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In this work, we propose a multi-level protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged Elastic Band (NEB) method driven by a cheap electronic structure method. Forces recalculated at the more accurate electronic structure theory for a set of points on the path are fitted with a machine learning technique (in our case symmetric gradient domain machine learning or sGDML) to produce a semi-local reactive potential energy surface (PES), embracing reactants, products and transition state (TS) regions. This approach has been successfully applied to a unimolecular (Bergman cyclization of enediyne) and a bimolecular (SN2 substitution) reaction. In particular, we demonstrate that with only 50 to 150 energy-force evaluations with the accurate reference methods (here complete-active-space self-consistent field, CASSCF, and coupled-cluster singles and doubles, CCSD) it is possible to construct a semi-local PES giving qualitative agreement for stationary-point geometries, intrinsic reaction coordinates and barriers. Furthermore, we find a qualitative agreement in vibrational frequencies and reaction rate coefficients. The key aspect of the method's performance is its multi-level nature, which not only saves computational effort but also allows extracting meaningful information along the reaction path, characterized by zero gradients in all but one direction. Agnostic to the nature of the TS and computationally economic, the protocol can be readily automated and routinely used for mechanistic reaction studies. [ABSTRACT FROM AUTHOR]

Chemical reactions between Be+ ions and H2 molecules have significance in the fields of ultracold chemistry and astrophysics, but the corresponding dynamics studies on the ground-state reaction have not been reported because of the lack of a global potential energy surface (PES). Herein, a globally accurate ground-state BeH2+ PES is constructed using the neural network model based on 18,657 ab initio points calculated by the multi-reference configuration interaction method with the aug-cc-PVQZ basis set. On the newly constructed PES, the state-to-state quantum dynamics calculations of the Be+(2S) + H2(v0 = 0; j0 = 0) and Be+(2S) + D2(v0 = 0; j0 = 0) reactions are performed using the time-dependent wave packet method. The calculated results suggest that the two reactions are dominated by the complex-forming mechanism and the direct abstraction process at relatively low and high collision energies, respectively, and the isotope substitution has little effect on the reaction dynamics characteristics. The new PES can be used to further study the reaction dynamics of the BeH2+ system, such as the effects of rovibrational excitations and alignment of reactant molecules, and the present dynamics data could provide an important reference for further experimental studies at a finer level. [ABSTRACT FROM AUTHOR]

In this study, the mechanism of the reaction between 4-methyl aniline and hydroxyl free radicals was computed using the M06-2X and CCSD(T) methods, along with the 6-311++G(3df,2p) basis set. The kinetics of the reaction were calculated utilizing the transition state theory and the microcanonical Rice–Ramsperger–Kassel–Marcus theory. The calculated results revealed that NH-C6H4-CH3 was the key product of the system. The total rate coefficient of the system, k_total = 2.04 × 10−18 T2.07 exp[(11.2 kJ/mol)/RT] cm3/s, was found under the 300–2000 K interval, with P = 760 Torr. At the ambient conditions, the velocity of this reaction was about ten times larger than that of the reaction between C6H5CH3 and hydroxyl free radicals, but it was smaller than the aniline + OH rate. [ABSTRACT FROM AUTHOR]

The impact of the chalcogen atomic electronegativity (O, S, and Se atoms) of new organic molecules on excited-state dynamical reactions is self-evident. Inspired by this kind of distinguished photochemical characteristic, in this work, we performed a computational investigation of chalcogen-substituted 3,6-bis(4,5-dihydroxyoxazo-2-yl)benzene-1,2-diol (BDYBD) derivatives (i.e., BDYBD-O, BDYBD-S, and BDYBD-Se). In this paper, we pay close attention to characteristic BDYBD derivatives that contain intramolecular double hydrogen bonds (O1–H2···N3 and O4–H5···N6). The main goal of this study was to explore how changes in atomic electronegativity affect the way hydrogen bonds interact and how excited molecules affect transfer protons. We go into further detail in the main text of the paper. By fixing our attention to geometrical variations and infrared (IR) vibrational spectra between the S0 and S1 states, exploring hydrogen bonding behaviors using the core-valence bifurcation (CVB) index, and simulating hydrogen bonding energy (EHB) via the atom in molecule (AIM) method, we clarified the photo-induced strengthened dual hydrogen bonding interactions that facilitate the excited-state dual-proton transfer (ESDPT) behavior of BDYBD derivatives. The reorganization of charge stemming from photoexcitation further verifies the tendencies of ESDPT reactions. We relied on constructing potential energy surfaces (PESs) by adopting a restrictive optimization approach, and herein, we finally clarify the gradual ESDPT mechanism of BDYBD derivatives. Particularly, we confirm that the variation in chalcogen atomic electronegativity has a regulatory effect on the ESDPT behavior of BDYBD derivatives; that is, the lower the atomic electronegativity, the more favorable it is for the gradual ESDPT reaction. [ABSTRACT FROM AUTHOR]

A theoretical approach based on Periodic Boundary Conditions (PBC) and a Linear Combination of Atomic Orbitals (LCAO) in the framework of the density functional theory (DFT) is used to investigate the molecular mechanism that rules the piezoelectric behavior of poly(vinylidene fluoride) (PVDF) polymer in the crystalline β-phase. We present several computational tests highlighting the peculiar electrostatic potential energy landscape the polymer chains feel when they change their orientation by a rigid rotation in the lattice cell. We demonstrate that a rotation of the permanent dipole through chain rotation has a rather low energy cost and leads to a lattice relaxation. This justifies the macroscopic strain observed when the material is subjected to an electric field. Moreover, we investigate the effect on the molecular geometry of the expansion of the lattice parameters in the (a, b) plane, proving that the rotation of the dipole can take place spontaneously under mechanical deformation. By band deconvolution of the IR and Raman spectra of a PVDF film with a high content of β-phase, we provide the experimental phonon wavenumbers and relative band intensities, which we compare against the predictions from DFT calculations. This analysis shows the reliability of the LCAO approach, as implemented in the CRYSTAL software, for calculating the vibrational spectra. Finally, we investigate how the IR/Raman spectra evolve as a function of inter-chain distance, moving towards the isolated chain limit and to the limit of a single crystal slab. The results show the relevance of the inter-molecular interactions on the vibrational dynamics and on the electro-optical features ruling the intensity pattern of the vibrational spectra. [ABSTRACT FROM AUTHOR]

The fundamental unit for comprehending the physicochemical properties of water, the Zundel cation configuration H5O2+, has yet to be exhaustively evaluated in terms of its interaction with terahertz (THz) electromagnetic waves, characterized by sub-picosecond oscillation periods or pulse widths. In this study, we embark on an investigation of the broad resonance and high-field nonresonant effects of intense THz radiation (ITR) on Zundel cations, utilizing a multifaceted methodological approach that includes density functional theory (DFT) calculations, finite difference time domain (FDTD) algorithm of the Schrödinger equation, and ab initio molecular dynamics (AIMD) simulations. Our analysis reveals that the proton potential energy surface (PES) varies in response to the external electric (E) field, suggesting that the interaction frequency of the central proton with the electromagnetic wave encompasses the THz band. This resonance effect is associated with proton behavior that may oscillate or demonstrate periodic tunneling. Moreover, our work uncovers the high-field nonresonant effects of ITR on Zundel cations, manifesting in proton transfer and vibrational excitation of the system. Our findings contribute to the understanding of the interaction between Zundel species and electromagnetic waves by presenting a microscopic view of proton transfer as informed by wavefunction evolution. [ABSTRACT FROM AUTHOR]

Photophysical properties of a series of bis(arylydene)cycloalkanone dyes with various donor substituents are studied using quantum chemistry. Their capacity for luminescence and nonradiative relaxation through trans–cis isomerization is related to their structure, in particular, to the donor capacity of the substituents and the degree of conjugation due to the central cycloalkanone moiety. It is shown that cyclohexanone central moiety introduces distortions and disrupts the conjugation, thus leading to a nonmonotonic change in their properties. The increasing donor capacity of the substituents causes increase in the HOMO energy (rise in the oxidation potential) and decrease in the HOMO–LUMO gap, which results in the red shift of the absorption spectra. The ability of the excited dye to relax through fluorescence or through trans–cis isomerization is governed by the height of the barrier between the Franck–Condon and S1–S0 conical intersection regions on the potential energy surface of the lowest π-π* excited state. This barrier also correlates with the donor capacity of the substituents and the degree of conjugation between the central and donor moieties. The calculated fluorescence and trans–cis isomerization rates are in good agreement with the observed fluorescence quantum yields. [ABSTRACT FROM AUTHOR]

Inspired by the distinguished regulated photochemical and photophysical properties of 2-(2′-hydroxyphenyl)benzazole derivatives, in this work, the novel bis(2′-benzothiazolyl)hydroquinone (BBTHQ) fluorophore is explored, looking at its photo-induced behaviors associated with different substituted atomic electronegativities, i.e., BBTHQ-SO, BBTHQ-SS and BBTHQ-Se compounds. From the structural changes, infrared (IR) vibrational variations and simulated core-valence bifurcation (CVB) indexes for the dual hydrogen bonds for the three BBTHQ derivatives, we see that low atomic electronegativity could be conducive to enhancing hydrogen bonding effects in the S1 state. Particularly, the O4-H5⋯N6 of BBTHQ-SO and the O1-H2⋯N3 of BBTHQ-SSe could be strengthened to be more intensive in the S1 state, respectively. Looking into the charge recombination induced by photoexcitation, we confirm a favorable ESDPT trend deriving from the charge reorganization of the dual hydrogen bonding regions. By constructing the potential energy surfaces (PESs) along with the ESDPT paths for the BBTHQ-SO, BBTHQ-SS and BBTHQ-Se compounds, we not only unveil stepwise ESDPT behaviors, but also present an atomic electronegativity-regulated ESDPT mechanism. [ABSTRACT FROM AUTHOR]

In this work the rovibrational spectrum of the acetylide anion HCC − is investigated using high-level electronic structure methods and variational rovibrational calculations. Using a composite approach the potential energy surface and dipole surface is constructed from explicitly correlated coupled-cluster accounting for corrections due to core-valence correlation, scalar relativistic effects and higher-order excitation effects. Previous approaches for approximating the latter are critically evaluated. Employing the composite potential, accurate spectroscopic parameters determined from variational calculations are presented. In comparison to the few available reference data the present results show excellent agreement with ground state rotational constants within 0.005% of the experimental value. Intensities determined from the variational calculations suggest the bending fundamental transition ν 2 around 510 cm − 1 to be the best target for detection. The rather weak CD stretching fundamental ν 1 in deuterated isotopologues show a second-order resonance with the (0 , 2 0 , 1) state and the consequences are discussed in some detail. The spectroscopic parameters and band intensities provided for a number of vibrational bands in isotopologues of the acetylide anion should facilitate future spectroscopic investigations. [ABSTRACT FROM AUTHOR]

The LiNa2 reactive system has recently received great attention in the experimental study of ultracold chemical reactions, but the corresponding theoretical calculations have not been carried out. Here, we report the first globally accurate ground-state LiNa2 potential energy surface (PES) using a Gaussian process model based on only 1776 actively selected high-level ab initio training points. The constructed PES had high precision and strong generalization capability. On the new PES, the quantum dynamics calculations on the Li(2S) + Na2(v = 0, j = 0) → LiNa + Na reaction were carried out in the 0.001–0.01 eV collision energy range using an improved time-dependent wave packet method. The calculated results indicate that this reaction is dominated by a complex-forming mechanism at low collision energies. The presented dynamics data provide guidance for experimental research, and the newly constructed PES could be further used for ultracold reaction dynamics calculations on this reactive system. [ABSTRACT FROM AUTHOR]

The hydrogen abstraction reaction OH + H2S→H2O + SH plays an important role in acid rain formation, air pollution and climate change. In this work, the product energy disposals of the reaction and its isotopic variants OD + H2S and OD + D2S are calculated on a new ab-initio-based ground electronic state potential energy surface (PES) using the quasi-classical trajectory method. The PES is developed by fitting a total of 72,113 points calculated at the level of UCCSD(T)-F12a/aug-cc-pVTZ and using the fundamental invariant-neural network method, resulting in a total RMSE of 4.14 meV. The product H2O formed in the OH + H2S reaction at 298 K is found to be largely populated in the first overtone states of its symmetric and asymmetric stretching modes, while the vibrational distributions of the products HOD and D2O in the isotopically substituted reactions are visibly different. The computed product vibrational state distributions agree reasonably well with experimental results and are rationalized by the sudden vector projection model. [ABSTRACT FROM AUTHOR]

Here, it is shown that the M3B12 (M = Cu-Au) clusters' global minima consist of an elongated planar B12 fragment connected by an in-plane linear M3 fragment. This result is striking since this B12 planar structure is not favored in the bare cluster, nor when one or two metals are added. The minimum energy structures were revealed by screening the potential energy surface using genetic algorithms and density functional theory calculations. Chemical bonding analysis shows that the strong electrostatic interactions with the metal compensate for the high energy spent in the M3 and B12 fragment distortion. Furthermore, metals participate in the delocalized π-bonds, which infers an aromatic character to these species. [ABSTRACT FROM AUTHOR]

The inelastic scattering of N2 molecules from silica surfaces, taken at 100 K, has been investigated by adopting a semiclassical collision model in conjunction with the appropriate treatment of the long-range interaction forces. Such forces promote the formation of the precursor state that controls all basic elementary processes occurring at the gas–surface interphase. The probabilities for the different elementary surface processes triggered by quartz are determined and compared with those recently obtained for another silica polymorph (cristobalite). In addition, the final roto-vibrational distributions of N2 molecules undergoing inelastic scattering have been characterized. N2 molecules, impinging on both considered surfaces in low-medium vibrational states, preserve the initial vibrational state, while those inelastically scattered are rotationally excited and translationally colder. The surface temperature effect, investigated by raising the temperature itself from 100 K up to 1000 K, emerges more sharply for the cristobalite polymorph, mainly for the molecules impinging in the ground roto-vibrational state and with low collision energies. [ABSTRACT FROM AUTHOR]

Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections. [ABSTRACT FROM AUTHOR]

This paper studies the mechanism of electrochemically induced carbon–bromine dissociation in 1-Br-2-methylnaphalene in the reduction regime. In particular, the bond dissociation of the relevant radical anion is disassembled at a molecular level, exploiting quantum mechanical calculations including steady-state, equilibrium and dissociation dynamics via dynamic reaction coordinate (DRC) calculations. DRC is a molecular-dynamic-based calculation relying on an ab initio potential surface. This is to achieve a detailed picture of the dissociation process in an elementary molecular detail. From a thermodynamic point of view, all the reaction paths examined are energetically feasible. The obtained results suggest that the carbon halogen bond dissociates following the first electron uptake follow a stepwise mechanism. Indeed, the formation of the bromide anion and an organic radical occurs. The latter reacts to form a binaphthalene intrinsically chiral dimer. This paper is respectfully dedicated to Professors Anny Jutand and Christian Amatore for their outstanding contribution in the field of electrochemical catalysis and electrosynthesis. [ABSTRACT FROM AUTHOR]

This paper is a detailed review of the chemistry of medium-size reactive systems using the following hydrogen abstraction reactions with ethane, X + C2H6 → HX + C2H5; X ≡ H, F(2P), Cl(2P), O(3P) and OH, and focusing attention mainly on the theoretical developments. These bimolecular reactions range from exothermic to endothermic systems and from barrierless to high classical barriers of activation. Thus, the topography of the reactive systems changes from reaction to reaction with the presence or not of stabilized intermediate complexes in the entrance and exit channels. The review begins with some reflections on the inherent problems in the theory/experiment comparison. When one compares kinetics or dynamics theoretical results with experimental measures, one is testing both the potential energy surface describing the nuclei motion and the kinetics or dynamics method used. Discrepancies in the comparison may be due to inaccuracies of the surface, limitations of the kinetics or dynamics methods, and experimental uncertainties that also cannot be ruled out. The paper continues with a detailed review of some bimolecular reactions with ethane, beginning with the reactions with hydrogen atoms. The reactions with halogens present a challenge owing to the presence of stabilized intermediate complexes in the entrance and exit channels and the influence of the spin-orbit states on reactivity. Reactions with O(3P) atoms lead to three surfaces, which is an additional difficulty in the theoretical study. Finally, the reactions with the hydroxyl radical correspond to a reactive system with ten atoms and twenty-four degrees of freedom. Throughout this review, different strategies in the development of analytical potential energy surfaces describing these bimolecular reactions have been critically analyzed, showing their advantages and limitations. These surfaces are fitted to a large number of ab initio calculations, and we found that a huge number of calculations leads to accurate surfaces, but this information does not guarantee that the kinetics and dynamics results match the experimental measurements. [ABSTRACT FROM AUTHOR]

Working cycle of conventional light-driven molecular rotary motors (LDMRMs), especially Feringa-type motors, usually have four steps, two photoisomerization steps, and two thermal helix inversion (THI) steps. THI steps hinder the ability of the motor to operate at lower temperatures and limit the rotation speed of LDMRMs. A three-stroke LDMRM, 2-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDIY), is proposed, which is capable of completing an unidirectional rotation by two photoisomerization steps and one thermal helix inversion step at room temperature. On the basis of trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EM nonadiabatic photoisomerization dynamics of DDIY were systematically analyzed. Quantum yields of EP→ZP and ZP→EM photoisomerization of DDIY are ca. 34% and 18%, respectively. Both EP→ZP and ZP→EM photoisomerization processes occur on an ultrafast time scale (ca. 100–300 fs). This three-stroke LDMRM may stimulate further research for the development of new families of more efficient LDMRMs. [ABSTRACT FROM AUTHOR]

Here, it is shown that the M 3 B 12 (M = Cu-Au) clusters' global minima consist of an elongated planar B 12 fragment connected by an in-plane linear M 3 fragment. This result is striking since this B 12 planar structure is not favored in the bare cluster, nor when one or two metals are added. The minimum energy structures were revealed by screening the potential energy surface using genetic algorithms and density functional theory calculations. Chemical bonding analysis shows that the strong electrostatic interactions with the metal compensate for the high energy spent in the M 3 and B 12 fragment distortion. Furthermore, metals participate in the delocalized π-bonds, which infers an aromatic character to these species.

GAGs exhibit a high level of conformational and configurational diversity, which remains untapped in terms of the recognition and modulation of proteins. Although GAGs are suggested to bind to more than 800 biologically important proteins, very few therapeutics have been designed or discovered so far. A key challenge is the inability to identify, understand and predict distinct topologies accessed by GAGs, which may help design novel protein-binding GAG sequences. Recent studies on chondroitin sulfate (CS), a key member of the GAG family, pinpointing its role in multiple biological functions led us to study the conformational dynamism of CS building blocks using molecular dynamics (MD). In the present study, we used the all-atom GLYCAM06 force field for the first time to explore the conformational space of all possible CS building blocks. Each of the 16 disaccharides was solvated in a TIP3P water box with an appropriate number of counter ions followed by equilibration and a production run. We analyzed the MD trajectories for torsional space, inter- and intra-molecular H-bonding, bridging water, conformational spread and energy landscapes. An in-house phi and psi probability density analysis showed that 1→3-linked sequences were more flexible than 1→4-linked sequences. More specifically, phi and psi regions for 1→4-linked sequences were held within a narrower range because of intra-molecular H-bonding between the GalNAc O5 atom and GlcA O3 atom, irrespective of sulfation pattern. In contrast, no such intra-molecular interaction arose for 1→3-linked sequences. Further, the stability of 1→4-linked sequences also arose from inter-molecular interactions involving bridged water molecules. The energy landscape for both classes of CS disaccharides demonstrated increased ruggedness as the level of sulfation increased. The results show that CS building blocks present distinct conformational dynamism that offers the high possibility of unique electrostatic surfaces for protein recognition. The fundamental results presented here will support the development of algorithms that help to design longer CS chains for protein recognition. [ABSTRACT FROM AUTHOR]

The potential energy surfaces (PES) for the reaction of 1-bromo-3,3,3- trifluoropropene (CF3CHCBrH) with hydroxyl (OH) free radicals is probed theoretically at the CCSD/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of theory. All the possible stationary and first-order saddle points along the reaction paths were verified by the vibrational analysis. The calculations account for all the product channels. Based on the calculated CCSD/aug-cc-pVDZ potential energy surface, the possible reaction mechanism is discussed. Six distinct reaction pathways of 1-bromo-3,3,3-trifluoropropene (BTP) with OH are investigated. The geometries, reaction enthalpies and energy barriers are determined. Canonical transition-state theory with Wigner tunneling correction was used to predict the rate constants for the temperature range of 290-3,000 K without any artificial adjustment, and the computed rate constants for elementary channels can be accurately fitted with three-parameter Arrhenius expressions. OH addition reaction channel and the H atom abstraction channels related to the carbon-carbon double bond are found to be the main reaction channels for the reaction of 1-bromo-3,3,3-trifluoropropene (CF3CHCBrH) with hydroxyl (OH) free radicals while the products leading to CF3CHCH + BrOH and COHF2CHCBrH + F play a negligible role. [ABSTRACT FROM AUTHOR]

Knowledge of energy exchange rate constants in inelastic collisions is critically required for accurate characterization and simulation of several processes in gaseous environments, including planetary atmospheres, plasma, combustion, etc. Determination of these rate constants requires accurate potential energy surfaces (PESs) that describe in detail the full interaction region space and the use of collision dynamics methods capable of including the most relevant quantum effects. In this work, we produce an extensive collection of vibration-to-vibration (V–V) and vibration-to-translation/rotation (V–T/R) energy transfer rate coefficients for collisions between CO and N 2 molecules using a mixed quantum-classical method and a recently introduced (A. Lombardi, F. Pirani, M. Bartolomei, C. Coletti, and A. Laganà, Frontiers in chemistry, 7, 309 (2019)) analytical PES, critically revised to improve its performance against ab initio and experimental data of different sources. The present database gives a good agreement with available experimental values of V–V rate coefficients and covers an unprecedented number of transitions and a wide range of temperatures. Furthermore, this is the first database of V–T/R rate coefficients for the title collisions. These processes are shown to often be the most probable ones at high temperatures and/or for highly excited molecules, such conditions being relevant in the modeling of hypersonic flows, plasma, and aerospace applications. [ABSTRACT FROM AUTHOR]

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se–S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies. [ABSTRACT FROM AUTHOR]

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm−1 (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species. [ABSTRACT FROM AUTHOR]

Based on a combination of valence-bond and molecular mechanics functions which were fitted to high-level ab initio calculations, we constructed an analytical full-dimensional potential energy surface, named PES-2020, for the hydrogen abstraction title reaction for the first time. This surface is symmetrical with respect to the permutation of the three hydrogens in ammonia, it presents numerical gradients and it improves the description presented by previous theoretical studies. In order to analyze its quality and accuracy, stringent tests were performed, exhaustive kinetics and dynamics studies were carried out using quasi-classical trajectory calculations, and the results were compared with the available experimental evidence. Firstly, the properties (geometry, vibrational frequency and energy) of all stationary points were found to reasonably reproduce the ab initio information used as input; due to the complicated topology with deep wells in the entrance and exit channels and a "submerged" transition state, the description of the intermediate complexes was poorer, although it was adequate to reasonably simulate the kinetics and dynamics of the title reaction. Secondly, in the kinetics study, the rate constants simulated the experimental data in the wide temperature range of 25–700 K, improving the description presented by previous theoretical studies. In addition, while previous studies failed in the description of the kinetic isotope effects, our results reproduced the experimental information. Finally, in the dynamics study, we analyzed the role of the vibrational and rotational excitation of the CN(v,j) reactant and product angular scattering distribution. We found that vibrational excitation by one quantum slightly increased reactivity, thus reproducing the only experimental measurement, while rotational excitation strongly decreased reactivity. The scattering distribution presented a forward-backward shape, associated with the presence of deep wells along the reaction path. These last two findings await experimental confirmation. [ABSTRACT FROM AUTHOR]

The oxidative decarboxylation of the iron(II) α-hydroxy acid (mandelic acid) complex model, biomimetic of Rieske dioxygenase, has been investigated at the density functional level. The explored mechanism sheds light on the role of the α-hydroxyl group on the dioxygen activation. The potential energy surfaces have been explored in different electronic spin states. The rate-determining step of the process is the proton transfer. The oxidative decarboxylation preferentially takes place on the quintet state. [ABSTRACT FROM AUTHOR]

The conversion reaction of NO to NO3− ion catalyzed by the end-on [Cr(III)(n-TMC)(O2)(Cl)]+ superoxo and side-on [Cr(IV)(n-TMC)(O2)(Cl)]+ peroxo non-heme complexes (n = 12, 13, 14 and 15), which are biomimetic systems of nitric oxide dioxygenases (NODs), has been explored using a computational protocol in the framework of density functional theory. Results show that the potential energy profiles for the studied reactions lie above the reagent energies, regardless of the used catalyst. Both the O-O bond breaking in the biomimetics and the NO3− ion formation require low energy barriers suggesting an efficient catalytic power of the studied systems. The rate-determining step depends on ligand size. [ABSTRACT FROM AUTHOR]

We built a full-dimensional analytical potential energy surface of the ground electronic state of Li2H from ca. 20,000 ab initio multi-reference configuration interaction calculations, including core–valence correlation effects. The surface is flexible enough to accurately describe the three dissociation channels: Li (2s 2S) + LiH (1Σ+), Li2 (1Σg+) + H (1s 2S) and 2Li (2s 2S) + H (1s 2S). Using a local fit of this surface, we calculated pure (J = 0) vibrational states of Li2H up to the barrier to linearity (ca. 3400 cm−1 above the global minimum) using a vibrational self-consistent field/virtual state configuration interaction method. We found 18 vibrational states below this barrier, with a maximum of 6 quanta in the bending mode, which indicates that Li2H could be spectroscopically observable. Moreover, we show that some of these vibrational states are highly correlated already ca. 1000 cm−1 below the height of the barrier. We hope these calculations can help the assignment of experimental spectra. In addition, the first low-lying excited states of each B1, B2 and A2 symmetry of Li2H were characterized. [ABSTRACT FROM AUTHOR]

We built a full-dimensional analytical potential energy surface of the ground electronic state of Li₂H from ca. 20,000 ab initio multi-reference configuration interaction calculations, including core⁻valence correlation effects. The surface is flexible enough to accurately describe the three dissociation channels: Li (2s ²S) + LiH (¹Σ⁺), Li₂ (¹Σ g ⁺) + H (1s ²S) and 2Li (2s ²S) + H (1s ²S). Using a local fit of this surface, we calculated pure ( J = 0) vibrational states of Li₂H up to the barrier to linearity (ca. 3400 cm -1 above the global minimum) using a vibrational self-consistent field/virtual state configuration interaction method. We found 18 vibrational states below this barrier, with a maximum of 6 quanta in the bending mode, which indicates that Li₂H could be spectroscopically observable. Moreover, we show that some of these vibrational states are highly correlated already ca. 1000 cm -1 below the height of the barrier. We hope these calculations can help the assignment of experimental spectra. In addition, the first low-lying excited states of each B₁, B₂ and A₂ symmetry of Li₂H were characterized.