Physics - Chemical Physics Publications (50)

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Physics - Chemical Physics Publications

A five-dimensional coupled states (5D-CS) approximation is used to compute cross sections and rate coefficients for CO+H2 collisions. The 5D-CS calculations are benchmarked against accurate six-dimensional close-coupling (6D-CC) calculations for transitions between low-lying rovibrational states. Good agreement between the two formulations is found for collision energies greater than 10 cm-1. Read More


The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation corrections. The direct integration simulation has several characteristics beneficial to free-energy calculations. Read More


Reverse Monte Carlo modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, SPC/E, has been performed. The strictly rigid geometry of SPC/E water molecules had to be loosened somewhat, in order to be able to produce a good fit to both sets of experimental data. In the final particle configurations, regularly shaped water molecules and straight hydrogen bonding angles were found to be consistent with diffraction results. Read More


We present the results of Gaussian-based ground-state and excited-state equation-of-motion coupled-cluster theory with single and double excitations for three-dimensional solids. We focus on diamond and silicon, which are paradigmatic covalent semiconductors. In addition to ground-state properties (the lattice constant, bulk modulus, and cohesive energy), we compute the quasiparticle band structure and band gap. Read More


A central difficulty of state-specific Multi-Reference Coupled Cluster (MR-CC) formalisms concerns the definition of the amplitudes of the single and double excitation operators appearing in the exponential wave operator. If the reference space is a complete active space (CAS) the number of these amplitudes is larger than the number of singly and doubly excited determinants on which one may project the eigenequation, and one must impose additional conditions. The present work first defines a state-specific reference-independent operator $\hat{\tilde{T}}^m$ which acting on the CAS component of the wave function $|\Psi_0^m \rangle$ maximizes the overlap between $(1+\hat{\tilde{T}}^m)|\Psi_0^m \rangle$ and the eigenvector of the CAS-SD CI matrix $|\Psi_{\rm CAS-SD}^m \rangle$. Read More


Metal atoms and small clusters introduced into superfluid helium (He II) concentrate there in quantized vortices to form (by further coagulation) the thin nanowires. The nanowires' thickness and structure are well predicted by a double-staged mechanism. On the first stage the coagulation of cold particles in the vortex cores leads to melting of their fusion product, which acquires a spherical shape due to surface tension. Read More


Wavefunctions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included \textit{a posteriori}. In this article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allow us to describe both static/nondynamic and dynamic electron correlation effects. Read More


First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. Read More


Coherent control of chaotic molecular systems, using laser-assisted alignment of sulphur dioxide (SO$_2$) molecules in the presence of a static electric field as an example, is considered. Conditions for which the classical version of this system is chaotic are established, and the quantum and classical analogs are shown to be in very good correspondence. It is found that the chaos present in the classical system does not impede the alignment, neither in the classical nor the quantum system. Read More


This article provides an introduction to and review of the field of computer-aided molecular design (CAMD). It is intended to be approachable for the absolute beginner as well as useful to the seasoned CAMD practitioner. We begin by discussing various quantitative structure-property relationships (QSPRs) which have been demonstrated to work well with CAMD problems. Read More


Stable luminescent pi-radicals with doublet emission have aroused a growing interest for functional molecular materials. We have demonstrated a neutral pi-radical dye (4-N-carbazolyl-2,6-dichlorophenyl)bis(2,4,6-trichlorophenyl)-methyl (TTM-1Cz) with remarkable doublet emission, which could be used as triplet sensitizer to initiate the photophysical process of triplet-triplet annihilation photon upconversion (TTA-UC). Dexter-like excited doublet-triplet energy transfer (DTET) was confirmed by theoretical calculation. Read More


Recently, high-resolution spectroscopy of slow beams of metastable helium molecules (He$_2^*$) generated by multistage Zeeman deceleration was used in combination with Rydberg-series extrapolation techniques to obtain the lowest rotational interval in the molecular helium ion at a precision of 18 MHz [Jansen et al. Phys. Rev. Read More


Although the existence of quasi-bound rotational levels of the $X^+ \ ^2\Sigma_g^+$ ground state of H$_2^+$ has been predicted a long time ago, these states have never been observed. Calculated positions and widths of quasi-bound rotational levels located close to the top of the centrifugal barriers have not been reported either. Given the role that such states play in the recombination of H(1s) and H$^+$ to form H$_2^+$, this lack of data may be regarded as one of the largest unknown aspects of this otherwise accurately known fundamental molecular cation. Read More


We study the strong coupling between the molecular excited state and the plasmonic modes of silver hole arrays with a resonant frequency very close to the asymptotic line of the plasmonic dispersion relation. When the molecular transition state is relatively high and lies at the nonlinear regime of the dispersion relation. We demonstrate that the strong coupling regime can be achieved between the two sub-systems at low molecular densities with negligible damping of the electromagnetic field. Read More


HfF$^+$ cation is a very promising system to search for the electron electric dipole moment (EDM), and corresponding experiment is carried out by E. Cornell group. Here we theoretically investigate the cation to search for another T,P-odd effect -- the nuclear magnetic quadrpole moment (MQM) interaction with electrons. Read More


The use of eco-friendly materials for the environment has been addressed as a critical issue in the development of systems for renewable energy applications. In this regard, the investigation of organic photovoltaic (OPV) molecules for the implementation in solar cells, has become a subject of intense research in the last years. The present work is a systematic study at the B3LYP level of theory performed for a series of 50 OPV materials. Read More


A Density Functional study predicting a heterogeneous-catalyzed reaction giving rise to biodiesel, was performed. Triacetin was used as a model of triglyceride in the presence of an Au(111) surface as the heterogeneous catalyst substrate. Explicit methoxy molecules were implemented as an alcohol solvent to understand the reaction trajectory along the well known three-step transesterification process. Read More


Chemical reactions can be surprisingly efficient at ultracold temperatures ( < 1mK) due to the wave nature of atoms and molecules. The study of reactions in the ultracold regime is a new research frontier enabled by cooling and trapping techniques developed in atomic and molecular physics. In addition, ultracold molecular gases that offer diverse molecular internal states and large electric dipolar interactions are sought after for studies of strongly interacting many-body quantum physics. Read More


Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally-measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first principles. Since the exact quantum solution scales exponentially with system size, there has been considerable effort in formulating reliable linear-scaling methods involving exact quantum statistics and approximate quantum dynamics modelled with classical-like trajectories. Here we review recent progress in the field with the development of methods including Centroid Molecular Dynamics (CMD), Ring Polymer Molecular Dynamics (RPMD) and Thermostatted RPMD (TRPMD). Read More


We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo (QMC) solution of the electronic part with the path integral (PI) formalism for the quantum nuclear dynamics. On the one hand, the PI molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. Read More


Catalytic swimmers have attracted much attention as alternatives to biological systems for examining collective microscopic dynamics and the response to physico-chemical signals. Yet, understanding and predicting even the most fundamental characteristics of their individual propulsion still raises important challenges. While chemical asymmetry is widely recognized as the cornerstone of catalytic propulsion, different experimental studies have reported that particles with identical chemical properties may propel in opposite directions. Read More


Ionic liquids are solvent-free electrolytes, some of which possess an intriguing self-assembly property. Using a mean-field framework (based on Onsager's relations) we show that bulk nano-structures arise via type-I and II phase transitions (PT), which directly affect the electrical double layer (EDL) structure. Ginzburg-Landau equation is derived and PT are related to temperature, potential and interactions. Read More


Solid mixed conductors with significant ionic as well as electronic conduction play a pivotal role for mass transfer and storage as required in battery electrodes. Single-phase materials with simultaneously high electronic and ionic conductivity at room temperature are hard to come by and therefore multi-phase systems with separate ion and electron channels have been put forward instead. Here, we explore bilayer graphene as a true single phase mixed conductor and demonstrate ultrafast lithium diffusion exceeding diffusion in bulk graphite by an order of magnitude and even surpassing diffusion of sodium chloride in liquid water. Read More


We present an exact single-electron picture that describes the correlated electron dynamics in strong laser fields. Our approach is based on the factorization of the electronic wavefunction as a product of a marginal and a conditional amplitude. The marginal amplitude, which depends only on one electronic coordinate and yields the exact one-electron density and current density, obeys a time-dependent Schr\"odinger equation with an effective time-dependent potential. Read More


The probability of non-radiative transitions in photochemical dynamics is determined by the so-called derivative couplings, the couplings between different electronic states through the nuclear degrees of freedom. Efficient and accurate evaluation of the derivative couplings is, therefore, of central importance to realizing reliable computer simulation methodologies for photochemical reactions. In this work, the derivative couplings for multistate multireference second-order perturbation theory (MS-CASPT2) and its 'extended' variant (XMS- CASPT2) are studied, in which we present an algorithm for their analytical evaluation. Read More


In this paper for the first time we report the results of molecular dynamics simulation of electrode/electrolyte interface of Li-O2 cathode under potential close to experimental values in 1M dimethyl sulfoxide (DMSO) solution of LiPF6 salt. Electric potential profiles, solvent structuring near the electrode surface and salt ions distributions are presented and discussed here as well as potentials of mean force (PMF) of oxygen and its reduction products. The latter would be of a great use for the future theoretical studies of reaction kinetics as PMF being essentially the work term is a required input for the reaction rate constant estimations. Read More


Partially-self-consistent gap-renormalization GW (grGW) is introduced to calculate quasiparticle (QP) energies within the many-body perturbation theory of Hedin. Self-consistency of the Green's function is obtained by renormalization of the band gap, removing the most significant approximation of the single-shot $\text{G}_{0}\text{W}_{0}$ approach. The formalism is performed as a post-processing step and thus, can be implemented within any GW algorithm which calculates the full frequency-dependent self-energies. Read More


A third-order multireference perturbation theory based on the driven similarity renormalization group approach (DSRG-MRPT3) is presented. The DSRG-MRPT3 method has several appealing features: a) it is intruder free, b) it is size consistent, c) it leads to a non-iterative algorithm with ${\cal O}(N^6)$ scaling, and d) it includes reference relaxation effects. The DSRG-MRPT3 scheme is benchmarked on the potential energy curves of F$_2$, H$_2$O$_2$, C$_2$H$_6$, and N$_2$ along the F-F, O-O, C-C, and N-N bond dissociation coordinates, respectively. Read More


Reversible in operando control of friction is an unsolved challenge crucial to industrial tribology. Recent studies show that at low sliding velocities, this control can be achieved by applying an electric field across electrolyte lubricants. However, the phenomenology at high sliding velocities is yet unknown. Read More


We present an approach using a combination of coupled channel scattering calculations with a machine- learning technique based on Gaussian Process regression to determine the sensitivity of the rate constants for non-adiabatic transitions in inelastic atomic collisions to variations of the underlying adiabatic interaction potentials. Using this approach, we improve the previous computations of the rate constants for the fine-structure transitions in collisions of O(3Pj) with atomic H. We compute the error bars of the rate constants corresponding to 20 % variations of the ab initio potentials and show that this method can be used to determine which of the individual adiabatic potentials are more or less important for the outcome of different fine-structure changing collisions. Read More


Recently, a general expression for Eckart-frame Hamilton operators has been obtained by the gateway Hamiltonian method ({\it J. Chem. Phys. Read More


We report on changes in the Raman spectrum of live Escherichi coli (E.coli) that result from exposure to lethal fluences of 300 nm (UV-B) and 405 nm (violet) photons. In the first instance, the energy per photon of 4. Read More


Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are integrated. In this context, Markov state models (MSMs) are extremely popular because they can be used to compute stationary quantities and long-time kinetics from ensembles of short simulations, provided that these short simulations are in "local equilibrium" within the MSM states. However, in the last over 15 years since the inception of MSMs, it has been controversially discussed and not yet been answered how deviations from local equilibrium can be detected, whether these deviations induce a practical bias in MSM estimation, and how to correct for them. Read More


A spectroscopic study of Rydberg states of helium ($n$ = 30 and 45) in magnetic, electric and combined magnetic and electric fields with arbitrary relative orientations of the field vectors is presented. The emphasis is on two special cases where (i) the diamagnetic term is negligible and both paramagnetic Zeeman and Stark effects are linear ($n$ = 30, $B \leq$ 120 mT and $F$ = 0 - 78 V/cm ), and (ii) the diamagnetic term is dominant and the Stark effect is linear ($n$ = 45, $B$ = 277 mT and $F$ = 0 - 8 V/cm). Both cases correspond to regimes where the interactions induced by the electric and magnetic fields are much weaker than the Coulomb interaction, but much stronger than the spin-orbit interaction. Read More


Frequency-modulation (FM) spectroscopy has been extended to the vacuum-ultraviolet (VUV) range of the electromagnetic spectrum. Coherent VUV laser radiation is produced by resonance-enhanced sum-frequency mixing ($\nu_{\mathrm{VUV}}=2\nu_{\mathrm{UV}}+\nu_2$) in Kr and Xe using two near-Fourier-transform-limited laser pulses of frequencies $\nu_{\mathrm{UV}}$ and $\nu_2$. Sidebands generated in the output of the second laser ($\nu_2$) using an electro-optical modulator operating at the frequency $\nu_{\mathrm{mod}}$ are directly transfered to the VUV and used to record FM spectra. Read More


We demonstrate nuclear magnetic resonance (NMR) spectroscopy of picoliter-volume solutions with a nanostructured diamond chip. Using optical interferometric lithography, diamond surfaces were nanostructured with dense, high-aspect-ratio nanogratings, enhancing the surface area by more than a factor of 15 over mm^2 regions of the chip. The nanograting sidewalls were doped with nitrogen-vacancy (NV) centers so that more than 10 million NV centers in a (25 micrometer)^2 laser spot are located close enough to the diamond surface (5 nm) to detect the NMR spectrum of 1 pL of fluid lying within adjacent nanograting grooves. Read More


In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. Read More


We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface and having various degrees of solvent exposure. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response, as measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain atoms and (iii) water molecules. Read More


Individual Kekule valence structures of biphenylene and related hydrocarbons are treated perturbatively by modelling them as sets of weakly-interacting uniform double bonds. Total pi-electron energies of these structures are then expressed in the form of power series with respect to the resonance parameter of uniform single bonds. On this basis, the Kekule structures concerned are ordered according to their relative stabilities and thereby importances when building up the actual electronic structures. Read More


This work defines density factor as the ratio of before ignition density to after ignition density of the ignition mixture. This work provides an estimation method for explosive limits of various fuels under room temperature and pressure by showing that for a large universe of fuels, constant adiabatic flame temperature and density factor are appropriate approximations at the lower explosive limit while only a constant density factor might be an appropriate approximation at the upper explosive limit. Thus the assumption of constant adiabatic flame temperature can be used in calculating lower explosive limit while the assumption of constant density factor can be used in approximating upper explosive limit. Read More


Density functional theory (DFT) has become the most popular approach to electronic structure across disciplines, especially in material and chemical sciences. Last year, at least 30,000 papers used DFT to make useful predictions or give insight into an enormous diversity of scientific problems, ranging from battery development to solar cell efficiency and far beyond. The success of this field has been driven by usefully accurate approximations based on known exact conditions and careful testing and validation. Read More


Time-resolved direct frequency comb spectroscopy (TRFCS) was used to study the kinetics of the deuterated analogue of the OH+CO->H+CO2 reaction, which is important for atmospheric and combustion chemistry. Complementing our recent work on quantifying the formation rate of the transient trans-DOCO radical, we report measurements of the kinetics of the activated product channel, D+CO2, at room temperature. Simultaneous measurements of the time-dependence of OD and CO2 concentrations allowed us to directly determine the formation rate, branching yield, and dependence on pressure and bath gas of the activated product. Read More


In this thesis, we study the interplay of phase separation and wetting in multicomponent systems. For this purpose, we have examined the phase separation pattern of a binary mixture (AB) in presence of stationary spherical particles (C) which prefers one of the components of the binary (say, A). Binary AB is composed of critical composition(50:50) and off-critical compositions(60:40, 40:60). Read More


This paper presents the first MD simulations of a model, which we have designed for understanding the development of electro-induced instability of a thin toluene emulsion film in contact with saline aqueous phase. This study demonstrates the charge accumulation role in toluene film rupture when a DC electric field is applied. The critical value of the external field at which film ruptures, thin film charge distribution, capacitance, number densities and film structure have been obtained in simulating the system within NVT and NPT ensembles. Read More


The validity of the dissipative quantum model of olfaction has not been examined yet and therefore the model suffers from the lack of experimental support. Here, we generalize the model and propose a numerical analysis of the dissipative odorant-mediated inelastic electron tunneling mechanism of olfaction, to be used as a potential examination in experiments. Our analysis gives several predictions on the model such as efficiency of elastic and inelastic tunneling of electrons through odorants, sensitivity thresholds in terms of temperature and pressure, isotopic effect on sensitivity, and the chiral recognition for discrimination between the similar and different scents. Read More


We report on two-photon photoassociation (PA) spectroscopy of ultracold heteronuclear LiRb molecules. This is used to determine the binding energies of the loosely bound levels of the electronic ground singlet and the lowest triplet states of LiRb. We observe strong two-photon PA lines with power broadened line widths greater than 20 GHz at relatively low laser intensity of 30 W/cm$^{2}$. Read More