Impact of Deuteration and Temperature on Furan Ring Dynamics.

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories.

About the Aromaticity of symm-Triaminotrinitrobenzene.

Aromaticity and structural features of the isolated symm-triaminotrinitrobenzene (TATB) were examined using the nonempirical ab initio quantum chemical method and molecular dynamics at the Car-Parrinello level. Different criteria of the aromaticity were combined with the study of conformational flexibility of molecule and analysis of the electron density distribution. It was found that the cooperative effect of the resonance-assisted hydrogen bonds results in the ultimate decreasing aromaticity of the benzene ring in TATB.

Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car-parrinello and path integral molecular dynamics.

Car-Parrinello and path integrals molecular dynamics (CPMD and PIMD) simulations were carried out for the 10π-electron aromatic systems: 2-hydroxy-2,4,6-cycloheptatrien-1-one, commonly known as Tropolone (I) and 2-hydroxy-2,4,6-cycloheptatriene-1-thione, called Thiotropolone (II) in vacuo and in the solid state. The extremely fast proton transfer (FPT) and "prototropy" tautomerism in the keto-enol (thione-enethiol) systems have been analyzed on the basis of CPMD and PIMD methods level. Comparisons of two-dimensional (2D) free-energy landscapes of reaction coordinate δ-parameter and R or R distances shows that the OH… tautomer to be more favorable in the Thiotropolone.

Car-Parrinello and Path Integral Molecular Dynamics Study of the Proton Transfer in the Intramolecular Hydrogen Bonds in the Ketohydrazone-Azoenol System.

Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD) simulations were carried out for 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) (Sudan I) in vacuo and in the solid state at 298 K. The fast proton transfer (FPT) and tautomerism in the ketohydrazone-azoenol systems have been analyzed on the basis of CPMD and PIMD methods level. The two-dimensional free-energy landscape of reaction coordinate δ-parameter and R distances shows the NH tautomer to be more favorable in the gas phase as well as in the solid state according to the CP and PI results, respectively.

Hydrogen detachment driven by a repulsive 1πσ* state - an electron localization function study of 3-amino-1,2,4-triazole.

Electron localization function analysis reveals the details of a charge induced hydrogen detachment mechanism of 3-amino-1,2,4-triazole, identified recently to be responsible for phototautomerization of the molecule. In this process vertical excitation to the πσ* state is followed by the barrier-less migration of a H atom along the N-H bond toward the conical intersection with the S0 ground state. The most striking feature revealed for the πσ* state is partial ejection of σ* electrons outside the molecule, even beyond the NH group, at the Franck-Condon point.

Experimental and Theoretical Study of the Kinetics and Mechanism of the Reaction of Chlorine Atoms with CHCHClCH and CDCDClCD.

The overall rate constants for H-abstraction (k) from CHCHClCH and D-abstraction (k) from CDCDClCD by chlorine atoms in the temperature range 298-528.5 K were determined and are described by the expressions: k = (3.52 ± 0.

Matrix-isolation and computational study of the HXeY⋯H2O complexes (Y = Cl, Br, and I).

The HXeY⋯H2O complexes (Y = Cl, Br, and I) are studied theoretically and experimentally. The calculations at the CCSD(T)/def2-TZVPPD level of theory predict two stable structures for Y = Cl and Br and one structure for Y = I, with interaction energies up to about -7 kcal mol(-1). In the experiments, we have identified several infrared absorption bands originating from the H-Xe stretching mode of these complexes in a xenon matrix.

Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone.

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations. A study on intramolecular hydrogen bonding in 1-phenyl-1,3-butadione (I) and 1-deuteroxy-2-deutero-1-phenylbut-1-en-3-one (II) crystals has been carried out at 160 K and 300 K on the CPMD method level and at 300 K on the PIMD method level. The analysis of the two-dimensional free-energy landscape of reaction coordinate δ-parameter and ROO distances shows that the hydrogen (deuter) between the two oxygen atoms adopts a slightly asymmetrical position in the single potential well.

Electron localization function study on the chemical bonding in a real space for tetrahedrane, cubane, adamantane, and dodecahedrane and their perfluorinated derivatives and radical anions.

The nature of chemical bonding in caged cycloalkanes CnXn, CnFn(-•), (n = 4, 8, 20; X = H, F), and C10X16, C10F16(-•), (X = H, F) has been investigated using topological analysis of the ELF function, electron density, and the Laplacian of electron density at density functional theory (DFT) level. The bonding analysis performed for the perfluorinated radical anion of dodecahedrane (C20F20(-•)), bestowing an additional electron, shows an unexpected local maximum of the ELF inside the carbon cage. The presence of such an attractor confirms the sigma stellation concept presented by Irikura (J.

Effects of xenon insertion into hydrogen bromide. Comparison of the electronic structure of the HBr···CO2 and HXeBr···CO2 complexes using quantum chemical topology methods: electron localization function, atoms in molecules and symmetry adapted perturbation theory.

Quantum chemistry methods have been applied to study the influence of the Xe atom inserted into the hydrogen-bromine bond (HBr → HXeBr), particularly on the nature of atomic interactions in the HBr···CO2 and HXeBr···CO2 complexes. Detailed analysis of the nature of chemical bonds has been carried out using topological analysis of the electron localization function, while topological analysis of electron density was used to gain insight into the nature of weak nonbonding interactions. Symmetry-adapted perturbation theory within the orbital approach was applied for greater understanding of the physical contributions to the total interaction energy.

Reaction of atomic hydrogen with formic acid.

We study the reaction of atomic hydrogen with formic acid and characterize the radical products using IR spectroscopy in a Kr matrix and quantum chemical calculations. The reaction first leads to the formation of an intermediate radical trans-H2COOH, which converts to the more stable radical trans-cis-HC(OH)2via hydrogen atom tunneling on a timescale of hours at 4.3 K.

Tuning of character of the N-O bond in HONO from covalent to protocovalent by different types of intramolecular interactions.

Quantum-chemical calculations of the H-O-N=O molecule in the equilibrium and transition states and the complexes of the HONO with BH3, study of the intramolecular interactions using NBO theory, and investigation of the electron distribution on the basis of topological analysis of the ELF function clearly indicate the influence of the n-π* conjugation and n-σ* hyperconjugation interactions on a par with exchange repulsion of lone pairs the character of the N-O bond. It is shown that repulsion between lone pairs of oxygen and nitrogen atoms causes the elongation of the N-O bond only but character of this bond remains covalent. The interaction between lone pair of the terminal oxygen atom and antibonding orbital of the N-O bond (n-σ* hyperconjugation) coincides with influence of repulsion and reinforces it changing the character of the N-O bond from covalent to protocovalent.

Spectroscopic and computational characterization of the HCO···H2O complex.

The complexes of HCO with water are prepared in a Kr matrix and characterized by IR spectroscopy with the aid of ab initio calculations. The calculations at the UCCSD(T)/aug-cc-pVTZ level of theory predict three structures of the HCO···H2O complex. In the "linear" structure I, a hydrogen atom of water interacts with the oxygen atom of HCO.

Investigations of the very short hydrogen bond in the crystal of nitromalonamide via Car-Parrinello and path integral molecular dynamics.

In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account.

FONO: a difficult case for theory. The ELF and ELI-D topological studies on the chemical bonding using correlated wavefunctions.

The complicated nature of the chemical bonding in cis and trans isomers of F-O-N=O is discussed based on the results obtained from the topological analysis of electron localization function (η) (ELF), electron localizability index (Y(D)(σ)), and electron density (ρ). The calculations have been performed for correlated wavefunctions using the CCSD and CASSCF methods. The F-O1 bond with non-bonding basins, V(F) and V(')(O1), belongs to the protocovalent type (η,Y(D)(σ)) and its total population ranges between 0.

Experimental and computational study of the HXeI···HY complexes (Y = Br and I).

The complexes of HXeI with hydrogen halides HY (Y = Br and I) are studied computationally and experimentally in a xenon matrix. The calculations at the CCSD(T)∕def2-TZVPPD level of theory predict several energy minima for the HXeI···HY complexes with interaction energies from -4.69 to -0.

Ab Initio Molecular Dynamics Study of the Very Short O-H···O Hydrogen Bonds in the Condensed Phases.

In this paper are presented the results of theoretical studies of the structure and proton motion in very short O···O intramolecular hydrogen bonds in two molecular crystals. A comparison was conducted between 3-cyano-2,4-pentanedione (I) and 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione (II) in the solid state. The dynamics of proton motion in the O-H···O hydrogen bond were investigated in he NVT ensemble at 298 and 50 K, respectively, for crystals I and II using Car-Parrinello and path integral molecular dynamics.

Entropy versus aromaticity in the conformational dynamics of aromatic rings.

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

High kinetic stability of HXeBr upon interaction with carbon dioxide: HXeBr···CO2 complex in a xenon matrix and HXeBr in a carbon dioxide matrix.

We investigate the conditions when noble-gas hydrides can be found in real environments and report on the preparation and identification of the HXeBr···CO(2) complex in a xenon matrix and HXeBr in a carbon dioxide matrix. The H-Xe stretching mode of the HXeBr···CO(2) complex in a xenon matrix is observed at 1557 cm(-1), showing a spectral shift of +53 cm(-1) from the HXeBr monomer. The calculations at the CCSD(T)/aug-cc-pVTZ-PP(Xe,Br) level of theory give two stable structures for the HXeBr···CO(2) complex with frequency shifts of +55 and +103 cm(-1), respectively.

On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment.

Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the acetic acid dimer in the gas phase.

In the paper are described studies of the double proton transfer (DPT) processes in the cyclic dimer of acetic acid in the gas phase using Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD). Structures, energies and proton trajectories have been determined. The results show the double proton transfer in 450 K.

Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO.

The ground-state electronic structure of peroxynitrous acid (HOONO) and its singlet biradicaloid form (HO···ONO) have been studied using topological analysis of the electron localization function (ELF), together with the electron localizability indicator (ELI-D), at the DFT (B3LYP, M05, M052X, and M06), CCSD, and CASSCF levels. Three isomers of HOONO (cis-cis, cis-perp, and trans-perp) have been considered. The results show that from all functionals applied, only B3LYP yields the correct geometrical structure.

Proton transfer dynamics in the propionic acid dimer from path integral molecular dynamics calculations.

The double proton transfer process in the cyclic dimer of propionic acid in the gas phase was studied using a path integral molecular dynamics method. Structures, energies and proton trajectories were determined. Very large amplitude motions of the skeleton of a propionic acid molecule were observed during the simulations, and almost free rotation of the C(2)H(5) group around the C(α)-C bond.

Ab initio and quantum chemical topology studies on the isomerization of HONO to HNO2. Effect of the basis set in QCT.

The article focus on the isomerization of nitrous acid HONO to hydrogen nitryl HNO(2). Density functional (B3LYP) and MP2 methods, and a wide variety of basis sets, have been chosen to investigate the mechanism of this reaction. The results clearly show that there are two possible paths: 1) Uncatalysed isomerisation, trans-HONO --> HNO(2), involving 1,2-hydrogen shift and characterized by a large energetic barrier 49.

Quantum chemical topology study on the electronic structure of cis- and trans-FONO.

The electronic structure of cis- and trans-FONO has been studied using topological analysis of the electron localization function at the B3LYP/aug-cc-pVTZ computational level. In cis-FONO with "normal" F-O bond length (1.428-1.