text large_stringlengths 7 3.02k |
|---|
The Alchemical Transfer Method (ATM) is herein validated against the relative binding free energies of a diverse set of protein-ligand complexes. We employed a streamlined setup workflow, a bespoke force field, and the AToM-OpenMM software to compute the relative binding free energies (RBFE) of the benchmark set prepa... |
This article presents a study of the excited state relaxation dynamics of N-salycylidene-o-aminophenol (SOAP) in ethanol solution. Femtosecond transient absorption (TA) spectroscopy and theoretical calculations are used in combination to establish the mechanism of the excited state relaxation and type of molecular spe... |
Uncertainty quantification (UQ) to detect samples with large expected errors (outliers) is applied to reactive molecular potential energy surfaces (PESs). Three methods - Ensembles, Deep Evidential Regression (DER), and Gaussian Mixture Models (GMM) - were applied to the H-transfer reaction between ${\it syn-}$Criegee... |
DNA base-gold interactions are studied theoretically at the DFT level using Au3 and Au4 clusters as simple catalytic models for Au particles. The bonding between DNA bases and gold clusters occurs via the anchoring of a Au atom to the N or O atoms of the bases. |
The weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. |
Compact solid discharge products enable energy storage devices with high gravimetric and volumetric energy densities, but solid deposits on active surfaces can disturb charge transport and induce mechanical stress. In this Letter we develop a nanoscale continuum model for the growth of Li2O2 crystals in lithium-oxygen... |
By means of the Jastrow correlated antisymmetrized geminal power (JAGP) wave function and quantum Monte Carlo (QMC) methods, we study the ground state properties of the oligoacene series, up to the nonacene. The JAGP is the accurate variational realization of the resonating-valence-bond (RVB) ansatz proposed by Paulin... |
Large molecular representation models pre-trained on massive unlabeled data have shown great success in predicting molecular properties. However, these models may tend to overfit the fine-tuning data, resulting in over-confident predictions on test data that fall outside of the training distribution. |
We report a new deep learning message passing network that takes inspiration from Newton's equations of motion to learn interatomic potentials and forces. With the advantage of directional information from trainable latent force vectors, and physics-infused operators that are inspired by the Newtonian physics, the... |
The use of aqueous electrolytes in energy storage devices is traditionally limited by the voltage stability window of water at 1.23 V. We present the use of a microemulsion based electrolyte which, although mostly water by mass, has a voltage stability window of up to 5 V. This allows the cost and safety benefits of aq... |
A large proportion of organic molecules relevant to medicine and biotechnology contain one or more ionizable groups, which means that fundamental physical and chemical properties (e.g. the charge of the molecule) depend on the pH of the surroundings via the corresponding pKa values of the molecules. As drug- and mater... |
Predicting the quantum dynamics of promising solid-state and molecular quantum technology candidates remains a formidable challenge. Yet, accessing these dynamics is key to understanding and controlling decoherence mechanisms -- a prerequisite for designing better qubits, sensors, and memories. |
In a previous paper, we introduced Ehrenfest+R dynamics for a two-level system and showed how spontaneous emission can be heuristically included such that, after averaging over an ensemble of Ehrenfest+R trajectories, one can recover both coherent and incoherent electromagnetic fields. In the present paper, we now sho... |
We apply a recently developed quasi-diabatic (QD) scheme to the symmetric quasi-classical (SQC) approach for accurate quantum dynamics propagation. By using the adiabatic states as the quasi-diabatic states during a short-time quantum dynamics propagation, the QD scheme allows directly interfacing diabatic SQC method ... |
Rovibronic energy levels are determined for four low-lying electronic states (\X, \A, \Sa, and \Sc) of the imidogen free radical ($^{14}$NH) using the \Marvel\ (Measured Active Rotational-Vibrational Energy Levels) technique. Compilation of transitions from both laboratory measurements and solar spectra, found in 18 p... |
Although molten carbonates only represent, at most, a very minor phase in the Earth's mantle, they are thought to be implied in anomalous high-conductivity zones in its upper part (70-350 km). Besides the high electrical conductivity of these molten salts is also exploitable in fuel cells. |
We discuss a symmetry-adapted algebraic (or vibron) model for molecular spectroscopy. The model is formulated in terms of tensor operators under the molecular point group. |
Vibrational frequency calculations performed under the harmonic approximation are widespread across chemistry. However, it is well-known that the calculated harmonic frequencies tend to systematically overestimate experimental fundamental frequencies; a limitation commonly overcome with multiplicative scaling factors.... |
Deep saline aquifers are one of the best options for large-scale and long-term hydrogen storage. Predicting the diffusion coefficient of hydrogen molecules at the conditions of saline aquifers is critical for modelling hydrogen storage. |
The Gibbs-Thomson (GT) equation describes the shift of the crystallization temperature for a confined fluid with respect to the bulk as a function of pore size. While this century old relation is successfully used to analyze experiments, its derivations found in the literature often rely on nucleation theory arguments... |
Below band gap formation of solvated electrons in neutral water clusters using pump-probe photoelectron imaging is compared with recent data for liquid water and with above band gap excitation studies in the liquid and clusters. Similar relaxation times in the order of 200 fs and 1-2 ps are retrieved for below and abo... |
Understanding the behavior of complex molecular systems is a fundamental problem in physical chemistry. To describe the long-time dynamics of such systems, which is responsible for their most informative characteristics, we can identify a few slow collective variables (CVs) while treating the remaining fast variables ... |
Derivatives of BODIPY are popular fluorophores due to their synthetic feasibility, structural rigidity, high quantum yield, and tunable spectroscopic properties. While the characteristic absorption maximum of BODIPY is at 2.5 eV, combinations of functional groups and substitution sites can shift the peak position by +... |
We have developed a deep learning algorithm for chemical shift prediction for atoms in molecular crystals that utilizes an atom-centered Gaussian density model for the 3D data representation of a molecule. We define multiple channels that describe different spatial resolutions for each atom type that utilizes cropping... |
In this paper we report a semianalytical model of the mass transfer impedance in microfluidic electrochemical chips (MEC). It is based on the molar advection diffusion equation in a microfluidic channel with a Poiseuille flow and an electrochemical reaction at the interface of deposited electrodes. |
Perturbative methods are attractive to describe the electronic structure of molecular systems because of their low-computational cost and systematically improvable character. In this work, a two-step perturbative approach is introduced combining multi-state Rayleigh-Schrödinger (effective Hamiltonian theory) and state... |
Calculations of time-resolved fluorescence anisotropy from a pair of chromophores coupled by an excitation transfer interaction are presented. For the purpose of investigating the effects of nuclear motion on the energy transfer and anisotropy, an illustrative model is developed that provides each chromophore with a s... |
Light-induced chemical processes are ubiquitous in nature and have widespread technological applications. For example, photoisomerization can allow a drug with a photo-switchable scaffold such as azobenzene to be activated with light. |
Devices based on deep-blue emitting iridium (III) complexes with N-heterocyclic carbene (NHC) ligands have recently been shown to give excellent performance as phosphorescent organic light-emitting diodes (PHOLEDs). To facilitate the design of even better deep-blue phosphorescent emitters we carried out density functi... |
The use of ultrafast pump-probe conductivity (PPC) for studies of photoelectron dynamics in nonpolar molecular liquids has been based upon the perturbation of geminate recombination dynamics of trapped electrons by their laser photoexcitation into the conduction band. Such a method is unsuitable for the studies of ele... |
The structure of three laminar premixed rich flames has been investigated: a pure methane flame and two methane flames doped by allene and propyne, respectively. The gases of the three flames contain 20.9% (molar) of methane and 33.4% of oxygen, corresponding to an equivalence ratio of 1.25 for the pure methane flame.... |
The design of better heterogeneous catalysts for applications such as fuel cells and electrolyzers requires a mechanistic understanding of electrocatalytic reactions and the dependence of their activity on operating conditions such as pH. A satisfactory explanation for the unexpected pH dependence of electrochemical pr... |
Autoignition experiments of stoichiometric mixtures of s-, t-, and i-butanol in air have been performed using a heated rapid compression machine (RCM). At compressed pressures of 15 and 30 bar and for compressed temperatures in the range of 715-910 K, no evidence of a negative temperature coefficient region in terms o... |
In Reply to Comment on Dynamically maintained steady-state pressure gradients, Sheehan offered his responses to the fifteen proposed resolutions to Duncan's paradox. This comment on Sheehan's reply aims to point out that it is epicatalysis that results in Duncan's paradox and the violation of the second la... |
Obtaining the exciton dynamics of large photosynthetic complexes by using mixed quantum mechanics/molecular mechanics (QM/MM) is computationally demanding. We propose a machine learning technique, multi-layer perceptrons, as a tool to reduce the time required to compute excited state energies. |
It is shown that the energy spectrum of the pure vibrational levels of the molecule consisting of two atoms interacting with each other via the modified Rosen-Morse potential, the analytical expressions for the vibrational partition function and enthalpy of the diatomic molecule, obtained in the paper Prediction of ent... |
In single particle imaging experiments, beams of individual nanoparticles are exposed to intense pulses of x-rays from free-electron lasers to record diffraction patterns of single, isolated molecules. The reconstruction for structure determination relies on signal from many identical particles. |
Protection of silver mirror stacks from environmental degradation before launching is crucial for space applications. Hereby, we report a comparative study of the advanced protection of silver mirror stacks for space telescopes provided by SiO2 and Al2O3 coatings in conditions of accelerated aging by sulfidation. |
We study the electronic structure of two types of transition metal complexes, the inverted-sandwich-type and open-lantern-type, by the electronic stress tensor. In particular, the bond order b_e measured by the energy density which is defined from the electronic stress tensor is studied and compared with the conventio... |
We propose a new, cyclic-voltammetry based experimental technique that can not only differentiate between discontinuous and continuous phase transitions in an adsorbate layer, but also quite accurately recover equilibrium behavior from dynamic analysis of systems with a continuous phase transition. The Electrochemical... |
Chemical structure elucidation is a serious bottleneck in analytical chemistry today. We address the problem of identifying an unknown chemical threat given its mass spectrum and its chemical formula, a task which might take well trained chemists several days to complete. |
The recently introduced multisite tensor network path integral (MS-TNPI) method [Bose and Walters, J. Chem. Phys., 2022, 156, 24101.] for simulation of quantum dynamics of extended systems has been shown to be effective in studying one-dimensional systems. Quantum transport in these systems are typically studied at a ... |
A theoretical rate constant for the associative detachment reaction Rb($^{2}S$)$+$OH$^{-}$($^{1}\Sigma^{+}$)$\rightarrow \,$ RbOH($^{1}\Sigma^{+}$)$+\,e^{-}$ of 4$\,\times$10$^{-10}$cm$^{3}$s$^{-1}$ at 300 K has been calculated. This result agrees with the experimental rate constant of 2$^{+2}_{-1}\,\times10^{-10}$cm$... |
The mode specific dissociative chemisorption dynamics of ammonia on the Ru(0001) surface is investigated using a quasi-classical trajectory (QCT) method on a new global potential energy surface (PES) with twelve dimensions. The PES is constructed by fitting 92524 density functional theory points using the permutation ... |
A density-functional theory is developed based on the Maxwell--Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical curre... |
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently proposed by Bereau and Kremer (2016). |
We explore the recently introduced $\eta$-ensemble approach to compute the free energy directly from \emph{ab initio} path integral Monte Carlo (PIMC) simulations [T. ~Dornheim \emph{et al. |
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow. With this structure, we can extend theories of nonequilibrium systems with qua... |
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by ... |
We have measured the dependence of the relative integral cross section of the reaction Li+HF-->LiF+H on the collision energy using crossed molecular beams. By varying the intersection angle of the beams from 37° to 90° we covered the energy range 25 meV < E_tr < 131 meV. |
Ammonia, a critical chemical fertilizer and a potential hydrogen carrier, can be sustainably synthesized from atmospheric nitrogen and water under ambient conditions through photocatalysis. In this study, high-entropy oxides with d0 and mixed d0+d10 cationic configurations are introduced as a new group of catalysts fo... |
Unexpected spectral features are observed in the two photon spectrum of the pure water in the forward direction when an 80 femtosecond laser pulse is focused at 10^10Wcm-2 or less. Such intensity is much lower than the breakdown or stimulated threshold of the liquid water. |
Integrating external heat into electrolysers can reduce the electrical power demand for carbon-neutral hydrogen production. Efficient operation requires detailed models that incorporate heat availability and its effect on startup costs. |
We point out that most of the classical thermodynamics results in the paper have been known in the literature, see Kestin and Woods, for quite some time and are not new, contrary to what the authors imply. As shown by Kestin, these results are valid for quasistatic irreversible processes only and not for arbitrary irr... |
For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. |
We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigur... |
We examine the application of the recently developed dual basis methods of Head-Gordon and co-workers to double hybrid density functional computations. Using the B2-PLYP, B2GP-PLYP, DSD-BLYP and DSD-PBEP86 density functionals, we assess the performance of dual basis methods for the calculation of conformational energy... |
It is still a matter of controversy whether the relative difference in hole and electron transport in solution-processed organic semiconductors is either due to intrinsic properties linked to chemical and solid-state structure or to extrinsic factors, as device architecture. We here isolate the intrinsic factors affec... |
Quantum coherence is highly involved in photochemical functioning of complex molecular systems. Co-existence and intermixing of electronic and/or vibrational coherences, while never unambiguously identified experimentally, has been proposed to be responsible for this phenomenon. |
The efficiency of natural light harvesting systems is largely determined by their ability to transfer excitations from the antenna to the energy trapping center before recombination. Exciton diffusion length similarly limits organic photovoltaics and demands bulk heterojunction architectures. |
Nuclear magnetic resonance (NMR) investigations of electrochemical systems require gas-tight and non-metallic cell housings. This contribution reports on the development and evaluation of a cylindrical battery container in combination with a numerically optimized saddle coil that is suitable for NMR investigations of ... |
Metal halide perovskites (MHPs) are gaining increasing attention as low-cost, high-performance semiconductors for optoelectronics. In particular, their solution processing is compatible with the large-scale manufacturing of thin-film devices, including solar cells and light-emitting diodes. |
The multi-reference Coupled Cluster method first proposed by Meller et al (J. Chem. Phys. 1996) has been implemented and tested. Guess values of the amplitudes of the single and double excitations (the ${\hat T}$ operator) on the top of the references are extracted from the knowledge of the coefficients of the Multi R... |
A variational solution to the rovibrational problem in curvilinear vibrational coordinates has been implemented and used to investigate the nuclear motions in several linear triatomic molecules, like HCN, OCS, and HCP. The dependence of the rovibrational energy levels on the rotational quantum numbers and the l-doubli... |
Understanding the mechanisms of efficient and robust energy transfer in light-harvesting systems provides new insights for the optimal design of artificial systems. In this paper, we use the Fenna-Matthews-Olson (FMO) protein complex and phycocyanin 645 (PC 645) to explore the general dependence on physical parameters... |
Fluctuations-driven complex oscillations are experimentally observed in cellular systems such as hepatocytes, cardiac cells, neuronal cells, etc. These systems are generally operating in regimes far from thermodynamic equilibrium. |
By adding a non-linear core correction to the well established Dual Space Gaussian type pseudopotentials for the chemical elements up to the third period, we construct improved pseudopotentials for the Perdew Burke Ernzerhof (PBE) functional and demonstrate that they exhibit excellent accuracy. Our benchmarks for the ... |
Mean-field mixed quantum--classical dynamics could provide a much-needed means to inexpensively model quantum electrodynamical phenomena, by describing the optical field and its vacuum fluctuations classically. However, this approach is known to suffer from an unphysical transfer of energy out of the vacuum fluctuatio... |
A first principle reciprocating quantum refrigerator is investigated with the purpose of determining the limitations of cooling to absolute zero. We find that if the energy spectrum of the working medium possesses an uncontrollable gap, then there is a minimum achievable temperature above zero. |
The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent probe to simply measure |
Recently a new wave of interest to spectroscopy of radioactive compounds has raised due to successful applications of the new experimental ISOL/CRIS technique to optical spectroscopy of radium monofluoride molecules. This opens great prospects to searches of the effects connected with ``new physics'' which poi... |
Traditional QSAR/QSPR and inverse QSAR/QSPR methods often assume that chemical properties are dictated by single molecules, overlooking the influence of molecular interactions and environmental factors. In this paper, we introduce a novel QSAR/QSPR framework that can capture the combined effects of multiple molecules ... |
In chemical reactions, trajectories typically turn from reactants to products when crossing a dividing surface close to the normally hyperbolic invariant manifold (NHIM) given by the intersection of the stable and unstable manifolds of a rank-1 saddle. Trajectories started exactly on the NHIM in principle never leave ... |
We present a recently developed projector quantum Monte Carlo method for calculations of electronic structure in systems with spin-orbit interactions. The method solves for many-body eigenstates in the presence of spin-orbit using the fixed-phase <a href="http://approximation.The" rel="external noopener nofollow" clas... |
In the context of high-accuracy computational thermochemistry, the valence CCSD correlation component of molecular atomization energies present the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermoc... |
We have revisited the MOBH35 (Metal-Organic Barrier Heights, 35 reactions) benchmark [Iron, M. A.; Janes, T. J. Phys. Chem. A 2019, 123 (17), 3761-3781; ibid. 2019, 123, 6379-6380] for realistic organometallic catalytic reactions, using both canonical CCSD(T) and localized orbital approximations to it. For low levels ... |
Electrolytes mediate interactions between the cathode and anode and determine performance characteristics of batteries. Mixtures of multiple solvents are often used in electrolytes to achieve desired properties, such as viscosity, dielectric constant, boiling point, and melting point. |
The results of our investigation of ion implantation of PLGA show that the PLGA films undergo crosslinking, carbonization and etching. The PLGA coating degrades in water by a hydrolysis reaction. |
Tantalum doped rutile nanorods were hydrothermally grown on FTO substrates using a new seeding approach. This approach allows the incorporation of high concentrations of up to 4.8 at% tantalum as active doping and results in a significant enhancement of photoelectrochemical water splitting rate (1.8 mA/cm2 at a potent... |
In order to find out capable chemical evolution step from astronomically created organic in interstellar space to biological organic on the earth, infrared spectrum of nitrogen substituted carbon pentagon-hexagon coupled polycyclic aromatic hydrocarbon was analyzed by the density functional theory. Ionization was mode... |
Some rate of oxidation and reduction side-reactions will inevitably coexist in most rechargeable batteries, contributing to reversible and irreversible self-discharge. While parasitic reduction traps electrons, parasitic oxidation donates electrons to the cells inventory and can lead to temporary capacity gain. |
Minimizing the energy of an $N$-electron system as a functional of a two-electron reduced density matrix (2-RDM), constrained by necessary $N$-representability conditions (conditions for the 2-RDM to represent an ensemble $N$-electron quantum system), yields a rigorous lower bound to the ground-state energy in contrast... |
The kinetics of a 2A + B2 = 2AB reaction on supported metal catalyst with spillover effects is investigated using Dynamic Monte Carlo simulations. In the presented model A particles can adsorb reversibly on both metal clusters and the support whereas B2 particles can adsorb dissociatively only on metal clusters. |
Estimates of the exchange interaction parameter (J) between electronic magnetic momenta residing in the d-shells of several divalent first row transition metal ions, and those residing on the [TCNE]$^-$. anion-radicals (TCNE = tetracyanoethylene) that are bonded to the metal ion are obtained by the use of the EHCF met... |
The rapid expansion of biomolecular datasets presents significant challenges for computational biology. Quantum computing emerges as a promising solution to address these complexities. |
Droplets provide unique opportunities for the investigation of laser-induced surface chemistry. Chemical reactions on the surface of charged droplets are ubiquitous in nature and can provide critical insight into more efficient processes for industrial chemical production. |
We investigate two key representative semiclassical approaches for propagating resonant energy transfer between a pair of electronic two-level systems (donor and acceptor) with coupled Maxwell-Liouville equations. On the one hand, when the electromagnetic (EM) field is treated classically and Coulomb interactions are ... |
We present the coupled-cluster singles and doubles method formulated in terms of truncated pair-natural orbitals (PNO) that are optimized to minimize the effect of truncation. Compared to the standard ground-state PNO coupled-cluster approaches, in which truncated PNOs derived from first-order Møller-Plesset (MP1) amp... |
We present semiclassical approximations to Green's functions of multidimensional systems, extending Gutzwiller's work to the classically forbidden region. Based on steepest-descent integrals over these functions, we derive an instanton method for computing the rate of nonadiabatic reactions, such as electron t... |
Density matrix embedding theory (DMET) is a quantum embedding theory for strongly correlated systems. From a computational perspective, one bottleneck in DMET is the optimization of the correlation potential to achieve self-consistency, especially for heterogeneous systems of large size. |
Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a m... |
Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. We show that existing force fields that place all non-Coulomb forces on the Drude core and ... |
In the lithium-ion battery literature, discharges followed by a relaxation to equilibrium are frequently used to validate models and their parametrizations. Good agreement with experiment during discharge is easily attained with a pseudo-two-dimensional model such as the Doyle-Fuller-Newman (DFN) model. |
Synchrotron X-ray diffraction experiments and molecular dynamics simulations have been performed on simple aliphatic aldehydes, from propanal to nonanal. The performance of the OPLS all-atom interaction potential model for aldehydes has been assessed via direct comparison of simulated and experimental total scattering... |
Nuclear spin hyperpolarization enables real-time observation of metabolism and intermolecular interactions in vivo. 1-13C-Pyruvate is the leading hyperpolarized tracer currently under evaluation in several clinical trials as a promising molecular imaging agent. |
We provide a rigorous derivation of a class of double-hybrid approximations, combining Hartree-Fock exchange and second-order Moller-Plesset correlation with a semilocal exchange-correlation density functional. These double-hybrid approximations contain only one empirical parameter and use a density-scaled correlation... |
Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. |
Machine Learning Interatomic Potentials (MLIPs) are a highly promising alternative to force-fields for molecular dynamics (MD) simulations, offering precise and rapid energy and force calculations. However, Quantum-Mechanical (QM) datasets, crucial for MLIPs, are fragmented across various repositories, hindering acces... |
Autoignition experiments for n-butanol have been performed using a heated rapid compression machine at compressed pressures of 15 and 30 bar, in the compressed temperature range of 675-925 K, and for equivalence ratios of 0.5, 1.0, and 2.0. Over the conditions studied, the ignition delay decreases monotonically as tem... |
The experimental study of hydrogen bonds and their symmetrisation under extreme conditions is predominantly driven by diffraction methods, despite challenges of localising or probing the hydrogen subsystems directly. Until recently, H-bond symmetrisation has been addressed in terms of either nuclear quantum effects, s... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.