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Showing papers in "Molecular Physics in 2011"


Journal ArticleDOI
TL;DR: In this paper, a set of pre-computed molecular integrals can be used to explicitly create a quantum circuit, i.e., a sequence of elementary quantum operations, that, when run on a quantum computer, obtains the energy of a molecular system with fixed nuclear geometry using the quantum phase estimation algorithm.
Abstract: Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient methods for the exact simulation of quantum systems on classical computers presents a limitation of current computational approaches. We report, in detail, how a set of pre-computed molecular integrals can be used to explicitly create a quantum circuit, i.e. a sequence of elementary quantum operations, that, when run on a quantum computer, obtains the energy of a molecular system with fixed nuclear geometry using the quantum phase estimation algorithm. We extend several known results related to this idea and discuss the adiabatic state preparation procedure for preparing the input states used in the algorithm. With current and near future quantum devices in mind, we provide a complete example using the hydrogen molecule of how a chemical Hamiltonian can be simulated using ...

441 citations


Journal ArticleDOI
TL;DR: Explicitly correlated MP2-F12 and CCSD(T)-F12 methods with orbital-pair-specific Slater-type geminals are proposed in this article, where the fixed amplitude ansatz of Ten-no is used, and different exponents of the Slater geminal functions can be chosen for core-core, core-valence, and valence-valences pairs.
Abstract: Explicitly correlated MP2-F12 and CCSD(T)-F12 methods with orbital-pair-specific Slater-type geminals are proposed. The fixed amplitude ansatz of Ten-no is used, and different exponents of the Slater geminal functions can be chosen for core–core, core–valence, and valence–valence pairs. This takes care of the different sizes of the correlation hole and leads to improved results when inner-shell orbitals are correlated. The complications and the extra computational cost as compared to corresponding calculations with a single geminal are minor. The improved accuracy of the method is demonstrated for spectroscopic properties of Br2, As2, Ga2, Cu2, GaCl, CuCl, and CuBr, where the d-orbitals are treated as core.

186 citations


Journal ArticleDOI
TL;DR: In this paper, it was shown that the correlation energy within the adiabatic-connection fluctuation dissipation theorem is exact in a Kohn-Sham framework while for Hartree-Fock reference states this is not the case.
Abstract: Random-phase approximation (RPA) correlation methods based on Kohn–Sham density-functional theory and Hartree–Fock are derived using the adiabatic-connection fluctuation dissipation theorem. It is shown that the correlation energy within the adiabatic-connection fluctuation-dissipation theorem is exact in a Kohn–Sham framework while for Hartree–Fock reference states this is not the case. This shows that Kohn–Sham reference states are probably better suited to describe electron correlation for use in RPA methods than Hartree–Fock reference states. Both, Kohn–Sham and Hartree–Fock RPA methods are related to each other both by comparing the underlying correlation functionals and numerically through the comparison of total energies and reaction energies for a set of small organic molecules.

145 citations


Journal ArticleDOI
TL;DR: In this paper, the importance of polarization effects on a series of examples concerning the structural properties, such as the stabilization of particular crystal structures or the formation of highly-coordinated multivalent ions in the melts, as well as the dynamic properties such as diffusion of ionic species is discussed.
Abstract: Ionic solids and melts are compounds in which the interactions are dominated by electrostatic effects. However, the polarization of the ions also plays an important role in many respects as has been clarified in recent years thanks to the development of realistic polarizable interaction potentials. After detailing these models, we illustrate the importance of polarization effects on a series of examples concerning the structural properties, such as the stabilization of particular crystal structures or the formation of highly-coordinated multivalent ions in the melts, as well as the dynamic properties such as the diffusion of ionic species. The effects on the structure of molten salt interfaces (with vacuum and electrified metal) is also described. Although most of the results described here concern inorganic compounds (molten fluorides and chlorides, ionic oxides...), the particular case of the room-temperature ionic liquids, a special class of molten salts in which at least one species is organic, will a...

122 citations


Journal ArticleDOI
TL;DR: In this article, Brogioli et al. employed a modified Poisson-Boltzmann free energy density functional to calculate the ionic adsorption and desorption onto and from the charged electrodes, from which the electric work of a cycle is deduced.
Abstract: A huge amount of entropy is produced at places where fresh water and seawater mix, for example at river mouths. This mixing process is a potentially enormous source of sustainable energy, provided it is harnessed properly, for instance by a cyclic charging and discharging process of porous electrodes immersed in salt and fresh water, respectively [D. Brogioli, Phys. Rev. Lett. 103, 058501 (2009)]. Here we employ a modified Poisson–Boltzmann free-energy density functional to calculate the ionic adsorption and desorption onto and from the charged electrodes, from which the electric work of a cycle is deduced. We propose optimal (most efficient) cycles for two given salt baths involving two canonical and two grand-canonical (dis)charging paths, in analogy to the well-known Carnot cycle for heat-to-work conversion from two heat baths involving two isothermal and two adiabatic paths. We also suggest a slightly modified cycle which can be applied in cases that the stream of fresh water is limited.

97 citations


Journal ArticleDOI
TL;DR: In this paper, a dynamical density functional theory for Brownian particles with an arbitrary shape was derived, which constitutes a microscopic framework to explore the collective dynamical behavior of biaxial particles in non-equilibrium.
Abstract: Starting from the many-particle Smoluchowski equation, we derive a dynamical density functional theory for Brownian particles with an arbitrary shape. Both passive and active (self-propelled) particles are considered. The resulting theory constitutes a microscopic framework to explore the collective dynamical behavior of biaxial particles in non-equilibrium. For spherical and uniaxial particles, earlier derived dynamical density functional theories are recovered as special cases. Our study is motivated by recent experimental progress in preparing colloidal particles with many different biaxial shapes.

92 citations


Journal ArticleDOI
TL;DR: In this article, the geometrical features of the first and second monolayers of water using a Matsui Akaogi (MA) force field for the TiO2 surface and a flexible single point charge model for the water molecules were reported.
Abstract: We have carried out classical molecular dynamics of various surfaces of TiO2 with its interface with water. We report the geometrical features of the first and second monolayers of water using a Matsui Akaogi (MA) force field for the TiO2 surface and a flexible single point charge model for the water molecules. We show that the MA force field can be applied to surfaces other than rutile (110). It was found that water OH bond lengths, H–O–H bond angles and dipole moments do not vary due to the nature of the surface. However, their orientation within the first and second monolayers suggest that planar rutile (001) and anatase (001) surfaces may play an important role in not hindering removal of the products formed on these surfaces. Also, we discuss the effect of surface termination in order to explain the layering of water molecules throughout the simulation box.

83 citations


Journal ArticleDOI
TL;DR: In this article, a theoretical study of the HXYH (X, Y, O, S and Se) monomers and dimers has been carried out by means of MP2 computational methods.
Abstract: A theoretical study of the HXYH (X, Y = O, S and Se) monomers and dimers has been carried out by means of MP2 computational methods. For the monomers, isomerization (H2X=Y//HXYH) and rotational transition state barriers have been calculated. Additionally, the molecular electrostatic potential of the isolated monomers has also been analysed. Due to the chiral nature of these compounds, homo and heterochiral dimers have been explored. The number of minima found for the dimers range between 13 and 22. The electron density of the complexes has been characterized with the Atoms in Molecules (AIM) methodology finding a large variety of interactions. The DFT-SAPT method has been used to analyse the components of the interaction energies. Concerning chalcogen–chalcogen interactions, although the most stable minima are formed through hydrogen bonds (especially if OH groups are present in the molecules) as the size of the atoms involved in the interaction increase, the chalcogen–chalcogen contacts become more impor...

81 citations


Journal ArticleDOI
TL;DR: In this article, the electronic properties of N-doped graphenes, including graphitic, pyridinic, and pyrrolic nitrogens, were investigated in stage-1 Li-graphite intercalation compounds and their electronic properties were investigated.
Abstract: First-principles calculations are used to investigate the electronic properties of N-doped graphenes, including graphitic, pyridinic and pyrrolic nitrogens. The pristine, graphitic and pyridinic N-doped graphenes are also employed in stage-1 Li–graphite intercalation compounds and their electronic properties were investigated. The results indicate that the pristine graphene shows a zero-gap semiconducting behaviour, while the conductive behaviour in graphitic graphene changes to n-type. The pyridinic and pyrrolic defects make a p-type semiconductor. In the Li intercalation compounds, the greatest contribution of Li atoms to the total density of states is from the hybridization of 2s and 2p states in the conduction band.

78 citations


Journal ArticleDOI
TL;DR: In this article, a theoretical study was performed to examine intermolecular halogen bond properties in one-dimensional NCX chains (X=Cl and Br). Geometries, binding energies, and charge-transfer of linear (NCCl)2−10 and (NCBr)2-10 chains were investigated by means of second-order Moller-Plesset perturbation theory (MP2) and DFT methods.
Abstract: A theoretical study was performed to examine intermolecular halogen bond properties in one-dimensional NCX chains (X=Cl and Br). Geometries, binding energies, and charge-transfer of linear (NCCl)2–10 and (NCBr)2–10 chains were investigated by means of second-order Moller–Plesset perturbation theory (MP2) and DFT methods. All MP2, B3LYP and M06/aug-cc-pVTZ results indicate that the magnitudes of the interaction energies increase with increasing halogen size. Considering MP2/aug-cc-pVTZ results, it can be seen that the (NCBr)10 cluster is bound −12.72 kcal/mol more strongly than (NCCl)10. The n-dependent trend of charge-transfer is reasonably correlated with cooperative effects in halogen bond energies. According to the quantum theory of atoms in molecules, the capability of the (NCX)2–10 clusters for electron localization, at the C–X ··· N bond critical point (BCPs), depends on the cluster size and thereby leads to cooperative changes in the C–X ··· N strength, and charge-transfer. It is also revealed that...

68 citations


Journal ArticleDOI
TL;DR: In this paper, the authors studied the properties (surface pressure, compression and shear moduli, texture) of silica nanoparticle layers at the air-water interface and found that the dependence of the mechanical properties on particle hydrophobicity is closely related to the foamability and stability of the foams made from dispersions.
Abstract: We have studied the properties (surface pressure, compression and shear moduli, texture) of silica nanoparticle layers at the air–water interface. Particle hydrophobicity or, equivalently, the contact angle between particles, air and water, is the main factor that influences surface organization and surface elastic moduli. The surface layers are denser for particles of higher hydrophobicity. The compression and shear moduli, as well as the yield and melt strains, present a maximum for contact angles around 90°. The dependence of the mechanical properties on particle hydrophobicity is closely related to the foamability and stability of the foams made from dispersions.

Journal ArticleDOI
TL;DR: In this article, the effect of size, solvent molecular weight and molecular architecture on GS dispersability and GS-Octane nanocomposite was analyzed using both equilibrium and non-equilibrium simulations.
Abstract: Dispersing nanoparticles in a polymer can enhance both mechanical and transport properties. Nanocomposites with high thermal conductivity could be obtained by using thermally conductive nanoparticles. Carbon-based nanoparticles are extremely promising, although high resistances to heat transfer from the nanoparticles to the polymer matrix could cause significant limitations. This work focuses on graphene sheets (GS) dispersed within n-octane. Although pristine GS agglomerate, equilibrium molecular dynamic simulations suggest that when the GS are functionalized with short branched hydrocarbons along the GS edges, they remain well dispersed. Results are reported from equilibrium and non-equilibrium molecular dynamics simulations to assess the effective interactions between dispersed GS, the self-assembly of GS, and the heat transfer through the GS–octane nanocomposite. Tools are designed to understand the effect of GS size, solvent molecular weight and molecular architecture on GS dispersability and GS–octa...

Journal ArticleDOI
TL;DR: In this article, the density profile of a colloidal liquid near a wall under shear flow was analyzed using a dynamical density functional theory and it was shown that the center of mass of the density distribution increases with shear rate, i.e. shear increases the potential energy of the particles.
Abstract: Using a dynamical density functional theory we analyse the density profile of a colloidal liquid near a wall under shear flow. Due to the symmetries of the system considered, the naive application of dynamical density functional theory does not lead to a shear induced modification of the equilibrium density profile, which would be expected on physical grounds. By introducing a physically motivated dynamic mean field correction we incorporate the missing shear induced interparticle forces into the theory. We find that the shear flow tends to enhance the oscillations in the density profile of hard spheres at a hard wall and, at sufficiently high shear rates, induces a non-equilibrium transition to a steady state characterized by planes of particles parallel to the wall. Under gravity, we find that the centre of mass of the density distribution increases with shear rate, i.e. shear increases the potential energy of the particles.

Journal ArticleDOI
TL;DR: In this article, the solvent-mediated critical Casimir force acting on colloidal particles immersed in a binary liquid mixture of water and 2,6-lutidine and close to substr...
Abstract: We study theoretically and experimentally the solvent-mediated critical Casimir force acting on colloidal particles immersed in a binary liquid mixture of water and 2,6-lutidine and close to substr...

Journal ArticleDOI
TL;DR: In this paper, density functional theory calculations were explored to investigate the antioxidant activity of flavonoid compounds such as apigenin and scutellarein, and the results revealed that scutellearein exhibits higher degree of antioxidant activity than apigein.
Abstract: The potent antioxidant activity of flavonoids relevant to their ability to scavenge reactive oxygen species is the most important function of flavonoids. Density functional theory calculations were explored to investigate the antioxidant activity of flavonoid compounds such as apigenin and scutellarein. The biological characteristics are dependent on electronic parameters, describing the charge distribution on the rings of the flavonoid molecules. The computation of structural and various molecular descriptors such as polarizability, dipole moment, energy gap, homolytic O–H bond dissociation enthalpies (BDEs), ionization potential (IP), electron affinity, hardness, softness, electronegativity, electrophilic index and density plot of molecular orbital for neutral as well as radical species were carried out and studied. The B3LYP/6-311G(d,p) basis set was adopted for all the computations. This computation reveals that scutellarein exhibits higher degree of antioxidant activity than apigenin. Their dipole mo...

Journal ArticleDOI
TL;DR: In this article, the authors show that the MLR form can readily accommodate the inclusion of "damping functions" in the description of the long-range potential tail, and that inclusion of such terms leads to much more realistic short-range extrapolation behaviour.
Abstract: The recently introduced [Mol. Phys. 105, 663 (2007)] ‘Morse/long-range’ (or MLR) potential energy function is a very flexible form which explicitly incorporates the theoretically predicted inverse-power-sum long-range tail, is smooth and differentiable everywhere, and includes the well depth , equilibrium distance r e, and long-range interaction coefficients Cm as explicit parameters. This form is being used increasingly commonly in direct-potential-fit analyses of experimental data. The present work shows that the MLR form can readily accommodate the inclusion of ‘damping functions’ in the description of the long-range potential tail, and that inclusion of such terms leads to much more realistic short-range extrapolation behaviour. Illustrative applications to the ground electronic states of MgH, Li2 and ArXe are presented.

Journal ArticleDOI
Uwe Manthe1
TL;DR: In this paper, the authors present a review of the state-of-the-art work in the area of thermal rate constants for reactions proceeding via barriers and highlight key method developments as well as important applications.
Abstract: In recent years the accurate and truly predictive calculation of thermal rate constants has become feasible for reactive systems consisting of more than only three or four atoms and results for benchmark six atom reactions as were presented. The present article reviews research focusing on the accurate calculation of rates for reactions proceeding via barriers and highlights key method developments as well as important applications in the area. It discusses the quantum transition state concept which allows one to rigorously and efficiently compute averages with respect to thermal or micro-canonical ensembles and to interpret the results using intuitive pictures. Schemes for the construction of accurate high-dimensional potential energy surfaces required in quantum dynamics simulations and for performing efficient multi-dimensional wave packet dynamics calculations are also reviewed. As a result of the large number of accurate reaction rate calculations for diverse reactions which have been presented in ab...

Journal ArticleDOI
TL;DR: In this paper, the influence of the electrode on the interfacial capacitance of a planar double layer at and around zero surface charge was studied using a modified Poisson-Boltzmann theory for 1:1 electrolytes.
Abstract: The influence of polarization of the electrode on the interfacial capacitance of a restricted primitive model planar double layer at and around zero surface charge is studied using a modified Poisson–Boltzmann theory for 1:1 electrolytes. The polarization, which occurs due to a dielectric discontinuity at the electrode–electrolyte interface, is treated by imagining fictitious image charges within the electrode, which mimic surface polarization charges. Specifically, the cases (i) when the electrode is a metallic conductor with infinite relative permittivity and (ii) when the electrode is a low relative permittivity insulator are investigated. The capacitance around zero surface charge is seen to undergo a gradual transition from having a camel-shaped form with a minimum at low electrolyte concentrations to having a maximum at higher concentrations consistent with the trends observed in earlier works in the absence of surface polarization. However, the transition envelope shifts to the lower concentration ...

Journal ArticleDOI
TL;DR: In this article, deeply supercooled water droplets held containerless in an acoustic levitator were investigated with high-energy X-ray scattering and the temperature dependence of the Xray structure function was found to be nonlinear.
Abstract: Deeply supercooled water droplets held containerless in an acoustic levitator are investigated with high-energy X-ray scattering. The temperature dependence of the X-ray structure function is found to be nonlinear. Comparison with two popular computer models reveals that structural changes are predicted too abrupt by the TIP5P-E model, while the rate of change predicted by TIP4P-Ew is in much better agreement with experiment. The abrupt structural changes, predicted by the TIP5P-E model to occur in the temperature range between 260 and 240 K as water approaches the homogeneous nucleation limit, are unrealistic. Both models underestimate the distance between neighbouring oxygen atoms and overestimate the sharpness of the OO distance distribution.

Journal ArticleDOI
TL;DR: The radial distribution function of liquid water, as obtained by the computer simulations of several classical models of water, is re-examined in this article and two intriguing features are shown.
Abstract: The radial distribution function of liquid water, as obtained by the computer simulations of several classical models of water, is re-examined herein and shown to display two intriguing features. These consist of a compact ‘three-peaks structure’ over three molecular diameters, which is followed by an apparent loss of the packing correlations beyond A. This is in contrast to simple liquids for which the correlations decay continuously with distance. This structure is reproduced for many widely used classical force field models of water and by scattering experiments as well. It is also preserved in aqueous binary mixtures of organic solvents, even up to equimolar mixture in some cases. The analysis of the structure factor highlights the role played by the competition between the packing effect and the hydrogen bonding interactions. This analysis, in terms of competition of two length scales, is also supported by a simple core-soft model, which reproduces the structural features outlined above.

Journal ArticleDOI
TL;DR: In this paper, the intermolecular interactions in F3CX and NCH(CNH) triads were analyzed at the MP2/cc-pVTZ computational level.
Abstract: MP2 calculations with the cc-pVTZ basis set were used to analyse the intermolecular interactions in F3CX ··· NCH(CNH) ··· NCH(CNH) triads (X=Cl, Br), which are connected via hydrogen and halogen bonds. Molecular geometries, binding energies, and infrared spectra of the dyads and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention was given to parameters such as the cooperative energies, cooperative dipole moments, and many-body interaction energies. All studied complexes, with the simultaneous presence of a halogen bond and a hydrogen bond, show cooperativity with energy values ranging between −1.32 and −2.88 kJ mol−1. The electronic properties of the complexes were analysed using the Molecular Electrostatic Potential (MEP), electron density shift maps and the parameters derived from the Atoms in Molecules (AIM) methodology.

Journal ArticleDOI
TL;DR: In this article, the infrared spectrum of the rare isotopologue has been investigated in the range 2190 −2250 cm−1 with a frequency-comb-referenced cavity ring-down spectrometer.
Abstract: The infrared spectrum of the rare isotopologue has been investigated in the range 2190–2250 cm−1 with a frequency-comb-referenced cavity ring-down spectrometer. Thirty-three ro-vibrational transitions of the ν3 fundamental band have been detected. Their absolute frequency was measured with a relative uncertainty ranging from to . The experimental frequencies were fitted to the conventional Hamiltonian of a linear molecule and a new set of spectroscopic parameters for the fundamental vibrational state has been improved for this species.

Journal ArticleDOI
TL;DR: In this article, the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture, and an efficient circuit design is shown for a two-qubit Grover search algorithm providing quadratic speedup over the classical counterpart.
Abstract: We present a new global optimization algorithm in which the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture. To demonstrate the efficiency of the method, a standard suite of single and multi-dimensional optimization functions along with the energies and the geometric structures of Lennard-Jones clusters are given as well as the application of the algorithm on quantum circuit design problems. We show that as an improvement over previous methods, the algorithm scales as N 2.5 for the Lennard-Jones clusters of N-particles. In addition, an efficient circuit design is shown for a two-qubit Grover search algorithm which is a quantum algorithm providing quadratic speedup over the classical counterpart.

Journal ArticleDOI
TL;DR: In this paper, a hardness equalization principle for polyatomic molecules analogous to the electronegativity equalisation principle was proposed, and a radial-dependent electrostatic definition of hardness of atoms suggested by the present authors was derived.
Abstract: Relying upon the commonality of the basic philosophy of the origin and development of electronegativity and hardness, we have attempted to explore whether a hardness equalization principle can be conceived for polyatomic molecules analogous to the electronegativity equalization principle. Starting from the new radial-dependent electrostatic definition of hardness of atoms suggested by the present authors and assuming that the hardness equalization principle is operative and valid, we have derived a formula for evaluating the hardness of polyatomic molecule, , where n is the number of ligands, ri is the atomic radius of the ith atom and C is a constant. The formula has been used to calculate the hardness values of 380 polyatomic molecules with widely divergent physico-chemical properties. The computed hardness data of a set of representative molecules are in good agreement with the corresponding hardness data evaluated quantum mechanically. The hardness data of the present work are found to be quite effica...

Journal ArticleDOI
TL;DR: In this article, the authors used a model based on the White-Bear version of fundamental measure theory to test recent predictions, due to Evans and co-workers, that capillary condensation in a capped capillary slit is a continuous interfacial critical phenomenon related to the complete wetting transition.
Abstract: We use a model Density Functional, based on the White-Bear version of Fundamental Measure theory, to test recent predictions, due to Evans and co-workers, that capillary condensation in a capped capillary-slit is a continuous interfacial critical phenomenon related to the complete wetting transition. Using a model with a square-well intermolecular fluid–fluid attraction we first determine accurately the location of the first-order capillary evaporation transition in an infinite (open) hard-wall capillary slit. Extending the density functional model to allow for a two-dimensional order-parameter profile, we then study the adsorption as the chemical potential is reduced to capillary evaporation but now in a capillary-slit that is capped at one end. The equilibrium density profiles obtained show that, sufficiently close to the phase boundary, a meniscus separating liquid-like and vapour-like phases forms near the capped end, and that as capillary evaporation is approached, continuously unbinds from the cappe...

Journal ArticleDOI
TL;DR: In this article, the use of B-spline basis sets is explored in the context of a vibrational program for automatic potential energy surface (PES) construction and multimode anharmonic vibrational wave function calculation.
Abstract: The use of B-spline basis sets is explored in the context of a vibrational program for automatic potential energy surface (PES) construction and multimode anharmonic vibrational wave function calculation. Results are compared with calculations using localized Gaussians and harmonic oscillator basis functions. Potential energy surfaces are constructed in an iterative fashion using a recently developed adaptive density-guided approach. The basis set requirements for an accurate representation of the vibrational wave functions are met by both B-spline basis sets as well as the well-known distributed Gaussian basis sets. Furthermore, the property of minimal support of the B-spline functions makes the use of B-spline basis more advantageous compared to harmonic oscillator basis functions, when combined with the adaptive procedure for PES construction used in this work. The methodology is tested for model potentials and water and subsequently applied to study vibrational states of dioxirane and diazirinone. The...

Journal ArticleDOI
TL;DR: Molecular dynamic simulations were carried out using various sizes of nanocrystals as a probe to explore the transport of nanomaterials across dipalmitoylphosphatidylcholine bilayers and the changes in the structural and mechanical properties of DPPC bilayers during the permeation.
Abstract: Biological membranes are one of the major structural elements of cells, and play a key role as a selective barrier and substrate for many proteins that facilitate transport and signaling processes. Understanding the structural and mechanical properties of lipid membranes during permeation of nanomaterials is of prime importance in determining the toxicity of nanomaterials to living cells. It has been shown that the interaction between lipid membranes and nanomaterials and the disruption of lipid membranes are often determined by physicochemical properties of nanomaterials, such as size, shape and surface composition. In this work, molecular dynamic simulations were carried out using various sizes of nanocrystals as a probe to explore the transport of nanomaterials across dipalmitoylphosphatidylcholine (DPPC) bilayers and the changes in the structural and mechanical properties of DPPC bilayers during the permeation. A coarse-grained model was used to provide insight at large time and length scales. In this...

Journal ArticleDOI
TL;DR: In this paper, an efficient and versatile method to calculate the components of the pressure tensor for hard-body fluids of generic shape from the perspective of molecular simulation is presented, after considering all possible repulsive contributions exerted by molecules upon their surroundings during an anisotropic system expansion.
Abstract: An efficient and versatile method to calculate the components of the pressure tensor for hard-body fluids of generic shape from the perspective of molecular simulation is presented. After due consideration of all the possible repulsive contributions exerted by molecules upon their surroundings during an anisotropic system expansion, it is observed that such a volume change can, for non-spherical molecules, give rise to configurations where overlaps occur. This feature of anisotropic molecules has to be taken into account rigorously as it can lead to discrepancies in the calculation of tensorial contributions to the pressure. Using the condition of detailed balance as a basis, a perturbation method developed for spherical molecules has been extended so that it is applicable to non-spherical and non-convex molecules. From a series of ‘ghost’ anisotropic volume perturbations the residual contribution to the components of the pressure tensor may be accurately calculated. Comparisons are made with prior method...

Journal ArticleDOI
TL;DR: In this article, the nonthermal effects of external electric and electromagnetic fields in the microwave to far-infrared frequency range and at (r.m.s.) electric field intensities of 10−3 to 0.25 V/Ar.
Abstract: The non-thermal effects of external electric and electromagnetic fields in the microwave to far-infrared frequency range and at (r.m.s.) electric field intensities of 10−3 to 0.25 V/Ar.m.s. on neat salts of 1,3-dimethyl-imidazolium hexafluorophosphate ([dmim][PF6]) and 1-butyl-3-methyl-imidazolium hexafluorophosphate ([bmim][PF6]) have been investigated by means of non-equilibrium molecular dynamics simulation. Significant alterations in molecular mobility were found vis-a-vis zero-field conditions. Using Green–Kubo and transient time correlation function analysis, the electrical conductivity of these ionic liquids has been estimated. The results indicate that ionic liquids respond most significantly to frequencies much lower than those of smaller polar solvents such as water, although the mechanism of the field response is almost exclusively translational.

Journal ArticleDOI
TL;DR: A benchmark of explicitly correlated CCSD(T)-F12 methods for the dimers Ga2, As2, Br2 and diatomic molecules AsN, BrO, HBr, GaF, GaCl, GaBr, AsF, AsCl, BrF, and BrCl is presented in this paper.
Abstract: A benchmark of explicitly correlated CCSD(T)-F12 methods for the dimers Ga2, As2, Br2 and diatomic molecules AsN, BrO, HBr, GaF, GaCl, GaBr, AsF, AsCl, BrF, and BrCl is presented. Equilibrium distances, harmonic vibrational frequencies, and dissociation energies are compared with extensive conventional CCSD(T) calculations using a variety of orbital basis sets and different ansatze for the explicitly correlated wavefunctions. Correlation of the 3d electrons has a strong effect, in particular on the equilibrium distances, and it is shown that this can be recovered very efficiently by the explicit correlation treatment. It is found that CCSD(T)-F12 calculations with new F12-specific cc-pVnZ-F12 basis sets give comparable accuracy to standard CCSD(T) calculations with very much larger aug-cc-pwCV(n+2)Z basis sets. The effects of higher order valence electron correlation (up to CCSDTQP) are also investigated in conventional calculations and are found to be significant in some cases.