A new four-dimensional ab initio potential energy surface and predicted infrared spectra for the He–CS2 complex

Theoretical investigation on degradation of CH[triple bond, length as m-dash]CCH2OH by NO3 radicals in the atmosphere

A detailed computational investigation is executed on the reaction between NO3 and CH[triple bond, length as m-dash]CCH2OH at the CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) level. Addition/elimination and H-abstraction mechanisms are found for the NO3 + CH[triple bond, length as m-dash]CCH2OH reaction, and they could compete with each other. The most feasible addition/elimination pathway through a series of central-C addition, 1,4-H migration to generate intermediates IM1 (CHCONO2CH2OH) and IM3 (CH2CONO2CH2O), and then IM3 directly decompose into product P2 (CH2CONO2CHO + H). The dominant H-abstraction pathway is abstracting the H atom of the -CH2- group to generate h-P1 (CHCCHOH + HNO3). RRKM-TST theory was used to compute the kinetics and product branching ratios of the NO3 + CH[triple bond, length as m-dash]CCH2OH reaction at 200-3000 K. The rate constants at 298 K are consistent with the experimental values. The lifetime of CH[triple bond, length as m-dash]CCH2OH is estimated to be 59.72 days at 298 K. The implicit solvent model was used to examine the solvent effect on the total reaction. Based on the quantitative structure-activity relationship (QSAR) model, the toxicity during the degradation process is increased towards fish, and decreased towards daphnia and green algae.

Insights into Hildebrand Solubility Parameters - Contributions from Cohesive Energies or Electrophilicity Densities?

We introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non- or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.

Unusual Dynamics and Vibrational Fingerprints of van der Waals Dimers Formed by Linear Molecules and Rare-Gas Atoms

Detailed structural, dynamical, and vibrational analyses have been performed for systems composed of linear triatomic molecules solvated by a single rare-gas atom, He, Ne, or Ar. Among the chromophores of these van der Waals (vdW) dimers, there are four neutral molecules (CO2, CS2, N2O, and OCS) and six molecular cations (HHe2+, HNe2+, HAr2+, HHeNe+, HHeAr+, and HNeAr+), both of apolar and polar nature. Following the exploration of bonding preferences, high-level four-dimensional (4D) potential energy surfaces (PESs) have been developed for 24 vdW dimers, keeping the two intramonomer bond lengths fixed. For these 24 complexes, over 1500 bound vibrational states have been obtained via quasi-variational nuclear-motion computations, employing exact kinetic-energy operators together with the accurate 4D PESs and their 2D/3D cuts. The reduced-dimensional (2D to 4D) dimer models have been compared with full-dimensional (6D) ones in the cases of the neutral CO2·Ar and charged HHe2+·He dimers, corroborating the high accuracy of the 2D to 4D vibrational energies. The reduced-dimensional models suggest that (a) while the equilibrium structures are T-shaped and planar, the effective ground-state structures are nonplanar, (b) certain bound states belong to collinear molecular structures, even when they are not minima, (c) the vdW vibrations are heavily mixed and many states have amplitudes corresponding to both the T-shaped and collinear structures, (d) there are a few dimers, for which even some of the vdW fundamentals lie above the first dissociation limit, and (e) the vdW vibrations are almost fully decoupled from the intramonomer bending motion.

Identifying the acidic or basic behavior of surface water: a QM/MM-MD study

Controversies on the water surface were theoretically addressed with the help of large scale quantum mechanical molecular dynamics (QMMD) simulations on water surface model systems with and without excess hydroniums and hydroxides. It was revealed that the thermodynamic surface structures of these ions strongly depend on their location and dipole orientation. Fast hydronium diffusion by proton transfer establishes a wider kinetic depth distribution (∼6 Å) than that predicted by its thermodynamic affinity for the water surface, while slow hydroxide is shallowly trapped below the outermost molecular layer (3-4 Å). In addition, the anisotropic orientation of surface water dipole can generate a substantial magnitude of surface potential, which extends to a depth of a few molecular layers. With these distinctively different surface properties of two ions and water molecules, the seemingly contradictory observations of acidic and negatively charged water surfaces may be successfully explained. That is, the negative surface charge of neutral water mostly stems from intrinsic water properties such as water dipole orientation and electron density spillage at the surface, rather than surface OH- ions. The enhanced acidity of the water surface can be attributed in large part to the kinetic depth profile of ion density in addition to static thermodynamic origin. Furthermore, the different depth profiles of the two ions may differently affect the surface-sensitive spectroscopic observations.

Tetragonal-zircon BiVO4: a better polymorph for the formation of coherent type-II heterostructures for water splitting applications

The monoclinic-scheelite (m-s) polymorph of BiVO4 has the highest photocatalytic activity, whereas tetragonal-zircon (t-z) has the lowest photocatalytic activity, which may be due to a higher band gap. However, t-z has the highest crystal symmetry, which makes it a more suitable candidate to form coherent type-II interfaces for the efficient separation of electron-hole pairs. Furthermore, the method of preparation (e.g. low temperature and moderate pH) of t-z is more facile compared to the m-s polymorph. Hence, in this report, we construct coherent isomaterial and heteromaterial type-II heterostructures by facet engineering of low index surfaces of t-z polymorph with different semiconductor materials (e.g. ZnO, TiO2, CdSe, and ZnS) by screening the band gap, band edge positions, and lattice misfit strain. On the basis of the calculated band-edge positions, the polymorphs of BiVO4 can form 212 combinations of the type-II interface, which reduces to 17 coherent interfaces with lattice misfit strain between 1.55% to 28.5% when translational symmetry, atomic positions, lattice mismatch, and bond complementarity have been imposed. Furthermore, the current study suggests that t-z polymorphs can form more coherent interfaces (4 out of 168), which may be due to its highest symmetry structure in comparison to previously formed 67 isomaterial and heteromaterial type-II heterostructure combinations of BiVO4 (1 out of 67), which suggests that t-z can be a suitable candidate for the formation of type-II coherent interfaces for PEC/PC applications.

Full-dimensional neural network potential energy surface and dynamics of the CH2OO + H2O reaction

An accurate global full-dimensional machine learning-based potential energy surface (PES) of the simplest Criegee intermediate (CH₂OO) reaction with water monomer was developed based on the high level of extensive CCSD(T)-F12a/aug-cc-pVTZ calculations. This analytical global PES not only covers the regions of reactants to hydroxymethyl hydroperoxide (HMHP) intermediates, but also different end product channels, which facilities both the reliable and efficient kinetics and dynamics calculations. The rate coefficients calculated by the transition state theory with the interface to the full-dimensional PES agree well with the experimental results, indicating the accuracy of the current PES. Extensive quasi-classical trajectory (QCT) calculations were performed both from the bimolecular reaction CH₂OO + H₂O and from HMHP intermediate on the new PES. The product branching ratios of hydroxymethoxy radical (HOCH₂O, HMO) + OH radical, formaldehyde (CH₂O) + H₂O₂ and formic acid (HCOOH) + H₂O were calculated. The reaction yields dominantly HMO + OH, because of the barrierless pathway from HMHP to this channel. The computed dynamical results for this product channel show the total available energy was deposited into the internal rovibrational excitation of HMO, and the energy release in OH and translational energy is limited. The large amount of OH radical found in the current study implies that the CH₂OO + H₂O reaction can provide crucially OH yield in Earth's atmosphere.

FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation

We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/.

DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.

Conceptual density functional theory under pressure: Part I. XP-PCM method applied to atoms

High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback-Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns.

Structural evolution, photoelectron spectra and vibrational properties of anionic GdGe n - (n = 5-18) nanoalloy clusters: a DFT insight

The structural growth of Gd-doped germanium anionic nanoclusters, GdGe n - (n = 5-18), has been explored via quantum chemistry calculations using the mPW2PLYP method and an unprejudiced structural searching technique known as ABCluster. The optimized geometries exhibited that when n = 10-14, the structural evolution favors the Gd-linked configuration where the Gd atom as a connector bridges two Ge subgroups, while the Gd atom is encapsulated in a closed cage-like Ge frame when n = 15-18. The properties like magnetic moment, charge transfer, relative stability, HOMO-LUMO gap, photoelectron spectra, and infrared and Raman spectra have been predicted. The information of these spectra could provide extra approaches to experimentally determine the electronic structures and equilibrium configuration of these compounds. The largest spin magnetic moment of 7 μ B is attained via half-filled 4f states. The GdGe16 - nanocluster is determined to be a superatom because its total valence of 75 electrons can be distributed to the orbital sequence of 1S21P6(4f7)1D101F142S22P21G182P42D10, which complies with not only Hund's rule, but also the spherical jellium model. Particularly, its UV-Vis spectra match well with solar energy distribution. Such materials act as nano multifunctional building units potentially used in solar energy converters or ultra-highly sensitive near-infrared photodetectors.

Gas phase acidity of water clusters

In the present work, we have estimated the gas-phase acidity of different water clusters, i.e., (H₂O)_n, n = 1-20, 30, 35, 42, 54, 80, and 100. The present work indicates that the gas-phase acidity of the terminal hydrogen atom increases with the size of water clusters and starts converging at (H₂O)₃₀. Furthermore, the present work also indicates that the gas-phase acidity of a terminal hydrogen atom is higher than that of the corresponding bulk hydrogen atom for the same size of water cluster.

Si doped T-graphene: a 2D lattice as an anode electrode in Na ion secondary batteries

Heteroatom doping into 2-dimensional lattices of materials such as graphene brings revolutionary reform in the field of materials endowing the parent material with remarkable properties.

CBDPS 1.0: A Python GUI Application for Machine Learning Models to Predict Bitter-Tasting Children's Oral Medicines

Bitter tastes are innately aversive and are thought to help protect animals from consuming poisons. Children are extremely sensitive to drug tastes, and their compliance is especially poor with bitter medicine. Therefore, judging whether a drug is bitter and adopting flavor correction and taste-masking strategies are key to solving the problem of drug compliance in children. Although various machine learning models for bitterness and sweetness prediction have been reported in the literature, no learning model or bitterness database for children's medication has yet been reported. In this study, we trained four different machine learning models to predict bitterness. The goal of this study was to develop and validate a machine learning model called the "Children's Bitter Drug Prediction System" (CBDPS) based on Tkinter, which predicts the bitterness of a medicine based on its chemical structure. Users can enter the Simplified Molecular-Input Line-Entry System (SMILES) formula for a single compound or multiple compounds, and CBDPS will predict the bitterness of children's medicines made from those XGBoost-Molecular ACCess System (XgBoost-MACCS) model yielded an accuracy of 88% under cross-validation.

Theoretical calculation of a full-dimensional ab initio potential energy surface and prediction of infrared spectra for Xe-CS2

An effective four-dimensional (4D) ab initio potential energy surface (PES) for Xe-CS2 which explicitly involves the intramolecular Q 1 symmetric stretching and Q 3 antisymmetric stretching vibrational coordinates of CS2 is constructed. The computations are carried out employing single- and double-excitation coupled-cluster theory with a non-iterative perturbation treatment of triple excitations [CCSD(T)] method with a large basis set. Two vibrationally averaged potentials at the ground and ν 1 + ν 3 (ν 1 = 1, ν 3 = 1) excited states are obtained by integrating the 4D potentials over the Q 1 and Q 3 coordinates. The potentials have a T-shaped global minimum and two equivalent linear local minima. The radial discrete variable representation/angular finite basis representation and the Lanczos algorithm are employed to calculate the rovibrational energy levels for Xe-CS2. The infrared band origin shift associated with the fundamental band of CS2 is predicted, which is red-shifted by -1.996 cm-1 in the ν 1 + ν 3 region. In addition, we further predict the spectroscopic parameters for the ground and the ν 1 + ν 3 excited states of Xe-CS2. Compared with the previous Rg-CS2 (Rg = He, Ne, Ar, Kr) complexes, we found that the complexes of the rare gas atoms with CS2 display obvious regularities.

Adsorption and migration of alkali metals (Li, Na, and K) on pristine and defective graphene surfaces

In this paper, a computational study of Li, Na, and K adsorption and migration on pristine and defective graphene surfaces is conducted to gain insight into the metal storage and mobility in carbon-based anodes for alkali metal batteries. Atomic level studies of the metal adsorption and migration on the graphene surface can help address the challenges faced in the development of novel alkali metal battery technologies, as these systems act as convenient proxies of the crystalline carbon surface in carbon-based materials including graphite, hard carbons and graphene. The adsorption of Li and K ions on the pristine graphene surface is shown to be more energetically favourable than Na adsorption. A collection of defects expected to be found in carbonaceous materials are investigated in terms of metal storage and mobility, with N- and O-containing defects found to be the dominant defects on these carbon surfaces. Metal adsorption and migration at the defect sites show that defect sites tend to act as metal trapping sites, and metal diffusion around the defects is hindered when compared to the pristine surface. We identify a defect where two C sites are substituted with O and one C site with N as the dominant surface defect, and find that this defect is detrimental to metal migration and hence the battery cycling performance.

Using density based indexes to characterize excited states evolution

With the aim of offering new computational tools helping in the description of photochemical reactions and phenomena occurring at the excited state, we present in this work the capability of a density based index (Π) in locating decay channels from higher to lower excited states. The Π index, previously applied to disclose non-radiative decay channels from the first excited state to the ground state, is very simple in its formulation and can be evaluated, practically with no extra computational cost, and coupled to any quantum method able to provide excited states densities. Indeed, this index relies only on the knowledge of energetics and electron densities of the different electronic states involved in the decay. In the present work, we show the proficiency of the Π index in the general case of decay between excited states by applying it to two model systems well characterized both theoretically and experimentally. In both cases, this descriptor was successful in spotting the regions where excited states are more likely to decay, thus suggesting its potential interest for further application in the design of new compounds. © 2018 Wiley Periodicals, Inc.

Exploring chemical space with alchemical derivatives: alchemical transformations of H through Ar and their ions as a proof of concept

Alchemical derivatives have been used previously to obtain information about transformations in which the number of electrons is unchanged. Here an approach for combining changes in both the number of electrons and the nuclear charge is presented.

Covalent Organic Framework Electrocatalysts for Clean Energy Conversion

Covalent organic frameworks (COFs) are promising for catalysis, sensing, gas storage, adsorption, optoelectricity, etc. owning to the unprecedented combination of large surface area, high crystallinity, tunable pore size, and unique molecular architecture. Although COFs are in their initial research stage, progress has been made in the design and synthesis of COF-based electrocatalysis for the oxygen reduction reaction, oxygen evolution reaction, hydrogen evolution reaction, and CO₂ reduction in energy conversion and fuel generation. Design principles are also established for some of the COF materials toward rational design and rapid screening of the best electrocatalysts for a specific application. Herein, the recent advances in the design and synthesis of COF-based catalysts for clean energy conversion and storage are presented. Future research directions and perspectives are also being discussed for the development of efficient COF-based electrocatalysts.

Transition states of spin-forbidden reactions

New approximation method for locating stationary points on lowest spin-coupled potential energy surface (PES) using density functional calculations.

Steric charge

Steric charge is an informative descriptor providing novel insights to appreciate the steric effect and stereoselectivity for chemical processes and transformations.

Identification and characterization of intramolecular γ-halo interaction in d0 complexes: a theoretical approach

A mechanistic investigation to detect intramolecular M⋯X-C type interactions in d⁰ neutral and cationic complexes was carried out through a benchmark study employing different density functional methods. As γ-halogen is involved in M⋯X-C type interactions, it is denoted as a γ-halo interaction and the respective conformers are designated as halo-conformers. By analyzing the geometrical parameters of halo-conformers, it was observed that, irrespective of the nature of the metal and the halogen, the C_γ-X bond distance increases compared to the usual C-X bond, which brings the M and X centers close enough to generate a weak interaction. Generation of the M⋯X-C interaction was confirmed by performing NBO, AIM and Wiberg bond index analyses, from which the persistence of γ-halo interaction was seen to be prominent. Moreover, for each neutral and cationic complex, the values of Wiberg bond order are in good agreement with the AIM results. The effect of the metal center, as well as γ-halogen substitution, on γ-halo interaction was also studied in the present work. To justify the practical subsistence of the halo-conformers, we checked the stability of the conformers with respect to their β-conformers by comparing the zero-point-corrected electronic energies. Therefore, the entire study was designed in such a way that it can provide evidence in support of intramolecular M⋯X-C interactions, where, instead of the C-H bond, the C_γ-X bond will interact with the central transition metal.

Benchmarking the DFT methodology for assessing antioxidant-related properties: quercetin and edaravone as case studies

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.

Potential benefits of melatonin in organ transplantation: a review

Organ transplantation is a useful therapeutic tool for patients with end-stage organ failure; however, graft rejection is a major obstacle in terms of a successful treatment. Rejection is usually a consequence of a complex immunological and nonimmunological antigen-independent cascade of events, including free radical-mediated ischemia-reperfusion injury (IRI). To reduce the frequency of this outcome, continuing improvements in the efficacy of antirejection drugs are a top priority to enhance the long-term survival of transplant recipients. Melatonin (N-acetyl-5-methoxytryptamine) is a powerful antioxidant and ant-inflammatory agent synthesized from the essential amino acid l-tryptophan; it is produced by the pineal gland as well as by many other organs including ovary, testes, bone marrow, gut, placenta, and liver. Melatonin has proven to be a potentially useful therapeutic tool in the reduction of graft rejection. Its benefits are based on its direct actions as a free radical scavenger as well as its indirect antioxidative actions in the stimulation of the cellular antioxidant defense system. Moreover, it has significant anti-inflammatory activity. Melatonin has been found to improve the beneficial effects of preservation fluids when they are enriched with the indoleamine. This article reviews the experimental evidence that melatonin is useful in reducing graft failure, especially in cardiac, bone, otolaryngology, ovarian, testicular, lung, pancreas, kidney, and liver transplantation.