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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]

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]

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]

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]