Dissociative electron attachment to gas phase valine: a combined experimental and theoretical study

Using a crossed electron/molecule beam technique the dissociative electron attachment (DEA) to gas phase L-valine, (CH(3))(2)CHCH(NH(2))COOH, is studied by means of mass spectrometric detection of the product anions. Additionally, ab initio calculations of the structures and energies of the anions and neutral fragments have been carried out at G2MP2 and B3LYP levels. Valine and the previously studied aliphatic amino acids glycine and alanine exhibit several common features due to the fact that at low electron energies the formation of the precursor ion can be characterized by occupation of the pi* orbital of the carboxyl group. The dominant negative ion (M-H)(-) (m/Z=116) is observed at electron energies of 1.12 eV. This ion is the dominant reaction product at electron energies below 5 eV. Additional fragment ions with m/Z=100, 72, 56, 45, 26, and 17 are observed both through the low lying pi* and through higher lying resonances at about 5.5 and 8.0-9.0 eV, which are characterized as core excited resonances. According to the threshold energies calculated here, rearrangements play a significant role in the formation of DEA fragments observed from valine at subexcitation energies.     

The electrophilic addition of thiols to olefins: A theoretical and experimental study

Density functional theory with the B3LYP hybrid functional and 6–31G* basis set was used to study the geometric and electronic structure of H₂C = CHR (R = H, CH₃, C₂H₅, C₃H₇, C₄H₉, and C₅H₁₁) olefins, their carbocations formed in the addition of the proton to the olefins, R′-S-H aliphatic thiols (R′ = H, CH₃, C₂H₅, and C₃H₇), the products of the addition of thiols to carbocations, and the final products of the addition of thiols to olefins. The proton affinity of the olefins and the products of the addition of thiols to olefins was calculated. The conclusion was drawn that the limiting stage in the nonradical addition of thiols to olefins catalyzed by acids was proton transfer from the protonated reaction product to the olefin. The theoretical results were compared with the experimental data on the electrophilic addition of polymercaptan to heptene-1.     

Kinetics and mechanism of 2-pyridylacetic acid pyrolysis in the gas phase: A joint experimental and theoretical study

A combination of the experimental and theoretical study was carried out on the reaction mechanism associated with the pyrolysis of 2-pyridylacetic acid in the gas phase. Methylpyridine and carbon dioxide were analyzed as the products, using a static system over the pressure range of 18–55 torr and the temperature of 541.2–583.4 K. The experimental kinetic data show that the pyrolysis process is homogeneous, unimolecular and proceeds through a concerted mechanism. Theoretical studies at the B3LYP level using the 6-31G^* basis set confirmed an asynchronous concerted mechanism for the reaction. Computed kinetic and activation parameters are in good agreement with the experimental one.     

Structural aspects of the anti-cancer drug oxaliplatin: A combined theoretical and experimental study

The conformational behavior of the third generation antitumor drug, oxaliplatin, has been explored by GGA-PW91 density functional calculations and FT-IR spectra. The difference in the biological activities of cisplatin and oxaliplatin are attributed to the presence of the DACH ligand in the latter. The trans forms of the ligand are found to be more stable than the cis form, but, of the two equally stable enantiomers, the trans-l (1R,2R) one is found to be more potent biologically. Since very minor differences are observed in the electronic structures of the two enantiomers, their difference in activity is attributed to the chiral recognition of the ligand by DNA. The calculated vibrational frequencies are in good agreement with our experimental FT-IR spectrum. Calculations have also been performed on the cis isomer and its monohydrate. Comparison between the theoretically predicted geometries and the experimental ones yielded good correspondence, validating our methodology.     

A theoretical study on the mechanism and thermodynamics of ozone-water gas phase reaction

Ozone water reaction including a complex was studied at the MP2/6-311++G(d,p) and CCSD/6-311++G(2df,2p)//MP2/6-311++G(d,p) levels of theory. The interaction between water oxygen and central oxygen of ozone produces stable H₂O-O₃ complex with no barrier. With decomposition of this complex through H-abstraction by O₃ and O-abstraction by H₂O, three possible product channels were found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the preferred mechanism. Thermodynamic data at T = 298.15 K and atmospheric pressure have been calculated. The results show that the production of hydrogen peroxide is the main reaction channel with ΔG = ?21.112 kJ mol^-1.     

Nitrosation, thiols, and hemoglobin: energetics and kinetics

Nitrosothiols are powerful vasodilators. Although the mechanism of their formation near neutral pH is an area of intense research, neither the energetics nor the kinetics of this reaction or of subsequent reactions have been addressed. The following considerations may help to guide experiments. (1) The standard Gibbs energy for the homolysis reaction RSNO → RS(?) + NO(?)(aq) is +110 ± 5 kJ mol(-1). (2) The electrode potential of the RSNO, H(+)/RSH, NO(?)(aq) couple is -0.20 ± 0.06 V at pH 7. (3) Thiol nitrosation by NO(2)(-) is favorable by 37 ± 5 kJ mol(-1) at pH 7. (4) N(2)O(3) is not involved in in vivo nitrosation mechanisms for thermodynamic--its formation from NO(2)(-) costs 59 kJ mol(-1)--or kinetic--the reaction being second-order in NO(2)(-)--reasons. (5) Hemoglobin (Hb) cannot catalyze formation of N(2)O(3), be it via the intermediacy of the reaction of Hb[FeNO(2)](2+) with NO(?) (+81 kJ mol(-1)) or reaction of Hb[FeNO](3+) with NO(2)(-) (+88 kJ mol(-1)). (6) Energetically and kinetically viable are nitrosations that involve HNO(2) or NO(?) in the presence of an electron acceptor with an electrode potential higher than -0.20 V. These considerations are derived from existing thermochemical and kinetics data.     

Kinetics and mechanisms of the unimolecular elimination of 2,2-diethoxypropane and 1,1-diethoxycyclohexane in the gas phase: experimental and theoretical study

The gas-phase thermal elimination of 2,2-diethoxypropane was found to give ethanol, acetone, and ethylene, while 1,1-diethoxycyclohexane yielded 1-ethoxycyclohexene and ethanol. The kinetics determinations were carried out, with the reaction vessels deactivated with allyl bromide, and the presence of the free radical suppressor cyclohexene and toluene. Temperature and pressure ranges were 240.1-358.3 °C and 38-102 Torr. The elimination reactions are homogeneous, unimolecular, and follow a first-order rate law. The rate coefficients are given by the following Arrhenius equations: for 2,2-diethoxypropane, log k(1) (s(-1)) = (13.04 ± 0.07) - (186.6 ± 0.8) kJ mol(-1) (2.303RT)(-1); for the intermediate 2-ethoxypropene, log k(1) (s(-1)) = (13.36 ± 0.33) - (188.8 ± 3.4) kJ mol(-1) (2.303RT)(-1); and for 1,1-diethoxycyclohexane, log k = (14.02 ± 0.11) - (176.6 ± 1.1) kJ mol(-1) (2.303RT)(-1). Theoretical calculations of these reactions using DFT methods B3LYP, MPW1PW91, and PBEPBE, with 6-31G(d,p) and 6-31++G(d,p) basis set, demonstrated that the elimination of 2,2-diethoxypropane and 1,1-diethoxycyclohexane proceeds through a concerted nonsynchronous four-membered cyclic transition state type of mechanism. The rate-determining factor in these reactions is the elongation of the C-O bond. The intermediate product of 2,2-diethoxypropane elimination, that is, 2-ethoxypropene, further decomposes through a concerted cyclic six-membered cyclic transition state mechanism.     

Role of triple bond in 1,2-diphenylacetylene crystal: A combined experimental and theoretical study

We have performed a combined experimental and theoretical study of the molecular system of 1,2-diphenylacetylene. The occurrence of two different geometries of the molecule in the crystal structure, one being planar and the other tilted by approximately 6 degrees , has been investigated in relation to the nature of the acetylenic linker. The experimental charge density analysis shows that the acetylenic linker exhibits a noncylindrical density reminiscent of the strong conjugation present in the molecule. The pi-orbitals of the acetylenic linker derived from density functional theory (DFT) calculations are found to sustain a variety of conjugation lengths between the phenyl rings, thereby giving flexibility to the molecule to arrange itself in various packing conformations in the crystal. It is interesting that the energy involved for such distortions is only kBT, allowing several polymorphic forms of the crystal structure as reported in the literature. The distortions entertained by the molecule and the corresponding changes in the charge density distribution and energy are all relevant to molecular electronics.     

Electronic states of o-nitrobenzaldehyde: a combined experimental and theoretical study

The experimental UV/vis absorption spectrum of ortho-nitrobenzaldehyde (o-NBA) has been assigned by means of MS-CASPT2/CASSCF, TD-DFT, and RI-CC2 theoretical computations. Additional information on the nature of the absorbing bands was obtained by comparing the o-NBA spectrum with that of related compounds, as, e.g., nitrobenzene and benzaldehyde. For wavelengths larger than approximately 280 nm, the absorption spectrum of o-NBA is dominated by a series of weak n pi* absorptions from the NO2 and CHO groups. These weak transitions are followed in energy by a more intense band, peaking at 250 nm and arising from charge transfer pi pi* excitations involving mainly benzene and nitro orbitals. Finally, the most intense band centered at 220 nm has its origin in the overlap of two different absorptions: the first one localized in the NO2 substituent and the second one arising from a charge transfer excitation involving the NO2 and the CHO fragments, respectively.     

A combined experimental and theoretical study of carboxylate coordination modes: a structural probe

The variations of the frequency differences of symmetric and asymmetric stretching vibrations in a series of carboxylato Fe(II) complexes have been theoretically studied. It is shown that structural information can be obtained from a direct comparison between the difference (Delta = nu(as) - nu(s)) in the asymmetric (nu(as)) and symmetric (nu(s)) carboxylate vibrations of the free anion and that of the coordinated species. The coordination mode approaches C(2v) symmetry as Delta decreases with respect to its value for the noncoordinated carboxylate. The use of IR spectroscopy in the resolution of speculated crystallographic structures is suggested.     

Chiral interactions in azobenzene dimers: a combined experimental and theoretical study

To investigate interchromophore interactions in azobenzene polymers, we have undertaken a thorough spectroscopic analysis of the azodye [(S)-3-pivaloyloxy-1-(4'-nitro-4-azobenzene)pyrrolidine] by modeling the repeating unit of poly[(S)-3-methacryloyloxy-1-(4'-nitro-4-azobenzene)pyrrolidine) and its dimeric derivative whose synthesis is presented here. The analysis of the electronic and Raman spectra of the azodye in several solvents is based on a previously proposed model for polar chromophores in solution. Electronic and CD spectra of the dimeric unit are collected and analyzed within the framework of a new model. On the basis of the information collected from the spectroscopic analysis of the solvated dye, this model accounts for interchromophore interactions in the dimer. The large CD signal measured for the dimer (amounting to about a third of the signal measured for the polymer) suggests the presence of important chiral interactions in the dimeric unit, and is modeled in terms of a right-handed relative orientation of the two chromophores.     

Activation of leinamycin by thiols: a theoretical study

Reaction of thiols with the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin (1) results in the conversion of this antitumor antibiotic to a DNA-alkylating episulfonium ion (5). While the products formed in this reaction have been rationalized by a mechanism involving initial attack of thiol on the central sulfenyl sulfur (S2') of the 1,2-dithiolan-3-one 1-oxide ring, the carbonyl carbon (C3') and the sulfinyl sulfur (S1') of this heterocycle are also expected to be electrophilic. Therefore, it is important to consider whether nucleophilic attack of thiol at these sites might contribute either to destruction of the antibiotic or conversion to its episulfonium ion form. To address this question, we have used computational methods to examine the attack of methyl thiolate on each of the three electrophilic centers in a simple analogue of the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin. Calculations were performed at the MP2/6-311+G(3df,p)//B3LYP/6-31G level of theory with inclusion of solvent effects. The results indicate that the most reasonable mechanism for thiol-mediated activation of leinamycin involves initial attack of thiolate at the S2'-position of the antibiotic's 1,2-dithiolan-3-one 1-oxide heterocycle, followed by conversion to the 1,2-oxathiolan-5-one intermediate (3).     

Anion-binding properties of the tripyrrolemethane group: a combined experimental and theoretical study

Tripyrrolemethane- and bistripyrrolemethane-containing systems were recently reported to be efficient and selective hosts for anions. Nevertheless, the basic intrinsic properties of tripyrrolemethane as a ligand for anions have not yet been explored. Here we report the study of the anion-binding properties of the tripyrrolemethane group. We applied a combined experimental and theoretical approach to determine the affinity of the tripyrrolemethane system for different anions in the gas phase, in solution and in the crystalline state. In the crystal, the tripyrrolemethane group forms a number of different complexes with the bromide ion, some involving the participation of more than one ligand species. Despite the very similar basicity of fluoride and dihydrogen phosphate, the tripyrrolemethane ligand exhibits a clear preference for the fluoride anion in solution, which indicates an anion-binding system and not merely deprotonation. Although the affinity of the tripyrrolemethane ligand for other ions was negligible in solution, gas-phase studies show that complexation with larger halide ions is favoured over complexation with fluoride.     

Room-temperature palladium-catalyzed Negishi-type coupling: a combined experimental and theoretical study

An air-stable, bulky electron-accepting phosphine ligand (phosphabarrelene) allows the easy reduction of a Pd(II) precursor to a Pd(0) complex, highly active in room-temperature Negishi-type cross-coupling. DFT calculations show that the use of the electron-accepting ligand favors both transmetalation (TM) and reductive-elimination (RE) processes (see scheme; OA = oxidative addition).     

A combined experimental and theoretical study on the conformation of multiarmed chiral aryl ethers

Four series of multiarmed chiral aryl ethers carrying two, three, five, or eight side-chains on a variety of aromatic core molecules (2-5) were prepared. The structure and conformation of 2 and 3 (in the solid state) were determined by the X-ray crystallographic analyses. While a pair of alternated (anti) conformers (i.e, up-down and down-up) were found in the crystal of 2, three side-arms in 3 were aligned in the same direction to give a C(3)-symmetric syn-conformation. Examinations by dispersion-corrected density functional (DFT-D) calculations revealed that two out of six anti- and two out of four syn-conformers of 2 are energetically most important. Two calculated structures of anti-conformers are in good agreement with those found in the solid state by X-ray analysis. Similarly, relevant conformations of syn-3, fully alternated 4, and C(5)-symmetric 5 were optimized at the DFT-D-B-LYP/TZVP level. The structure and conformation of the side-arms in 2-5 in solution were further studied by temperature dependent (1)H NMR and UV-vis spectroscopy. In addition, comparative experimental and theoretical CD spectral studies were carried out in order to elucidate the contribution of the thermodynamically less-stable minor isomers in solution. The CD spectral changes observed for 2 and 3 at varying temperatures were quite different, while the parent chiral arene 1, as well as 4 and 5, only showed an increased intensity of the negative Cotton effect for the (1)L(b) band. The latter behavior is readily accounted for in terms of the conformational freezing of the chiral groups at low temperatures. The unusual CD spectral behavior observed for 2 and 3 was rationalized by the conformational alteration of the side-arms. Because of attractive van der Waals interactions between the aromatic units of the arms in nonpolar solvents, the syn-conformations become gradually more important for 2 at low temperatures, which eventually results in a weak positive Cotton effect for the (1)L(b) band. This was also supported by the SCS-MP2/TZVPP single-point energy calculations for the relevant conformers of 2. For 3, the contribution of the C(3)-symmetrical conformer becomes more important than the less-symmetrical isomers at low temperatures. The conformations of 2 and 3 in their excited states as well as in the oxidized states were also examined.     

Tautomerism in 7-hydroxyquinoline: a combined experimental and theoretical study in water

Tautomerism in the ground and excited states of 7-hydroxyquinoline (7HQ) was studied in different solvents using steady-state and lifetime spectroscopic measurements, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Equilibrium between the enol and the keto/zwitterion tautomers exists in 7HQ, which is solvent-dependent. Of the solvents used in this study, only in water does the absorbance spectrum of 7HQ show absorption from both the enol and zwitterion tautomers. In addition, in aqueous media, fluorescence is observed from the zwitterion tautomer only, which is attributed to self-quenching of the enol fluorescence by energy transfer to the ground-state zwitterion tautomer and energetically favorable excited-state proton transfer. Solvation of the hydrogen bonding sites of 7HQ was studied in binary mixtures of 1,4-dioxane and water, and three water molecules were estimated to connect the polar sites and induce intermolecular proton transfer. The results are confirmed by DFT calculations showing that three water molecules are the minimum number required to form a stable solvent wire. Mapping the water density around the polar sites using MD simulations shows well-defined hydrogen bonds around the amino and hydroxyl groups of the enol tautomer and slightly less well-defined hydrogen bonds for the zwitterion tautomer. The presence of three-member water wires connecting the polar centers in 7HQ is evident in the MD simulations. The results point to the unique spectral signatures of 7HQ in water, which make this molecule a potential probe to detect the presence of water in nanocavities of macromolecules.     

Thermochemistry of biphenylcarboxylic and dicarboxylic acids. A combined experimental and theoretical study

The standard molar enthalpies of combustion and sublimation of 2- and 4-biphenylcarboxylic acid, 2,2'- and 4,4'-biphenyldicarboxylic acid were measured and the gas-phase enthalpies of formation, at T= 298.15 K, were determined. Ab initio calculations were performed and a theoretical study on molecular structure of all the biphenyl acid isomers has been carried out. Calculated enthalpies of formation using appropriate isodesmic reactions are compared with experimental values, and a good agreement is observed. Estimates of enthalpies of formation for the isomers, which were not studied experimentally, are presented. All the acids containing at least one ortho COOH are comparatively less stable than their isomers having just meta or para COOH group(s).