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The solvent-induced interactions (SII) between flexible solutes can be separated into two distinct components: the solvation-induced conformational effect, and the joint solvation interaction (JSI). The JSI quantifies the thermodynamic effect of the solvent simultaneously accommodating the solutes, generalizing the ty...
The solvated electron represents an elementary quantum system in a liquid environment. Electrons solvated in water have raised strong interest because of their prototypical properties, their role in radiation chemistry, and their relevance for charge separation and transport.
Resonant vibrational and rotation-vibration excitation cross sections for electron-CO scattering are calculated in the 0-10 eV energy range for all 81 vibrational states of CO, assuming that the excitation occur via the 2{\Pi} shape resonance. Static exchange plus polarization calculations performed using the R-matrix...
A variationally computed $^{28}$SiH$_4$ rotation-vibration line list applicable for temperatures up to $T=1200\,$K is presented. The line list, called OY2T, considers transitions with rotational excitation up to $J=42$ in the wavenumber range $0$--$5000\,$cm$^{-1}$ (wavelengths $\lambda> 2\,\mu$m).
In this chapter we focus first on the theoretical methods and relevant computational approaches to calculate the electronic structure of atoms, molecules, and clusters containing heavy elements for which relativistic effects become significant. In particular, we discuss the mean-field approximation of the Dirac equati...
We investigate the electronic stress tensor of the hydrogen molecular ion for the ground state using the exact wave function and wave functions approximated by gaussian function basis set expansion. The spatial distribution of the largest eigenvalue, corresponding eigenvectors, tension and kinetic energy density are c...
A linear-scaling algorithm is presented for computing the Hartree-Fock (HF) exchange matrix using concentric atomic density fitting. The algorithm utilizes the stronger distance dependence of the three-center electron repulsion integrals along with the rapid decay of the density matrix to accelerate the construction o...
Neutron scattering and molecular dynamics studies were performed on a concentrated aqueous tetramethylammonium (TMA) chloride solution to gain insight into the hydration shell structure of TMA, which is relevant for understanding its behavior in biological contexts of, e.g., properties of phospholipid membrane headgrou...
Recently, two-photon fluorescent probes based on anthocyanidins molecules have attracted extensive attention due to their outstanding photophysical properties. However, there are only a few two-photon excited fluorescent probes that really meet the requirements of relatively long emission wavelengths (>600 nm), lar...
The interpretation of electrochemical impedance spectroscopy data by fitting it to equivalent circuit models has been a standard method of analysis in electrochemistry. However, the inversion of the data from the frequency domain to a distribution function of relaxation times (DFRT) has gained considerable attention f...
We comment a recent work titled "Direct evidence for hidden one-dimensional Fermi surface of hexagonal K0.25WO3". In this paper the authors report photoemission and theoretical results on the K0.25WO3 system which led them to propose that a Charge Density Wave (CDW), associated with hidden one-dimensional band...
In order to resolve a significant uncertainty in the heat of vaporization of silicon -- a fundamental parameter in gas-phase thermochemistry -- $\Delta H^\circ_{f,0}$[Si(g)] has been determined from a thermochemical cycle involving the precisely known experimental heats of formation of SiF_4(g) and F(g) and a benchmark...
We predict anti-alignment dynamics in the excited state of H2+ or related homonuclear dimers in the presence of a strong field. This effect is a general indirect outcome of the strong transition dipole and large polarizabilities typically used to control or to induce alignment in the ground state.
We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires only one quantum calculation for each molecular dynamics step in contrast to multi...
We present various types of reduced models including five vibrational modes and three electronic states for the pyrazine molecule in order to investigate the lifetime of electronic coherence in a rigid and neutral system. Using an ultrafast optical pumping in the ground state (1 1 A g ), we prepare a coherent superpos...
It is well assessed that the charge transport through a chiral potential barrier can result in spin-polarized charges. The possibility of driving this process through visible photons holds tremendous potential for several aspects of quantum information science, e.g., the optical control and readout of qubits.
Broadband inversion pulses that rotate all magnetization components 180 degrees about a given fixed axis are necessary for refocusing and mixing in high-resolution NMR spectroscopy. The relative merits of various methodologies for generating pulses suitable for broadband refocusing are considered.
Molecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translational and r...
Unambiguously identifying molecules in spectra is of fundamental importance for a variety of scientific and industrial uses. Interpreting atmospheric spectra for the remote detection of volatile compounds requires information about the spectrum of each relevant molecule.
We present a new analysis of exchange and dispersion effects for calculating halogen-bonding interactions in a wide variety of complex dimers (69 total) within the XB18 and XB51 benchmark sets. Contrary to previous work on these systems, we find that dispersion plays a more significant role than exact exchange in accu...
Proton migration is a ubiquitous process in chemical reactions related to biology, combustion, and catalysis. Thus, the ability to control the movement of nuclei with tailored light, within a hydrocarbon molecule holds promise for far-reaching applications.
It has been shown that it is possible to transform a well-stirred chemical medium into a logic-gate simply by varying the chemistry's external conditions (feed rates, lighting conditions, etc). We extend this work, showing that the same method can be generalized to spatially-extended systems.
Steric or attractive interactions among reactants or between reactants and inert crowders can substantially influence the total rate of a diffusion-influenced reaction in the liquid phase. However, the role of the product species, that has typically different physical properties than the reactant species, has been dis...
The carbon chain ions HC$_3$O$^+$ and HC$_3$S$^+$ - longer variants of the famous "X-ogen" line carrier HCO$^+$ - have been observed for the first time using two cryogenic 22-pole ion trap apparatus (FELion, Coltrap) and two different light sources: the Free Electron Laser for Infrared eXperiments (FELIX), whic...
The presence of two chlorine atoms in 1,2-dichloroethene allows for isomerisation around the double bond. This isomerisation can lead to rich photochemistry.
We report spectra of various benzene isotopomers and their dimers in helium nanodroplets in the region of the first Herzberg-Teller allowed vibronic transition 610 1B2u<-1A1g (the A00 transition) at ~260 nm. Excitation spectra have been recorded using both beam depletion detection and laser-induced fluorescence.
The development of kinetic energy (KE) functionals is one of the current challenges in density functional theory (DFT). The Yukawa non-local KE functionals [Phys. Rev. B 103, 155127 (2021)] have been shown to describe accurately the Lindhard response of the homogeneous electron gas (HEG) directly in the real space, wi...
Electronic excitations and ionisations produced by electron impact are key processes in the radiation-induced damage mechanisms in materials of biological relevance, underlying important medical and technological applications, including radiotherapy, radiation protection in manned space missions and nanodevice fabricat...
Experimental and theoretical evidence point out to the crucial role of specific resonant intramolecular vibrational modes in the interpretation of long-lived coherences observed in two-dimensional spectra of some natural and synthetic light harvesting complexes. For the natural situation of illumination by incoherent ...
Ab initio methods based on the second-order and higher connected moments, or cumulants, of a reference function have seen limited use in the determination of correlation energies of chemical systems throughout the years. Moment-based methods have remained unattractive relative to more ubiquitous methods, such as pertu...
We propose an efficient ${\cal O}(N^2)$-parameter ansatz that consists of a sequence of exponential operators, each of which is a unitary variant of Neuscamman's cluster Jastrow operator. The ansatz can also be derived as a decomposition of T$_2$ amplitudes of the unitary coupled cluster with generalized singles a...
The augmented potential introduced by Levy and Zahariev [Phys. Rev. Lett. 113, 113002 (2014)] is shifted with respect to the standard exchange-correlation potential of Kohn-Sham density functional theory by a density-dependent constant that makes the total energy become equal to the sum of the occupied orbital energies...
Calculations are carried out to determine elastic scattering cross sections and resonance energies for low energy electron impact on uracil and on each of the DNA bases (thymine, cytosine, adenine, guanine), for isolated molecules in their equilibrium geometry. Our calculations are compared with available theory and e...
We assess the predictive power of alchemical perturbations for estimating fundamental properties in ionic crystals. Using density functional theory we have calculated formation energies, lattice constants, and bulk moduli for all sixteen iso-valence-electronic combinations of pure pristine alkali halides involving ele...
The non-relativistic electronic Hamiltonian, H(a)= Hkin + Hne + aHee, extended with coupling strength parameter (a), allows to switch the electron-electron repulsion energy off and on. First, the easier a=0 case is solved and the solution of real (physical) a=1 case is generated thereafter from it to calculate the tot...
We have derived a new method which allows to compute the full and the Pauli reference kinetic potentials for atoms and molecules in a real space representation. This is done by applying the optimized effective potential (OEP) method to {the} Kohn-Sham non-interacting kinetic energy expression.
Significant efforts have been devoted in the last decade towards improving the predictivity of coarse-grained models in molecular dynamics simulations and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research effort ...
We present Monte Carlo simulations on Eley-Rideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations.
Gold nanoparticles have been synthesized inside ethosomes, vesicles composed of phospholipid, ethanol and water, which could be very efficient not only in delivery probes to the skin but also as diagnostic and therapeutic multimodal agents. High efficiency encapsulation of gold nanoparticles is achieved by a simple st...
We combine the renormalized singles (RS) Green's function with the T-Matrix approximation for the single-particle Green's function to compute quasiparticle energies for valence and core states of molecular systems. The $G_{\text{RS}}T_0$ method uses the RS Green's function that incorporates singles contrib...
Owing to the presence of strong static correlation effects, accurate prediction of the electronic properties (e.g., the singlet-triplet energy gaps, vertical ionization potentials, vertical electron affinities, fundamental gaps, symmetrized von Neumann entropy, active orbital occupation numbers, and real-space represen...
We have developed a new method for fabrication of ultra-low noise silver-silver chloride (Ag-AgCl) reference electrode with dramatically high stability, useful in biomedical precise measurements. Low noise level and high stability are the most important features when evaluating reference electrode for example when use...
In this paper the Martin-Siggia-Rose formalism is used to derive a generalized Rouse equation for a test chain in a matrix which can undergo the glass transition. It is shown that the surrounding matrix renormalizes the static properties of the test chain.
Efficiently and accurately computing molecular Auger electron spectra for larger systems is limited by the increasing complexity of the scaling in the number of doubly ionized final states with respect to the system size. In this work, we benchmark the application of multiconfiguration pair-density functional theory w...
A full-dimensional molecular model of water, HBB2-pol, derived entirely from first principles, is introduced and employed in computer simulations ranging from the dimer to the liquid. HBB2-pol provides excellent agreement with the measured second and third virial coefficients and, by construction, reproduces the dimer...
When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, ai...
Development of the methods to exploit nuclear hyperpolarization and search for molecules whose nuclear spins can be efficiently hyperpolarized is an active area in nuclear magnetic resonance. Of particular interest are those molecules that have long nuclear relaxation times, making them to be suitable candidates as co...
The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation ...
Standard approximations for the exchange-correlation (XC) functional in Kohn-Sham density functional theory (KS-DFT) typically lead to unacceptably large errors when applied to strongly-correlated electronic systems. Partition-DFT (PDFT) is a formally exact reformulation of KS-DFT in which the ground-state density and...
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects, because it involves a complic...
A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function Reaction Dynamics (GFRD), and variations thereon -- each offering trade-offs...
We develop a second order correction to commonly used density functional approximations (DFA) to eliminate the systematic delocalization error. The method, based on the previously developed global scaling correction (GSC), is an exact quadratic correction to the DFA for the fractional charge behavior and uses the anal...
An analytical description of nucleation stage in a supersaturated vapor with instantly created supersaturation is given with taking into account the vapor concentration inhomogeneities arising as a result of depletion due to non-stationary diffusion onto growing droplets. This description suggests that the intensity o...
The hard sphere repulsion among ions can be considered in the Poisson-Nernst-Planck (PNP) equations by combining the fundamental measure theory (FMT). To reduce the nonlocal computational complexity in 3D simulation of biological systems, a local approximation of FMT is derived, which forms a local hard sphere PNP (LH...
In searching for novel photoactive liquid crystals, we have synthesized a series of five-ring pyridine-based bent-core compounds bearing different substituents at the peripheral phenyl rings (CH3O, Cl and NO2). Their mesomorphic behaviour has been investigated by polarizing optical microscopy, differential scanning ca...
We demonstrate a new technique in velocity map imaging (VMI) that allows spatial gating of the laser focal overlap region in time resolved pump-probe experiments. This significantly enhances signal-to-noise ratio by eliminating background signal arising outside the region of spatial overlap of pump and probe beams.
The role of internal motions and molecular geometry on $^1$H NMR relaxation times $T_{1,2}$ in hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for in{\it tra}molecular $G_R(t)$ and in{\it ter}molecular $G_T(t)$ $^1$H-$^1$H dipole-dipole interactions arising from r...
Despite the wide use of first-principles calculations to elucidate catalytic reaction mechanisms, the reliability of the theory remains unknown for reactions that initiate with O$_2$ adsorption, as few papers in the literature have systematically verified the accuracy of the calculations. Here, we have overcome this i...
A general expression is derived for the dipolar NMR spin-lattice relaxation rate $1/T_1$ of a system exhibiting Brownian dynamics in a discrete and finite configuration space. It is shown that this approach can be particularly useful to model the proton relaxation rate in molecular rotors.
In the framework of Kohn-Sham density-functional theory, systems with ground-state densities that are not pure-state v-representable in the non-interacting reference system (PSVR) occur frequently. In the present contribution, a new algorithm, which allows the solution of such systems, is proposed.
We present a new wavefunction ansatz that combines the strengths of spin projection with the language of matrix product states (MPS) and matrix product operators (MPO) as used in the density matrix renormalization group (DMRG). Specifically, spin-projected matrix product states (SP-MPS) are constructed as $\|\Psi^{(N,S...
Microscopic thermodynamic studies can elucidate specific molecular interactions. In this work, we report the microscopic thermodynamics in binary liquid mixtures, which elucidate the role of molecular structure in nonlinear solvent response using femtosecond optical tweezers (FOT).
Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, ...
We report microscopic calculations of free energies and entropies for intramolecular electron transfer reactions. The calculation algorithm combines the atomistic geometry and charge distribution of a molecular solute obtained from quantum calculations with the microscopic polarization response of a polar solvent expr...
Lipid nanoparticles (LNPs) are precisely engineered drug delivery carriers commonly produced through controlled mixing processes, such as nanoprecipitation. Since their delivery efficacy greatly depends on particle size, numerous studies have proposed experimental and theoretical approaches for tuning LNP size.
A novel route to the exponential trapping-time distribution within a solidlike state in water clusters is described. We propose a simple homogeneous network (SHN) model to investigate dynamics on the potential energy networks of water clusters.
To describe excited states, the electron density alone being insufficient, we use the noninteracting reference density matrix $\gamma_{s}({\bf x},{\bf x}')$ based on the recently established foundation for the $\Delta SCF$ theory, in which ground and excited state energies and densities are obtained from the minimu...
We describe the thermodynamic state of a single-phase fluid confined to a porous medium with Hill's thermodynamics of small systems, also known as nanothermodynamics. This way of defining small system thermodynamics, with a separate set of control variables, may be useful for the study of transport in non-deformab...
The crystal structures of potassium and cesium bistrifluoroacetates were determined at room temperature and at 20 K and 14 K, respectively, with the single crystal neutron diffraction technique. The crystals belong to the I2/a and A2/a monoclinic space groups, respectively, and there is no visible phase transition.
First steps towards developing a new perturbation theory for molecular liquids are taken. By choosing a new form of splitting the site-site potential functions between molecules, we will get a set of atomic fluids as the reference system with known structure and thermodynamics.
Self interaction error remains an impotrant problem in density functional theory. A number of approximations to exact exchange aimed to correct for this error while retainining computational efficiency had been suggested recently.
Non-perturbative high-harmonic generation (HHG) has recently been observed in the liquid phase, where it was demonstrated to have a different physical mechanism compared to gas and solid phases of matter. The currently best physical picture for liquid HHG eliminates scattered-electron contributions and identifies on-s...
In previous research, we tested the wave function format of a linear combination of several antisymmetrized geminal power states. A numerical problem in the geminal matrices was noted, which made the total energies of electronic systems with large numbers of electrons unstable.
For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to provide sufficiently accurate data, especially for molecules containing transition ...
We present a detailed analysis of the mechanism of the primary charge separation process in bacterial photosynthesis using real-time path integrals. Direct computer simulations as well as an approximate analytical theory have been employed to map out the dynamics of the charge separation process in many regions of the...
We present a study of mono(benzene)TM and bis(benzene)TM systems, where TM={Mo,W}. We calculate the binding energies by quantum Monte Carlo (QMC) approaches and compare the results with other methods and available experiments.
The infrared bar-spectrum of a single ammonia molecule encapsulated in nano-cage C$_{60}$ fullerene molecule is modelled using the site inclusion model successfully applied to analyze spectra of CO$_2$ isotopologues isolated in rare gas matrix. Calculations show that NH$_3$ can rotate freely on a sphere of radius 0.18...
This article reviews the application of fragment descriptors at different stages of virtual screening: filtering, similarity search, and direct activity assessment using QSAR/QSPR models. Several case studies are considered.
In this work we describe the rank-reduced variant of the equation-of-motion coupled cluster theory with complete inclusion of single, double, and triple excitations. The advantage of the proposed formalism in comparison with the canonical theory stems from the application of Tucker decomposition format to the ground- ...
A state-specific multireference coupled-cluster method based on Arponen's bivariational principle is presented, the bivar-MRCC method. The method is based on singlereference theory, and therefore has a relatively straightforward formulation and modest computational complexity.
Excitation energy transfer (EET) is one of the most important processes in both natural and artificial chemical systems including, for example, photosynthetic complexes and organic solar cells. The EET rate, however, is strongly suppressed when there is a large difference in the excitation energy between the donor and...
The optimal power performance of a first principle quantum heat engine model shows friction-like phenomena when the internal fluid Hamiltonian does not commute with the external control field. The model is based on interacting two-level-systems where the external magnetic field serves as a control variable.
Formation of microstructure in homogeneous associated liquids is analysed through the density-density pair correlation functions, both in direct and reciprocal space, as well as an effective local one-body density function. This is illustrated through a molecular dynamics study of two neat alcohols, namely methanol an...
Photoelectron angular distributions (PADs) of oriented polar molecules in response to different polarized lasers are systematically investigated. It is found that the PADs of polar CO molecules show three distinct styles excited by linearly, elliptically and circularly polarized lasers respectively.
We present the implementation of a variational finite element solver in the HelFEM program for benchmark calculations on diatomic systems. A basis set of the form $\chi_{nlm}(\mu,\nu,\phi)=B_{n}(\mu)Y_{l}^{m}(\nu,\phi)$ is used, where $(\mu,\nu,\phi)$ are transformed prolate spheroidal coordinates, $B_{n}(\mu)$ are fi...
Recent literatures reported blue-green emission from amyloid fibril as exclusive signature of fibril formation. This unusual visible luminescence is regularly used to monitor fibril growth.
Parity-violating energies $E_{PV}$ of the $H_2X_2$ X = O, S, Se, Te, Po) molecules are reported, calculated as analytical expectation values at the relativistic coupled-cluster singles-and-doubles (CCSD) level using property-optimized basis sets. Radiative corrections to the $E_{PV}$ was investigated using effective Q...
Rotational transitions in molecular hydrogen collisions are computed. The two most recently developed potential energy surfaces for the H2-H2 system are used from the following works:
A wide range of experiments have established that certain chemical reactions at metal surfaces can be driven by multiple hot electron mediated excitations of adsorbates. A high transient density of hot electrons is obtained by means of femtosecond laser pulses and a characteristic feature of such experiments is the em...
When creating training data for machine-learned interatomic potentials (MLIPs), it is common to create initial structures and evolve them using molecular dynamics to sample a larger configuration space. We benchmark two other modalities of evolving structures, contour exploration and dimer-method searches against mole...
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions.
Microfluidic systems hold great potential for the study of live microscopic cultures of cells, tissue samples, and small organisms. Integration of hyperpolarisation would enable quantitative studies of metabolism in such volume limited systems by high-resolution NMR spectroscopy.
The physical nature and the correct definition of hydrogen bond (H-bond) are considered. \,\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.
The article presents new model of equilibrium in open chemical systems suggesting a linear dependence of the reaction shift from equilibrium in presence of the external thermodynamic force. Basic equation of this model contains traditional logarithmic term and a non-traditional parabolic term.
The dissociation of a hydrogen molecule on MgO(001) films deposited on Mo(001) surface is investigated systematically using periodic density-functional theory method. The unusual adsorption behavior of heterolytic dissociative hydrogen molecule at neighboring surface oxygen and surface magnesium, is clarified here.
A dielectric model of electrostatic solvation is applied to describe potentials of mean force in water along reaction paths for: a) formation of a sodium chloride ion pair;
Considering the emblematic Hartree-Fock (HF) energy expression with single Slater determinant and the ortho-normal molecular orbits (MO) in it, expressed as a linear combination (LC) of atomic orbits (LCAO) basis set functions, the HF energy expression is in fact a 4th order polynomial of the LCAO coefficients, which i...
We report experimental results on three-dimensional momentum imaging measurements of anions generated via dissociative electron attachment to gaseous formamide. From the momentum images, we analyze the angular and kinetic energy distributions for NH$_2^{-}$, O$^{-}$, and H$^{-}$ fragments and discuss the possible elec...
Interactions of Cn (element 112) atoms with small Au clusters are studied using accurate ab initio scalar relativistic coupled cluster method for correlation treatment and two-component relativistic density functional theory (RDFT) to account for spin-dependent relativistic effect. The results demonstrate the failure ...
The Hartree-Fock (HF) wave function, commonly used for approximating molecular ground states, becomes nonideal in open shell systems due to the inherent multi-configurational nature of the wave function, limiting accuracy in Quantum Imaginary Time Evolution (QITE). We propose replacing the HF wave function with a spin...

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