Physics - Chemical Physics Publications (50)

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Physics - Chemical Physics Publications

Oxygen functional groups are one of the most important subjects in the study of electrochemical properties of carbon materials which can change the wettability, conductivity and pore size distributions of carbon materials, and can occur redox reactions. In the electrode materials of carbon-based supercapacitors, the oxygen functional groups have widely been used to improve the capacitive performance. In this paper, we not only analyzed the reasons for the increase of the capacity that promoted by oxygen functional groups in the charge-discharge cycling tests, but also analyzed the mechanism how the pseudocapacitance was provided by the oxygen functional groups in the acid/alkaline aqueous electrolyte. Read More


In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has been demonstrated that the overall yield is increased if certain bricks which occur on the outer faces of target structures are merged with adjacent bricks. However, it is not well understood by what mechanism such `boundary bricks' increase the yield, as they likely influence both the nucleation process and the final stability of the target structure. Read More


In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of $N$-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox [J. Read More


We report the three main ingredients to calculate three- and four-electron integrals over Gaussian basis functions involving Gaussian geminal operators: fundamental integrals, upper bounds, and recurrence relations. In particular, we consider the three- and four-electron integrals that may arise in explicitly-correlated F12 methods. A straightforward method to obtain the fundamental integrals is given. Read More


Methyl thionitrite CH3SNO is an important model of S-nitrosated cysteine aminoacid residue (CysNO), a ubiquitous biological S-nitrosothiol (RSNO) involved in numerous physiological processes. Here, we report accurate structure and properties of CH3SNO using accurate ab initio Feller-Peterson-Dixon (FPD) approach. The FPD scheme included CCSD(T)-F12/CBS extrapolated values, as well as corrections for the quadruple coupled cluster excitations, core-valence and scalar-relativistic effects. Read More


The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms (referred to herein as "flexible FFs"). The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas (IG) property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. Read More


We examine the olfactory discrimination of left- and right-handed enantiomers of chiral odorants based on the odorant-mediated electron transport from a donor to an acceptor of the olfactory receptors embodied in a biological environment. The chiral odorant is effectively described by an asymmetric double-well potential whose minima are associated to the left- and right-handed enantiomers. The introduced asymmetry is considered as an overall measure of chiral interactions. Read More


We have theoretically studied the uptake of a non-uniformly charged biomolecule, suitable to represent a globular protein or a drug, by a charged hydrogel carrier in the presence of a 1:1 electrolyte. Based on the analysis of a physical interaction Hamiltonian including monopolar, dipolar and Born (self-energy) contributions derived from linear electrostatic theory of the unperturbed homogeneous hydrogel, we have identified five different sorption states of the system, from complete repulsion of the molecule to its full sorption deep inside the hydrogel, passing through meta- and stable surface adsorption states. The results are summarized in state diagrams that also explore the effects of varying the electrolyte concentration, the sign of the net electric charge of the biomolecule, and the role of including excluded-volume (steric) or hydrophobic biomolecule-hydrogel interactions. Read More


We use an optical centrifuge to excite coherent rotational wave packets in N$_2$O, CS$_2$ and OCS molecules with rotational quantum numbers reaching up to J=465, 690 and 1186, respectively. Time-resolved rotational spectroscopy at such ultra-high levels of rotational excitation can be used as a sensitive tool to probe the molecular potential energy surface at inter-nuclear distances far from their equilibrium values. Significant bond stretching in the centrifuged molecules results in the growing period of the rotational revivals, which are experimentally detected using coherent Raman scattering. Read More


The spin-boson model is a simplified Hamiltonian often used to study non-adiabatic dynamics in large condensed phase systems, even though it has not been solved in a fully analytic fashion. Herein, we present an exact analytic expression for the dynamics of the spin-boson model in the infinitely slow bath limit and generalize it to approximate dynamics for faster baths. We achieve the latter by developing a hybrid approach that combines the exact slow-bath result with the popular NIBA method to generate a memory kernel that is formally exact to second order in the diabatic coupling but also contains higher-order contributions approximated from the second order term alone. Read More


We study the loss of coherence of electrochemical oscillations on meso- and nanosized electrodes with numeric simulations of the electrochemical master equation for a prototypical electrochemical oscillator, the hydrogen peroxide reduction on Pt electrodes in the presence of halides. On nanoelectrodes, the electrode potential changes whenever a stochastic electron-transfer event takes place. Electrochemical reaction rate coefficients depend exponentially on the electrode potential and become thus fluctuating quantities as well. Read More


We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range $f \approx$ 20-80 THz, with a maximum transfer percentage close to 1. Read More


A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we formulated the physical model and developed a numerical fluid dynamics integrator. In this study, we incorporated the fluid dynamics integrator with the Amber simulation engine to conduct atomistic simulations of biomolecules. At this stage of the development, only nonelectrostatic interactions, i. Read More


The combined all-electron and two-step approach is applied to calculate the molecular parameters which are required to interpret the ongoing experiment to search for the effects of manifestation of the T,P-odd fundamental interactions in the HfF$^+$ cation by Cornell/Ye group [Science 342, 1220 (2013); J. Mol. Spectrosc. Read More


We investigate the effective two- and three-body interactions mediated between non-active colloidal inclusions immersed in an active bath of chiral or non-chiral self-propelled particles (swimmers). We perform Brownian Dynamics simulations within a standard model comprising hard inclusions and swimmers in two spatial dimensions. In the absence of chirality, we corroborate previous findings by showing that strong, repulsive, two-body forces of medium range (up to surface separations of a few swimmer radii) emerge between colloidal inclusions in the active bath. Read More


The second law of photochemistry states that in most cases, no more than one molecule is activated for an excited-state reaction for each photon absorbed by a collection of molecules. In this work, we demonstrate that it is possible to trigger a many-molecule reaction using only one photon by strongly coupling the molecular ensemble to a confined light mode. The collective nature of the resulting hybrid states of the system (the so-called polaritons) leads to the formation of a polaritonic "supermolecule" involving the degrees of freedom of all molecules, opening a reaction path on which all involved molecules undergo a chemical transformation. Read More


We recalculate the leading relativistic corrections for the ground electronic state of the hydrogen molecule using variational method with explicitly correlated functions which satisfy the interelectronic cusp condition. The new computational approach allowed for the control of the numerical precision which reached about 8 significant digits. More importantly, the updated theoretical energies became discrepant with the known experimental values and we conclude that the yet unknown relativistic recoil corrections might be larger than previously anticipated. Read More


Following the Dirac-Frenkel time-dependent variational principle, transient dynamics of a one-dimensional Holstein polaron with diagonal and off-diagonal exciton-phonon coupling in an external electric field is studied by employing the multi-D$_2$ {\it Ansatz}, also known as a superposition of the usual Davydov D$_2$ trial states. Resultant polaron dynamics has significantly enhanced accuracy, and is in perfect agreement with that derived from the hierarchy equations of motion method. Starting from an initial broad wave packet, the exciton undergoes typical Bloch oscillations. Read More


Metal-organic frameworks (MOFs) are an attractive substrate for catalytic reactions due to the high area density of reaction sites and the ability to tailor an array of material attributes. This study focuses on a thermally stable crystalline UiO-66(Zr) MOF structure and the modulation of the electronic structure using two strategies to improve the catalytic conversion and selectivity of benzene alcohol to benzedehyate. Those two strategies include the functionalization of the organic struts with branched ligands and manually creating structural defects with unsaturated organic linkers. Read More


Treated traditionally by the Ehrenfest approximation, dynamics of a one-dimensional molecular crystal model with off-diagonal exciton-phonon coupling is investigated in this work using the Dirac-Frenkel time-dependent variational principle with the multi-D$_2$ {\it Ansatz}. It is shown that the Ehrenfest method is equivalent to our variational method with the single D$_2$ {\it Ansatz}, and with the multi-D$_2$ {\it Ansatz}, the accuracy of our simulated dynamics is significantly enhanced in comparison with the semi-classical Ehrenfest dynamics. The multi-D$_2$ {\it Ansatz} is able to capture numerically accurate exciton momentum probability and help clarify the relation between the exciton momentum redistribution and the exciton energy relaxation. Read More


Biluminescent organic emitters show simultaneous fluorescence and phosphorescence at room temperature. So far, the optimization of the room temperature phosphorescence (RTP) in these materials has drawn the attention of research. However, the continuous wave operation of these emitters will consequently turn them into systems with vastly imbalanced singlet and triplet populations, which is due to the respective excited state lifetimes. Read More


We present a generalization of the Debye-H\"uckel free-energy-density functional of simple fluids to the case of two-component systems with arbitrary interaction potentials. It allows one to obtain the two-component Debye-H\"uckel integral equations through its minimization with respect to the pair correlation functions, leads to the correct form of the internal energy density, and fulfills the virial theorem. It is based on our previous idea, proposed for the one-component Debye-H\"uckel approach, and which was published recently \cite{Piron16}. Read More


Accurate simulations of atomistic systems from first principles are limited by computational cost. In high-throughput settings, machine learning can potentially reduce these costs significantly by accurately interpolating between reference calculations. For this, kernel learning approaches crucially require a single Hilbert space accommodating any atomistic system. Read More


Quantum reactive scattering calculations are reported for the ultracold hydrogen-exchange reaction and its non-reactive atom-exchange isotopic counterparts, proceeding from excited rotational states. It is shown that while the geometric phase (GP) does not necessarily control the reaction to all final states one can always find final states where it does. For the isotopic counterpart reactions these states can be used to make a measurement of the GP effect by separately measuring the even and odd symmetry contributions, which experimentally requires nuclear-spin final-state resolution. Read More


The dynamics of unimolecular photo-triggered reactions can be strongly affected by the surrounding medium. An accurate description of these reactions requires knowing the free energy surface (FES) and the friction felt by the reactants. Most of theories start from the Langevin equation to derive the dynamics, but there are few examples comparing it with experiments. Read More


The ab initio description of the spectral interior of the absorption spectrum poses both a theoretical and computational challenge for modern electronic structure theory. Due to the often spectrally dense character of this domain in the quantum propagator's eigenspectrum for medium-to-large sized systems, traditional approaches based on the partial diagonalization of the propagator often encounter oscillatory and stagnating convergence. Alternatively, electronic structure methods which solve the molecular response problem through the solution of spectrally shifted linear systems, such as the complex polarization propagator, offer an alternative approach which is agnostic to the underlying spectral density or domain location. Read More


The salt-induced microheterogeneity (MH) formation in binary liquid mixtures is studied by small-angle X-ray scattering (SAXS) and liquid state theory. Previous experiments have shown that this phenomenon occurs for antagonistic salts, whose cations and anions prefer different components of the solvent mixture. However, so far the precise mechanism leading to the characteristic length scale of MHs remained unclear. Read More


We report the first experimental measurement of the near-threshold photo-ionization spectra of polycyclic aromatic hydrocarbon clusters made of pyrene C16H10 and coronene C24H12, obtained using imaging photoelectron photoion coincidence spectrometry with a VUV synchrotron beamline. The experimental results of the ionization energy are confronted to calculated ones obtained from simulations using dedicated electronic structure treatment for large ionized molecular clusters. Experiment and theory consistently find a decrease of the ionization energy with cluster size. Read More


We introduce a multimodel approach to the simulation of the optical properties of molecular dyes in solution, whereby the effects of thermal fluctuations and of dielectric screening on the absorption spectra are accounted for by explicit and implicit solvation models, respectively. Thermal effects are treated by averaging the spectra of molecular configurations generated by an ab initio molecular-dynamics simulation where solvent molecules are treated explicitly. Dielectric effects are then dealt with implicitly by computing the spectra upon removal of the solvent molecules and their replacement with an effective medium, in the spirit of a continuum solvation model. Read More


The combustion characteristics of ethanol/Jet A-1 fuel droplets having three different proportions of ethanol (10%, 30%, and 50% by vol.) are investigated in the present study. The large volatility differential between ethanol and Jet A-1 and the nominal immiscibility of the fuels seem to result in combustion characteristics that are rather different from our previous work on butanol/Jet A-1 blends. Read More


Revelation of the effects of isotope fractionation during fragmentation in electron ionization mass spectrometry (EI-MS) on compound-specific isotope analysis of chlorine and bromine (CSIA-Cl/Br) may be of crucial significance, yet a theoretical basis for elucidating the effects is absent. This study provides a solid theoretical deduction regarding the isotope fractionation taking place during fragmentation in EI-MS. Both intermolecular and intramolecular isotope fractionations present in dehalogenation processes, influencing the isotope ratios of detected ions. Read More


Context. Methane is among the main components of the ice mantles of insterstellar dust grains, where it is at the start of a rich solid-phase chemical network. Quantification of the photon-induced desorption yield of these frozen molecules and understanding of the underlying processes is necessary to accurately model the observations and the chemical evolution of various regions of the interstellar medium. Read More


The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and rationalizing it in the context of solvation entropy. Read More


With excellent efficiencies being reported from multiple labs across the world, device stability and the degradation mechanisms have emerged as the key aspects that could determine the future prospects of perovskite solar cells. However, the related experimental efforts remain scattered due to the lack of any unifying theoretical framework. In this context, here we provide a comprehensive analysis of ion migration effects in perovskite solar cells. Read More


Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. By developing quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, we show that these analytical results accurately predict the behavior of strongly anharmonic systems. Read More


Mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in two-dimensional electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct down-conversion from the highest-energy states to the lowest-energy pigments. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. Read More


A stochastic method is introduced for geometric modeling aerosol surface roughness with random field and discrete differential geometry theory. Optical scattering properties are computed for randomly oriented spheroidal particles with uniformly random surface roughness. Invariant imbedding T-Matrix and geometric optics method are applied to compute light scattering properties of aerosol particles covered from Rayleigh to geometric optics region. Read More


We report fabrication of an optically active, bio-electronic device based on thin film of purple membrane and single walled carbon nanotubes (SWNT). Two dimensional (2D) crystals of photoactive bacteriorhodopsin forms the optical center of the purple membrane where as pure SWNTs provides the necessary electronic support to the complex. Electro-optically functional and stable, hybrid complex was prepared using surface functionalization of SWNTs with indigenous, batch-process synthesized purple membrane. Read More


We present the fully general time-dependent multiconfiguration self-consistent-field method to describe the dynamics of a system consisting of arbitrary different kinds and numbers of interacting fermions and bosons. The total wave function is expressed as a superposition of different configurations constructed from time-dependent spin-orbitals prepared for each particle kind. We derive equations of motion followed by configuration-interaction (CI) coefficients and spin-orbitals for general, not restricted to full-CI, configuration spaces. Read More


We present the results of our calculations of the parity nonconserving electric dipole amplitudes ($E1_{PNC}$) for the $6s ~ ^2S_{1/2} - 5d ~ ^2D_{3/2;5/2}$ transitions of $^{133}$Cs employing a relativistic coupled-cluster (RCC) method. $E1_{PNC}$ values for the nuclear spin independent (NSI) and nuclear spin dependent (NSD) parity non-conservation (PNC) effects for different hyperfine levels of the $6s ~ ^2S_{1/2} - 5d ~ ^2D_{3/2}$ transition and only due to the NSD PNC interaction Hamiltonian for all possible hyperfine levels of the $6s ~ ^2S_{1/2} - 5d ~ ^2D_{5/2}$ transition are given. We have also performed calculations of several properties that are relevant for assessing the reliability of the calculations of the amplitudes of the above mentioned transitions. Read More


Capacitive deionization (CDI) is a fast-emerging technology most commonly applied to brackish water desalination. In CDI, salt ions are removed from the feedwater and stored in electric double layers (EDLs) within micropores of electrically charged porous carbon electrodes. Recent experiments have demonstrated that CDI electrodes exhibit selective ion removal based on ion size, with the smaller ion being preferentially removed in the case of equal-valence ions. Read More


H$_3^+$ is a ubiquitous and important astronomical species whose spectrum has been observed in the interstellar medium, planets and tentatively in the remnants of supernova SN1897a. Its role as a cooler is important for gas giant planets and exoplanets, and possibly the early Universe. All this makes the spectral properties, cooling function and partition function of H$_3^+$ key parameters for astronomical models and analysis. Read More


A combined ab initio and quantum dynamical study characterizes a family of bent neutral carbon dioxide molecules in terms of their vibrational levels, electric dipole moment surfaces, and infrared spectra in the gas phase. The considered isomers include the dioxiranylidene (cyclic) form of CO$_2$ with the equilibrium valence angle of 72$^\circ$, belonging to the ground electronic state, and four open structures with the valence angles of 118$^\circ$/119$^\circ$ (belonging to the singlet and triplet electronic states $2^1\!A'$ and $1^3\!A'$, respectively) and 127$^\circ$/128$^\circ$ (states $1^1\!A"$ and $1^3\!A"$, respectively). All studied bent structures possess permanent dipole moments. Read More


We consider a range of model potentials with metastable states undergoing molecular dynamics coupled to a thermal bath in the high friction regime, and consider how the optimal reaction coordinate depends on the diffusion anisotropy. For this we use our recently proposed method 'Spectral gap optimization of order parameters (SGOOP)' (Tiwary and Berne, Proc. Natl. Read More


Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure-function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Read More


The aim of this work is to study heat pump cycles, using CO 2 based mixtures as working fluids. Since adding other chemicals to CO 2 moves the critical point and generally equilibrium lines, it is expected that lower operating pressures as well as higher global efficiencies may be reached. A simple stage pure CO 2 cycle is used as reference, with fixed external conditions. Read More


Iodine (I$_2$) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by $\langle \cos^2 \theta_{2D} \rangle$, is measured as a function of the laser intensity. The results are well described by $\langle \cos^2 \theta_{2D} \rangle$ calculated for a gas of isolated molecules each with an effective rotational constant of 0. Read More


We present a general methodology to evaluate matrix elements of the effective core potentials (ECPs) within one-electron basis set of Slater-type orbitals (STOs). The scheme is based on translation of individual STO distributions in the framework of Barnett-Coulson method. We discuss different types of integrals which naturally appear and reduce them to few basic quantities which can be calculated recursively or purely numerically. Read More


The photoelectron spectrum of the $\textrm{X}^{+}\,{}^{2}\Pi \leftarrow \textrm{X}\,{}^{1}\Sigma^{+}$ photoionising transition in iododiacetylene, HC$_4$I, has been recorded using pulsed-field-ionisation zero-kinetic-energy (PFI-ZEKE) photoelectron spectroscopy with partial resolution of the rotational structure. The first adiabatic ionisation energy of HC$_4$I and the spin-orbit splitting of the X$^{+}\,{}^{2}\Pi$ state of HC$_4$I$^+$ are determined as $E^{\textrm{ad}}_{\textrm{I}}/(hc) = 74470.7(2)$ cm$^{-1}$ and $\Delta\tilde{\nu}_{\textrm{so}} = 1916. Read More


Supersonic beams of hydrogen atoms, prepared selectively in Rydberg-Stark states of principal quantum number $n$ in the range between 25 and 35, have been deflected by 90$^\circ$, decelerated and loaded into off-axis electric traps at initial densities of $\approx 10^6$ atoms/cm$^{-3}$ and translational temperatures of 150 mK. The ability to confine the atoms spatially was exploited to study their decay by radiative and collisional processes. The evolution of the population of trapped atoms was measured for several milliseconds in dependence of the principal quantum number of the initially prepared states, the initial Rydberg-atom density in the trap, and the temperature of the environment of the trap, which could be varied between 7. Read More