlR2(M = Ge, Sn, Pb)
- Author
-
Jing Xu and Yi-hong Ding
- Subjects
Crystallography ,chemistry.chemical_compound ,Nucleophile ,Chemistry ,Stereochemistry ,Transition metal carbene complex ,Biophysics ,Moiety ,Chemical stability ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Molecular Biology ,Carbene - Abstract
Design of stable heavier carbene analogues M(II) (M = Ge, Sn, Pb) with structural motifs different from the traditional di-coordinate analogues is extremely of interest and challengeable. In this paper, we computationally designed a novel class of tri-coordinate cyclic heavier analogues of carbenes covering a number of substituents, i.e., RM(μ-R)2AlR2 (M = Ge, Sn, Pb) 1, in which two sets of inter-molecular donor–acceptor interactions were formed between the di-coordinate carbene MR2 and the AlR3 moiety. The M-centre was found to undergo both the nucleophilic and insertion reactions, indicative of the ‘carbene’ character. We also designed c-1 starting from the known di-coordinate cyclic MR2 and AlR3 under 16 kinds of substituents [NR′2, OR′, PR′2, SR′(R′ = H, Me, iPr, Ph)]; c-1 also has favourable thermodynamic stability. After the only known cyclic tri-coordinate M(II) [M2,R4] inter-molecularly formed between two di-coordinate MR2, the presently designed new tri-coordinate cyclic heavier carbene analogue...
- Published
- 2014
- Full Text
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141. A molecular dynamics simulation on the convective heat transfer in nanochannels
- Author
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Song Ge, Youwei Gu, and Min Chen
- Subjects
Convective heat transfer ,Chemistry ,Bulk temperature ,Biophysics ,Thermodynamics ,Film temperature ,Laminar flow ,Heat transfer coefficient ,Condensed Matter Physics ,Churchill–Bernstein equation ,Nusselt number ,Physics::Fluid Dynamics ,Heat transfer ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
The understanding of the flow and heat transfer processes for fluid through micro- and nanochannels becomes imperative due to its wide application in micro- and nano-fluidic devices. In this paper, the method to simulate the convective heat transfer process in molecular dynamics is improved based on a previous study. With this method, we simulate a warm dense fluid flowing through a cold parallel-plate nanochannel with constant wall temperature. The characteristics of the velocity and temperature fields are analysed. The temperature difference between the bulk average temperature of fluid and the wall temperature decreases in an exponential form along the flow direction. The Nusselt number for the laminar flow in parallel-plate nanochannel is smaller than its corresponding value at macroscale. It could be attributed to the temperature jump at the fluid–wall interface, which decreases the temperature gradient near the wall. The results also reveal that the heat transfer coefficient is related to the surfac...
- Published
- 2014
- Full Text
- View/download PDF
142. Analysis method for comparison of two similar molecules using natural orbitals of the difference density matrix: application to substituent effects
- Author
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Daisuke Yamaki
- Subjects
Density matrix ,Chemistry ,Biophysics ,Substituent ,Electron ,Condensed Matter Physics ,Resonance (chemistry) ,Molecular physics ,Nitrobenzene ,chemistry.chemical_compound ,Atomic orbital ,Computational chemistry ,Molecule ,Physical and Theoretical Chemistry ,Molecular Biology ,Eigenvalues and eigenvectors - Abstract
In this paper, we propose an analysis method to compare the electronic states of two similar molecules using natural orbitals (NOs) of the difference density matrix. In this method, inert and unchanged orbital components of the electronic states can be excluded from the analysis. The difference can then be interpreted as being due to electron transfers between NO-pairs, whose eigenvalues have the same absolute values but opposite signs. As a demonstration, we show an application to the substituent effects on nitrobenzene by comparing nitrobenzene and benzene molecules. By investigating a small number of orbital pairs, our analysis method successfully and separately detects the inductive and the resonance effects.
- Published
- 2014
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- View/download PDF
143. Inhomogeneous contribution to the width of zero-field MARY line
- Author
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O.A. Anisimov, V.N. Verkhovlyuk, Yu. N. Molin, and S.V. Anishchik
- Subjects
Condensed matter physics ,Chemistry ,Biophysics ,Magnetic field effect ,Condensed Matter Physics ,Magnetic field ,Spin chemistry ,Radical ion ,Zero field ,Singlet state ,Physical and Theoretical Chemistry ,Molecular Biology ,Hyperfine structure ,Coherence (physics) - Abstract
The paper discusses the dependence of the singlet product yield in the recombination of radical ion pairs vs. external magnetic field in a situation when hyperfine couplings in one partner are much greater than those in the other partner. The theoretical calculations performed for the case of equivalent magnetic nuclei demonstrate a considerable effect of small hyperfine couplings on the shape of this dependence. In particular, the width of the low-field magnetic field effect (referred to as the ‘zero-field’ MARY line) is determined by weak hyperfine interactions along with spin coherence lifetime. The predictions are in a qualitative agreement with experimental results.
- Published
- 2014
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144. Accurate spectroscopic calculations of the 12 Λ-S states and 27 Ω states of NF+cation including the spin–orbit coupling effect
- Author
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D. H. Shi, Wei Yu, Jinfeng Sun, and Zunlue Zhu
- Subjects
Davidson correction ,Field (physics) ,Chemistry ,Biophysics ,Multireference configuration interaction ,Spin–orbit interaction ,Condensed Matter Physics ,Potential energy ,Bound state ,Complete active space ,Physical and Theoretical Chemistry ,Atomic physics ,Molecular Biology ,Basis set - Abstract
This paper studies the potential energy curves (PECs) of 27 Ω states generated from the 12 Λ-S states (X2Π, 12Σ+, 12Σ−, 22Σ−, A2Π, 12Δ, 14Σ+, 14Σ−, 24Σ−, 14Π, 24Π and 14Δ), which are attributed to the first dissociation channel of NF+ cation. Of these 12 states, only 22Σ− and 24Π are the repulsive ones, which are very different from those reported by G.-S. Kim and D. M. Hirst, Mol. Phys. 86, 1183–1193 (1995). In addition, the 12Δ and 14Σ− states are found to possess the double well. 14Σ+, 14Σ− and 14Δ are found to be the inverted states with the spin–orbit coupling effect taken into account, and 12Σ+, 12Σ−, 12Δ, 14Σ+, 24Σ− and 14Δ are found to be the weakly bound states. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with Davidson correction. The convergent behaviour of the present calculations is discussed with respect to the basis set and level of theory. All the PECs are ...
- Published
- 2014
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145. Taking one charge off a two-dimensional Wigner crystal
- Author
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L. Samaj, Moritz Antlanger, Emmanuel Trizac, Martial Mazars, Gerhard Kahl, Laboratoire de Physique Théorique d'Orsay [Orsay] (LPT), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Institut für Theoretische Physik and Center for Computational Materials Science, Vienna University of Technology (TU Wien), Institute of Physics, Slovak Academy of Science [Bratislava] (SAS), Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), and Starita, Sabine
- Subjects
Physics ,Planar projection ,Planar array ,Monte Carlo method ,Biophysics ,FOS: Physical sciences ,Condensed Matter - Soft Condensed Matter ,Condensed Matter Physics ,Energy minimization ,01 natural sciences ,[PHYS.COND.CM-SCM] Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] ,010305 fluids & plasmas ,Wigner crystal ,Lattice (order) ,Metastability ,Quantum mechanics ,0103 physical sciences ,Soft Condensed Matter (cond-mat.soft) ,Physical and Theoretical Chemistry ,010306 general physics ,Ground state ,[PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] ,Molecular Biology - Abstract
A planar array of identical charges at vanishing temperature forms a Wigner crystal with hexagonal symmetry. We take off one (reference) charge in a perpendicular direction, hold it fixed, and search for the ground state of the whole system. The planar projection of the reference charge should then evolve from a six-fold coordination (center of a hexagon) for small distances to a three-fold arrangement (center of a triangle), at large distances $d$ from the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimization and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that the $d=0$ and $d\to\infty$ limiting cases extend for finite values of $d$ from the respective starting points into two sequences of stable states, with intersecting energies at some value $d_t$; beyond this value the branches continue as metastable states., Comment: 17 pages, 11 figures
- Published
- 2014
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146. A conservative and a hybrid early rejection schemes for accelerating Monte Carlo molecular simulation
- Author
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Amgad Salama, Ahmad Kadoura, and Shuyu Sun
- Subjects
Canonical ensemble ,Computer science ,Quantum Monte Carlo ,Monte Carlo method ,Biophysics ,Condensed Matter Physics ,Rejection rate ,Reduction (complexity) ,Hybrid Monte Carlo ,Dynamic Monte Carlo method ,Statistical physics ,Physical and Theoretical Chemistry ,Molecular Biology ,Algorithm ,Monte Carlo molecular modeling - Abstract
Molecular simulation could provide detailed description of fluid systems when compared to experimental techniques. They can also replace equations of state; however, molecular simulation usually costs considerable computational efforts. Several techniques have been developed to overcome such high computational costs. In this paper, two early rejection schemes, a conservative and a hybrid one, are introduced. In these two methods, undesired configurations generated by the Monte Carlo trials are rejected earlier than it would when using conventional algorithms. The methods are tested for structureless single-component Lennard–Jones particles in both canonical and NVT-Gibbs ensembles. The computational time reduction for both ensembles is observed at a wide range of thermodynamic conditions. Results show that computational time savings are directly proportional to the rejection rate of Monte Carlo trials. The proposed conservative scheme has shown to be successful in saving up to 40% of the computational tim...
- Published
- 2014
- Full Text
- View/download PDF
147. Nuclear spin-spin coupling constants prediction based on XGBoost and LightGBM algorithms
- Author
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Tong Deng, Xin-xin Zhang, and Guo-zhu Jia
- Subjects
Physics ,Coupling constant ,010304 chemical physics ,Condensed matter physics ,Nuclear Theory ,Biophysics ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Molecular property ,0103 physical sciences ,Condensed Matter::Strongly Correlated Electrons ,Physical and Theoretical Chemistry ,Nuclear Experiment ,Spin (physics) ,Molecular Biology - Abstract
Nuclear magnetic resonance (NMR) is a robust method for the analysis of molecular complex structures, and the measurement of the nuclear spin–spin coupling constant is the key. In this paper, based...
- Published
- 2019
- Full Text
- View/download PDF
148. Frequency dependence of microwave-assisted electron-transfer chemical reactions
- Author
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Guennadi A. Kouzaev
- Subjects
Materials science ,010304 chemical physics ,Field (physics) ,Biophysics ,Frequency dependence ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Chemical reaction ,0104 chemical sciences ,Solvent ,Electron transfer ,Chemical physics ,Reagent ,0103 physical sciences ,Polar ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Molecular Biology ,Microwave - Abstract
In this paper, the electron transfer reactions in the microwave field are studied. A classical theory is developed for a mix of reagents and polar frequency-dispersive and lossy solvent filling vessels excited by microwaves. These reactors are described by a system of non-linear partial self-consistent differential equations for non-stationary microwave field, heat and liquid dynamics, and chemical molecular kinetics. A particular solution of this system is considered for the isothermic electron-transfer reactions in the microwave field varying its frequency with the calculation of the normalized Marcus rate coefficient. It is found that for the small normalized reaction free energy, the chemical reactions are supported by microwaves in a wide frequency band with an increased value of the exponent in the Marcus rate coefficient. At higher values of this energy, these reactions are driven only by conventional microwave heating. The restrictions for the given theory are reviewed, and further experimental and semi-classical and quantum-mechanical studies are found essential for practical applications of these findings.
- Published
- 2019
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149. Quantum chemical study on ·Cl-initiated degradation of ethyl vinyl ether in atmosphere
- Author
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Fengrong Zhang, Dandan Han, Haijie Cao, and Maoxia He
- Subjects
Quantum chemical ,010304 chemical physics ,Chemistry ,Biophysics ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Redox ,0104 chemical sciences ,Atmosphere ,Product analysis ,Reaction rate constant ,0103 physical sciences ,Ethyl vinyl ether ,Degradation (geology) ,Physical and Theoretical Chemistry ,Molecular Biology ,Nuclear chemistry - Abstract
A theoretical investigation on oxidation reaction of ethyl vinyl ether (EVE) and .Cl are carried out in this paper. By employing M06-2x/6-31 + g(d,p)//6-311++g(3df,2p) method, complex reaction mech...
- Published
- 2019
- Full Text
- View/download PDF
150. Comparison of three related imidazolium ionic liquids and their CS2 solutions
- Author
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Ruth M. Lynden-Bell
- Subjects
Materials science ,010304 chemical physics ,Biophysics ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Dication ,chemistry.chemical_compound ,chemistry ,Chemical physics ,0103 physical sciences ,Ionic liquid ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
The aim of this paper is to give examples showing how computer simulation can be used to obtain insight into the behaviour of ionic liquids. Three related ionic liquids with cations containing imid...
- Published
- 2019
- Full Text
- View/download PDF
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