Ab initio study on the thermochemistry of vinyl radical and cation

The ionization energy of the vinyl radical: a Mexican standoff with a happy ending

Theoretical approaches and experimental spectra are confirmed as the origin transition is shown to be forbidden in vinyl photoionization.

Computational investigations of physicochemical, pharmacokinetic, toxicological properties and molecular docking of betulinic acid, a constituent of Corypha taliera (Roxb.) with Phospholipase A2 (PLA2)

BACKGROUND

Betulinic acid (BA) is a natural triterpenoid compound and exhibits a wide range of biological and medicinal properties including anti-inflammatory activity. Therefore, this theoretical investigation is performed to evaluate (a) physicochemical properties such as acid dissociation constant (pKa), distribution coefficient (logD), partition coefficient (logP), aqueous solubility (logS), solvation free energy, dipole moment, polarizability, hyperpolarizability and different reactivity descriptors, (b) pharmacokinetic properties like human intestinal absorption (HIA), cellular permeability, skin permeability (P_Skin), plasma protein binding (PPB), penetration of the blood brain barrier (BBB), (c) toxicological properties including mutagenicity, carcinogenicity, risk of inhibition of hERG gene and (d) molecular mechanism of anti-inflammatory action which will aid the development of analytical method and the synthesis of BA derivatives.

METHODS

The physicochemical properties were calculated using MarvinSketch 15.6.29 and Gaussian 09 software package. The pharmacokinetic and toxicological properties were calculated on online server PreADMET. Further, the molecular docking study was conducted on AutoDock vina in PyRx 0.8.

RESULTS

The aqueous solubility increased with increasing pH due to the ionization of BA leading to decrease in distribution coefficient. The solvation energies in water, dimethyl sulfoxide (DMSO), acetonitrile, n-octanol, chloroform and carbon tetrachloride were - 41.74 kJ/mol, - 53.80 kJ/mol, - 66.27 kJ/mol, - 69.64 kJ/mol, - 65.96 kJ/mol and - 60.13 kJ/mol, respectively. From the results of polarizability and softness, it was clear that BA is less stable and hence, kinetically more reactive in water. BA demonstrated good human intestinal absorption (HIA) and moderate cellular permeability. Further, BA also exhibited positive CNS activity due to high permeability through BBB. The toxicological study revealed that BA was a mutagenic compound but noncarcinogenic in mice model. Moreover, molecular docking study of BA with PLA2 revealed that BA interacts with GLY22 & GLY29 through hydrogen bond formation and LEU2, PHE5, HIS6, ALA17, ALA18, HIS47 and TYR51 through different types of hydrophobic interactions. The binding affinity of BA was - 41.00 kJ/mol which is comparable to the binding affinity of potent inhibitor 6-Phenyl-4(R)-(7-Phenyl-heptanoylamino)-hexanoic acid (BR4) (- 33.89 kJ/mol).

CONCLUSIONS

Our computed properties may assist the development of analytical method to assay BA or to develop BA derivatives with better pharmacokinetic and toxicological profile.

Millimeter-wave spectroscopy of H(2)C=CD: Tunneling splitting and ortho-para mixing interaction

The H(2)C=CD isotopic species of vinyl radical produced in a supersonic jet expansion by ultraviolet laser photolysis was studied by millimeter-wave spectroscopy. Due to the tunneling motion of the α deuteron, the ground state is split into two components, 0(+) and 0(-). Tunneling-rotation transitions connecting the lower (0(+)) and upper (0(-)) components of the tunneling doublet were observed in the frequency region of 184-334 GHz, including three R- and two Q-branch transitions. Three and two pure rotational transitions in the K(a)=0 and 1 stacks, respectively, were also observed for each of the 0(+) and 0(-) states in the frequency region of 52-159 GHz. Least-squares analysis of the observed frequencies for the tunneling-rotation and pure rotational transitions with well resolved hyperfine structures yielded a set of precise molecular constants, among which the tunneling splitting in the ground state was determined to be ΔE(0)=1187.234(17) MHz, which is 1/14 that for H(2)C=CH. The potential barrier height derived from the observed tunneling splitting by an analysis of the tunneling dynamics using a one-dimensional model is 1545 cm(-1), consistent with the value 1568 cm(-1) obtained for the normal vinyl. The observed spectrum was found to be perturbed by a hyperfine interaction connecting ortho and para levels. The constant for the interaction, which we call the ortho-para mixing Fermi contact interaction, has been determined to be δa(F) ((β))=68.06(53) MHz. This is believed to be the first definite detection of such an interaction. By this interaction the ortho and para states of H(2)C=CD are mixed up to about 0.1%. The constant is more than 1000 times larger than spin-rotation interaction constants that cause ortho-para mixing in closed shell molecules and suggests extremely rapid conversion between the ortho and para nuclear spin isomers of H(2)C=CD.

Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods

The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.

A Photoelectron Photoion Coincidence Study of the Vinyl Bromide and Tribromoethane Ion Dissociation Dynamics: Heats of Formation of C2H3+, C2H3Br, C2H3Br+, C2H3Br2+, and C2H3Br3

The threshold photoelectron photoion coincidence (TPEPICO) technique has been used to measure accurate dissociative photoionization onsets of vinyl bromide and 1,1,2-tribromoethane. The reactions investigated and their 0 K onsets are C2H3Br + hnu --> C2H3+ + Br (11.902 +/- 0.008 eV); C2H3Br3 + hnu --> C2H3Br2+ + Br (10.608 +/- 0.008 eV); and (C2H3Br3 + hnu --> C2H3Br+ + 2Br (12.301 +/- 0.035 eV). The vinyl ion heat of formation (Delta(f)H degrees 298K = 1116.1 +/- 3.0 kJ/mol) has been calculated using W1 theory and used as an anchor along with the measured dissociation energies to determine the heats of formation, Delta(f)H degrees 298K, in kJ/mol, of the following bromine-containing species: C2H3Br (74.1 +/- 3.1), C2H3Br+ (1021.9 +/- 3.1), C2H3Br2+ (967.1 +/- 4.0), and C2H3Br3 (53.5 +/- 4.3). These results represent accurate and consistent experimental determinations of heats of formation for these bromine-containing species, which serve to correct the discrepancies in the literature for C2H3Br and C2H3Br+ and provide the first experimental determination for the enthalpies of formation of C2H3Br2+ and C2H3Br3.

Accurate ab initio predictions of ionization energies of hydrocarbon radicals: CH2, CH3, C2H, C2H3, C2H5, C3H3, and C3H5

The ionization energies for methylene (CH2), methyl (CH3), ethynyl (C2H), vinyl (C2H3), ethyl (C2H5), propargyl (C3H3), and allyl (C3H5) radicals have been calculated by the wave-function-based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled-cluster level with single and double excitations plus a quasiperturbative triple excitation [CCSD(T)]. When it is appropriate, the zero-point vibrational energy correction, the core-valence electronic correction, the scalar relativistic effect correction, the diagonal Born-Oppenheimer correction, and the high-order correlation correction have also been made in these calculations. The comparison between the computed ionization energy (IE) values and the highly precise experimental IE values determined in previous pulsed field ionization-photoelectron (PFI-PE) studies indicates that the CCSD(T)/CBS method is capable of providing accurate IE predictions for these hydrocarbon radicals achieving error limits well within +/-10 meV. The benchmarking of the CCSD(T)/CBS IE predictions by the PFI-PE experimental results also lends strong support for the conclusion that the CCSD(T)/CBS approach with high-level energy corrections can serve as a valuable alternative for reliable IE determination of radicals, particularly for those radicals with very unfavorable Franck-Condon factors for photoionization transitions near their ionization thresholds.

A high-resolution pulsed field ionization-photoelectron-photoion coincidence study of vinyl bromide

By employing the high-resolution pulsed field ionization-photoelectron (PFI-PE)-photoion coincidence method, we have examined the unimolecular dissociation reaction of energy-selected C(2)H(3)Br(+) to form C(2)H(3) (+)+Br near its threshold. The analysis of the breakdown curves for C(2)H(3)Br(+) and C(2)H(3) (+) yields a value of 11.9010+/-0.0015 eV for the 0 K dissociative photoionization threshold or appearance energy (AE) for C(2)H(3) (+) from C(2)H(3)Br. This AE(C(2)H(3) (+)) value, together with the ionization energy (IE) for C(2)H(3)Br (9.8200+/-0.0015 eV) obtained by PFI-PE and threshold photoelectron (TPE) measurements, has allowed the determination of the 0 K dissociation energy (D(0)) for the C(2)H(3) (+)-Br bond to be 2.081+/-0.002 eV. The 0 K AE(C(2)H(3) (+)) from C(2)H(3)Br obtained in this study corresponds to DeltaH(f0) ( composite function )(C(2)H(3) (+))=1123.7+/-1.9 kJ/mol. Combining the latter value and the known DeltaH(f0) ( composite function )(C(2)H(3))=306.7+/-2.1 kJ/mol, we calculated a value of 8.468+/-0.029 eV for the IE(C(2)H(3)), which is in accord with the result obtained in the previous photoionization efficiency study. We have also carried out high-level ab initio calculations for the IE(C(2)H(3)) at the Gaussian-3 and the CCSD(T,full)/CBS level of theory. The CCSD(T,full)/CBS prediction of 8.487 eV for the IE(C(2)H(3)-->bridged-C(2)H(3) (+)) is in good agreement with the IE(C(2)H(3)) value derived in the present experiment. Combining the 0 K AE(C(2)H(3) (+))=11.9010+/-0.0015 eV and the IE(C(2)H(3))=8.468+/-0.029 eV yields the value of 3.433+/-0.029 eV for D(0)(C(2)H(3)-Br). We have also recorded the TPE spectrum of C(2)H(3)Br in the energy range of 9.80-12.20 eV. Members (n=5-14) of four autoionizing Rydberg series converging to the C(2)H(3)Br(+)(A (2)A(')) state are observed in the TPE spectrum. The analysis of the converging limit of these Rydberg series and the vibrational TPE bands for C(2)H(3)Br(+)(A (2)A(')) has provided more precise values for the nu(6) (+) (1217+/-10 cm(-1)) and nu(8) (+) (478+/-8 cm(-1)) modes and the IE (10.9156+/-0.0010 eV) for the formation of C(2)H(3)Br(+)(A (2)A(')) from C(2)H(3)Br.

Determination of the proton tunneling splitting of the vinyl radical in the ground state by millimeter-wave spectroscopy combined with supersonic jet expansion and ultraviolet photolysis

The vinyl radical in the ground vibronic state produced in a supersonic jet expansion by 193 nm excimer laser photolysis of vinyl bromide was investigated by millimeter-wave spectroscopy. Due to the proton tunneling, the ground state is split into two components, of which the lower and higher ones are denoted as 0+ and 0-, respectively. Eight pure rotational transitions with Ka = 0 and 1 obeying a-type selection rules were observed for each of the 0+ and 0- states in the frequency region of 60-250 GHz. Tunneling-rotation transitions connecting the lower (0+) and upper (0-) components of the tunneling doublet, obeying b-type selection rules, were also observed in the frequency region of 190-310 GHz, including three R- and six Q-branch transitions. The observed frequencies of the pure rotational and tunneling-rotation transitions were analyzed by using an effective Hamiltonian in which the coupling between the 0+ and 0- states was taken into account. A set of precise molecular constants was obtained. Among others, the proton tunneling splitting in the ground state was determined to be DeltaE0 = 16,272(2) MHz. The potential barrier height was estimated to be 1580 cm(-1) from the proton tunneling splitting, by an analysis using a detailed one-dimensional model. The spin-rotation and hyperfine interaction constants were also determined for the 0+ and 0- states together with the off-diagonal interaction constants connecting the 0+ and 0- states, epsilonab + epsilonba for the spin-rotation interaction and Tab for the hyperfine interaction of the alpha (CH) proton. The hyperfine interaction constants, due to the alpha proton and the beta (CH2) protons, are consistent with those derived from electron spin resonance studies.

Computational chemistry: a useful (sometimes mandatory) tool in mass spectrometry studies

In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.