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Journal of Chemical Physics

Current research reports and chronological list of recent articles..

The international scientific Journal of Chemical Physics - JCP - publishes concise and definitive reports of significant research in methods and applications of chemical physics.

The publisher is the American Institute of Physics, AIP. The copyright and publishing rights of specialized products listed below are in this publishing house. This is also responsible for the content shown.

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Additional research articles see Current Chemistry Research Articles. Magazines with similar content (chemical physics):

 - Chemical Physics.

 - ChemPhysChem.

 - Faraday Discussions.

 - Journal of Physical Chemistry.

 - Physical Chemistry Chemical Physics PCCP.

Journal of Chemical Physics - Abstracts

Stereoinversion of tetrahedral p-block element hydrides

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The potential energy surfaces of 15 tetrahedral p-block element hydrides were screened on the multireference level. It was addressed whether stereoinversion competes against other reactions, such as reductive H2-elimination or hydride loss, and if so, along which pathway the stereomutation occurs. Importantly, stereoinversion transition structures for the ammonium cation (C4v) and the tetrahydridoborate anion (Cs) were identified for the first time. Revisiting methane’s Cs symmetric inversion transition structure with the mHEAT+ protocol revealed an activation enthalpy for stereoinversion, in contrast to all earlier studies, which is 5 kJ mol−1 below the C–H bond dissociation enthalpy. Square planar structures were identified lowest in energy only for the inversion of AlH4−, but a novel stepwise Cs-inversion was discovered for SiH4 or PH4+. Overall, the present contribution delineates essentials of the potential energy surfaces of p-block element hydrides, while structure–energy relations offer design principles for the synthetically emerging field of structurally constrained compounds.
Datum: 20.05.2022

Finite-temperature atomic relaxations: Effect on the temperature-dependent C44 elastic constants of Si and BAs

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The effect of atomic relaxations on the temperature-dependent elastic constants (TDECs) is usually taken into account at zero temperature by the minimization of the total energy at each strain. In this paper, we investigate the order of magnitude of this approximation on a paradigmatic example: the C44 elastic constant of diamond and zincblende materials. We estimate the effect of finite-temperature atomic relaxations within the quasi-harmonic approximation by computing ab initio the internal strain tensor from the second derivatives of the Helmholtz free-energy with respect to strain and atomic displacements. We apply our approach to Si and BAs and find a visible difference between the softening of the TDECs computed with the zero-temperature and finite-temperature atomic relaxations. In Si, the softening of C44 passes from 8.6% to 4.5%, between T = 0 K and T = 1200 K. In BAs, it passes from 8% to 7%, in the same range of temperatures. Finally, from the computed elastic constant corrections, we derive the temperature-dependent Kleinman parameter, which is usually measured in experiments.
Datum: 20.05.2022

Superconducting Li10Se electride under pressure

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Achieving a compound with interesting multiple coexisting states, such as electride, metallicity, and superconductivity, is of great interest in basic research and practical application. Pressure has become an effective way to realize high-temperature superconductivity in hydrides, whereas most electrides are semiconducting or insulating at high pressure. Here, we have applied swarm-intelligence structural search to identify a hitherto unknown C2/m Li10Se electride that is superconducting at high pressure. More interestingly, Li10Se is estimated to exhibit the highest Tc value of 16 K at 50 GPa, which is the lowest pressure among Li-based chalcogen electrides. This superconducting transition is dominated by Se-related low frequency vibration modes. The increasing electronic occupation of the Se 4d orbital and the decreasing amount of interstitial anion electrons with pressure heighten their coupling with low-frequency phonons, which is responsible for the enhancement of the Tc value. The finding of Li-based chalcogen superconducting electrides provides a reference for the realization of other superconducting electrides at lower pressures.
Datum: 20.05.2022

State-specific solvation for restricted active space spin–flip (RAS-SF) wave functions based on the polarizable continuum formalism

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The restricted active space spin–flip (RAS-SF) formalism is a particular form of single-reference configuration interaction that can describe some forms of strong correlation at a relatively low cost and which has recently been formulated for the description of charge-transfer excited states. Here, we introduce both equilibrium and nonequilibrium versions of a state-specific solvation correction for vertical transition energies computed using RAS-SF wave functions, based on the framework of a polarizable continuum model (PCM). Ground-state polarization is described using the solvent’s static dielectric constant and in the nonequilibrium solvation approach that polarization is modified upon vertical excitation using the solvent’s optical dielectric constant. Benchmark calculations are reported for well-studied models of photo-induced charge transfer, including naphthalene dimer, C2H4⋯C2F4, pentacene dimer, and perylene diimide (PDI) dimer, several of which are important in organic photovoltaic applications. For the PDI dimer, we demonstrate that the charge-transfer character of the excited states is enhanced in the presence of a low-dielectric medium (static dielectric constant ɛ0 = 3) as compared to a gas-phase calculation (ɛ0 = 1). This stabilizes mechanistic traps for singlet fission and helps to explain experimental singlet fission rates. We also examine the effects of nonequilibrium solvation on charge-separated states in an intramolecular singlet fission chromophore, where we demonstrate that the energetic ordering of the states changes as a function of solvent polarity. The RAS-SF + PCM methodology that is reported here provides a framework to study charge-separated states in solution and in photovoltaic materials.
Datum: 20.05.2022

Multiphase organization is a second phase transition within multi-component biomolecular condensates

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We present a mean-field theoretical model, along with molecular dynamics simulations, to show that the multiphase organization of multi-component condensates is a second phase transition. Whereas the first phase transition that leads to the separation of condensates from the bulk phase is driven by the overall attraction among the macromolecular components, the second phase transition can be driven by the disparity in the strength between the self- and cross-species attraction. At a fixed level of disparity in interaction strengths, both of the phase transitions can be observed by decreasing the temperature, leading first to the separation of condensates from the bulk phase and then to component demixing inside condensates. The existence of a critical temperature for demixing and predicted binodals are verified by molecular dynamics simulations of model mixtures.
Datum: 20.05.2022

Deuteron magnetic resonance study of glyceline deep eutectic solvents: Selective detection of choline and glycerol dynamics

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Glyceline, a green solvent considered for various electrochemical applications, represents a multi-component glass former. Viewed from this perspective, the choline cation and the hydrogen bond donor glycerol, the two major constituents forming this deep eutectic solvent, were studied using nuclear magnetic resonance in a selective manner by means of suitably deuteron-labeled isotopologues. Carried out from far above to far below the glass transition temperature, measurements and analyses of the spin-lattice and spin-spin relaxation times reveal that the reorientational dynamics of the components, i.e., of glycerol as well as of chain deuterated choline chloride are slightly different. Possible implications of this finding regarding the hydrogen-bonding pattern in glyceline are discussed. Furthermore, the deuterated methyl groups in choline chloride are exploited as sensitive probes of glyceline’s supercooled and glassy states. Apart from spin relaxometry, a detailed line shape analysis of the CD3 spectra yields valuable insights into the broad intermolecular and intramolecular energy barrier distributions present in this binary mixture.
Datum: 19.05.2022

Constrained iterative Hirshfeld charges: A variational approach

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties.
Datum: 19.05.2022

Plasmon-induced coherence, exciton-induced transparency, and Fano interference for hybrid plasmonic systems in strong coupling regime

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We present an analytical model describing the transition to a strong coupling regime for an ensemble of emitters resonantly coupled to a localized surface plasmon in a metal–dielectric structure. The response of a hybrid system to an external field is determined by two distinct mechanisms involving collective states of emitters interacting with the plasmon mode. The first mechanism is the near-field coupling between the bright collective state and the plasmon mode, which underpins the energy exchange between the system components and gives rise to exciton-induced transparency minimum in scattering spectra in the weak coupling regime and to emergence of polaritonic bands as the system transitions to the strong coupling regime. The second mechanism is the Fano interference between the plasmon dipole moment and the plasmon-induced dipole moment of the bright collective state as the hybrid system interacts with the radiation field. The latter mechanism is greatly facilitated by plasmon-induced coherence in a system with the characteristic size below the diffraction limit as the individual emitters comprising the collective state are driven by the same alternating plasmon near field and, therefore, all oscillate in phase. This cooperative effect leads to scaling of the Fano asymmetry parameter and of the Fano function amplitude with the ensemble size, and therefore, it strongly affects the shape of scattering spectra for large ensembles. Specifically, with increasing emitter numbers, the Fano interference leads to a spectral weight shift toward the lower energy polaritonic band.
Datum: 19.05.2022

Multidimensional minimum-work control of a 2D Ising model

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>A system’s configurational state can be manipulated using dynamic variation of control parameters, such as temperature, pressure, or magnetic field; for finite-duration driving, excess work is required above the equilibrium free-energy change. Minimum-work protocols in multidimensional control-parameter space have the potential to significantly reduce work relative to one-dimensional control. By numerically minimizing a linear-response approximation to the excess work, we design protocols in control-parameter spaces of a 2D Ising model that efficiently drive the system from the all-down to all-up configuration. We find that such designed multidimensional protocols take advantage of more flexible control to avoid control-parameter regions of high system resistance, heterogeneously input and extract work to make use of system relaxation, and flatten the energy landscape, making accessible many configurations that would otherwise have prohibitively high energy and, thus, decreasing spin correlations. Relative to one-dimensional protocols, this speeds up the rate-limiting spin-inversion reaction, thereby keeping the system significantly closer to equilibrium for a wide range of protocol durations and significantly reducing resistance and, hence, work.
Datum: 19.05.2022

Desorption of physisorbed molecular oxygen from coronene films and graphite surfaces

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We present a study on the adsorption and desorption of molecular oxygen (O2) on highly oriented pyrolytic graphite and coronene films deposited on it. To this end, density functional theory calculations were performed and experiments were made using the FORMOLISM device, which combines ultra-high vacuum, cryogenics, atomic or molecular beams, and mass spectrometry techniques. We first studied the desorption kinetics of dioxygen (O2) on a coronene film and graphite at 15 K using the thermally programed desorption technique. We observed that the desorption of O2 occurs at a lower temperature on coronene than on graphite. We deduce the binding energies that are 12.5 kJ/mol on graphite and 10.6 kJ/mol on coronene films (pre-exponential factor, 6.88 × 1014 s−1). The graphite surfaces partially covered with coronene show both adsorption energies. In combination with theoretical density function theory (DFT) calculations using graphene and coronene as surfaces, we observe that the experimental results are in good agreement with the theoretical calculations. For the adsorption of the O2 molecule, two orientations are possible: parallel or perpendicular to the surface. It seems that O2 is best bound parallel to the surface and has a preference for the internal sites of the coronene.
Datum: 19.05.2022

Generalization of the Tavis–Cummings model for multi-level anharmonic systems: Insights on the second excitation manifold

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Confined electromagnetic modes strongly couple to collective excitations in ensembles of quantum emitters, producing light–matter hybrid states known as polaritons. Under such conditions, the discrete multilevel spectrum of molecular systems offers an appealing playground for exploring multiphoton processes. This work contrasts predictions from the Tavis–Cummings model in which the material is a collection of two-level systems, with the implications of considering additional energy levels with harmonic and anharmonic structures. We discuss the exact eigenspectrum, up to the second excitation manifold, of an arbitrary number N of oscillators collectively coupled to a single cavity mode in the rotating-wave approximation. Elaborating on our group-theoretic approach [New J. Phys. 23, 063081 (2021)], we simplify the brute-force diagonalization of N2 × N2 Hamiltonians to the eigendecomposition of, at most, 4 × 4 matrices for arbitrary N. We thoroughly discuss the eigenstates and the consequences of weak and strong anharmonicities. Furthermore, we find resonant conditions between bipolaritons and anharmonic transitions where two-photon absorption can be enhanced. Finally, we conclude that energy shifts in the polaritonic states induced by anharmonicities become negligible for large N. Thus, calculations with a single or few quantum emitters qualitatively fail to represent the nonlinear optical response of the collective strong coupling regime. Our work highlights the rich physics of multilevel anharmonic systems coupled to cavities absent in standard models of quantum optics. We also provide concise tabulated expressions for eigenfrequencies and transition amplitudes, which should serve as a reference for future spectroscopic studies of molecular polaritons.
Datum: 19.05.2022

The influence of a solvent environment on direct non-covalent interactions between two molecules: A symmetry-adapted perturbation theory study of polarization tuning of π–π interactions by water

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>High-level quantum chemical computations have provided significant insight into the fundamental physical nature of non-covalent interactions. These studies have focused primarily on gas-phase computations of small van der Waals dimers; however, these interactions frequently take place in complex chemical environments, such as proteins, solutions, or solids. To better understand how the chemical environment affects non-covalent interactions, we have undertaken a quantum chemical study of π–π interactions in an aqueous solution, as exemplified by T-shaped benzene dimers surrounded by 28 or 50 explicit water molecules. We report interaction energies (IEs) using second-order Møller–Plesset perturbation theory, and we apply the intramolecular and functional-group partitioning extensions of symmetry-adapted perturbation theory (ISAPT and F-SAPT, respectively) to analyze how the solvent molecules tune the π–π interactions of the solute. For complexes containing neutral monomers, even 50 explicit waters (constituting a first and partial second solvation shell) change total SAPT IEs between the two solute molecules by only tenths of a kcal mol−1, while significant changes of up to 3 kcal mol−1 of the electrostatic component are seen for the cationic pyridinium–benzene dimer. This difference between charged and neutral solutes is attributed to large non-additive three-body interactions within solvated ion-containing complexes. Overall, except for charged solutes, our quantum computations indicate that nearby solvent molecules cause very little “tuning” of the direct solute–solute interactions. This indicates that differences in binding energies between the gas phase and solution phase are primarily indirect effects of the competition between solute–solute and solute–solvent interactions.
Datum: 18.05.2022

Analytical approach to chiral active systems: Suppressed phase separation of interacting Brownian circle swimmers

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We consider chirality in active systems by exemplarily studying the phase behavior of planar systems of interacting Brownian circle swimmers with a spherical shape. For this purpose, we derive a predictive field theory that is able to describe the collective dynamics of circle swimmers. The theory yields a mapping between circle swimmers and noncircling active Brownian particles and predicts that the angular propulsion of the particles leads to a suppression of their motility-induced phase separation, being in line with recent simulation results. In addition, the theory provides analytical expressions for the spinodal corresponding to the onset of motility-induced phase separation and the associated critical point as well as for their dependence on the angular propulsion of the circle swimmers. We confirm our findings by Brownian dynamics simulations. Agreement between results from theory and simulations is found to be good.
Datum: 18.05.2022

The “good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We characterize a concentrated 7.3 m CaCl2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca2+–Cl− interactions were primarily “hidden” in the Ca-NDIS signal due to overlapping with Ca2+–Ow and Ca2+–Hw contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models “on average,” the question “which model is the best” has not been answered but replaced by the question “which model is better for a given research.” An overall “good” model can still be inappropriate or, in some instances, “bad” and, unfortunately, produce erroneous results. The accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.
Datum: 18.05.2022

Field theory description of ion association in re-entrant phase separation of polyampholytes

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Phase separation of several different overall neutral polyampholyte species (with zero net charge) is studied in solution with two oppositely charged ion species that can form ion pairs through an association reaction. Hereby, a field theory description of the system, which treats polyampholyte charge sequence dependent electrostatic interactions as well as excluded volume effects, is given. Interestingly, analysis of the model using random phase approximation and field theoretic simulation consistently shows evidence of a re-entrant polyampholyte phase separation at high ion concentrations when there is an overall decrease of volume upon ion association. As an illustration of the ramifications of our theoretical framework, several polyampholyte concentration vs ion concentration phase diagrams under constant temperature conditions are presented to elucidate the dependence of phase separation behavior on the polyampholyte sequence charge pattern as well as ion pair dissociation constant, volumetric effects on ion association, solvent quality, and temperature.
Datum: 18.05.2022

The onset of solidification: From interface formation to the Stefan regime

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The onset of a solidification process is considered in a situation where the free surface of a warm liquid is touched by a sufficiently cold solid. The process is analyzed in terms of a model that takes into account the formation of a liquid–solid interface as the two media are brought in contact and then the appearance of the solidified liquid as a third bulk phase. As is shown, the temperature at the liquid–solid interface and then at the solidification front evolves in a non-monotone way, and when the solidification front appears and starts to move, its velocity is not a function of its temperature. The classical Stefan regime of solidification appears as a limit as the temperature at the solidification front evolves toward the melting temperature.
Datum: 18.05.2022

The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane–water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. We find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.
Datum: 18.05.2022

Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. II. Benchmarks and applications

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles.
Datum: 17.05.2022

Static self-induced heterogeneity in glass-forming liquids: Overlap as a microscope

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We propose and numerically implement a local probe of the static self-induced heterogeneity characterizing glass-forming liquids. This method relies on the equilibrium statistics of the overlap between pairs of configurations measured in mesoscopic cavities with unconstrained boundaries. By systematically changing the location of the probed cavity, we directly detect spatial variations of the overlap fluctuations. We provide a detailed analysis of the statistics of a local estimate of the configurational entropy, and we infer an estimate of the surface tension between amorphous states, ingredients that are both at the basis of the random first-order transition theory of glass formation. Our results represent the first direct attempt to visualize and quantify the self-induced heterogeneity underpinning the thermodynamics of glass formation. They pave the way for the development of coarse-grained effective theories and for a direct assessment of the role of thermodynamics in the activated dynamics of deeply supercooled liquids.
Datum: 17.05.2022

Rheological model for the alpha relaxation of glass-forming liquids and its comparison to data for DC704 and DC705

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Dynamic shear-modulus data are presented for two silicone oils DC704 and DC705 for frequencies between 1 mHz and 10 kHz at temperatures covering more than five decades of relaxation-time variation. Data are fitted to the alpha part of a phenomenological model previously shown to describe well the dynamic shear modulus of squalane, which has a large beta process [Hecksher et al., J. Chem. Phys. 146, 154504 (2017)]. That model is characterized by additivity of the alpha and beta shear compliance and by a high-frequency decay of the alpha process in proportion to ω−1/2, where ω is the angular frequency. The fits of the alpha part of this model to the DC704 and DC705 data are compared to fits by a Havriliak–Negami type model, a Barlow–Erginsav–Lamb model, and a Cole–Davidson type model. At all temperatures, the best fit is obtained by the alpha part of the squalane model. This strengthens the conjecture that so-called [math]-relaxation, leading to high-frequency loss decays proportional to ω−1/2, is generic to the alpha relaxation of supercooled liquids [J. C. Dyre, Phys. Rev. E 74, 021502 (2006); Nielsen et al., J. Chem. Phys. 130, 154508 (2009); and Pabst et al., J. Phys. Chem. Lett. 12, 3685–3690 (2021)].
Datum: 17.05.2022

Solution structures and ultrafast vibrational energy dissipation dynamics in cyclotetramethylene tetranitramine

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Steady-state and time-resolved infrared (IR) studies of cyclotetramethylene tetranitramine (HMX) were carried out, using the asymmetric nitro-stretch as probe, to investigate its solution structures and vibrational energy transfer processes in pure dimethyl sulfoxide (DMSO) and in a DMSO/water mixture. A linear IR spectrum in the nitro-stretching mode region shows two major bands and one minor band in DMSO but changes to the two major bands mainly picture when adding water as an antisolvent of HMX, suggesting a transition from well-solvated and less perfect β-conformation to a less-solvated and close-to-perfect β-conformation. The latter bears a similar asymmetric nitro-stretch vibration profile to the β-polymorph in the crystal form. Density functional theory computations of the nitro-stretching vibrations suggest that HMX in DMSO may be in a NO2 group rotated β-conformation. Two-dimensional IR cross-peak intensity reveals intramolecular energy transfer between the axial and equatorial nitro-groups in the β-HMX on the ps time scale, which is slightly faster in the mixed solvent case. The importance of water as an antisolvent in influencing the equilibrium solvation structure, as well as the vibrational and orientational relaxation dynamics of HMX, is discussed.
Datum: 17.05.2022

Effects of disorder on polaritonic and dark states in a cavity using the disordered Tavis–Cummings model

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We consider molecules confined to a microcavity of dimensions such that an excitation of the molecule is nearly resonant with a cavity mode. The molecular excitation energies are assumed to be Gaussianly distributed with mean ϵa and variance σ. We find an asymptotically exact solution for large number density [math]. Conditions for the existence of the polaritonic states and expressions for their energies are obtained. Polaritonic states are found to be quite stable against disorder. Our results are verified by comparison with simulations. When ϵa is equal to energy of the cavity state ϵc, the Rabi splitting is found to increase by [math], where [math] is the coupling of a molecular excitation to the cavity state. An analytic expression is found for the disorder-induced width of the polaritonic peak. Results for various densities of states and the absorption spectrum are presented. The dark states turn “gray” in the presence of disorder with their contribution to the absorption increasing with σ. Lifetimes of the cavity and molecular states are found to be important, and for sufficiently large Rabi splitting, the width of the polaritonic peaks is dominated by them. We also give analytical results for the case where the molecular levels follow a uniform distribution. We conclude that the study of the width of the polaritonic peaks as a function of the Rabi splitting can give information on the distribution of molecular energy levels. Finally, the effects of (a) orientational disorder and (b) spatial variation on the cavity field are presented.
Datum: 17.05.2022

Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Biotin-labeled proteins are widely used as tools to study protein–protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
Datum: 16.05.2022

Thermochemistry and mechanisms of the Pt+ + SO2 reaction from guided ion beam tandem mass spectrometry and theory

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The kinetic energy dependences of the reactions of Pt+ (2D5/2) with SO2 were studied using a guided ion beam tandem mass spectrometer and theory. The observed cationic products are PtO+ and PtSO+, with small amounts of PtS+, all formed in endothermic reactions. Modeling the kinetic energy dependent product cross sections allows determination of the product bond dissociation energies (BDEs): D0(Pt+–O) = 3.14 ± 0.11 eV, D0(Pt+–S) = 3.68 ± 0.31 eV, and D0(Pt+–SO) = 3.03 ± 0.12 eV. The oxide BDE agrees well with more precise literature values, whereas the latter two results are the first such measurements. Quantum mechanical calculations were performed for PtO+, PtS+, PtO2+, and PtSO+ at the B3LYP and coupled-cluster with single, double, and perturbative triple [CCSD(T)] levels of theory using the def2-XZVPPD (X = T, Q) and aug-cc-pVXZ (X = T, Q, 5) basis sets and complete basis set extrapolations. These theoretical BDEs agree well with the experimental values. After including empirical spin–orbit corrections, the product ground states are determined as PtO+ (4Σ3/2), PtS+ (4Σ3/2), PtO2+ (2Σg+), and PtSO+ (2A′). Potential energy profiles including intermediates and transition states for each reaction were also calculated at the B3LYP/def2-TZVPPD level. Periodic trends in the thermochemistry of the group 9 metal chalcogenide cations are compared, and the formation of PtO+ from the Pt+ + SO2 reaction is compared with those from the Pt+ + O2, CO2, CO, and NO reactions.
Datum: 16.05.2022

Elucidating the molecular orbital dependence of the total electronic energy in multireference problems

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The accurate resolution of the chemical properties of strongly correlated systems, such as biradicals, requires the use of electronic structure theories that account for both multi-reference and dynamic correlation effects. A variety of methods exist that aim to resolve the dynamic correlation in multi-reference problems, commonly relying on an exponentially scaling complete-active-space self-consistent-field (CASSCF) calculation to generate reference molecular orbitals (MOs). However, while CASSCF orbitals provide the optimal solution for a selected set of correlated (active) orbitals, their suitability in the quest for the resolution of the total correlation energy has not been thoroughly investigated. Recent research has shown the ability of Kohn–Shan density functional theory to provide improved orbitals for coupled cluster (CC) and Møller–Plesset perturbation theory (MP) calculations. Here, we extend the search for optimal and more cost effective MOs to post-configuration-interaction [post-(CI)] methods, surveying the ability of the MOs obtained with various density functional theory (DFT) functionals, as well as Hartree–Fock and CC and MP calculations to accurately capture the total electronic correlation energy. Applying the anti-Hermitian contracted Schrödinger equation to the dissociation of N2, the calculation of biradical singlet–triplet gaps, and the transition states of bicylobutane isomerization, we demonstrate that DFT provides a cost-effective alternative to CASSCF in providing reference orbitals for post-CI dynamic correlation calculations.
Datum: 16.05.2022

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to β-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation.
Datum: 16.05.2022

Controlling cluster size in 2D phase-separating binary mixtures with specific interactions

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.
Datum: 16.05.2022

Time-domain self-broadened and air-broadened nitrogen S-branch Raman linewidths at 80–200 K recorded in an underexpanded jet

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We report pure-rotational N2–N2, N2–air, and O2–air S-branch linewidths for temperatures of 80–200 K by measuring the time-dependent decay of rotational Raman coherences in an isentropic free-jet expansion from a sonic nozzle. We recorded pure-rotational hybrid femtosecond/picosecond coherent anti-Stokes Raman scattering (fs/ps CARS) spectra along the axial centerline of the underexpanded jet, within the barrel shock region upstream of the Mach disk. The dephasing of the pure-rotational Raman coherence was monitored using probe-time-delay scans at different axial positions in the jet, corresponding to varying local temperatures and pressures. The local temperature was obtained by fitting CARS spectra acquired at zero probe time delay, where the impact of collisions was minimal. The measured decay of each available Raman transition was fit to a dephasing constant and corrected for the local pressure, which was obtained from the CARS-measured static temperature and thermodynamic relationships for isentropic expansion from the known stagnation state. Nitrogen self-broadened transitions decayed more rapidly than those broadened in air for all temperatures, corresponding to higher Raman linewidths. In general, the measured S-branch linewidths deviated significantly in absolute and relative magnitudes from those predicted by extrapolating the modified exponential gap model to low temperatures. The temperature dependence of the Raman linewidth for each measured rotational state of nitrogen (J ≤ 10) and oxygen (N ≤ 11) was fit to a temperature-dependent power law over the measurable temperature domain (80–200 K) and extrapolated to both higher rotational states and room temperature. The measured and modeled low-temperature linewidth data provided here will aid low temperature gas-phase pressure measurements with fs/ps CARS.
Datum: 16.05.2022

Combined contributions of carotenoids and chlorophylls in two-photon spectra of photosynthetic pigment–protein complexes—A new way to quantify carotenoid dark state to chlorophyll energy transfer?

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Transitions into the first excited state of carotenoids, Car S1, are optically forbidden in conventional one-photon excitation (OPE) but are possible via two-photon excitation (TPE). This can be used to quantify the amount of Car S1 to Chlorophyll (Chl) energy transfer in pigment–protein complexes and plants by observing the chlorophyll fluorescence intensity after TPE in comparison to the intensity observed after direct chlorophyll OPE. A parameter, [math], can be derived that directly reflects relative differences or changes in the Car S1 → Chl energy transfer of different pigment–protein complexes and even living plants. However, very careful calibrations are necessary to ensure similar OPE and TPE excitation probabilities and transition energies. In plants, the exact same sample spot must be observed at the same time. All this is experimentally quite demanding. [math] also corrects intrinsically for direct chlorophyll TPE caused by larger chlorophyll excesses in the complexes, but recently it turned out that in certain TPE wavelengths ranges, its contribution can be quite large. Fortunately, this finding opens also the possibility of determining [math] in a much easier way by directly comparing values in TPE spectra observed at wavelengths that are either more dominated by Cars or Chls. This avoids tedious comparisons of OPE and TPE experiments and potentially allows measurement at even only two TPE wavelengths. Here, we explored this new approach to determine [math] directly from single TPE spectra and present first examples using known experimental spectra from Cars, Chl a, Chl b, LHC II, and PS 1.
Datum: 16.05.2022

Observation of rotationally dependent fine-structure branching ratios near the predissociation threshold N(2D5/2,3/2) + N(2D5/2,3/2) of 14N2

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Photofragment spin–orbit fine-structure branching ratios have long been predicted to depend on the rotational quantum number J′ by theory near the dissociation thresholds of several diatomic molecules, while this has rarely been observed in any photodissociation experiments yet. Here, we measured the fine-structure branching ratios N(2D5/2)/N(2D3/2) produced in the N(2D5/2,3/2) + N(2D5/2,3/2) channel at the b′1Σu+(v = 20) state of 14N2 by using our vacuum ultraviolet (VUV)-pump–VUV-probe time-sliced velocity-mapped ion imaging setup. It is found that 14N2 almost exclusively dissociates into the spin–orbit channel N(2D5/2) + N(2D3/2) at low rotational levels and gradually approaches the statistical or diabatic limit by distributing all possible spin–orbit channels at higher rotational levels. The strongly rotationally dependent fine-structure branching ratios should be due to the increasing strength of nonadiabatic Coriolis interaction among various dissociative states in the so-called “recoupling zone” as J′ increases. They are supposed to provide unprecedented information on the near threshold photodissociation dynamics of 14N2.
Datum: 16.05.2022

Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. I. Theory

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Reactions involving adsorbates on metallic surfaces and impurities in bulk metals are ubiquitous in a wide range of technological applications. The theoretical modeling of such reactions presents a formidable challenge for theory because nuclear quantum effects (NQEs) can play a prominent role and the coupling of the atomic motion with the electrons in the metal gives rise to important non-adiabatic effects (NAEs) that alter atomic dynamics. In this work, we derive a theoretical framework that captures both NQEs and NAEs and, due to its high efficiency, can be applied to first-principles calculations of reaction rates in high-dimensional realistic systems. More specifically, we develop a method that we coin ring polymer instanton with explicit friction (RPI-EF), starting from the ring polymer instanton formalism applied to a system–bath model. We derive general equations that incorporate the spatial and frequency dependence of the friction tensor and then combine this method with the ab initio electronic friction formalism for the calculation of thermal reaction rates. We show that the connection between RPI-EF and the form of the electronic friction tensor presented in this work does not require any further approximations, and it is expected to be valid as long as the approximations of both underlying theories remain valid.
Datum: 16.05.2022

Alignment and propulsion of squirmer pusher–puller dumbbells

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>The properties of microswimmer dumbbells composed of pusher–puller pairs are investigated by mesoscale hydrodynamic simulations employing the multiparticle collision dynamics approach for the fluid. An individual microswimmer is represented by a squirmer, and various active-stress combinations in a dumbbell are considered. The squirmers are connected by a bond, which does not impose any geometrical restriction on the individual rotational motion. Our simulations reveal a strong influence of the squirmers’ flow fields on the orientation of their propulsion directions, their fluctuations, and the swimming behavior of a dumbbell. The properties of pusher–puller pairs with an equal magnitude of the active stresses depend only weakly on the stress magnitude. This is similar to dumbbells of microswimmers without hydrodynamic interactions. However, for non-equal stress magnitudes, the active stress implies strong orientational correlations of the swimmers’ propulsion directions with respect to each other, as well as the bond vector. The orientational coupling is most pronounced for pairs with large differences in the active-stress magnitude. The alignment of the squirmers’ propulsion directions with respect to each other is preferentially orthogonal in dumbbells with a strong pusher and weak puller, and antiparallel in the opposite case when the puller dominates. These strong correlations affect the active motion of dumbbells, which is faster for strong pushers and slower for strong pullers.
Datum: 16.05.2022

An alternative, dynamic density functional-like theory for time-dependent density fluctuations in glass-forming fluids

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We propose an alternative theory for the relaxation of density fluctuations in glass-forming fluids. We derive an equation of motion for the density correlation function that is local in time and is similar in spirit to the equation of motion for the average non-uniform density profile derived within the dynamic density functional theory. We identify the Franz–Parisi free energy functional as the non-equilibrium free energy for the evolution of the density correlation function. An appearance of a local minimum of this functional leads to a dynamic arrest. Thus, the ergodicity breaking transition predicted by our theory coincides with the dynamic transition of the static approach based on the same non-equilibrium free energy functional.
Datum: 16.05.2022

Complex energies and transition dipoles for shape-type resonances of uracil anion from stabilization curves via Padé

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Absorption of slow moving electrons by neutral ground state nucleobases has been known to produce resonance metastable states. There are indications that such metastable states may play a key role in DNA/RNA damage. Therefore, herein, we present an ab initio non-Hermitian investigation of the resonance positions and decay rates for the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has already been successfully applied to many small molecular systems, and herein, we present the first application of RVP to a medium-sized system. The presented resonance energies are optimized with respect to the size of the basis set and compared with previous theoretical studies and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the optimal basis set. The ability to calculate ab initio energies and lifetimes of biologically relevant systems paves the way for studying reactions of such systems in which autoionization takes place, while the ability to also calculate their complex transition dipoles opens the door for studying photo-induced dynamics of such biological molecules.
Datum: 16.05.2022

Disrupting bonding in azoles through beryllium bonds: Unexpected coordination patterns and acidity enhancement

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Although triazoles and tetrazole are amphoteric and may behave as weak acids, the latter property can be hugely enhanced by beryllium bonds. To explain this phenomenon, the structure and bonding characteristics of the complexes between triazoles and tetrazoles with one and two molecules of BeF2 have been investigated through the use of high-level G4 ab initio calculations. The formation of the complexes between the N basic sites of the azoles and the Be center of the BeF2 molecule and the (BeF2)2 dimer leads to a significant bonding perturbation of both interacting subunits. The main consequence of these electron density rearrangements is the above-mentioned increase in the intrinsic acidity of the azole subunit, evolving from a typical nitrogen base to a very strong nitrogenous acid. This effect is particularly dramatic when the interaction involves the (BeF2)2 dimer, that is, a Lewis acid much stronger than the monomer. Although the azoles investigated have neighboring N-basic sites, their interaction with the (BeF2)2 dimer yields a monodentate complex. However, the deprotonated species becomes extra-stabilized because a second N–Be bond is formed, leading to a new five-membered ring, with the result that the azole-(BeF2)2 complexes investigated become stronger nitrogenous acids than oxyacids such as perchloric acid.
Datum: 16.05.2022

The nature of supermolecular bonds: Investigating hydrocarbon linked beryllium solvated electron precursors

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Beryllium ammonia complexes Be(NH3)4 are known to bear two diffuse electrons in the periphery of a Be(NH3)42+ skeleton. The replacement of one ammonia with a methyl group forms CH3Be(NH3)3 with one peripheral electron, which is shown to maintain the hydrogenic-type shell model observed for Li(NH3)4. Two CH3Be(NH3)3 monomers are together linked by aliphatic chains to form strongly bound beryllium ammonia complexes, (NH3)3Be(CH2)nBe(NH3)3, n = 1–6, with one electron around each beryllium ammonia center. In the case of a linear carbon chain, this system can be seen as the analog of two hydrogen atoms approaching each other at specific distances (determined by n). We show that the two electrons occupy diffuse s-type orbitals and can couple exactly as in H2 in either a triplet or singlet state. For long hydrocarbon chains, the singlet is an open-shell singlet nearly degenerate with the triplet spin state, which transforms to a closed-shell singlet for n = 1 imitating the σ-covalent bond of H2. The biradical character of the system is analyzed, and the singlet–triplet splitting is estimated as a function of n based on multi-reference calculations. Finally, we consider the case of bent hydrocarbon chains, which allows the closer proximity of the two diffuse electrons for larger chains and the formation of a direct covalent bond between the two diffuse electrons, which happens for two Li(NH3)4 complexes converting the open-shell to closed-shell singlets. The energy cost for bending the hydrocarbon chain is nearly compensated by the formation of the weak covalent bond rendering bent and linear structures nearly isoenergetic.
Datum: 16.05.2022

Hierarchical equations of motion approach to hybrid fermionic and bosonic environments: Matrix product state formulation in twin space

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>We extend the twin-space formulation of the hierarchical equations of motion approach in combination with the matrix product state representation [R. Borrelli, J. Chem. Phys. 150, 234102 (2019)] to nonequilibrium scenarios where the open quantum system is coupled to a hybrid fermionic and bosonic environment. The key ideas used in the extension are a reformulation of the hierarchical equations of motion for the auxiliary density matrices into a time-dependent Schrödinger-like equation for an augmented multi-dimensional wave function as well as a tensor decomposition into a product of low-rank matrices. The new approach facilitates accurate simulations of non-equilibrium quantum dynamics in larger and more complex open quantum systems. The performance of the method is demonstrated for a model of a molecular junction exhibiting current-induced mode-selective vibrational excitation.
Datum: 16.05.2022

Near-exact treatment of seniority-zero ground and excited states with a Richardson–Gaudin mean-field

The Journal of Chemical Physics, Volume 156, Issue 19, May 2022. <br/>Eigenvectors of the reduced Bardeen–Cooper–Schrieffer (BCS) Hamiltonian, Richardson–Gaudin (RG) states, are used as a variational wavefunction ansatz for strongly correlated electronic systems. These states are geminal products whose coefficients are solutions of non-linear equations. Previous results showed an un-physical apparent avoided crossing in ground state dissociation curves for hydrogen chains. In this paper, it is shown that each seniority-zero state of the molecular Coulomb Hamiltonian corresponds directly to an RG state. However, the seniority-zero ground state does not correspond to the ground state of a reduced BCS Hamiltonian. The difficulty is in choosing the correct RG state. The systems studied showed a clear choice, and we expect that it should always be possible to reason physically which state to choose.
Datum: 16.05.2022


Category: Current Chemistry Research

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