A bioinspired strategy for designing well-ordered nanotubular structures by templateless electropolymerization of thieno[3,4-b]thiophene-based monomers.

Here, a bioinspired strategy is used to prepare well-ordered nanotubular structures, as observed in animals and plants, such as gecko toe pads or corals. The nanotubes are obtained by templateless electropolymerization of thieno[3,4-b]thiophene-based monomers with various aromatic groups in an organic solvent (dichloromethane). The most interesting and robust structures were obtained with carbazole and pyrene substituents to the base monomer structure, since these groups participate significantly in the polymerization and also have strong π-stacking interactions. The addition of water to electropolymerization solvent significantly impacted the formation of nanotubes, as it caused the release of a significant amount of H2 and O2 bubbles, depending on the electropolymerization method. Identifying templateless approaches to vary nanotubular structures is very interesting, as these materials are sought-after for applications in water harvesting systems. This article is part of the theme issue 'Bioinspired materials and surfaces for green science and technology (part 3)'.

Chloromethane Degradation in Soils: A Combined Microbial and Two-Dimensional Stable Isotope Approach.

Chloromethane (CHCl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CHCl budget, and especially the CHCl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CHCl hydrogen and carbon and investigated bacterial diversity during CHCl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CHCl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 µg g dry wt. d for forest soil, from 0.1 to 0.9 µg g dry wt. d for grassland soil, and from 0.1 to 0.4 µg g dry wt. d for agricultural soil and increased with increasing temperature and CHCl supplementation. The measured mean stable hydrogen enrichment factor of CHCl of -50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CHCl degradation rates and ranged from -38 to -11‰. Bacterial community composition correlated with soil properties was independent from CHCl degradation or isotope enrichment. Nevertheless, increased abundance after CHCl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CHCl degradation, may play a role in the microbial CHCl sink in soil.

Recent advances in QM/MM free energy calculations using reference potentials.

BACKGROUND: Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. SCOPE OF REVIEW: Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. MAJOR CONCLUSIONS: The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. GENERAL SIGNIFICANCE: As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Accurate ab initio vibrational energies of methyl chloride.

Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.

Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

Theoretical foundation for the presence of oxacarbenium ions in chemical glycoside synthesis.

Glycoside formation in organic synthesis is believed to occur along a reaction path involving an activated glycosyl donor with a covalent bond between the glycosyl moiety and the leaving group, followed by formation of contact ion pairs with the glycosyl moiety loosely bound to the leaving group, and eventually solvent-separated ion pairs with the glycosyl moiety and the leaving group being separated by solvent molecules. However, these ion pairs have never been experimentally observed. This study investigates the formation of the ion pairs from a covalent intermediate, 2,3,4,6-tetra-O-methyl-α-d-glucopyranosyl triflate, by means of computational chemistry. Geometry optimization of the ion pairs without solvent molecules resulted in re-formation of the covalent α- and ß-triflates but was successful when four solvent (dichloromethane) molecules were taken into account. The DFT(M06-2X) computations indicated interconversion between the α- and ß-covalent intermediates via the α- and ß-contact ion pairs and the solvent-separated ion pairs. The calculated activation Gibbs energy of this interconversion was quite small (10.4-13.5 kcal/mol). Conformational analyses of the ion pairs indicated that the oxacarbenium ion adopts (4)H3, (2)H3/E3, (2)H3/(2)S0, E3, (2,5)B, and B2,5 pyranosyl ring conformations, with the stability of the conformers being strongly dependent on the relative location of the counteranion.

Solvent effects on the intramolecular conversion of trimethylsulfonium chloride to dimethyl sulfide and methyl chloride.

The formation of CH3Cl from (CH3)3SCl in various solvents has been studied based on M05/6-311+G(2d,p) DFT calculations to quantify the influence of the solvent on the stability of sulfonium cations. Four different pathways (one SN1, one backside and two frontside attacks for SN2) as well as the formation of different ion pairs (tripod, seesaw, and linear) are discussed to investigate the origin of the kinetic solvent effect (KSE) and the contribution of ion pairs to the overall reaction. Ion pairs are formed only in solvents with a permittivity ε lower than 28, but the reaction proceeds via a standard SN2 mechanism with a backside attack in all solvents. The formation of ion pairs does not change the order of the rate law, but it strongly influences the KSE, which can distinguish between reactions starting from free ions and those starting from ion pairs, in contrast to standard kinetic analysis.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Structural and dynamic properties of a hydrogen bond from the study of the CH3Cl-HCl complex and isotopic species.

The microwave (4-20 GHz range) and infrared (HCl and DCl stretch ranges) spectra of six isotopic species of the CH3Cl-HCl hydrogen bond complex have been recorded for the first time and analyzed with the support of high level ab initio calculations (MP2 and CCSD(T) levels). Accurate molecular parameters, including rotational, quartic centrifugal distortion, and nuclear-quadrupole coupling constants, vibrational frequencies, and anharmonic coupling constants, are presented in this paper. These parameters have then been used to estimate the hydrogen bond geometry and confirm the strong coupling between intramolecular and low frequency intermolecular modes. Experimental and theoretical evidence, in agreement with each other, tend to point out a free rotation of the CH3Cl unit in the complex, emphasizing the very peculiar dynamical properties of a hydrogen bond and, consequently, the necessity of taking those effects into account to correctly model the intra- and intermolecular interactions.

Density functional study of S(N) 2 substitution reactions for CH(3) Cl + CX(1) X(2•-) (X(1) X(2) = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II).

A systematic investigation on the S(N) 2 displacement reactions of nine carbene radical anions toward the substrate CH(3) Cl has been theoretically carried out using the popular density functional theory functional BHandHLYP level with different basis sets 6-31+G (d, p)/relativistic effective core potential (RECP), 6-311++G (d, p)/RECP, and aug-cc-pVTZ/RECP. The studied models are CX(1) X(2•-) + CH(3) Cl → X(2) X(1) CH(3) C(•) + Cl(-) , with CX(1) X(2•-) = CH(2) (•-) , CHF(•-) , CHCl(•-) , CHBr(•-) , CHI(•-) , CF(2) (•-) , CCl(2) (•-) , CBr(2) (•-) , and CI(2) (•-) . The main results are proposed as follows: (a) Based on natural bond orbital (NBO), proton affinity (PA), and ionization energy (IE) analysis, reactant CH(2) (•-) should be a strongest base among the anion-containing species (CX(1) X(2•-) ) and so more favorable nucleophile. (b) Regardless of frontside attacking pathway or backside one, the S(N) 2 reaction starts at an identical precomplex whose formation with no barrier. (c) The back-S(N) 2 pathway is much more preferred than the front-S(N) 2 one in terms of the energy gaps [ΔE cent≠(front)-ΔE cent≠(back)], steric demand, NBO population analysis. Thus, the back-S(N) 2 reaction was discussed in detail. On the one hand, based on the energy barriers (ΔE cent≠ and ΔE ovr≠) analysis, we have strongly affirmed that the stabilization of back attacking transition states (b-TSs) presents increase in the order: b-TS-CI(2) < b-TS-CBr(2) < b-TS-CCl(2) < b-TS-CHI < b-TS-CHBr < b-TS-CHCl < b-TS-CF(2) < b-TS-CHF < b-TS-CH(2) . On the other hand, depended on discussions of the correlations of ΔE ovr≠ with influence factors (PA, IE, bond order, and ΔE def≠), we have explored how and to what extent they affect the reactions. Moreover, we have predicted that the less size of substitution (α-atom) required for the gas-phase reaction with α-nucleophile is related to the α-effect and estimated that the reaction with the stronger PA nucleophile, holding the lighter substituted atom, corresponds to the greater exothermicity given out from reactants to products.

Physical and physicochemical factors effecting transport of chlorohydrocarbon gases from lung alveolar air to blood as measured by the causation of narcosis.

This systematic investigation examines gas transport in the lung for two sets of chlorohydrocarbons (CHCs): the chloromethanes (C1) and chloroethanes (C2). The C1 series includes chloromethane, methylene chloride, chloroform, and carbon tetrachloride, and the C2 series includes chloroethane, 1,2-dichloroethane, 1, 1, 2-trichloroethane, and 1, 1, 2, 2-tetrachloroethane. Most CHC gases cause narcosis. The comprehensive narcosis work of Lehmann and colleagues on CHCs was used as a basis for the narcosis endpoint in the present examination. The sites for narcosis are located in the brain (midline cortex and posterior parietal area), the spine, and at many peripheral nerve sites. Central nervous system (CNS) exposure executes a multisite, neural transmission set of inhibitions that promotes rapid loss of consciousness, sensory feeling, and current and stored memory while providing temporary amnesia. Absorption into the system requires dissolution into many lipid membranes and binding to lipoproteins. Lipophilicity is a CHC property shared with many anesthetics according to the Meyer-Overton Rule. Many structurally different lipid chemicals produce the narcosis response when the lipid concentration exceeds -67 mM. This suggests narcotic or anesthetic dissolution into CNS membranes until the lipid organization is disrupted or perturbed. This perturbation includes loading of Na(+)- and K(+)-channel transmembrane lipoprotein complexes and disrupting their respective channel functional organizations. The channel functions become attenuated or abrogated until the CHC exposure ceases and CHC loading reverses. This investigation demonstrates how the CHC physical and chemical properties influence the absorption of these CHCs via the lung and the alveolar system on route to the blood. Narcosis in test animals was used here as an objective biological endpoint to study the effects of the physical factors Bp, Vp, Kd (oil: gas) partition, Henry's constant (HK), and water solubility (S%) on gas transport. Narcosis is immediate after gas exposure and requires no chemical activation only absorption into the blood and circulation to CNS narcotic sites. The three physical factors Bp, K(d) (oil: air), and S% vary directly with unitary narcosis (UN) whereas Vp and HK vary inversely with UN in linear log-log relationships for the C2 series but not for the C1 series. Physicochemical properties of C1 series gases indicate why they depart from what is usually assumed to be an Ideal Gas. An essential discriminating process in the distal lung is the limiting alveolar film layer (AFL) and the membrane layer of the alveolar acini. The AFL step influences gas uptake by physically limiting the absorption process. Interaction with and dissolution into aqueous solvent of the AFL is required for transport and narcotic activity. Narcotics or anesthetics must engage the aqueous AFL with sufficient strength to allow transport and absorption for downstream CNS binding. CHCs that do not engage well with the AFL are not narcotic. Lipophilicity and amphipathicity are also essential solvency properties driving narcotics' transport through the alveolar layer, delivery to the blood fats and lipoproteins, and into critical CNS lipids, lipoproteins, and receptor sites that actuate narcosis. AFL disruption is thought to be strongly related to a number of serious pulmonary diseases such acute respiratory distress syndrome, infant respiratory distress syndrome, emphysema, chronic obstructive pulmonary disease, asthma, chronic bronchitis, pneumonia, pulmonary infections, and idiopathic pulmonary fibrosis. The physical factors (Bp, Vp, Kd [oil: gas] partition, Henry's constant, and water solubility [S%]) combine to affect a specific transport through the AFL if lung C > C(0) (threshold concentration for narcosis). The degree of blood CHC absorption depends on dose, lipophilicity, and lung residence time. AFL passage can be manipulated by physical factors of increased pressure (kPa) or increased gas exposure (moles). Molecular lipophilicity facilitates narcosis but lipophilicity alone does not explain narcosis. Vapor pressure is also required for narcosis. Narcotic activity apparently requires stereospecific processing in the AFL and/or down-stream inhibition at stereospecific lipoproteins at CNS inhibitory sites. It is proposed that CHCs likely cannot proceed through the AFL without perturbation or disruption of the integrity of the AFL at the alveoli. CHC physicochemical properties are not expected to allow their transport through the AFL as physiological CO(2) and O(2) naturally do in respiration. This work considers CHC inspiration and systemic absorption into the blood with special emphasis on the CHC potential perturbation effects on the lipid, protein liquid layer supra to the alveolar membrane (AFL). A heuristic gas transport model for the CHCs is presented as guidance for this examination. The gas transport model can be used to study absorption for other gas delivery endpoints of environmental concern such as carcinogens.

Sampling the proton transfer reaction coordinate in mixed quantum-classical molecular dynamics simulations.

An umbrella sampling approach based on the vibrational energy gap is presented and examined for exploring the reaction coordinate for a proton transfer (PT) reaction. The technique exploits the fact that for a PT reaction the energy gap between the vibrational ground and excited states of the transferring proton reaches a minimum at the transition state. Umbrella sampling is used within mixed quantum-classical simulations to identify the transition state configurations and explore the reaction free energy curve and vibrationally nonadiabatic coupling. The method is illustrated by application to a model phenol-amine proton transfer reaction complex in a nanoconfined solvent. The results from this new umbrella sampling approach are consistent with those obtained from previous umbrella sampling calculations based on a collective solvent coordinate. This sampling approach further provides insight into the vibrationally nonadiabatic coupling for the proton transfer reaction and has potential for simulating vibrational spectra of PT reaction complexes in solution.

Near-thermal reactions of Au(+)(1S,3D) with CH3X (X = F,Cl).

Reactions of Au(+)((1)S) and Au(+)((3)D) with CH(3)F and CH(3)Cl have been carried out in a drift cell in He at a pressure of 3.5 Torr at both room temperature and reduced temperatures in order to explore the influence of the electronic state of the metal on reaction outcomes. State-specific product channels and overall two-body rate constants were identified using electronic state chromatography. These results indicate that Au(+)((1)S) reacts to yield an association product in addition to AuCH(2)(+) in parallel steps with both neutrals. Product distributions for association vs HX elimination were determined to be 79% association/21% HX elimination for X = F and 50% association/50% HX elimination when X = Cl. Reaction of Au(+)((3)D) with CH(3)F also results in HF elimination, which in this case is thought to produce (3)AuCH(2)(+). With CH(3)Cl, Au(+)((3)D) reacts to form AuCH(3)(+) and CH(3)Cl(+) in parallel steps. An additional product channel initiated by Au(+)((3)D) is also observed with both methyl halides, which yields CH(2)X(+) as a higher-order product. Kinetic measurements indicate that the reaction efficiency for both Au(+) states is significantly greater with CH(3)Cl than with CH(3)F. The observed two-body rate constant for depletion of Au(+)((1)S) by CH(3)F represents less than 5% of the limiting rate constant predicted by the average dipole orientation model (ADO) at room temperature and 226 K, whereas CH(3)Cl reacts with Au(+)((1)S) at the ADO limit at both room temperature and 218 K. Rate constants for depletion of Au(+)((3)D) by CH(3)F and CH(3)Cl were measured at 226 and 218 K respectively, and indicate that Au(+)((3)D) is consumed at approximately 2% of the ADO limit by CH(3)F and 69% of the ADO limit by CH(3)Cl. Product formation and overall efficiency for all four reactions are consistent with previous experimental results and available theoretical models.

Resonant inelastic x-ray scattering of methyl chloride at the chlorine K edge.

We present a combined experimental and theoretical study of isolated CH(3)Cl molecules using resonant inelastic x-ray scattering (RIXS). The high-resolution spectra allow extraction of information about nuclear dynamics in the core-excited molecule. Polarization-resolved RIXS spectra exhibit linear dichroism in the spin-orbit intensities, a result interpreted as due to chemical environment and singlet-triplet exchange in the molecular core levels. From analysis of the polarization-resolved data, Cl 2p(x, y) and 2p(z) electronic populations can be determined.

Dissociative photoionization of methyl chloride studied with threshold photoelectron-photoion coincidence velocity imaging.

Utilizing threshold photoelectron-photoion coincidence (TPEPICO) velocity imaging, dissociation of state-selected CH(3)Cl(+) ions was investigated in the excitation energy range of 11.0-18.5 eV. TPEPICO time-of-flight mass spectra and three-dimensional time-sliced velocity images of CH(3)(+) dissociated from CH(3)Cl(+)(A(2)A(1) and B(2)E) ions were recorded. CH(3)(+) was kept as the most dominant fragment ion in the present energy range, while the branching ratio of CH(2)Cl(+) fragment was very low. For dissociation of CH(3)Cl(+)(A(2)A(1)) ions, a series of homocentric rings was clearly observed in the CH(3)(+) image, which was assigned as the excitation of umbrella vibration of CH(3)(+) ions. Moreover, a dependence of anisotropic parameters on the vibrational states of CH(3)(+)(1(1)A') provided a direct experimental evidence of a shallow potential well along the C-Cl bond rupture. For CH(3)Cl(+)(B(2)E) ions, total kinetic energy released distribution for CH(3)(+) fragmentation showed a near Maxwell-Boltzmann profile, indicating that the Cl-loss pathway from the B(2)E state was statistical predissociation. With the aid of calculated Cl-loss potential energy curves of CH(3)Cl(+), CH(3)(+) formation from CH(3)Cl(+)(A(2)A(1)) ions was a rapid direct fragmentation, while CH(3)Cl(+)(B(2)E) ions statistically dissociated to CH(3)(+) + Cl via internal conversion to the high vibrational states of X(2)E.

Dissociation mechanisms of excited CH3X (X = Cl, Br, and I) formed via high-energy electron transfer using alkali metal targets.

High-energy electron transfer dissociation (HE-ETD) on collisions with alkali metal targets (Cs, K, and Na) was investigated for CH(3)X(+) (X = Cl, Br, and I) ions by a charge inversion mass spectrometry. Relative peak intensities of the negative ions formed via HE-ETD strongly depend on the precursor ions and the target alkali metals. The dependency is explained by the exothermicities of the respective dissociation processes. Peak shapes of the negative ions, especially of the X(-) ions, which comprise a triangle and a trapezoid, also strongly depend on the precursor ions and the target alkali metals. The trapezoidal part of the I(-) peak observed with the Na target is more dominant and much broader than that with the Cs target. This dependence on the targets shows an inverse relation between the peak width and the available energy, which corresponds to the exothermicity assuming formation of fragment pair in their ground internal states. From a comparison of the kinetic energy release value calculated from the trapezoidal shape of I(-) with the available energy of the near-resonant level on the CH(3)I potential energy curve reported by ab initio calculations, the trapezoidal part is attributed to the dissociation to CH(3) + I((2)P(3/2)) via the repulsive (3)Q(1) state of CH(3)I, which is not dominant in the photo-dissociation of CH(3)I. The observation of trapezoid shape of the CH(2)I(-) peak with the Cs target indicates spontaneous dissociation via repulsive potential from the (3)R(2) Rydberg state, although the correlation between the (3)R(2) Rydberg state and relevant repulsive states has not been reported by any theoretical calculation.

Reactions of atomic metal anions in the gas phase: competition between electron transfer, proton abstraction and bond activation.

Bare metal anions K(-), Rb(-), Cs(-), Fe(-), Co(-), Ni(-), Cu(-), and Ag(-), generated by electrospray ionization of the corresponding oxalate or tricarballylate solutions, were allowed to react with methyl and ethyl chloride, methyl bromide, nitromethane, and acetonitrile in the collision hexapole of a triple-quadrupole mass spectrometer. Observed reactions include (a) the formation of halide, nitride, and cyanide anions, which was shown to be likely due to the insertion of the metal into the C-X, C-N, and C-C bonds, (b) transfer of H(+) from the organic molecule, which is demonstrated to most likely be due to the simple transfer of a proton to form neutral metal hydride, and (c) in the case of nitromethane, direct electron transfer to form the nitromethane radical anion. Interestingly, Co(-) was the only metal anion to transfer an electron to acetonitrile. Differences in the reactions are related to the differences in electron affinity of the metals and the Δ(acid)H° of the metals and organic substrates. Density functional theory calculations at the B3-LYP/6-311++G(3df,2p)//B3-LYP/6-31+G(d) level of theory shed light on the relative energetics of these processes and the mechanisms by which they take place.

Hybrid quantum mechanical/molecular mechanics study of the S(N)2 reaction of CH3Cl+OH- in water.

The S(N)2 mechanism for the reaction of CH(3)Cl + OH(-) in aqueous solution was investigated using combined quantum mechanical and molecular mechanics methodology. We analyzed structures of reactant, transition, and product states along the reaction pathway. The free energy profile was calculated using the multilayered representation with the DFT and CCSD(T) level of theory for the quantum-mechanical description of the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process. We find that solvation energy contribution raises the reaction barrier by ~18.9 kcal/mol and the reaction free energy by ~24.5 kcal/mol. The presence of the solvent also induces perturbations in the electronic structure of the solute leading to an increase of 3.5 kcal/mol for the reaction barrier and a decrease of 5.6 kcal/mol for the reaction free energy, respectively. Combining the results of two previous calculation results on CHCl(3) + OH(-) and CH(2)Cl(2) + OH(-) reactions in water, we demonstrate that increase in the chlorination of the methyl group (from CH(3)Cl to CHCl(3)) is accompanied by the decrease in the free energy reaction barrier, with the CH(3)Cl + OH(-) having the largest barrier among the three reactions.

Proton transfer in phenol-amine complexes: phenol electronic effects on free energy profile in solution.

Free energy profiles for the proton transfer reactions in hydrogen-bonded complex of phenol with trimethylamine in methyl chloride solvent are studied with the reference interaction site model self-consistent field method. The reactions in both the electronic ground and excited states are considered. The second-order Møller-Plesset perturbation (MP) theory or the second-order multireference MP theory is used to evaluate the effect of the dynamical electron correlation on the free energy profiles. The free energy surface in the ground state shows a discrepancy with the experimental results for the related hydrogen-bonded complexes. To resolve this discrepancy, the effects of chloro-substitutions in phenol are examined, and its importance in stabilizing the ionic form is discussed. The temperature effect is also studied. In contrast to the ground state, the ππ* excited state of phenol-trimethylamine complex exhibits the proton transfer reaction with a low barrier. The reaction is almost thermoneutral. This is attributed to the reduction of proton affinity of phenol by the ππ* electronic excitation. We further examine the possibility of the electron-proton-coupled transfer in the ππ* state through the surface crossing with the charge transfer type πσ* state.