Search

Vibronic coupling in the energetically lowest first four electronic states of CH2F+2is 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. Extensiveab initioquantum 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. [ABSTRACT FROM AUTHOR]

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-extensivitya posterioricorrections 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. [ABSTRACT FROM AUTHOR]

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 vectorsk. Confirming our earlier work, we found exponential decay for splay and twist correlations, and oscillatory exponential decay for the bend correlation. In this 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 tok2for smallk, 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. [ABSTRACT FROM PUBLISHER]

In this paper, dedicated to Prof. Jean-Pierre Hansen, I will summarise the development of lattice-Boltzmann methods for simulating the dynamics of colloidal suspensions. I will describe the main ideas and subsequent improvements, and place them in the wider context of particle-based methods for fluid dynamics. [ABSTRACT FROM PUBLISHER]

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. [ABSTRACT FROM PUBLISHER]

In this paper, various implementations of the analytic Hartree–Fock and hybrid density functional energy second derivatives are studied. An approximation-free four-centre implementation is presented, and its accuracy is rigorously analysed in terms of self-consistent field (SCF), coupled-perturbed SCF (CP-SCF) convergence and prescreening criteria. The CP-SCF residual norm convergence threshold turns out to be the most important of these. Final choices of convergence thresholds are made such that an accuracy of the vibrational frequencies of better than 5 cm−1compared to the numerical noise-free results is obtained, even for the highly sensitive low frequencies (<100–200 cm−1). The effects of the choice of numerical grid for density functional exchange–correlation integrations are studied and various weight derivative schemes are analysed in detail. In the second step of the work, approximations are introduced in order to speed up the computation without compromising its accuracy. To this end, the accuracy and efficiency of the resolution of identity approximation for the Coulomb terms and the semi-numerical chain of spheres approximation to the exchange terms are carefully analysed. It is shown that the largest performance improvements are realised if either Hartree–Fock exchange is absent (pure density functionals) and otherwise, if the exchange terms in the CP-SCF step of the calculation are approximated by the COSX method in conjunction with a small integration grid. Default values for all the involved truncation parameters are suggested. For vancomycine (176 atoms and 3593 basis functions), the RIJCOSX Hessian calculation with the B3LYP functional and the def2-TZVP basis set takes ∼3 days using 16 Intel® Xeon® 2.60GHz processors with the COSX algorithm having a net parallelisation scaling of 11.9 which is at least ∼20 times faster than the calculation without the RIJCOSX approximation. [ABSTRACT FROM PUBLISHER]

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 Y3Ga5O12crystal. The method is founded on the two-spin-orbit-parameter model where in addition to the contributions from the spin-orbit parameter of central dnion (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 parametersg//,g⊥andD) in Y3Ga5O12: Cr3+are reasonably explained. The impurity-induced local lattice distortion of Cr3+in Y3Ga5O12crystal is also estimated through the calculations. The results are discussed. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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−1of 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. The cation–oxygen distances (Na–O or Mg–O) show two signals, corresponding to the first and second coordination shells, which indicates that the ions behave as in bulk water. [ABSTRACT FROM PUBLISHER]

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 surface wettabilities, which differs from that in the macroscopic condition. [ABSTRACT FROM PUBLISHER]

We report here on the first study of topological effects for the NHH system, as carried out by treating simultaneously the two dominant effects of this system, namely, the Jahn–Teller (JT) effect and the Renner–Teller (RT) effect. Both the effects were treated rigorously as demanded by the Born–Oppenheimer approach. No approximations were made and in those cases where convergence was required, it was achieved by including the required number of states. The study concentrates on calculating the privileged adiabatic-to-diabatic transformation (ADT) angle γ12,along closed contours, which is the only needed angle to carry out the ADT in the case of relatively low energies. For this purpose, three coupled A′-states are usually considered and only in the last two extreme cases, where the area in configuration space becomes relatively large, namely 15–35 Å2, we had also to include an A″state (the second Δ-state), a situation that enforces the more elaborate (JT/RT) effect. In this paper, we also report on potential energies as calculated along the above-mentioned contours. Among them are considered the energies associated with the two adiabatic Δ-states, 1A′ and 1A″, of different symmetry and therefore are responsible for the RT effect. These states are expected to be degenerate along the collinear axis. It was revealed that these states, in contrast to the Renner theory, are not degenerate along a finite interval of the collinear axis at the vicinity of the JT conical intersection (JT-CI). In other words, the JT-CI annihilates the RT degeneracy along this interval. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 MR2and the AlR3moiety. The M-centre was found to undergo both the nucleophilic and insertion reactions, indicative of the ‘carbene’ character. We also designedc-1starting from the known di-coordinate cyclic MR2and AlR3under 16 kinds of substituents [NR′2, OR′, PR′2, SR′(R′ = H, Me,iPr, Ph)];c-1also 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 analogues should expand the higher coordinate M(II) family and await future laboratory synthesis. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this paper, we theoretically investigate the asymmetric molecular high-order harmonic emission and the attosecond X-ray pulse generation when the asymmetric molecular HeH2+ion is exposed to an intense chirped pulse. It is found that the molecular harmonics are strongly dependent on the internuclear distanceRas well as the chirp parameter, showing a smooth and intense harmonic plateau atR= 8.0 a.u. and β = 0.4. Further, by adding a subharmonic controlling pulse with the optimised conditions, a supercontinuum with a bandwidth of 602 eV can be obtained. Finally, by properly superposing the selected harmonics in the supercontinuum region, a series of isolated X-ray pulses with durations of sub-80 as are directly generated. [ABSTRACT FROM AUTHOR]

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 andNVT-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 time in the canonical ensemble and up to 30% in theNVT-Gibbs ensemble when compared to standard algorithms. In addition, it preserves the exact Markov chains produced by the Metropolis scheme. Further enhancement forNVT-Gibbs ensemble is achieved by combining this technique with the bond formation early rejection one. The hybrid method achieves more than 50% saving of the central processing unit (CPU) time. [ABSTRACT FROM AUTHOR]

For many decades, quantum chemical method development has been dominated by algorithms which involve increasingly complex series of tensor contractions over one-electron orbital spaces. Procedures for their derivation and implementation have evolved to require the minimum amount of logic and rely heavily on computationally efficient library-based matrix algebra and optimised paging schemes. In this regard, the recent development of exact stochastic quantum chemical algorithms to reduce computational scaling and memory overhead requires a contrasting algorithmic philosophy, but one which when implemented efficiently can achieve higher accuracy/cost ratios with small random errors. Additionally, they can exploit the continuing trend for massive parallelisation which hinders the progress of deterministic high-level quantum chemical algorithms. In the Quantum Monte Carlo community, stochastic algorithms are ubiquitous but the discrete Fock space of quantum chemical methods is often unfamiliar, and the methods introduce new concepts required for algorithmic efficiency. In this paper, we explore these concepts and detail an algorithm used for Full Configuration Interaction Quantum Monte Carlo (FCIQMC), which is implemented and available inMOLPROand as a standalone code, and is designed for high-level parallelism and linear-scaling with walker number. Many of the algorithms are also in use in, or can be transferred to, other stochastic quantum chemical methods and implementations. We apply these algorithms to the strongly correlated chromium dimer to demonstrate their efficiency and parallelism. [ABSTRACT FROM PUBLISHER]

The high-order perturbation formulas of spin-Hamiltonian parameters (gfactorsgiand hyperfine structure constantsAi,i=x,y,z) based on the two-mechanism model for d1ions in rhombic tetrahedral clusters with the ground stateare derived in this paper. In the model, besides the contributions to spin-Hamiltonian parameters due to the crystal-field (CF) mechanism in the widely applied CF theory, those due to the charge-transfer (CT) mechanism are taken into account. From these formulas, the six spin-Hamiltonian parametersgiandAifor the rhombic Mo5+tetrahedral centres in ZrSiO4crystal are calculated with four adjustable parameters. The calculated results are in reasonable agreement with the experimental values. The calculations show that for the exact and complete calculations of spin-Hamiltonian parameters of the high valence state dnions in crystals, the contributions due to CT mechanism should not be neglected. Some information on the defect structure of Mo5+impurity centres in ZrSiO4crystal is also acquired from the calculations. The results are discussed. [ABSTRACT FROM PUBLISHER]

The paper presents results ofab initiomodelling of formation energies of vacancy–hydrogen complexesVHnand an extended variant of thermodynamic theory describing equilibrium concentrations of such complexes. A single H atom is shifted from vacancy to a neighbouring O-site by 1.19 Å. Two H atoms in a vacancy form a dumbbell with H–H distance of 2.38 Å being much greater than in H2molecule. Configurations of three, four and five H atoms in a vacancy are more complex, and H–H distances gradually increase showing repulsion between hydrogen atoms. Binding energy of aVHn−1complex with the next hydrogen atom to formVHnis 0.60, 0.61, 0.39, 0.37 and 0.31 forn= 1–5, which is close to other researchers’ data. These results were used to construct an improved variant of thermodynamic description of vacancy–hydrogen interaction in a bcc solid solution taking into account both binding energies and hydrogen atom configurations in differentVHncomplexes. Calculations show that at low temperatures most vacancies are bound to several hydrogen atoms, and the equilibrium concentration of vacancies themselves significantly increases, in accordance with existing experiments. [ABSTRACT FROM AUTHOR]

Using the complete active space self-consistent field (CASSCF) method followed by the internally contracted multi-reference configuration interaction (MRCI) approach in combination with the correlation-consistent basis sets, this paper studies the potential energy curves of X2Σ+, 22Σ+, 32Σ+, 12Σ−, A2Π, 22Π, 32Π, 12Δ, 14Σ+, 24Σ+, 14Σ−, 14Π, 24Π and 14Δ Λ-S states of BeBr molecule and the corresponding 30 Ω states for the first time. All the Λ-S states correlate to the first two dissociation channels, Be(1Sg) + Br(2Pu) and Be(3Pu) + Br(2Pu), of BeBr molecule. Of these Λ-S states, the 32Π and 24Π are found to be repulsive without the spin–orbit coupling, whereas 14Π, 24Π, 32Π and 24Σ+are found to be repulsive with the spin–orbit coupling included. A2Π and 22Σ+possess the double well whether the spin–orbit coupling effect is included or not. Only 14Σ+, 14Σ−, 12Π and 22Π are found to be the inverted Λ-S states. The spin–orbit coupling is accounted for by the state interaction approach with Breit–Pauli Hamiltonian using the all-electron cc-pCVTZ basis set. The potential energy curves determined by the internally contracted MRCI method are corrected for size-extensivity errors by means of the Davidson correction. Core–valence correlation correction is calculated with a cc-pCVTZ basis set. Scalar relativistic correction is included using the third-order Douglas–Kroll Hamiltonian approximation at the level of cc-pVTZ basis set. The spectroscopic parameters of all the Λ-S and Ω bound states are evaluated. The spectroscopic parameters are compared with those reported in the literature. Fair agreement is found between the present results and available measurements. In particular, the energy splitting of 204.43 cm−1in the A2Π Λ-S state agrees well with the measurements of 201 cm−1. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. [ABSTRACT FROM PUBLISHER]

The ability to manipulate matter to create non-conventional structures is one of the key issues of material science. The understanding of assembling mechanism at the nanoscale allows us to engineer new nanomaterials, with physical properties intimately depending on their structure. This paper describes new strategies to obtain and characterise metal nanostructures via the combination of a top-down method, such as electron beam lithography, and a bottom-up technique, such as the chemical electroless deposition. We realised silver nanoparticle aggregates within well-defined patterned holes created by electron beam lithography on silicon substrates. The quality characteristics of the nanoaggregates were verified by using scanning electron microscopy and atomic force microscopy imaging. Moreover, we compared the experimental findings to molecular dynamics simulations of nanoparticles growth. We observed a very high dependence of the structure characteristics on the pattern nanowell aspect ratio. We found that high-quality metal nanostructures may be obtained in patterns with well aspect ratio close to one, corresponding to a maximum diameter of 50 nm, a limit above which the fabricated structures become less regular and discontinuous. When regular shapes and sizes are necessary, as in nanophotonics, these results suggest the pattern characteristics to obtain isolated, uniform and reproducible metal nanospheres. [ABSTRACT FROM AUTHOR]

This paper presents the methodology developed in order to thoroughly characterise a solvent extraction system containing high solute concentrations. The chemical system selected is N,N-(2-ethylhexyl)isobutyramide (DEHiBA) diluted in one alkane with increasing concentration of uranium(VI). Combining experiments with theoretical calculations allowed a deeper understanding of the extraction mechanism. A thermodynamic study was performed by the classical van't Hoff method and also by direct calorimetry to provide the enthalpies of extraction and specific heats. Dedicated methods like vapour pressure osmometry and electrospray ionisation mass spectrometry analysis provide information about the stoichiometry of the extracted species. Spectroscopic investigations with ultraviolet–visible and Fourier transform infrared probed the uranium coordination. Finally, a combination of molecular dynamics simulations, and small and wide-angle X-ray scattering experiments investigated the organisation in the organic phase beyond the molecular scale. It was shown that the high concentrations of uranium extracted have no influence on the stoichiometry of the complexes and the coordination of uranium in the inner sphere. The thermodynamic properties related to the extraction process and obtained with a fine consideration of the activity coefficients showed to be the same as those found with trace concentration. However, an unexpected organisation beyond the molecular scale was observed with an important role of nitrates as bridging ligands which could explain some physico-chemical properties. This approach could be applied to other chemical systems (other N,N-dialkylamides or other cations) to identify the origin of the different affinities between ligands and the difference of selectivity between cations. [ABSTRACT FROM AUTHOR]

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 sixfold coordination (centre of a hexagon) for small distances to a threefold arrangement (centre of a triangle), at large distancesdfrom the plane. The aim of this paper is to describe the corresponding non-trivial lattice transformation. For that purpose, two numerical methods (direct energy minimisation and Monte Carlo simulations), together with an analytical treatment, are presented. Our results indicate that thed= 0 andd→ ∞ limiting cases extend for finite values ofdfrom the respective starting points into two sequences of stable states, with intersecting energies at some valuedt; beyond this value the branches continue as metastable states. [ABSTRACT FROM AUTHOR]

In this paper, we report measured Rosenkranz N2- and O2-broadening, induced pressure-shift and mixing coefficients for OCS in the ν1+ ν3band, using a multi-pressure fitting technique applied to the measured shapes of the lines, including the interference effects caused by the line overlaps. These measurements were made by analysing six laboratory absorption spectra recorded at 0.004 cm−1resolution using the Fourier transform spectrometer Bruker IFS125HR located at the Laboratoire Interuniversitaire des Systèmes Atmosphériques, in Créteil. The spectra have been recorded in the 1850–3000 cm−1wave number range at 295 K, using a multipass absorption cell with an optical path of 3.249 m. The total sample pressures ranged from 5.97 to 83.28 Torr with OCS volume mixing ratios between 0.001 and 0.013 in nitrogen or oxygen. We have been able to determine the N2- and O2-pressure-broadening coefficients of 81 ν1+ ν3transitions with rotational quantum numberJup to 50. The measured N2- and O2-broadening coefficients range from 0.0815 ± 0.0698 to 0.1169 ± 0.1027 cm−1atm−1at 295 K, respectively. Most of the measured pressure shifts are positive. The reported N2- and O2-induced pressure-shift coefficients vary from about −0.0103 ± 0.0092 to 0.0097 ± 0.0092 cm−1atm−1, respectively. We have examined the dependence of the measured broadening parameters on the quantum numberm(m= −Jfor the P branch andm=J +1 for the R branch) and also developed an empirical expression to describe the broadening coefficients in terms of |m|. On average, this empirical expression reproduces the measured broadening coefficients to within 2%. Using a semi-classical Robert and Bonamy formalism, the theoretical broadening coefficients have been calculated at room temperature and compared with the experimental results. The theoretical results of the broadening coefficients are in very good overall agreement with the experimental data (2%). [ABSTRACT FROM PUBLISHER]

In this paper we study the level of accuracy of the electronic wave functions which is necessary to describe properly the atomic effects during nuclear β -decay. In the case of the β−-decay in the Li atom into Be+ion, we compare the numerical values of the transition probabilities from the,,low-lying states of the initial atom and final ion calculated using both Hylleraas-configuration interaction and configuration interaction (CI) with Slater orbital wave functions. In addition, using the CI method the transition probabilities from,,andlow-lying states have been calculated. The average of the absolute deviation of the transition probabilities distribution for low-lyingstates is <0.15%, forstates it is <0.5% and larger for D and higher energy states. The numerical results demonstrate that for low-lying states the atomic effect parameters in β-decay can be calculated with sufficient accuracy using CI wave functions constructed with Slater orbitals. This result opens a new avenue for the accurate calculation of atomic effects during the β-decay in heavier atoms and molecules. [ABSTRACT FROM PUBLISHER]

Application of Hamilton–Jacobi (HJ) equation to reaction systems which involve energy barrier(s) leading to the product is relatively new. Such problems are described by a new class of HJ equation, called the generalised HJ equation. This new HJ equation renders an anisotropic propagation for the wave front. In this paper, we describe the adaptation of the fast marching method (FMM) and the generalised HJ equation to understand a new class of reaction process where the energy barrier does not lead to the product; instead, a new class of states are detected along the reaction path of such reactions. These states are valley-ridge inflection point, branching point and potential energy ridge. Such reactions are characterised as bifurcation reactions. We have identified a new classical wave front, called the reaction action front (RAF) which distinctly separates the reaction system into a reactant zone and a product zone connected by a third zone, called ‘neck’. The RAF is an important tool to understand the bifurcation reaction and the associated reaction paths. We have also introduced a convenient way to compute the reaction path force (RPF) using the FMM. The RPF for a bifurcation reaction significantly differs from the reactions with energy barrier, and so, the RPF provides vital information about the occurrence of branching of a path. The method has been tested for the isomerisation reaction of methoxy radical (H3C) to hydroxymethylene radical (H2ĊOH). [ABSTRACT FROM AUTHOR]

In this paper, the authors have applied the infinite-order two-component (IOTC) method to study the X-ray spectra of noble gases. The effect of spin–orbit coupling is introduced via the restricted active space interaction (RASSI) method with the use of the atomic mean-field AMFI integrals. For the deep core energies the discrepancies between the experimental and calculated values can be still quite large. To explain these differences the quantum electrodynamic corrections have been calculated such as Breit energy, self-energy and vacuum polarisation. The comparison between results of the IOTC method and the Douglas–Kroll–Hess (DKHn) approximation has been presented as well. [ABSTRACT FROM AUTHOR]

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ−phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond. [ABSTRACT FROM PUBLISHER]

Anab initioanalysis of the periodic array of Au/Si nanostructure composed of gold clusters linked to silicon quantum dot (QD) co-doped by aluminium and phosphorus along [111] direction is presented in this paper. The density functional theory (DFT) is used to compute the electronic structure of the simulated system. Non-adiabatic coupling implemented in the form of dissipative equation of motion for reduced density matrix is used to study the phonon-induced relaxation in the simulated system. The density of states clearly shows that the formation of Au–Si bonds contributes states to the band gap of the model. Dynamics of selected photo-excitations shows that hole relaxation in energy and in space is much faster than electron relaxation, which is due to the higher density of states of the valence band. [ABSTRACT FROM PUBLISHER]

In this paper we show how it is possible to obtain the pKaof a weak acid (H4SiO4) bound to a highly charged cation (La3+) from DFT-based molecular dynamics in a relatively simple, tunable and efficient way. This was done by combining molecular dynamics in bulk water of a La3+/H4SiO4complex with the single sweep method. At this end, we have first performed molecular dynamics runs where a high temperature is assigned on the defined reaction coordinate, here the O–H distance. Then we performed constrained molecular dynamics simulations for selected values of the reaction coordinate along the observed dissociation pathway. The average forces obtained from those constrained simulations are then interpolated to get a final free energy curve. The pKais obtained by integrating the resulting free energy curve and that of a reference calculation, the autodissociation of water. We then show that the pKaof the silanol groups away from La3+is close to the first pKaof silisic acid, while the pKaof the silanol groups interacting with La3+is about three units lower. [ABSTRACT FROM AUTHOR]

Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case, however, that the interparticle forces drive motion on many time scales, and the efficiency of a calculation is limited by the choice of time step, which must be sufficiently small that the fastest force components are accurately integrated. Multiple time-stepping algorithms partially alleviate this inefficiency by assigning to each time scale an appropriately chosen step-size. As the fast forces are often computationally cheaper to evaluate than the slow forces, this results in a significant gain in efficiency. However, such approaches are limited by resonance phenomena, wherein motion on the fastest time scales limits the step sizes associated with slower time scales. In atomistic models of biomolecular systems, for example, resonances limit the largest time step to around 5-6 fs. Stochastic processes promote mixing and ergodicity in dynamical systems and reduce the impact of resonant modes. In this paper, we introduce a set of stochastic isokinetic equations of motion that are shown to be rigorously ergodic, largely free of resonances, and can be integrated using a multiple time-stepping algorithm which is easily implemented in existing molecular dynamics codes. The technique is applied to a simple, illustrative problem and then to a more realistic system, namely, a flexible water model. Using this approach outer time steps as large as 100 fs are shown to be possible. [ABSTRACT FROM AUTHOR]

In this paper, we set the stage for molecular dynamics studies of the transport properties of molten salts in the presence of external electric and magnetic fields by introducing an original propagator to integrate the equations of motion. Using this algorithm, we compute, within linear response theory, transport properties of molten sodium chloride focusing, in particular, on the conductivity tensor at different intensities of the magnetic field. Finally, in view of full non-equilibrium calculations on the system in which an electric field is also applied, an adapted thermalisation mechanism, which extends to these systems Nosé–Hoover thermostatting, is derived. [ABSTRACT FROM AUTHOR]

In this paper, we propose a straightforward generalisation of the linear response theory on a finite time-horizon to systems in non-equilibrium that are subject to external forcing. We briefly revisit the standard linear response result for equilibrium systems, where we consider Langevin dynamics as a special case, and then give an alternative derivation using a change-of-measure argument that does not rely on any stationarity or reversibility assumption. This procedure easily enables us to calculate the second-order correction to the linear response formula (which may or may not be useful in practice). Furthermore, we outline how the novel non-equilibrium linear response formula can be used to compute optimal controls of molecular systems for cases in which one wants to steer the system to maximise a certain target expectation value. We illustrate our approach with simple numerical examples. [ABSTRACT FROM AUTHOR]

Granular materials are not in thermodynamic equilibrium. Nevertheless, concepts borrowed from equilibrium statistical mechanics are extensively used to characterise granular systems. One often-invoked concept is the so-called granular entropy. In this paper, we consider what it would take to compute granular entropy numerically. Our focus is the analogy (or, more accurately, lack thereof) between statistical mechanical ensembles, as used in Monte Carlo simulations of thermal systems, and preparation protocols used in the generation of granular packings. Attempts to phrase the description of granular media in ‘thermal’ Monte Carlo language reveal some awkward problems. Whilst some of these problems had been reported in the existing literature, the present perspective yields new insights. [ABSTRACT FROM AUTHOR]

In this paper, we review what molecular dynamics has brought to the understanding of the thermal diffusion effect in simple fluid mixtures. We describe the various methods that have been developed by the community during the last decades to study this non-equilibrium phenomenon. We present how these methods have been used to quantitatively predict transport coefficients. Finally, in the light of important advances in experimental setup that have brought accurate and reliable data in this area, we assess how molecular simulations contribute to the understanding of molecular mechanisms of the thermal diffusion effect and the elaboration of accurate macroscopic models. [ABSTRACT FROM AUTHOR]

In the present paper, we have used density functional theory to study electronic properties of bilayer graphene and graphyne doped with B and N impurities in the presence of electric field. It has been demonstrated that a band gap is opened in the band structures of the bilayer graphene and graphyne by B and N doping. We have also investigated influence of electric field on the electronic properties of BN-doped bilayer graphene and graphyne. It is found that the band gaps induced by B and N impurities are increased by applying electric field. Our results reveal that doping with B and N, and applying electric field are an effective method to open and control a band gap which is useful to design carbon-based next-generation electronic devices. [ABSTRACT FROM AUTHOR]

Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O–H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D–H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur. Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials. [ABSTRACT FROM AUTHOR]

Spectroscopic observables can be used for monitoring relaxation processes of molecules. In particular, electron spin resonance of stable multi-radicals is sensitive to the details of the rotational and internal dynamics in rigid and flexible molecules. Integration with advanced theoretical/computational methods proves to be particularly effective to acquire direct information on long-range relaxation processes, based on molecular dynamics, multi-scale approaches and coarse-graining treatments. Together, experimental data and computational interpretation provide a way to understand the effect of chemical changes on specific systems. In this paper we review computational tools aimed at the characterisation of dynamical properties of molecules gathered from electron spin resonance measurements. Stochastic models are employed, based on a number of structural parameters that are calculated at atomistic and/or mesoscopic level depending on their nature. Open source software tools built as user-friendly ‘virtual spectroscopes’ targeted for use by experimentalists are provided as a kind of extension of the laboratory equipment. An overview of their range of applicability is provided. [ABSTRACT FROM PUBLISHER]

We have systematically studied micro-heterogeneous mixtures of the room temperature ionic liquid 1-butyl-3-methyl-imidazolium tetrafluoroborate ([bmim+][BF4−]) and water using continuous wave electron paramagnetic resonance (CW EPR) and the spin-probing methodology. Using cryo TEM, a mesoscopic picture of the micro-heterogeneous mixtures could be revealed. Six spin-probes differing in polarity, charge and Lewis basicity have been used to map the dependence of the micro-polarity and rotation motion of the probe on the ionic liquid (IL) concentration. The electron paramagnetic resonance (EPR) spectra of all probe molecules have been found to be unimodal. The critical aggregation concentration has been determined and the local water concentration sensed by the probes extracted from the Mukerjee hydrophilicity index. Surprisingly, four probes of the piperidinoxyl type were found to sense very similar local water concentrations irrespective of the substituent, monovalent ionic or H-bonding, at the 4-position. Using a simple geometrical model of the primary IL aggregates observed in the micro-heterogeneous concentration range, we show that these probes cannot be statically located within the aggregates on the EPR timescale. Instead, diffusive trajectories of the probe molecules extend into the aqueous phase, i.e. aqueous and [bmim+][BF4−]-rich phases are sampled by the probes in swift succession. No details of the internal structure of the [bmim+][BF4−] aggregates can in general be elucidated by the spin-probing methodology under these conditions. On the other hand, the dianionic Fremy's salt binds to the surface of the IL aggregates thereby sampling predominantly the aqueous phase. At large IL concentrations, a micro-viscosity drastically smaller than the macroscopic viscosity is typically observed. Supplementary Materials (Figures S1–S5) for this paper are available online on the journal website. [ABSTRACT FROM PUBLISHER]

This paper reports incorporation of the perturbative triples correction within the explicitly correlated Mukherjee’s multireference coupled cluster method using the SP ansatz. In accord with the standard approximation, these corrections are not directly entered by the correlation factor amplitudes, but the explicitly correlated part of the effective Hamiltonian is included in full. The performance of the new method is tested on singlet methylene, potential curve of fluorine molecule and automerisation barrier of cyclobutadiene. It has been found that the convergence pattern of the MkCCSD(T)-F12 results with increasing basis set is improved by approximately one cardinal number, as compared to conventional MkCCSD(T). This improvement appears at the level of single and double excitations, whereas no significant impact of the explicit treatment of the electron correlation on the (T) correction has been observed, in analogy to a single-reference approach. [ABSTRACT FROM PUBLISHER]

To date no experiment has reached the level of sensitivity required to observe weak nuclear force-induced parity violation (PV) energy differences in chiral molecules. In this paper, we present the approach, adopted at Laboratoire de Physique des Lasers (LPL), to measure frequency differences in the vibrational spectrum of enantiomers. We review different spectroscopic methods developed at LPL leading to the highest resolutions, as well as 20 years of CO2laser stabilisation work enabling such precise measurements. After a first attempt to observe PV vibrational frequency shifts using sub-Doppler saturated absorption spectroscopy in a cell, we are currently aiming at an experiment based on Doppler-free two-photon Ramsey interferometry on a supersonic beam. We report on our latest progress towards observing PV with chiral organo-metallic complexes containing a heavy rhenium atom. [ABSTRACT FROM AUTHOR]

In this paper, we present a simple strategy for the elimination of the translational kinetic energy contamination of the total energy in pre-Born–Oppenheimer calculations carried out in laboratory-fixed Cartesian coordinates (LFCCs). The simple expressions for the coordinates and the operators are thus preserved throughout the calculations, while the mathematical form and the parametrisation of the basis functions are chosen so that the translational and rotational invariances are respected. The basis functions are constructed using explicitly correlated Gaussian functions (ECGs) and the global vector representation. First, we observe that it is not possible to parametrise the ECGs so that the system is at rest in LFCCs and at the same time the basis functions are square integrable with a non-vanishing (positive-definite) norm. Then, we work out a practical strategy to circumvent this problem by making use of the properties of the linear transformation between the LFCCs and translationally invariant and centre-of-mass Cartesian coordinates as well as the transformation properties of the corresponding basis function parameter matrices. By exploiting these formal mathematical relationships, we can identify and separate the translational contamination terms in the matrix representation of the kinetic energy operator in the LFCC formalism. We present numerical examples for the translational contamination and its elimination for the two lowest rotational energy levels of the singlet hydrogen molecule, corresponding to para- and ortho-H2, respectively, treated as four-particle quantum systems. [ABSTRACT FROM AUTHOR]

A recent paper by Hamm and Stock [Phys. Rev. Lett.109, 173201 (2012)] has introduced the concept of vibrational conical intersections as a potential source of ultrafast vibrational relaxation, using the coupling between high-frequency OH modes and low-frequency intramolecular hydrogen bonding modes of malonaldehyde as an example. Here, the question is addressed whether such conical intersections may also appear for intermolecular hydrogen bonds. To that end, the water dimer [(H2O)2] is studied as a minimal model for the hydrogen bonding in liquid water. Although a significant separation of time scales between intramolecular and intermolecular degrees of freedom exists in (H2O)2, a standard normal-mode description is found to lead to a complete breakdown of the adiabatic ansatz. This is due to strong nonlinear couplings between high- and low-frequency normal modes, which in turn give rise to large overall non-adiabatic couplings. A valid adiabatic picture is obtained, on the other hand, when internal coordinates are employed. The resulting adiabatic potential energy surfaces indeed exhibit low-lying conical intersections, whose possible relevance for ultrafast relaxation and energy transfer in water is discussed. [ABSTRACT FROM AUTHOR]

The recently developed time-dependent (TD) Monte Carlo (MC) importance sampling method [Tao and Miller; JCP135, 024104 (2011)] provides an efficient implementation of the semi-classical (SC) initial value representation (IVR) methodology for the evaluation of time correlation functions. The key idea in this TD-SC-IVR method is to perform importance sampling of trajectories for the MC averages in the SC calculations with a sampling function that includes information about thefinal(time-evolved) values of the coordinates and momenta of trajectories in addition to (the usual) information of their initial values. This paper shows how this approach deals with electronically non-adiabatic dynamics, i.e. dynamics that involves coupled multiple electronic states. We suggest that a state-resolved sampling function may facilitate the efficient implementation of TD-SC-IVR for such processes. This is illustrated by application to the calculation of the nuclear momentum distribution function (i.e. the nuclear energy-loss spectrum) for a benchmark non-adiabatic scattering problem. [ABSTRACT FROM AUTHOR]

We have developed and implemented a general formalism for fast numerical solution of time-independent linear partial differential equations as well as integral equations through the application of numerically separable integral operators ind≥ 1 dimensions using the non-standard (NS) form. The proposed formalism is universal, compact and oriented towards the practical implementation into a working code using multiwavelets. The formalism is applied to the case of Poisson and bound-state Helmholtz operators ind= 3. Our algorithms are fully adaptive in the sense that the grid supporting each function is obtained on the fly while the function is being computed. In particular, when the functiong=O fis obtained by applying an integral operatorO, the corresponding grid is not obtained by transferring the grid from the input functionf. This aspect has significant implications that will be discussed in the numerical section. The operator kernels are represented in a separated form with finite but arbitrary precision using Gaussian functions. Such a representation combined with the NS form allows us to build a sparse, banded representation of Green’s operator kernel. We have implemented a code for the application of such operators in a separated NS form to a multivariate function in a finite but, in principle, arbitrary number of dimensions. The error of the method is controlled, while the low complexity of the numerical algorithm is kept. The implemented code explicitly computes all the 22dcomponents of thed-dimensional operator. Our algorithms are described in detail in the paper through pseudo-code examples. The final goal of our work is to be able to apply this method to build a fast and accurate Kohn–Sham solver for density functional theory. [ABSTRACT FROM AUTHOR]

For a molecule with a complicated electronic structure, the solution of the Kohn–Sham equations of density functional theory (DFT) may require the use of an ensemble density matrix rather than a pure-state density matrix. In this paper, we first outline how an ensemble density matrix may be parameterised in a form, which ensures that all occupation numbers are between zero and two and that the total number of electrons is constant. A previously developed method for the optimisation of both orbitals and occupation numbers is summarised, and a time-independent linear response method for ensemble densities is developed. The optimisation and linear response methods are applied to the energy, dipole moment and static polarisability of the ground state of ozone at various bond angles. When comparing the results of pure-state and ensemble DFT calculations, it is found that the latter gives better agreement with wave-function methods and in particular provides smooth and differentiable potential and property curves. [ABSTRACT FROM AUTHOR]

Radiative forces from near-resonant laser light can be used for cooling and slowing the motion of diatomic molecules. While radiative-force slowing can be efficient in reducing the longitudinal velocity of molecules in a beam, this method has so far resulted in relatively low fluxes of slow molecules available for loading into a trap. This is primarily due to the divergence of the molecular beam, which increases in inverse proportion to the forward velocity. In this paper, we discuss methods to transversely confine molecules as they are slowed by radiative forces. We focus in particular on a promising method that uses a microwave field tuned to the blue of a rotational transition in the molecule, to provide the confining force. We argue that with a realistic design, this approach can improve the useful flux of slow molecules from radiative slowing by a factor of ~ 100. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been performed to investigate the aqueous binary mixtures of alcohols, including methanol, ethylene glycol (EG) and glycerol of molalities ranging from 1 to 5 m at the temperatures of 273, 288 and 298 K, respectively. The primary purpose of this paper is to investigate the mechanism of water self-diffusion in water-alcohol mixtures from the point of view of hydrogen bonding. The effects of temperature and concentration on water self-diffusion coefficient are evaluated quantitatively in this work. Temperature and concentration to some extent affect the hydrogen bonding statistics and dynamics of the binary mixtures. It is shown that the self-diffusion coefficient of water molecules decreases as the concentration increases or the temperature decreases. Moreover, calculations of mean square displacements of water molecules initially with different numbernof H-bonds indicate that the water self-diffusion coefficient decreases asnincreases. We also studied the aggregation of alcohol molecules by the hydrophobic alkyl groups. The largest cluster size of the alkyl groups clearly increases as the concentration increases, implying the emergence of a closely connected network of water and alcohols. The clusters of water and alcohol that interacted could block the movement of water molecules in binary mixtures. These findings provide insight into the mechanisms of water self-diffusion in aqueous binary mixtures of methanol, EG and glycerol. [ABSTRACT FROM PUBLISHER]

Density functional theory calculations were used to study the titanium (Ti) adsorption on perfect and defected (4, 0) BC3nanotubes, considering Stone–Wales and vacancy defects. The binding energy values for these nanotubes were larger than the corresponding values for carbon nanotubes. The charge transfer from the Ti atom to nanotube was observed for all systems studied. The most exothermic binding process occurred for the Ti adsorption on a native VBdefect, which showed minimum structural deformation with respect to a perfect BC3tube. In the case of a nanotube with a reconstructed carbon vacancy, the adsorption of Ti generated a half-metallic anti-ferromagnet. The results obtained in this paper are relevant for spintronics and hydrogen adsorption applications. [ABSTRACT FROM PUBLISHER]