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studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods.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. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.

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. Values of the HOMA index indicate that it could be classified as low-aromatic in equilibrium state at zero temperature but completely nonaromatic at room temperature. An extremely high flexibility of the molecule is also not typical for aromatic rings. The electron delocalization in H-bonded O═N-C═C-N-H quasi-aromatic rings was found to be greater than that in the benzene ring of 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 RO…O or RO…S distances shows that the OH… tautomer to be more favorable in the Thiotropolone. The hydrogen between the oxygen and the sulfur atoms adopts a starkly asymmetrical position in the double potential well. The values of the energy barriers for the FPT were calculated and suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the 2D average index of π-delocalization 〈λ〉 landscape of time evolutions of RO1…O2 and RC7O2 or RC7S1 distances for the both crystals indicate that hydrogen bonds in the crystals of Tropolone (I) and Thiotropolone (II) have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds and also low-barrier hydrogen bonds. In the crystal of the Thiotropolone (II), we found the hydrogen bond OH…S existing without the equilibrium of the two tautomers whereas in the crystal of the Tropolone (I) has been confirmed the hydrogen bond OH…O existing with the equilibrium of the two tautomers. It was also found the significant differences in frequency, speed, and the image of the FPT in the studied crystals. © 2018 Wiley Periodicals, Inc.

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 RN···O 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. The hydrogen between the nitrogen and the oxygen atoms adopts a starkly asymmetrical position in the double potential well. The molecular geometry and energy barrier for the intramolecular proton transference were calculated, and the value found suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the two-dimensional average index of π-delocalization ⟨λ⟩ landscape of time evolutions of RN1···O1 and RC1═O1 distances for both the crystals indicate that the hydrogen bonds in the crystals of 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) have characteristic properties for the type of bonding model: resonance-assisted hydrogen bonds and low-barrier hydrogen bonds, without the existence of equilibrium in the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.

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 1πσ* 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 1πσ* state is partial ejection of σ* electrons outside the molecule, even beyond the NH group, at the Franck-Condon point. Further gradual spatial localization of the electron around the proton moving along the N-H stretching coordinate gives a plausible explanation for the repulsive character of the 1πσ* potential energy surface with the proton wading through the region of space where some negative charge is accumulated ('a virtual acceptor'), dragging some electron density. This mechanism resembles the one postulated for the hydrogen transfer from a donor molecule (D-H) to an acceptor one (A) in a class of vertically excited molecules with a preexisting inter- or intramolecular D-HA motif, even though the acceptor molecule is absent. The present analysis demonstrates also that the bond evolution and changes in the electron density along the excited state reaction path can be effectively studied with the use of an electron localization function.

Experimental and Theoretical Study of the Kinetics and Mechanism of the Reaction of Chlorine Atoms with CH3CHClCH3 and CD3CDClCD3.

The overall rate constants for H-abstraction (kH) from CH3CHClCH3 and D-abstraction (kD) from CD3CDClCD3 by chlorine atoms in the temperature range 298-528.5 K were determined and are described by the expressions: kH = (3.52 ± 0.21) × 10-11 exp(-184 ± 19/T) cm3 molecule-1 s-1 and kD = (1.91 ± 0.16) × 10-11 exp(-185 ± 31/T) cm3 molecule-1 s-1 respectively. The results of the experiment show that the value of the kinetic isotope effect (kH/kD) for the overall rate constants is temperature independent and is equal to 1.85 ± 0.17. A theoretical examination of these reaction mechanisms revealed some unusual properties, such as negative values of the activation energy for the H-abstraction reaction from the secondary carbon atom. Moreover, it was proved that in the radical process of H-abstraction from the primary carbon atom of 2-chloropropane the created R-Cl···Cl complex is the most stable structure responsible for the value of the activation energy of this transformation.

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. When the nuclear quantum effects are taken into account, very large delocalization of the bridging proton is observed. These studies indicate that hydrogen bonds in the crystal of benzoylacetone have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds (RAHB) without existing the equilibrium of the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.

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. Phys. Chem. A 2008, 112, 983) and essential change of the electron localization inside the cage. The basin belongs to the rare asynaptic type, V(asyn), and its mean electron population is 0.26 (0.36e). The value of the integrated spin density, 0.13e, shows that both spin-up and spin-down electrons reside in the vicinity of the cage center. A similar attractor has been found for perfluorinated radical anion of adamantane (C10F16(-•)). However, the saturation of the basis set suggests that such an attractor may be an artifact. For both caged perfluorinated tetrahedrane and cubane (CnFn (-•), n = 4, 8), no valence attractors are present inside the cage. Unpaired electron density is concentrated mainly on the C-C bonding basins. The results obtained in this study are complementary to those based on the molecular orbital theory presented by Irikura.

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. These open-shell species are observed for the first time as well as a reaction between atomic hydrogen and formic acid. The structural assignment is aided by extensive deuteration experiments and ab initio calculations at the UMP2 and UCCSD(T) levels of theory. The simplest geminal diol radical trans-cis-HC(OH)2 identified in the present work as the final product of the reaction should be very reactive, and further reaction channels are of particular interest. These reactions and species may constitute new channels for the initiation and propagation of more complex organic species in the interstellar clouds.

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. The monomer-to-complex frequency shifts of this mode are up to +82 cm(-1) (Y = Cl), +101 cm(-1) (Y = Br), and +138 cm(-1) (Y = I), i.e., the shift is smaller for more strongly bound molecules. Based on the agreement of the experimental and theoretical results, the observed bands are assigned to the most stable planar structure with an O-H⋯Y-Xe hydrogen bond.

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. In contrary, the n-π* conjugation interaction between lone pairs of the bridged oxygen atom and π-orbital of the N=O double bond leads to the strengthening of the N-O bond making it more covalent.

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 0.2 and 0.4e. The central N-O1 bond in the cis form is protocovalent (η, Y(D)(σ)) with two basins, V(N) and V(O1). The total population oscillates between 0.7 and 0.9e. In the trans isomer, topology of ELF depends on used method. At the CCSD level only one non-bonding basin, V(N), is observed (η). Its population is about 0.5e. According to the definition of a heteronuclear charge-shift (CS) bond, only N-O1 bond in trans-FONO belongs to the CS class. A relation between η- and ρ-topology and N-O1 bond length is discussed.

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. In structure II, the hydrogen atom of HCO interacts with the oxygen atom of water. The "cyclic" structure III has the C-H···O and O-H···O hydrogen bonds simultaneously. In the experiment, the HCO···H2O complex is produced by photolysis of HCOOH/HY/Kr (Y = Br and Cl) matrices followed by thermal annealing at about 30 K, which promotes the H + CO···H2O → HCO···H2O reaction. The analysis of the spectroscopic data shows that the main product has structure III whereas the formation of structure II is less efficient. The experiments show no evidence of the weakest structure I. The experiments with deuterated formic acid (DCOOH) provide additional support of the proposed assignment.

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. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.

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 -0.23 kcal mol(-1). We have identified three bands of the HXeI···HI complexes in the H-Xe stretching region with the monomer-to-complex blue shifts from +37 to +96 cm(-1), and three bands of the HXeI···HBr complexes with blue shifts from +88 to +157 cm(-1). The structural assignments are done on the basis of the strong H-Xe and HY stretching bands and the decomposition rates upon broadband IR irradiation. The experimental bands with larger shifts are assigned to the most stable structures of the HXeI···HY complexes with the Y-H···I hydrogen bond.

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.

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. Very large delocalization of the bridging proton was noted especially in the path integral simulation where quantum effects are taken into account. The infrared spectrum was calculated, and a comparative vibrational analysis was performed. CPMD vibrational results appear to be in qualitative agreement with the experimental ones.

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 basis of the calculations, the experimentally observed band is assigned to the more stable structure with a "parallel" geometry. The HXeBr molecule was prepared in a carbon dioxide matrix and has the H-Xe stretching frequency of 1646 cm(-1), meaning a strong matrix shift and stabilization of the H-Xe bond. The deuterated species DXeBr in a carbon dioxide matrix absorbs at 1200 cm(-1). This is the first case where a noble-gas hydride is prepared in a molecular solid. The thermal stabilities of HXeBr and HXeBr···CO(2) complex in a xenon matrix and HXeBr in a carbon dioxide matrix were examined. We have found a high thermal stability of HXeBr in carbon dioxide ice (at least up to 100 K), i.e., under conditions that may occur in nature.

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. In the classical dynamics (CPMD) a clear process mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. The DPT mechanism is also asynchronic when quantum tunneling has been allowed in the simulation. It has been found that the calculated values of barrier height for the proton transfer depends very strongly on the used approaches. Barrier received from the free-energy profile at the CPMD level is around 4.5 kcal mol(-1) whereas at the PIMD level is reduced to 1 kcal mol(-1). The nature of bonding in acetic acid dimer and rearrangement of electron density due to the proton movement has been also studied by the topological analysis of Electron Localization Function and Electron Localizability Indicator function.