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We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird [J. Comp. Phys., 151, (1999)]. |
Gaining a detailed understanding of water transport behavior through ultra-thin polymer membranes is increasingly becoming necessary due to the recent interest in exploring applications such as water desalination using nanoporous membranes. Current techniques only measure bulk water transport rates and do not offer di... |
The new capacity of X-ray free-electron laser (XFEL) facilities to produce multi-color X-ray femtosecond pulses paves the way to explore ultrafast phenomena in matter induced by X-ray photons. In the present study, we exploit the site selectivity and the high temporal resolution of a two-color X-ray femtosecond pump-p... |
We develop a new scheme for determining molecular partial atomic charges (PACs) with external electrostatic potential (ESP) closely mimicking that of the molecule. The PACs are the "minimal corrections" to a reference-set of PACs necessary for reproducing exactly the tensor components of the Cartesian zero- fi... |
Density measurements from single-sinker magnetic suspension densimeters need to be corrected to compensate for the magnetic effects of the measuring cell materials and the fluid on the coupling transmission system. While the magnetic effect of the densimeter materials can be easily determined, the fluid effect require... |
Some aspects of direct ion transfer across the water/1,2-dichloroethane are analyzed using a very simple model based on thermodynamic considerations. It was concluded that ion solvation by water molecules may occur in some particular cases in the organic phase, delivering an important contribution to the Gibbs free en... |
The allyl radical (C3H5) is a well-characterized hydrocarbon radical, renowned for its pivotal role as an intermediate species in high-energy environments. Its core excited states can elucidate intricate details pertaining to its electronic and structural properties. |
The generalized relativistic effective core potential (GRECP) approach is employed in the framework of multireference single- and double-excitation configuration interaction (MRD-CI) method to calculate the spin-orbit (SO) splitting in the $^2P^o$ ground state of the Tl atom and spectroscopic constants for the $0^+$ gr... |
The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. |
We introduce state-averaging into the method of Monte Carlo configuration interaction (SA-MCCI) to allow the stable and efficient calculation of excited states. We show that excited potential curves for H$_{3}$, including a crossing with the ground state, can be accurately reproduced using a small fraction of the FCI ... |
A measurement method of constant-current-discharging voltage decay is established to characterize the band bending effect in the heterojunction of conducting glass/TiO2 for typical dye-sensitized solar cells. Furthermore, a dark-state electron transport regarding the TiO2 conduction band bending is proposed based upon... |
In this article, we present an emerging field of quantum chemistry at finite temperature. We discuss its recent developments on both theoretical and experimental <a href="http://fronts.We" rel="external noopener nofollow" class="link-external link-http">this http URL</a> describe and analyze several experimental inves... |
We proposed in Ref. [<a href="https://arxiv.org/abs/1812.09285v2" data-arxiv-id="1812.09285v2" class="link-https">arXiv:1812.09285v2</a>] a way to improve energy density functionals in the density functional theory based on the combination of the inverse Kohn-Sham method and the density functional perturbation theory.... |
Wetting is a widespread phenomenon, most prominent in a number of cases, both in nature and technology. Droplets of pure water with initial radius ranging from 20 to 80 [Å] spreading on graphitic surfaces are studied by molecular dynamics simulations. |
The use of optical cavities to control chemical reactions has been of great interest recently, following demonstrations of enhancement, suppression, and negligible effects on chemical reaction rates depending on the specific reaction and cavity frequency. In this work, we study the reaction rate inside imperfect cavit... |
We consider mechanisms of directed transport in a ratchet model comprising, besides the external freedom where transport occurs, a chemical freedom that replaces the familiar external driving by an autonomous dynamics providing energy input, and an internal freedom representing a functional mode of a motor molecule. T... |
A two-state model Hamiltonian is proposed to model the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. |
Using a reverse-engineering method we construct a meta-generalized gradient approximation (meta-GGA) angle-averaged exchange-correlation hole model which has a general applicability. It satisfies known exact hole constraints and can exactly recover the exchange-correlation energy density of any reasonable meta-GGA exc... |
Synthesizing new metal-organic frameworks (MOFs) is a challenging task, as the size, morphology, polymorph and type and number of defects present on the synthesis product may depend on many variables, including temperature, solvent, concentration and nature of reactants, among others. A deeper understanding on how syn... |
Solid-state micro/nanopores play an important role in the sensing field because of their high stability and controllable size. Aiming at problems of complex processes and high costs in pore manufacturing, we propose a convenient and low-cost micro/nanopore fabrication technique based on the needle punching method. |
The correlation energies of various atoms in their excited-states are estimated by modelling the Coulomb hole following the previous work by Chakravorty and Clementi. The parameter in the model is fixed by making the corresponding Coulomb hole to satisfy the exact constraint of charge neutrality. |
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. |
A single--pore model for performance of the cathode catalyst layer (CCL) in a PEM fuel cell is developed. The model takes into account oxygen transport though the CCL depth and through the thin Nafion film, separating the pore from Pt/C species. Analytical solution to model equations reveals the limiting current densit... |
It is known that the nuclear-spin-dependent parity-violating contributions to the NMR shielding and the nuclear spin-rotation tensors (${\bf \sigma}^{PV}$ and ${\bf M}^{PV}$, respectively) are formally related each other within the non-relativistic (NR) regime. Such a formal relationship is not any longer valid within... |
Density-functional theory requires ever better exchange-correlation (xc) functionals for the ever more precise description of many-body effects on electronic structure. Universal constraints on the xc energy are important ingredients in the construction of improved functionals. |
An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. |
In this work we explore the potential of a new data-driven approach to the design of exchange-correlation (XC) functionals. The approach, inspired by convolutional filters in computer vision and surrogate functions from optimization, utilizes convolutions of the electron density to form a feature space to represent lo... |
The mechanisms for photodissociation of methyl halides (CH$_3$X, X= Cl, Br, I) have been studied for these molecules when adsorbed on thin films of C$_6$H$_6$ or C$_6$F$_6$ on copper single crystals, using time-of-flight spectroscopy with 248nm and 193nm light. For CH$_3$Cl and CH$_3$Br monolayers adsorbed on C$_6$H$_... |
Previously-determined empirical energy levels are used to construct a rovibronic model for the $\mathrm{X}\,^4\Sigma^-$, $\mathrm{A}'\,^4\Phi$, $\mathrm{A}\,^4\Pi$, $\mathrm{B}\,^4\Pi$, $\mathrm{C}\,^4\Sigma^-$, $\mathrm{D}\,^4\Delta$, $\mathrm{1}\,^2\Delta$, $\mathrm{1}\,^2\Sigma^+$, $\mathrm{1}\,^2\Phi$, $\mathrm... |
An adaptation of the full configuration interaction quantum Monte Carlo (FCIQMC) method is presented, for correlated electron problems containing heavy elements and the presence of significant relativistic effects. The modified algorithm allows for the sampling of the four-component spinors of the Dirac--Coulomb(--Bre... |
One of the most popular subjects now being researched in molecular science is strong light-matter coupling. The introduction of vibrational strong coupling and the formation vibro-polaritonic states tend to modify chemical reactivity, energy transfer, and many other physical properties of the coupled system. |
We present new interaction potential curves, calculated from first-principle, for the He$(^3$S)$...$H$_2$ and He$(^3$S)$...$Ar systems, relevant in Penning's ionization experiments. Two different approaches were applied: supermolecular using coupled cluster theory (CC) and perturbational within symmetry-adapted pe... |
An accurate knowledge of cage occupancy of methane is central for understanding the physical-chemical properties of gas hydrates, the actual inventory of natural gas in hydrate deposits and the description of gas exchange processes. Here we report the absolute cage occupancies, the cage occupancy ratios and hydration ... |
Organic-inorganic hybrid perovskites are considered to be most promising photovoltaic materials. Highest efficiencies of perovskite solar cells have been achieved by using appropriate cation and anion mixtures. |
A model for the current-voltage characteristic of the junction between an Ion-Sensitive-Membrane and an electrolyte solution is derived and compared with numerical simulations of the Poisson-Nernst-Planck model for ion transport. The expression resembles that of a semiconductor pn junction with a non-ideality factor o... |
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are summarized and put into perspective. |
The latest experimental [Noll et al. Atmos. Chem. Phys. 20(2020)5269] and theoretical [Brooke et al. J. Quant. Spectr. Rad. Transfer 168(2016)142] data on the OH emission intensities are analyzed with use of the NIDL. It is found that the calculated intensities of the $\Delta v>6$ transitions should not be trusted.... |
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of rapidly determining multiple pathways between known states. |
This paper presents in detail our fast semistochastic heat-bath configuration interaction (SHCI) method for solving the many-body Schrodinger equation. We identify and eliminate computational bottlenecks in both the variational and perturbative steps of the SHCI algorithm. |
We study the structure and dynamics of liquid water in contact with Pd and Au (111) surfaces using \emph{ab initio} molecular dynamics simulations with and without van der Waals interactions. Our results show that the structure of water at the interface of these two metals is very different. |
The current paper investigates the impact of gluconate, D-sorbitol, D-mannitol and D-galactitol on calcium speciation at high pH values by i) solubility measurements of portlandite (Ca(OH)2) and |
The notion of the n-th order local energy, generated by the n-th power of the Hamiltonian, has been introduced. The n-th order two-particle coalescence conditions have been derived from the requirements that the n-th order local energy at the coalescence point is non-singular and equal to the n-th power of the Hamilto... |
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the application of existing ML methods. |
We perform the calculation of all relativistic and quantum electrodynamic corrections of the order of $\alpha^6\,m$ to the ground electronic state of a hydrogen molecule and present improved results for the dissociation and the fundamental transitions energies. These results open the window for the high-precision spec... |
In this work, we propose a geometrical model for the study of conformational properties of a starburst dendrimer with the topology of a truncated Bethe lattice. A convenient embedding of the Bethe lattice in the hyperbolic plane is used to study the architecture of the dendrimer. |
A formulation is presented to efficiently model ionic conduction inside, i.e. across and along, grain boundaries. Efficiency and accuracy is achieved by reducing it to a two-dimensional manifold while guaranteeing the conservation of mass and charge at the intersection of multiple grain boundaries. |
The inverse problem of Kohn-Sham density functional theory (DFT) is often solved in an effort to benchmark and design approximate exchange-correlation potentials. The forward and inverse problems of DFT rely on the same equations but the numerical methods for solving each problem are substantially different. |
We present a theoretical model for the study of exciton dynamics in J-aggregated monolayers of fluorescent dyes. The excitonic evolution is described by a Monte-Carlo wave function approach which allows for a unified description of the quantum (ballistic) and classical (diffusive) propagation of an exciton on a lattic... |
We present the development of a new astrochemical research tool HILTRAC, the Highly Instrumented Low Temperature ReAction Chamber. The instrument is based on a pulsed form of the CRESU (Cinétique de Réaction en Écoulement Supersonique Uniforme, meaning reaction kinetics in a uniform supersonic flow) apparatus, with th... |
Densified SiO2 glasses, obtained from different pressure and temperature routes have been annealed over a wide range of temperature far below the glass transition temperature (500$^\circ$C-900$^\circ$C). Hot and cold compressions were useful to separate the effects of pressure and the compression temperature. |
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 throu... |
Density functional theory (DFT) calculations have been performed for the high-spin (HS) and low-spin (LS) isomers of a series of iron(II) spin crossover complexes with nitrogen ligands. The calculated charge densities have been analyzed in the framework of the quantum theory of atoms in molecules (QTAIM). |
There have existed for a long time a paradigm that TiO phases at ambient conditions are stable only if structural vacancies are available. Using an evolutionary algorithm, we perform an ab initio search of possible zero-temperature polymorphs of TiO in wide pressure interval. |
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced by external driving in at least one such system. |
Modulating heterogeneous microstructure in room temperature ionic liquids (RTILs) by external stimuli is an important approach for understanding and designing the external field induced chemical reactions in natural and applicable systems. Here, we report for the first time the redistribution of oxygen molecules in RT... |
Extensive all-atom molecular dynamics calculations on the water-squalane interface for nine different loadings with sorbitan monooleate (SPAN80), at $T=300$K, are analyzed for the surface tension equation of state, desorption free energy profiles as they depend on loading, and to evaluate escape times for absorbed SPAN... |
We describe a new method for pulsed spin order transfer (SOT) of parahydrogen induced polarization (PHIP) that enables close to 100 % polarization in incompletely 2H-labeled molecules by exciting only the desired protons in a frequency-selective manner. While a selective pulse (SP) on 1H at the beginning of pulsed SOT... |
In a recent comment, Ruth Signorell raises a number of issues that she considers to question the validity of our approach to determine mean free paths for electron scattering in liquid water and our comparison with the results on amorphous ice by Michaud, Wen, and Sanche. Here, we show that these critiques are unjusti... |
Since their discovery in 1822, supercritical fluids have been of enduring interest, and have started to be deployed in many important applications. Theoretical understanding of the supercritical state is lacking, and is seen to limit further industrial deployment. |
Exchange-correlation potentials vxc and energy densities exc are derived for integer and fractional electron counts using an orbital-averaged Kohn-Sham inversion procedure. The reference densities for inversion come from full configuration interaction in a Slater orbital basis. |
The effect of three-body interatomic contributions in the equation of state of 4He are investigated. A recent two-body potential together with the Cohen and Murrell (Chem. |
Long-range charge-transfer excitations pose a major challenge for time-dependent density functional approximations. We show that spin-symmetry-breaking offers a simple solution for molecules composed of open-shell fragments, yielding accurate excitations at large separations when the acceptor effectively contains one ... |
The hydration structure of Ba^{2+} ion is important for understanding blocking mechanisms in potassium ion channels. Here, we combine statistical mechanical theory, ab initio molecular dynamics simulations, and electronic structure methods to calculate the hydration free energy and local hydration structure of Ba^{2+}... |
The comment of Guseinov is irrelevant and also unjust. In contrast to his comment, we show that the obtained electric multipole moment values for some first-row diatomic molecules are original and better than his values (I.I. Guseinov, E. Akin, and A.M. |
We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in |
In an effort to increase the speed and efficiency of ballistic energy transport via oligomeric chains, we performed measurements of the transport in compounds featuring long alkyl chains of up to 37 methylene units. Compounds of the N3-(CH2)n-COOMe type (denoted as aznME) were synthesized with n = 5, 10, 15, 19, 28, 3... |
The hierarchical triple-helix structure of collagen type I, Col I, is essential for extracellular matrix support and integrity. However, current reconstruction strategies face challenges such as chain mismatch, preventing proper fibril formation. |
We have developed and experimentally demonstrated an improved electrostatic deflector for the spatial separation of molecules according to their dipole-moment-to-mass ratio. The device features a very open structure that allows for significantly stronger electric fields as well as for stronger deflection without molec... |
Electronic open-shell ground-state properties of selected alkali-metal (AM) - alkaline-earth-metal (AEM) polar molecules are investigated. We determine potential energy curves of the 2{\Sigma}+ ground state at the coupled-cluster singles and doubles with partial triples (CCSD(T)) level of electron correlation. |
We report an investigation of the low-lying excited states of the YbF molecule--a candidate molecule for experimental measurements of the electron electric dipole moment--with 2-component based multi-reference configuration interaction (MRCI), equation of motion coupled cluster (EOM-CCSD) and the extrapolated intermedi... |
A light-driven molecular motor system is investigated using a multi-state Brownian ratchet model described by a single effective coordinate with multiple electronic states in a dissipative environment. The rotational motion of the motor system is investigated on the basis of wavepacket dynamics. |
We address a molecular dissociation mechanism that is known to occur when a H 2 molecule approaches a catalyst with its molecular axis parallel to the surface. It is found that molecular dissociation is a form of quantum dynamical phase transition associated to an ana- lytic discontinuity of quite unusual nature: the ... |
Electron transmission through chiral molecules induced by circularly polarized light can be very different for mirror-image structures, a peculiar fact given that the electronic energy spectra of the systems are identical. We propose that this asymmetry - as large as 10% for resonance transport- arises from different ... |
When a cell-sized water droplet, with a diameter of several tens of micro meter, is placed in oil containing phospholipids, a stable cell-sized vesicle is spontaneously formed as a water-in-oil phospholipid emulsion (W/O CE) with a phospholipid monolayer. We transferred the lipid vesicle thus formed in the oil phase t... |
The development of kinetic energy functional (KEF) is known as one of the most difficult subjects in the electronic density functional theory (DFT). In particular, the sound description of chemical bonds using a KEF is a matter of great significance in the field of theoretical physics and chemistry. |
Nuclear Magnetic Resonance (NMR) is one of the most powerful experimental techniques to characterize the structure of molecules and confined liquids. Nevertheless, the complexity of the systems under investigation usually requires complementary computational studies to interpret the NMR results. |
Phase-modulated wave-packet interferometry is combined with mass-resolved photoion detection to investigate rubidium atoms attached to helium nanodroplets in a molecular beam experiment. The spectra of atomic Rb electronic states show a vastly enhanced sensitivity and spectral resolution when compared to conventional ... |
Electrode-electrolyte interfaces are crucial for electrochemical energy conversion and storage. At these interfaces, the liquid electrolytes form electrical double layers (EDLs). |
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range of tools to support simulations of finite size systems, extended systems with pe... |
The absorption spectrum of the MnO$_{4}$$^{-}$ ion has been a test-bed for quantum-chemical methods over the last decades. Its correct description requires highly-correlated multiconfigurational methods, which are incompatible with the inclusion of finite-temperature and solvent effects due to their high computational... |
Photodetachment spectroscopy of OH- and H3O2- anions has been performed in a cryogenic 22-pole radiofrequency multipole trap. Measurements of the detachment cross section as a function of laser frequency near threshold have been analysed. |
Smooth model potentials with parameters selected to reproduce the spectrum of one-electron atoms are used to approximate the singular Coulomb potential. Even when the potentials do not mimic the Coulomb singularity, much of the spectrum is reproduced within the chemical accuracy. |
We present the first report of optical absorption spectroscopy of H$^{36}\! $Cl, a radioactive isotopologue of hydrogen chloride. |
Recent atomic force microscopy (AFM) can measure force curves between a probe and a sample surface in several solvents. The force curve is thought as the solvation structure in some cases, because its shape is generally oscilltive and pitch of the oscillation is about the same as diameter of the solvent. |
In this work, an extension of the Madrid-2019 force field is presented. We have added the cations Rb + and Cs + and the anions F$^-$, Br$^-$ and I$^-$. |
The rise of machine learning has greatly influenced the field of computational chemistry, and that of atomistic molecular dynamics simulations in particular. One of its most exciting prospects is the development of accurate, full-dimensional potential energy surfaces (PESs) for molecules and clusters, which, however, ... |
Energy transport theories are being revisited at the nanoscale, as macroscopic laws known since a century are broken at dimensions smaller than those associated with energy carriers. For thermal radiation, where the typical dimension is provided by Wien's wavelength, Planck's law and associated concepts descri... |
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. Here, we derive a simple, closed-form formula for the apparent surface charge (ASC), as well as for the electric field, generated by a molec... |
High-harmonic generation (HHG) spectrum from a LiH molecule induced by an intense laser pulse is computed and analyzed with potential energy surfaces for electron motion (ePES) constructed from a model of localized electron wave packets (EWP) with valence-bond spin-coupling. The molecule has two valence ePES with bind... |
Identifying signatures of quantum coherent behaviour in photoactive systems that are maintained in stationary states away from thermal equilibrium is an open problem of wide interest in a variety of physical scenarios, including single photosynthetic complexes subjected to continuous incoherent illumination. Here we c... |
Ab initio thermodynamics is a widespread, computationally efficient approach to predict the stable configuration of a surface in contact with a surrounding (gas or liquid) environment. In a prevalent realization of this approach, this stable configuration is simply equated with the structure in a considered candidate ... |
The transition between two distinct mechanisms for the laser-induced field-free orientation of CO molecules is observed via measurements of orientation revival times and subsequent comparison to theoretical calculations. In the first mechanism, which we find responsible for the orientation of CO up to peak intensities... |
Removing suspended solids and colloids are one of the most important water treatment processes. In this research, experimental tests have been done to assess the effects of pH and different doses of PACL on turbidity removal efficiency. |
Vibrational spectra can be computed without storing full-dimensional vectors by using low-rank sum-of-products (SOP) basis functions. We introduce symmetry constraints in the SOP basis functions to make it possible to separately calculate states in different symmetry subgroups. |
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. |
It is known that the presence of cations like Ca++ or Pb++ in the water subphase alters the pressure-area isotherms for fatty acid monolayers. The corresponding lattice constant changes have been studied using x-ray diffraction. |
The ability to control chemical reactions by coupling organic molecules to confined light in a cavity has recently attracted much attention. While most previous studies have focused on single-mode photonic or plasmonic cavities, here we investigate the effect of hybrid metallodielectric cavities on photoisomerization ... |
Preconcentration of the target compound is a critical step that ensures the accuracy of the subsequent chemical analysis. In this work, we present a straightforward yet effective liquid-liquid extraction approach based on surface nanodroplets (i.e., nanoextraction) for offline analysis of highly diluted sample solutio... |
Densities, $\rho$, and speeds of sound, $u$, of 2-propanone + aniline, + N-methylaniline, or + pyridine systems have been measured at (293.15, 298.15 and 303.15) K and atmospheric pressure using a vibrating tube densimeter and sound analyser Anton Paar model DSA-5000. The $\rho$ and $u$ values were used to calculate e... |
The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between bases and the structure of the DNA environment. |
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