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The one photon and the two photon S1←S0 spectra of jet-cooled p-ethynyltoluene have been measured for the first time, and a detailed vibronic analysis for both spectra has been attained. Mass analyzed resonance enhanced multiphoton ionization spectroscopy is the employed technique. In the one photon spectrum, the allowed component (origin and Franck-Condon bands) is much weaker than the forbidden component, and the same mechanisms as in the one photon spectrum of phenylacetylene are observed. The methyl torsional transitions are active. The 000 band is at 35 483 cm-1. The two photon spectrum is very strong and bears a resemblance to the two photon spectrum of phenylacetylene. The potential barrier of the methyl rotor in the S1 state has been determined as V6=-12 cm-1 with BCH3=5.55 cm-1. Ab initio calculations, MP2(full)/cc-pVTZ and CAS/cc-pVTZ, have been implemented for the geometry optimization and the normal mode vibration computation in the S0 and S1 states. [ABSTRACT FROM AUTHOR]

The molecular geometries, conformational energies, and zero-point energies of di(trimethylsilylene)methylene are obtained from high-level quantum chemistry calculations. Molecular mechanics and Monte Carlo calculations for isolated polymer chains together with molecular dynamics runs for the modeled dimer have provided excellent results in terms of conformational and thermodynamic properties.

Interpolated variational transition state theory calculations with centrifugal-dominant, small-curvature tunneling coefficients have been carried out for the case of the deuterium kinetic isotope effect (KIE) in the reaction OH+12CD4→HDO+12CD3 and for the 13C KIE for the reaction OH+13CH4→H2O+13CH3. The interpolated variationally optimized generalized transition states predict notably different nontunneling KIEs than the conventional ones, and factorization analyses of the KIEs are presented to illustrate the origin of the differences. The zero-point energies at the variational transition states differ from those at the saddle point by up to 0.19 kcal/mol for the OH+12CD4 reaction and by up to 0.34 kcal/mol for the OH+13CH4 reaction. The incorporation of multidimensional tunneling effects partly cancels the effect of variational optimization of the transition state. [ABSTRACT FROM AUTHOR]

We have carried out ab initio calculations for the reaction OH+CH4→H2O+CH3 using second-order Mo\ller–Plesset perturbation theory, employing a very large basis set and scaling all correlation energy for the final energy calculation, but optimizing the equilibrium and transition state structures without scaling (MP-SAC2//MP2). We found that inclusion of correlation energy has an important effect on the geometry, barrier height, and vibrational frequencies of the transition state. The final calculated values for the forward and reverse classical barrier heights are 7.4 and 20.6 kcal/mol, respectively. We have used these with interpolated canonical variational transition state theory and the centrifugal-dominant small-curvature tunneling approximation, including information at the reactants, products, transition state, and two other points along the minimum energy path, to predict the rate constants for the above reaction in the temperature range from 223 to 2400 K. The calculated rate constants agree well with experiment over a wide temperature range. [ABSTRACT FROM AUTHOR]

In this paper we optimize several algorithms for the computation of reaction rates based on information calculated along minimum energy reaction paths and we evaluate the efficiencies of the optimized algorithms. The investigations are based on the calculation of chemical reaction rate constants using variational transition state theory and multidimensional semiclassical transmission coefficients including reaction path curvature. Several methods are evaluated and compared by a systematic set of applications to test cases involving the hydrogen-atom transfer reactions CH3+H2→CH4+H and OH+H2→H2O+H. For each method we present general recommendations for all algorithmic choices other than gradient step size so that future calculations may be carried out reasonably efficiently by varying only one parameter. In the process of these optimizations we have found that the accuracy of the Euler stabilization method can be significantly increased by choosing the auxiliary parameters differently than in previous work; the optimized algorithm is called ES1*. Our final recommendations for future work are (i) when the Hessian/gradient computational cost ratio is low (<=3): the Page–McIver algorithm with the Hessian recalculated at every step, with a cubic starting step, and with curvature calculated from the derivative of the gradient, and (ii) when the Hessian/gradient computational cost ratio is moderate or large: the ES1* algorithm with a Hessian step size three times larger than the gradient step size, with a quadratic starting step, and with curvature calculated from the derivative of the gradient. [ABSTRACT FROM AUTHOR]

Geometries for possible transition states and energy minima of the potential-energy surface for the reaction between BrO and CIO radicals and for conformers of CIOOBr peroxide are identified and harmonic frequency calculations are carried out. The results of the study assist in the qualitative understanding of the mechanism and kinetics of BrO + CIO reaction.

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the “isolated” carboxylic (–COOH) and amide (–NH) interactions in neat DMSO via1H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the –COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems. [ABSTRACT FROM AUTHOR]

The 13C longitudinal relaxation times (T1) of three biomolecule groups of major significance to proteins and cells – protein amino acids (AAs), acetyl-amino acids (Ac-AAs) and betaines – and the 14N linewidths (Δν1/2) of Ac-AAs and betaines were measured in aqueous solutions at acidic and neutral pH, by NMR spectroscopy, to estimate the effect of the molecular weight (Mw) on 13C longitudinal relaxation times and 14N linewidths, respectively. 13C relaxation times indicate that AAs and Ac-AAs strongly interact with the same number of water molecules at acidic and neutral pH, respectively, whereas both 13C and 14N results indicate that their Mw values at acidic pH (protonated, positively charged AAs and zero-charged Ac-AAs) increase relatively to those at pH 6.0 (zwitterionic AAs and negatively charged Ac-AAs) that translates into their extra hydration with an excess of one water molecule. Both 13C and 14N relaxation times revealed that betaines retain their hydration grade in both their ionization states at two pH values, while exhibiting their hydration differences from AAs and Ac-AAs and pointing out the “controlling” role of the amino and imino groups in the extra hydration of protonated AAs and Ac-AAs, enlightening the so far unknown significant role of the N-terminus and the −NH near the C-terminus in peptide solvation. Moreover, DFT calculations of the interacting water molecules through hydrogen bonds with Ala, Ac-Ala and Ala betaine molecules in their protonated and neutral pH forms are in absolute agreement with NMR results. Finally, a fully promising method arises with a view on hydration–solvation studies of oligopeptides and other bio-organic molecules by 13C relaxation. [ABSTRACT FROM AUTHOR]

Two different effective-core-potential methodologies, augmented with extra polarization functions are used at the MP2 level of theory to investigate the isomers of I-containing peroxides of the type XOOI, XIO2, IXO2, XOIO and IOXO (X=Cl, Br, I). The reliability of the results is checked against the all-electron calculations of Misra and Marshall [J. Phys. Chem. A, 102 (1998) 9056] for the IOOI family. Contrary to what has been well established for the chlorine and bromine analogs, the present study confirms the interesting observation that the I-containing peroxide isomers, XOOI, are not the most stable structures in each subfamily. [Copyright &y& Elsevier]

Two different effective-core-potential methodologies, augmented by extra polarization functions were used to investigate a number of iodine triatomics of the type XOI, XIO and IXO (X = Cl, Br, I). The procedures were tested first on the well-studied ClOCl, BrOBr, ClOBr and IOI systems and they were shown to reproduce the full-electron calculation results with reasonable consistency. The results exhibit the same tendencies as the corresponding Cl and Br analogues and produce the greater stability for the isomer with the least electronegative atom in the middle. [Copyright &y& Elsevier]

Abstract: Ab initio calculations have been performed for both H-atom and Cl-atom abstraction reactions by the hydroxyl radical. Geometry optimization and vibrational frequencies analysis were performed for reactants, transition state and products at the MP2(full)/cc-pVTZ level of theory. On the basis of the ab initio data, the rate constants have been deduced over a wide temperature range, 200–2000 K, using conventional transition state theory, including Wigner tunneling correction and the hindered rotor approximation. Calculated transition state rate constants with Wigner tunneling correction are in good agreement with experimental results. The tunneling contribution becomes important at ambient temperatures, resulting in the exhibited non-Arrhenius behavior of the rate constant. [Copyright &y& Elsevier]

Abstract: In this work, magnetometry and EPR spectroscopy studies on the binuclear Mn(II) complex [Mn2{(OPPh2)2N}4] (1) established antiferromagnetic interactions between the two S =5/2 Mn(II) centers being at 3.378Å from each other. The magnitude of the J AB coupling constant, in the framework of the formalism, was determined to be −4.5±0.5cm−1, by the temperature dependence of the magnetic susceptibility of 1. This value is comparable with the one of the previously studied [Mn2{(OPPh2)[OP(OEt)2]N}4(H2O)2] complex (−3.5cm−1), which bears similar type of ligands. The antiferromagnetic nature of the coupling within the binuclear Mn2O4 core of 1 was unequivocally confirmed also by EPR studies on frozen CH2Cl2 solutions at various temperatures. Density functional broken-symmetry calculations confirmed the above experimental findings and provided J AB values in close agreement with the experiment. Comparisons with literature binuclear Co(II) or Mn(II) complexes were made. [Copyright &y& Elsevier]

Abstract: Ab initio calculations were conducted for both reaction pathways of the CH3Br and OH system. Geometry optimization and vibrational frequencies analysis were performed for reactants, pre-reaction complex, transition states, post-reaction complex and products at the MP2(full)/6-311+G(d,p), MP2(full)/6-311+G(3df,2pd) and MP2(full)/cc-pVTZ levels of theory. Energetic results were further refined by CCSD(T,full) calculations, using optimized geometric parameters of the MP2(full)/cc-pVTZ level, i.e., CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ. Based on MP2(full)/cc-pVTZ and CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ data, rate constants were deduced in the 200–2000K temperature range, using conventional transition state theory and Wigner tunneling correction. Calculated rate constants, including tunneling corrections, were found to be in excellent agreement with experimental results. [Copyright &y& Elsevier]

The mechanisms for the OH radical and Cl atom gas-phase reaction kinetics of substituted aromatic compounds remain a topic of atmospheric and combustion chemistry research. 4-Chlorobenzotrifluoride ( p -chlorobenzotrifluoride, p -ClC 6 H 4 CF 3 , PCBTF) is a commonly used substituted aromatic volatile organic compound (VOC) in solvent-based coatings. As such, PCBTF is classified as a volatile chemical product (VCP) whose release into the atmosphere potentially impacts air quality. In this study, rate coefficients, k 1 , for the OH + PCBTF reaction were measured over the temperature ranges 275-340 and 385-940 K using low-pressure discharge flow-tube reactors coupled with a mass spectrometer detector in the ICARE/CNRS (Orléans, France) laboratory. k 1 (298-353 K) was also measured using a relative rate method in the thermally regulated atmospheric simulation chamber (THALAMOS; Douai, France). k 1 ( T ) displayed a non-Arrhenius temperature dependence with a negative temperature dependence between 275 and 385 K given by k s 1 (275-385 K) = (1.50 ± 0.15) × 10 -14 exp((705 ± 30)/T) cm 3 molecule -1 s -1 s k 1 (298 K) = (1.63 ± 0.03) × 10 -13 cm 3 molecule -1 s -1 and a positive temperature dependence at elevated temperatures given by k 1 (470-950 K) = (5.42 ± 0.40) × 10 -12 exp(-(2507 ± 45) /T) cm 3 molecule -1 s -1 s k 1 (298 K) results are in reasonable agreement with two previous 296 K (760 Torr, syn. air) relative rate measurements. The rate coefficient for the Cl-atom + PCBTF reaction, k 2 , was also measured in THALAMOS using a relative rate technique that yielded k 2 (298 K) = (7.8 ± 2) × 10 -16 cm 3 molecule -1 s -1 . As part of this work, the UV and infrared absorption spectra of PCBTF were measured (NOAA; Boulder, CO, USA). On the basis of the UV absorption spectrum, the atmospheric instantaneous UV photolysis lifetime of PCBTF (ground level, midlatitude, Summer) was estimated to be 3-4 days, assuming a unit photolysis quantum yield. The non-Arrhenius behavior of the OH + PCBTF reaction over the temperature range 275 to 950 K is interpreted using a mechanism for the formation of an OH-PCBTF adduct and its thermochemical stability. The results from this study are included in a discussion of the OH radical and Cl atom kinetics of halogen substituted aromatic compounds for which only limited temperature-dependent kinetic data are available.

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via 1 H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

How many solvent molecules and in what way do they interact directly with biomolecules? This is one of the most challenging questions regarding a deep understanding of biomolecular functionalism and solvation. We herein present a novel NMR spectroscopic study, achieving for the first time the quantification of the directly interacting water molecules with several neutral dipeptides. Our proposed method is supported by both molecular dynamics simulations and density functional theory calculations, advanced analysis of which allowed the identification of the direct interactions between solute-solvent molecules in the zwitterionic L-alanyl-L-alanine dipeptide-water system. Beyond the quantification of dipeptide-water molecule direct interactions, this NMR technique could be useful for the determination and elucidation of small to moderate bio-organic molecular groups' direct interactions with various polar solvent molecules, shedding light on the biomolecular micro-solvation processes and behaviour in various solvents.

The one photon and the two photon S(1)<--S(0) spectra of jet-cooled p-ethynyltoluene have been measured for the first time, and a detailed vibronic analysis for both spectra has been attained. Mass analyzed resonance enhanced multiphoton ionization spectroscopy is the employed technique. In the one photon spectrum, the allowed component (origin and Franck-Condon bands) is much weaker than the forbidden component, and the same mechanisms as in the one photon spectrum of phenylacetylene are observed. The methyl torsional transitions are active. The 0(0) (0) band is at 35 483 cm(-1). The two photon spectrum is very strong and bears a resemblance to the two photon spectrum of phenylacetylene. The potential barrier of the methyl rotor in the S(1) state has been determined as V(6)=-12 cm(-1) with B(CH(3) )=5.55 cm(-1). Ab initio calculations, MP2(full)/cc-pVTZ and CAS/cc-pVTZ, have been implemented for the geometry optimization and the normal mode vibration computation in the S(0) and S(1) states.