Electronic and relaxation contribution to linear molecular polarizability. An analysis of the experimental values

Pristine and aurum-decorated tungsten ditellurides as sensing materials for VOCs detection in exhaled human breath: DFT analysis

In this research, we employed density functional theory (DFT) to evaluate the sensing capabilities of transition metal-decorated two-dimensional WTe2 TMDs nanosheets toward VOCs such as (acetone, ethanol, methanol, toluene, and formaldehyde) that are exhaled in human breath and can serve as potential biomarkers for detecting specific physiological disorders and also gases interfering in exhaled breath (CO2 and H2O) detection. Au can be physically decorated onto the surface of WTe2. We analyzed the density of states (DOS), adsorption energy, charge transfer, and sensing behavior. The pristine WTe2 monolayer, exhibiting a semiconductor characteristic with a band gap of 0.63 eV, transitions to a metallic state upon Au-decoration, due to its actively stable nature and promising negative adsorption energy value, it triggers the emergence of novel states within the DOS. Computed adsorption energies of VOCs range from -0.08 to -0.57 eV, with greater interaction distances confirming the physisorption behavior of these VOCs biomarkers on Au-WTe2. Ethanol displays greater sensitivity compared to other considered VOCs. Au-WTe2 exhibits promising potential as a viable option for detecting VOCs in breath analysis applications at room temperature, owing to its excellent adsorption capabilities and sensitivity. Overall, our results highlight aurum-decorated tungsten ditelluride's potential as an efficient nano-sensor for detecting VOCs associated with early-stage lung cancer diagnoses.

Formation of S-Bearing Complex Organic Molecules in Interstellar Clouds via Ice Reactions with C2H2, HS, and Atomic H

The chemical network governing interstellar sulfur has been the topic of unrelenting discussion for the past few decades due to the conspicuous discrepancy between its expected and observed abundances in different interstellar environments. More recently, the astronomical detections of CH3CH2SH and CH2CS highlighted the importance of interstellar formation routes for sulfur-bearing organic molecules with two carbon atoms. In this work, we perform a laboratory investigation of the solid-state chemistry resulting from the interaction between C2H2 molecules and SH radicals-both thought to be present in interstellar icy mantles-at 10 K. Reflection absorption infrared spectroscopy and quadrupole mass spectrometry combined with temperature-programmed desorption experiments are employed as analytical techniques. We confirm that SH radicals can kick-start a sulfur reaction network under interstellar cloud conditions and identify at least six sulfurated products: CH3CH2SH, CH2CHSH, HSCH2CH2SH, H2S2, and tentatively CH3CHS and CH2CS. Complementarily, we utilize computational calculations to pinpoint the reaction routes that play a role in the chemical network behind our experimental results. The main sulfur-bearing organic molecule formed under our experimental conditions is CH3CH2SH, and its formation yield increases with the ratios of H to other reactants. It serves as a sink to the sulfur budget within the network, being formed at the expense of the other unsaturated products. The astrophysical implications of the chemical network proposed here are discussed.

Unraveling a Cavity-Induced Molecular Polarization Mechanism from Collective Vibrational Strong Coupling

We demonstrate that collective vibrational strong coupling of molecules in thermal equilibrium can give rise to significant local electronic polarizations in the thermodynamic limit. We do so by first showing that the full nonrelativistic Pauli-Fierz problem of an ensemble of strongly coupled molecules in the dilute-gas limit reduces in the cavity Born-Oppenheimer approximation to a cavity-Hartree equation for the electronic structure. Consequently, each individual molecule experiences a self-consistent coupling to the dipoles of all other molecules, which amount to non-negligible values in the thermodynamic limit (large ensembles). Thus, collective vibrational strong coupling can alter individual molecules strongly for localized "hotspots" within the ensemble. Moreover, the discovered cavity-induced polarization pattern possesses a zero net polarization, which resembles a continuous form of a spin glass (or better polarization glass). Our findings suggest that the thorough understanding of polaritonic chemistry, requires a self-consistent treatment of dressed electronic structure, which can give rise to numerous, so far overlooked, physical mechanisms.

Cavity Born-Oppenheimer Hartree-Fock Ansatz: Light-Matter Properties of Strongly Coupled Molecular Ensembles

Experimental studies indicate that optical cavities can affect chemical reactions through either vibrational or electronic strong coupling and the quantized cavity modes. However, the current understanding of the interplay between molecules and confined light modes is incomplete. Accurate theoretical models that take into account intermolecular interactions to describe ensembles are therefore essential to understand the mechanisms governing polaritonic chemistry. We present an ab initio Hartree-Fock ansatz in the framework of the cavity Born-Oppenheimer approximation and study molecules strongly interacting with an optical cavity. This ansatz provides a nonperturbative, self-consistent description of strongly coupled molecular ensembles, taking into account the cavity-mediated dipole self-energy contributions. To demonstrate the capability of the cavity Born-Oppenheimer Hartree-Fock ansatz, we study the collective effects in ensembles of strongly coupled diatomic hydrogen fluoride molecules. Our results highlight the importance of the cavity-mediated intermolecular dipole-dipole interactions, which lead to energetic changes of individual molecules in the coupled ensemble.

Ab Initio and Statistical Rate Theory Exploration of the CH (X2Π) + OCS Gas-Phase Reaction

The first theoretical results regarding the gas-phase reaction mechanism and kinetics of the CH (X2Π) + OCS reaction are presented here. This reaction has a proposed importance in the removal of OCS in regions of the interstellar medium (ISM) and has the potential to form the recently observed HCS/HSC isomers, with both constitutional isomers having recently been observed in the L483 molecular cloud in a 40:1 ratio. Statistical rate theory simulations were performed on stationary points along the reaction potential energy surface (PES) obtained from ab initio calculations at the RO-CCSD(T)/aug-cc-pV(Q+d)Z//M06-2X-D3/aug-cc-pV(Q+d)Z level of theory over the temperature and total density range of 150-3000 K and 1011-1024 cm-3, respectively, using a Master Equation analysis. Exploration of the reaction potential energy surface revealed that all three pathways identified to create CS + HCO products required surmounting barriers of 16.5 kJ mol-1 or larger when CH approached the oxygen side of OCS, rendering this product formation negligible below 1000 K, and certainly under low-temperature ISM conditions. In contrast, when CH approaches the sulfur side of OCS, only submerged barriers are found along the reaction potential energy surface to create HCCO + S or CO + HCS, both of which are formed via a strongly bound OCC(H)S intermediate (-358.9 kJ mol-1). Conversion from HCS to HSC is possible via a barrier of 77.8 kJ mol-1, which is still -34.1 kJ mol-1 below the CH + OCS entrance channel. No direct route from CH + OCS to H + CO + CS was found from our ab initio calculations. Rate theory simulations suggest that the reaction has a strong negative temperature dependence, in accordance with the barrierless addition of CH to the sulfur side of OCS. Product branching fractions were also determined from MESMER simulations over the same temperature and total density range. The product branching fraction of CO + HCS reduces from 79% at 150 K to 0.0% at 800 K, while that of HCS dissociation to H + CS + CO increases from 22% at 150 K to 100% at 800 K. The finding of CO + HCS as the major product at the low temperatures relevant to the ISM, instead of H + CS + CO, is in opposition to the current supposition used in the KIDA database and should be adapted in astrochemical models as another source of the HCS isomer.

Unifying Charge-Flow Polarization Models

We show that several models where electric polarization in molecular systems is modeled by charge-flow between atoms can all be considered as different manifestations of a general underlying mathematical structure. The models can be classified according to whether they employ atomic or bond parameters and whether they employ atom/bond hardness or softness. We show that an ab initio calculated charge response kernel can be considered as the inverse screened Coulombic matrix projected onto the zero-charge subspace, and this may provide a method for deriving charge screening functions to be used in force fields. The analysis suggests that some models contain redundancies, and we argue that a parameterization of charge-flow models in terms of bond softness is preferable as it depends on local quantities and decay to zero upon bond dissociation, while bond hardness depends on global quantities and increases toward infinity upon bond dissociation.

Broadening of the ν2 Raman Band of CH4 by C3H8 and C4H10

Raman spectroscopy is a promising method for the analysis of natural gas. It is necessary to account for the broadening effects on spectral lines to improve measurement accuracy. In this study, the broadening coefficients for methane lines in the region of the ν₂ band perturbed by propane, n-butane, and isobutane at room temperature were measured. We estimated the measurement errors of the concentration of oxygen and carbon dioxide in the case of neglecting the broadening effects on the methane spectrum by the pressure of C₂-C₆ alkanes. The obtained data are suited for the correct simulation of the methane spectrum in the hydrocarbon-bearing gases and can be used to improve the accuracy of the analysis of natural gas by Raman spectroscopy.

Solvation Effects on Polarizability of Aromatic Fluids

Elucidating solvation effects on polarizability in condensed phases is important for the description of the optical and dielectric behavior of high-refractive-index molecular materials. We study these effects via the polarizability model combining electronic, solvation, and vibrational contributions. The method is applied to well-characterized highly polarizable liquid precursors: benzene, naphthalene, and phenanthrene. We find that the solvation and vibrational terms are of opposite signs and cancel almost exactly for benzene, but for naphthalene and phenanthrene, a 2.5 and 5.0% decrease relative to the equilibrium electronic polarizability of the respective monomer, α₁^e, is predicted, respectively. The increase in electronic polarizability affects interaction polarizability of all contacts, which is the main reason for the increasing importance of solvation contribution. The calculated refractive indices agree very well with experiment for all three systems.

An integrated ion trap for the photon-ion spectrometer at PETRA III

We have added a multipole ion trap to the existing photon-ion spectrometer at PETRA III (PIPE). Its hybrid structure combines a ring-electrode trap with a segmented 16-pole trap. The interaction of gases and ions with extreme ultraviolet radiation from the beamline P04 is planned to be investigated with the newly installed multipole trap. The research focus lies on radiation-induced chemical reactions that take place in the interstellar medium or in the atmospheres of planets, including natural as well as man-made processes that are important in the Earth's atmosphere. In order to determine the mass-to-charge ratio of the stored ions as efficiently as possible, we are using an ion time-of-flight spectrometer. With this technique, all stored ions can be detected simultaneously. To demonstrate the possibilities of the trap setup, two experiments have been carried out: The photoionization of xenon and the ion-impact ionization of norbornadiene. This type of ion-impact ionization can, in principle, also take place in planetary atmospheres. In addition to ionization by photon or ion impact, chemical reactions of the trapped ions with neutral atoms or molecules in the gas phase have been observed. The operation of the trap enables us to simulate conditions similar to those in the ionosphere.

Design and Manipulation of a Minimalistic Hydrocarbon Nanocar on Au(111)

Nanocars are carbon-based single-molecules with a precise design that facilitates their atomic-scale control on a surface. The rational design of these molecules is important in atomic and molecular-scale manipulation to advance the development of molecular machines, as well as for a better understanding of self-assembly, diffusion and desorption processes. Here, we introduce the molecular design and construction of a collection of minimalistic nanocars. They feature an anthracene chassis and four benzene derivatives as wheels. After sublimation and adsorption on an Au(111) surface, we show controlled and fast manipulation of the nanocars along the surface using the tip of a scanning tunneling microscope (STM). The mechanism behind the successful displacement is the induced dipole created over the nanocar by the STM tip. We utilized carbon monoxide functionalized tips both to avoid decomposition and accidentally picking the nanocars up during the manipulation. This strategy allowed thousands of maneuvers to successfully win the Nanocar Race II championship.

Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions

Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals.

Time resolved transient transmission spectroscopy of TiCl4 and SnCl4

Herewith, for the first time, we present the vibrational spectra collected for liquid TiCl₄ and liquid SnCl₄ by use of time resolved transient transmission spectroscopy. Of our interest is the isotopically split isotropic ν₁ intramolecular vibrational band, the shape of which is very sensitive to intermolecular interactions. The high resolution spectra, obtained as fast Fourier transforms of the time domain signals acquired in transient transmission experiment, are compared with spontaneous Raman spectra. The dependence of the spectrum shape on intermolecular interactions has been established by diluting TiCl₄ and SnCl₄ in CS₂ at different concentrations. Fitting the simplified oscillatory model of a liquid to FFTs of time domain signals in transient transmission experiment we have found intermolecular force constants and decoherence lifetimes for all concentrations. Application of the pump-probe spectroscopic technique and windowed fast Fourier transform procedure allowed us to observe the evolution of the spectral shape, and thus of the intermolecular forces, after the liquid has been perturbed by the femtosecond pump pulse.

Fragmentation of interstellar methanol by collisions with He˙+: an experimental and computational study

Methanol is a key species in astrochemistry as its presence and reactivity provides a primary route to the synthesis of more complex interstellar organic molecules (iCOMs) that may eventually be incorporated in newly formed planetary systems. In the interstellar medium, methanol is formed by hydrogenation of CO ices on grains, and its fate upon collisions with interstellar ions should be accounted for to correctly model iCOM abundances in objects at various stages of stellar evolution. The absolute cross sections (CSs) and branching ratios (BRs) for the collisions of He˙⁺ ions with CH₃OH are measured, as a function of the collision energy, using a Guided Ion Beam Mass Spectrometer (GIB-MS). Insights into the dissociative electron (charge) exchange mechanism have been obtained by computing the entrance and exit multidimensional Potential Energy Surfaces (PESs) and by modelling the non-adiabatic transitions using an improved Landau-Zener-Stückelberg approach. Notably, the dynamical treatment reproducing the experimental findings includes a strong orientation effect of the system formed by the small He˙⁺ ion and the highly polar CH₃OH molecule, in the electric field gradient associated to the strongly anisotropic intermolecular interaction. This is a stereodynamical effect that plays a fundamental role in collision events occurring under a variety of conditions, with kinetic energy confined within intervals ranging from the sub-thermal to the hyper-thermal regime.

Ion Mobility and Fourier Transform Ion Cyclotron Resonance Collision Cross Section Techniques Yield Long-Range and Hard-Sphere Results, Respectively

We determined collision cross section (CCS) values for singly and doubly charged cucurbit[n]uril (n = 5-7), decamethylcucurbit[5]uril, and cyclohexanocucurbit[5]uril complexes of alkali metal cations (Li⁺-Cs⁺). These hosts are relatively rigid. CCS values calculated using the projection approximation (PA) for computationally modeled structures of a given host are nearly identical for +1 and +2 complexes, with weak metal ion dependence, whereas trajectory method (TM) calculations of CCS for the same structures consistently yield values 7-10% larger for the +2 complexes than for the corresponding +1 complexes and little metal ion dependence. Experimentally, we measured relative CCS values in SF₆ for pairs of +1 and +2 complexes of the cucurbituril hosts using the cross-sectional areas by Fourier transform ion cyclotron resonance ("CRAFTI") method. At center-of-mass collision energies <∼30 eV, CRAFTI CCS values are sensitive to the relative binding energies in the +1 and +2 complexes, but at collision energies >∼40 eV (sufficient that ion decoherence occurs on essentially every collision) that dependence is not evident. Consistent with the PA calculations, these experiments found that the +2 complex ions have CCS values ranging between 94 and 105% of those of their +1 counterparts (increasing with metal ion size). In contrast, but consistent with the TM CCS calculations, ion mobility measurements of the same complexes at close to thermal energies in much less polarizable N₂ find the CCS of +2 complexes to be in all cases 9-12% larger than those of the corresponding +1 complexes, with little metal ion dependence.

Upper bound for permanent orientation of symmetric-top molecule induced by linearly polarized electric fields

Many symmetric top molecules are among the most important polyatomic molecules. The orientation of a polyatomic molecule is a challenging task, which is at the heart of its quantum control and crucial for many subsequent applications in various fields. Most recent studies focus on the temporary orientation achieved via the quantum revivals. In this study, we reveal the underlying mechanism behind the observed permanent orientation and discuss strategies for a higher degree of permanent orientation. By a careful analysis of symmetry and unitary, it is possible to estimate an upper bound of [Formula: see text] for a molecule in its thermal equilibrium states using a linear field. We show that this bound can be reached for an oblate symmetric-top molecule in the high temperature limit. To demonstrate different possible schemes, we take CHCl3 as an example. Simply with designed microwave fields, one can permanently orient CHCl3 with a degree of ⟨cos  θ⟩ ≈ 0.045. We show that this value can be significantly increased by adding one or more pump pulses.

Reactions of Atomic Thorium and Uranium Cations with SF6 Studied by Guided Ion Beam Tandem Mass Spectrometry

The fundamental chemistry of the thorium and uranium fluorides continues to be an area of interest because of the use of thorium and uranium fluoride compounds in nuclear fuel systems. Here, we study the reaction of thorium cations with sulfur hexafluoride for the first time and revisit the reaction of uranium cations with sulfur hexafluoride. By using guided ion beam tandem mass spectrometry, we explore the reaction pathways that become accessible well above thermal energies (E ∼ 0.04 eV). Overall, we find that both Th⁺ and U⁺ react very efficiently with SF₆, approaching the collision limit at both thermal and elevated energies. The primary products observed at low energies include Th_1-3⁺, UF_1-4⁺, and SF_1-4⁺, all of which are formed in barrierless, exothermic processes. SF₅⁺ was also observed, although the pressure dependence of this channel reveals that SF₅⁺ forms exothermically through secondary reactions, which the energy dependences suggest result from reactions between ThF₂⁺ and UF₃⁺ with SF₆. At higher energies, both AnF₃⁺ products are observed to decay to AnF⁺ + F₂, and both SF₄⁺ and SF₂⁺ exhibit cross sections with endothermic features. For both systems, the rise in SF₄⁺ can be attributed to a secondary collision between AnF⁺ with SF₆ on the basis of the pressure dependence of the SF₄⁺ channel at higher energies, and the rise in SF₂⁺ appears to result from the decomposition of SF₃⁺ to SF₂⁺ + F.

Statistical vibrational autodetachment and radiative cooling rates of para-benzoquinone

We report measurements of the statistical vibrational autodetachment (VAD, also called thermionic emission) and radiative cooling rates of isolated para-benzoquinone (pBQ, C₆H₄O₂) radical anions using the cryogenic electrostatic ion storage ring facility DESIREE. The results are interpreted using master equation simulations with rate coefficients calculated using statistical detailed balance theory. The VAD rate is determined by measuring the time-dependent yield of neutral pBQ due to spontaneous electron emission from a highly-excited ensemble of anions formed in an electron-attachment ion source. Competition with radiative cooling quenches the VAD rate after a critical time of τ_c = 11.00(5) ms. Master equation simulations which reproduce the VAD yield provide an estimate of the initial effective vibrational temperature of the ions of 1100(20) K, and provide insight into the anion formation scenario. A second measurement of the radiative cooling rate of pBQ^- stored for up to 0.5 s was achieved using time-dependent photodetachment action spectroscopy across the ²A_u ← ²B_2g and ²B_2u ← ²B_2g transitions. The rate at which hot-band contributions fade from the action spectrum is quantified by non-negative matrix factorisation. This is found to be commensurate with the average vibrational energy extracted from the simulations, with 1/e lifetimes of 0.16(3) s and 0.1602(7) s, respectively. Implications for astrochemistry are discussed.

Development of computational design for reliable prediction of dielectric strengths of perfluorocarbon compounds

The development of robust computational protocols capable of accurately predicting the dielectric strengths of eco-friendly insulating gas candidates is crucial; however, it lacks relevant efforts significantly. Consequently, a series of computational protocols are employed in this study to enable the computational prediction of polarizability and ionization energy of eco-friendly, perfluorinated carbon-based candidates, followed by the equation-based prediction of their dielectric strength. The validation process associated with the prediction of the afore-mentioned variables for selected datasets confirms the suitability of the B3LYP-based prediction protocol for reproducing experimental values. Subsequently, the validation of dielectric strength prediction outlines the following three conclusions. (1) The referenced equation adopted from a previous study is incapable of predicting the dielectric strengths of 137 organic compounds present in our database. (2) Parameterization of the coefficients in the referenced equation leads to the accurate prediction of the dielectric strengths. (3) Incorporation of a novel variable, viz. molecular weight, into the referenced equation combined with the parameterization of the coefficients leads to a robust protocol capable of predicting dielectric strengths with high efficiencies even with a significantly smaller fitting dataset. This implies the development of a comprehensive solution capable of accurately predicting the dielectric strengths of a substantially large dataset.

Temperature dependence of the Kirkwood correlation factor and linear dielectric constant of simple isotropic polar fluids

The theory developed in an accompanying paper [Déjardin, Phys. Rev. E 105, 024109 (2022)10.1103/PhysRevE.105.024109] is used to compute the Kirkwood correlation factor of simple polar fluids of different nature. From this calculation, the theoretical static permittivity is readily obtained, which is compared with experimental values. This is accomplished by fitting only one parameter accounting for induction or dispersion forces and torques, which is necessarily connected with the individual molecular polarizability but not explicitly related to the physical properties due to the nonadditivity of such energies. Excellent agreement between theoretical and experimental static permittivities is obtained over a very broad temperature range for a number of associated and nonassociated liquids. Finally, limitations of the present theory are given.

Effects of alkylthio groups on phase transitions of organic molecules and liquid crystals: a comparative study with alkyl and alkoxy groups

The effects of the alkylthio groups on the phase transition behavior of organic liquid crystal molecules were examined by comparing them with the effects of alkyl and alkoxy groups.

Mixed-conducting properties of annealed polyacrylonitrile activated by n-doping of conjugated domains

Critical limiting factors in next generation electrode materials for rechargeable batteries include short lifetimes, poor reaction reversibility, and safety concerns. Many of these challenges are caused by detrimental interactions at the interfaces between electrode materials and the electrolyte. Thermally annealed polyacrylonitrile has recently shown empirical success in mitigating such detrimental interactions when used in conjunction with alloy anode materials, though the mechanisms by which it does so are not well understood. This is a common problem in the battery community: an additive or a coating improves certain battery characteristics, but without a deeper understanding of how or why, design rules to further motivate the design of new chemistries can't be developed. Herein, we systematically investigate the effect of heating parameters on the properties of annealed polyacrylonitrile to identify the structural basis for such beneficial properties. We find that sufficiently long annealing times and control over temperature result in the formation of conjugated imine domains. When sufficiently large, the conjugated domains can be electrochemically reduced in a Li-ion half-cell battery, effectively n-doping the polymeric matrix and allowing it to become a mixed-conductor, with the ability to conduct both the Li-ions and electrons needed for reversible lithiation of an interdispersed alloy active material like antimony. Not only do those relationships inform design principles for annealed polyacrylonitrile containing electrodes, but they also identify new strategies in the development of mixed-conducting materials for use in next generation battery electrodes.

Thermal annealing of polyacrylonitrile results in the formation of conjugated imine domains. When of sufficient size, these conjugated domains can be electrochemically activated to exhibit both electronic and ionic conductivity.

On the Electron Impact Integral Cross-Sections for Butanol and Pentanol Isomers

The need for a reliable and comprehensive database of cross-sections for many atomic and molecular species is immense due to its key role in R&D domains such as plasma modelling, bio-chemical processes, medicine and many other natural and technological environments. Elastic, momentum transfer and total cross-sections of butanol and pentanol isomers by the impact of 6–5000 eV electrons are presented in this work. The calculations were performed by employing the spherical complex optical potential formalism along with single-centre expansion and group additivity rule. The investigations into the presence of isomeric variations reveal that they are more pronounced at low and intermediate energies. Elastic, total cross-sections (with the exception of n-pentanol) and momentum transfer cross-sections for all pentanol isomers are reported here for the first time, to the best of our knowledge. Our momentum transfer cross-sections for butanol isomers are in very good agreement with the experimental and theoretical values available, and in reasonable consensus for other cross-sections.

Multiscale modeling shows that dielectric differences make NaV channels faster than KV channels

The generation of action potentials in excitable cells requires different activation kinetics of voltage-gated Na (Na_V) and K (K_V) channels. Na_V channels activate much faster and allow the initial Na⁺ influx that generates the depolarizing phase and propagates the signal. Recent experimental results suggest that the molecular basis for this kinetic difference is an amino acid side chain located in the gating pore of the voltage sensor domain, which is a highly conserved isoleucine in K_V channels but an equally highly conserved threonine in Na_V channels. Mutagenesis suggests that the hydrophobicity of this side chain in Shaker K_V channels regulates the energetic barrier that gating charges cross as they move through the gating pore and control the rate of channel opening. We use a multiscale modeling approach to test this hypothesis. We use high-resolution molecular dynamics to study the effect of the mutation on polarization charge within the gating pore. We then incorporate these results in a lower-resolution model of voltage gating to predict the effect of the mutation on the movement of gating charges. The predictions of our hierarchical model are fully consistent with the tested hypothesis, thus suggesting that the faster activation kinetics of Na_V channels comes from a stronger dielectric polarization by threonine (Na_V channel) produced as the first gating charge enters the gating pore compared with isoleucine (K_V channel).

Assessment of the proposed pseudo-potential theoretical model for the static and dynamic Raman scattering intensities: Multivariate statistical approach to quantum-chemistry protocols

Accurate calculation of molecular polarizabilities and Raman intensities required high-level correlated wave functions (CCSD) and large basis set with the inclusion of electronic correlation within experimental precision. These requirements, in terms of time and computation, are economically costly. Polarized Gaussian basis sets adapted to effective core potentials (ECPs) for the static and frequency dependent Raman intensities is presented. The results of the proposed basis sets at CCSD and DFT levels in comparison with Sadlej-pVTZ, as reference basis set, show quite a good quantitative agreement in the properties with a valuable reduction in the computational time and resources. Multivariate principal component analysis (PCA) was performed to study the assessment of the efficiency of proposed methodology and diagnose the inherent information related to the kind of normal vibrational mode of each molecule, based on the variations in the computed Raman intensities. The results, in the form of score-plots, explored a clear segregation and classification among the Raman intensities data, revealing its dependence on the excitation frequencies of laser and nature of the vibrational mode of each molecule of interest. Moreover, the projection of the loadings-plots of the PCs successfully enabled to classify the most correlated computational methods in to the same groups, and made isolations of the less efficient basis functions at the corresponding theoretical method.

A comparison of experimental and theoretical low energy positron scattering from furan

This paper presents a joint experimental and theoretical study of positron scattering from furan. Experimental data were measured using the low energy positron beamline located at the Australian National University and cover an energy range from 1 eV to 30 eV. Cross sections were measured for total scattering, total elastic and inelastic scattering, positronium formation, and differential elastic scattering. Two theoretical approaches are presented: the Schwinger multichannel method and the independent atom method with screening corrected additivity rule. In addition, our data are compared to corresponding electron scattering results from the same target with a number of significant differences observed and discussed.

Reinterpreting π-stacking

The nature of π-π interactions has long been debated. The term "π-stacking" is considered by some to be a misnomer, in part because overlapping π-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate π-π interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic saturated hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic π-π interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked π-π architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize π-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp² carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformational landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for π-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked π-π motif in protein crystal structures.

Simple corrections for the static dielectric constant of liquid mixtures from model force fields

Pair-wise additive force fields provide fairly accurate predictions, through classical molecular simulations, for a wide range of structural, thermodynamic, and dynamical properties of many materials. However, one key property that has not been well captured is the static dielectric constant, which characterizes the response of a system to an applied electric field and is important in determining the screening of electrostatic interactions through a system. A simple correction has been found to provide a relatively robust method to improve the estimate of the static dielectric constant from molecular simulations for a broad range of compounds. This approach accounts for the electronic contribution to molecular polarizability and assumes that the charges that couple a molecule to an applied electric field are proportional to the effective force field charges. In this work, we examine how this correction performs for systems at different temperatures and for binary mixtures. Using a value for the electronic polarizability, based on the experimental index of refraction, and a charge scaling factor, determined at a single temperature, we find that the static dielectric constant can be predicted remarkably well, in comparison to the experimentally measured values. This provides good evidence that the effective charges that appear in pair-wise additive force fields developed to reproduce the potential energy surface of a system are not the same as those that determine the static dielectric constant; however, they can be captured in a relatively simple manner, which is dependent on the particular force field.

Thermal evaporation of pyrene clusters

This work presents a study of the thermal evaporation and stability of pyrene (C16H10)n clusters. Thermal evaporation rates of positively charged mass-selected clusters are measured for sizes in the range n = 3-40 pyrene units. The experimental setup consists of a gas aggregation source, a thermalization chamber, and a time of flight mass spectrometer. A microcanonical Phase Space Theory (PST) simulation is used to determine the dissociation energies of pyrene clusters by fitting the experimental breakdown curves. Calculations using the Density Functional based Tight Binding combined with a Configuration Interaction (CI-DFTB) model and a hierarchical optimization scheme are also performed in the range n = 2-7 to determine the harmonic frequencies and a theoretical estimation of the dissociation energies. The frequencies are used in the calculations of the density of states needed in the PST simulations, assuming an extrapolation scheme for clusters larger than 7 units. Using the PST model with a minimal set of adjustable parameters, we obtain good fits of the experimental breakdown curves over the full studied size range. The approximations inherent to the PST simulation and the influence of the used parameters are carefully estimated. The derived dissociation energies show significant variations over the studied size range. Compared with neutral clusters, significantly higher values of the dissociation energies are obtained for the smaller sizes and attributed to charge resonance in line with CI-DFTB calculations.

Evaluation of Molecular Polarizability and of Intensity Carrying Modes Contributions in Circular Dichroism Spectroscopies

We re-examine the theory of electronic and vibrational circular dichroism spectroscopy in terms of the formalism of frequency-dependent molecular polarizabilities. We show the link between Fermi’s gold rule in circular dichroism and the trace of the complex electric dipole–magnetic dipole polarizability. We introduce the C++ code polar to compute the molecular polarizability complex tensors from quantum chemistry outputs, thus simulating straightforwardly UV-visible absorption (UV-Vis)/electronic circular dichroism (ECD) spectra, and infrared (IR)/vibrational circular dichroism (VCD) spectra. We validate the theory and the code by referring to literature data of a large group of chiral molecules, showing the remarkable accuracy of density functional theory (DFT) methods. We anticipate the application of this methodology to the interpretation of vibrational spectra in various measurement conditions, even in presence of metal surfaces with plasmonic properties. Our theoretical developments aim, in the long run, at embedding the quantum-mechanical details of the chiroptical spectroscopic response of a molecule into the simulation of the electromagnetic field distribution at the surface of plasmonic devices. Such simulations are also instrumental to the interpretation of the experimental spectra measured from devices designed to enhance chiroptical interactions by the surface plasmon resonance of metal nanostructures.

Holography with Photochromic Diarylethenes

Photochromic materials are attractive for the development of holograms for different reasons: they show a modulation of the complex refractive index, meaning they are suitable for both amplitude and phase holograms; they are self-developing materials, which do not require any chemical process after the light exposure to obtain the final hologram; the holograms are rewritable, making the system a convenient reconfigurable platform for these types of diffractive elements. In this paper, we will show the features of photochromic materials, in particular diarylethenes in terms of the modulation of a transparency and refractive index, which are mandatory for their use in holography. Moreover, we report on the strategies used to write binary and grayscale holograms and their achieved results. The outcomes are general, and they can be further applied to other classes of photochromic materials in order to optimize the system for achieving high efficiency and high fidelity holograms.

Polarization of Electron Density Databases of Transferable Multipolar Atoms

Polarizability is a key molecular property involved in either macroscopic (i.e., dielectric constant) and microscopic properties (i.e., interaction energies). In rigid molecules, this property only depends on the ability of the electron density (ED) to acquire electrostatic moments in response to applied electric fields. Databases of transferable electron density fragments are a cheap and efficient way to access molecular EDs. This approach is rooted in the relative conservation of the atomic ED between different molecules, termed transferability principle. The present work discusses the application of this transferability principle to the polarizability, an electron density-derived property, partitioned in atomic contributions using the Quantum Theory of Atoms In Molecules topology. The energetic consequences of accounting for in situ deformation (polarization) of database multipolar atoms are investigated in detail by using a high-quality quantum chemical benchmark.

Fine structures in Raman spectra of tetrahedral tetrachloride molecules in femtosecond coherent spectroscopy

Herewith, we present fast Fourier transforms of time resolved signals, obtained by use of the femtosecond transient transmission (TT) spectroscopy, for three tetrachlorides, CCl₄, SiCl₄, and GeCl₄, and chloroform, CHCl₃. Due to coherent excitation of molecules, the isotopic splitting of their spectral bands in the range of symmetric stretching vibration can be observed with high resolution not available in spontaneous Raman scattering. The intensity distribution in the isotopic fine structure pattern appears to differ for various studied molecules, which is explained by the role of intermolecular interactions and the local order of molecules in the liquids. In particular, in SiCl₄, the vibrational band exhibits anomalous ratios of the peak amplitudes, which do not agree with the natural abundance of the isotopologues. Using the simple oscillatory model of the liquid and fitting theoretical curves to the experimental results, we have been able to find the intermolecular force constants for all three liquids and to formulate the conclusion that the anomalous spectral pattern in SiCl₄ results from strong interactions between the closest Cl atoms belonging to adjacent molecules. Application of the windowed Fourier transform enables us to study the dynamics of intermolecular interactions. The strength of intermolecular interactions in CCl₄, SiCl₄, and GeCl4, found by the TT technique, is compared with the results obtained by means of the femtosecond optical Kerr effect spectroscopy.

Electron scattering from 1-butanol at intermediate impact energies: Total cross sections

We report experimental measurements of the absolute total cross sections (TCSs) for electron scattering from 1-butanol at impact energies in the range 80-400 eV. Those measurements were conducted by considering the attenuation of a collimated electron beam, at a given energy, through a gas cell containing 1-butanol, at a given pressure, and through application of the Beer-Lambert law to derive the required TCS. We also report theoretical results using the Independent-Atom Model with Screening Corrected Additivity Rule and Interference approach. Those results include the TCS, the elastic integral cross section (ICS), the ionization total ICS, and the sum over all excitation process ICSs with agreement at the TCS level between our measured and calculated results being encouraging.

Mechanistic studies on the dibenzofuran and dibenzo‑p‑dioxin formation reactions from anthracene

Polychlorinated dibenzo‑p‑dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are highly toxic, carcinogenic and mutagenic to humans. As precursors of PCDD/Fs, dibenzofuran (DF) and dibenzo‑p‑dioxin (DD) have received considerable public and scientific attention. To reduce the emission of PCDD/Fs, it is critical to explore the formation mechanisms of DF and DD. The present study delineated the DF and DD formation mechanisms from anthracene partial oxidation with the aid of high-accuracy quantum chemistry calculations. The rate constants of crucial elementary steps were obtained utilizing canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) correction. The results indicate that anthracene could be important precursor of DF and DD, because of the potential barriers for all the major elementary reactions are lower than 33.54kcalmol^-1. This work also reveals that water molecule plays an important catalytic effect during the formation of both DF and DD by lowering the barriers of about 27.24kcalmol^-1. For the water-assisted formation pathway, DF is the dominate product of anthracene partial oxidation with the highest barrier of 30.45kcalmol^-1. For the non-water-assisted formation pathway, DD is the dominate product with the highest barrier of 33.54kcalmol^-1.