Correlations between experimental matrix-isolation FT-IR and DFT(B3LYP) calculated data for isolated 1:1 H-bonded complexes of water and pyridine or imidazole derivatives

(1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

Collision-induced dissociation products of the protonated dipeptide carnosine: structural elucidation, fragmentation pathways and potential energy surface analysis

Collision-induced dissociation (CID) experiments on protonated carnosine, [carnosine + H](+), with several collision energies were shown to yield eleven different fragment ions with the generation of product ions [carnosine-H2O + H](+) and [carnosine-NH3 + H](+) being the lowest energy processes. Energy-resolved CID showed that at slightly higher collision energies the ions [histidine + H](+) and [histidine-H2O-CO + H](+) are formed. At even higher energies four other product ions were observed, however, attained relatively lower abundances. Quantum chemistry calculations, carried out at different levels of theory, were employed to probe fragmentation mechanisms that account for all the experimental data. All the adopted computational protocols give similar energetic trends, and the range of the calculated free energy barrier values for the generation of all the observed product ions is in agreement with the fragmentation mechanisms offered here.

Structures, energetics and vibrational frequency shifts of hydrated pyrimidine

More than 70 unique micro-hydrated structures of pyrimidine, ranging in size from 1 to 7 water molecules, have been characterized with the B3LYP density functional and the 6-311++G(2df,2pd) triple-ζ split-valence basis set. Explicitly correlated MP2-F12 single-point computations were performed on each structure with a correlation consistent triple-ζ basis set to estimate the relative and dissociation energies at the MP2 complete basis set (CBS) limit. Many of these new structures have significantly lower energies than those previously reported (by as much as 12.66 kcal mol(-1)). For clusters with 1 and 2 water molecules, the MP2-F12 relative and dissociation energies are virtually identical to the corresponding CCSD(T)-F12 values. As the number of hydrating waters increases, the structures in which the water molecules are clustered together at one of the N atoms have lower energies than those where the water molecules are more distributed around the pyrimidine ring. Micro-hydrated structures that effectively extend the low-energy hydrogen-bonding motifs to both sides of the ring, as would be expected in the bulk phase, reproduce the experimentally observed vibrational frequency shifts of ν(1) and ν(8b) in very dilute aqueous pyrimidine solutions to within 1 cm(-1) . Micro-hydrated structures of pyrimidine in which water molecules are clustered together have lower energies than structures in which the water molecules are more evenly spread around the pyrimidine ring.

Hydrogen-Bonding between Pyrimidine and Water: A Vibrational Spectroscopic Analysis

We present an experimental and a theoretical study on hydrogen-bonding between pyrimidine and water as the H-donor. The degree of hydrogen-bonding in this binary system varies with mixture composition. This was monitored experimentally by polarization-resolved linear Raman spectroscopy with the pyrimidine ring breathing mode nu1 as a marker band. A subsequent quantitative line shape analysis of the isotropic Raman intensity for 24 pyrimidine/water mixtures clearly revealed a splitting into three spectral components upon dilution with water. The two additional peaks have been assigned to distinct groups of hydrogen-bonded species that differ in the number of pyrimidine nitrogen atoms (N) involved in hydrogen-bonding to water hydrogen atoms (H). From the integrated Raman intensities for "free" and "hydrogen-bonded" pyrimidine, a concentration profile for these species was established. Our assignments and interpretations are supported by quantum mechanical calculations of structures and by vibrational spectra for pyrimidine and 10 pyrimidine/water complexes with increasing water content. Also, accurate structure-spectra correlations for different cluster subgroups have been determined; within each particular cluster subgroup the water content varies, and a perfect negative correlation between NH hydrogen-bond distances and nu1 wavenumbers was observed.

Determination of Critical Indices by “Slow” Spectroscopy: NMR Shifts by Statistical Thermodynamics and Density Functional Theory Calculations

The temperature dependencies of NMR shifts in the critical region of two coexisting phases have been simulated using statistical thermodynamics and graph-theory consideration of equilibrium processes of molecular association. Microparameters of magnetic screening of various water and water/pyridine structures used in the statistical averaging have been evaluated by density functional theory calculations (PBE1PBE and B3PW91 functionals in the 6-311++G** basis set). The gauge-including atomic orbital (GIAO) approach has been applied to ensure gauge invariance of the results. Solvent effects were taken into account by a polarized continuum model (PCM). NMR shifts "order parameters" (Deltadelta = |delta+ - delta-|) and "diameters" (phidelta = |(delta+ + delta-)/2 - deltaC|, where delta+, delta-, and deltaC are the chemical shifts of coexisting phases and at the critical point respectively) have been calculated in each case close to the lower critical solution point (TL) and processed using linear regression analysis of Deltadelta approximately |T - TL| and phidelta approximately |T - TL| in the log-log plot. It has been shown that the critical index beta can be evaluated with high precision from the slope of Deltadelta = f(T - TL) at any realistic set of model input parameters. The slope of diameter has been found to depend on both input beta and alpha values. The obtained phidelta slopes (0.58-0.63) are very close to 2beta values. The results are discussed within the concept of complete scaling. Results of simulation are compared and supported by experimental NMR data for water/2,6-lutidine, acetic anhydride/n-heptane, and acetic anhydride/cyclohexane systems.

Proton transfer in hydrogen-bonded pyridine/acid systems: the role of higher aggregation

In this work the role of higher molecular aggregation in the proton transfer processes within hydrogen bond (H-bond) is investigated. The H-bonded complex consisting of 4-cyanopyridine (CyPy) with trichloroacetic acid (TCA) has been studied in the solutions of acetonitrile, carbon tetrachloride, chloroform and dichloroethane as solvent by FTIR spectroscopy and quantum chemical DFT calculations. In order to illustrate the effect of increasing H-bond strength FTIR investigations have also been performed on solutions of CyPy with H(2)O, acetic-, trifluoroacetic- and methanesulfonic acids. Proton states in the H-bond have been monitored using vibrational CyPy ring modes in FTIR spectra. The stabilization of the CyPy/TCA complex in its protonated form upon increasing polarity of the solvent has been evidenced. It was shown that formation of the CyPy/(TCA)(2) aggregates in the solutions favors the proton transfer process. An X-ray diffraction study has been performed on a single 1 : 2 co-crystal of pyridine/3,5-dinitrobenzoic acid. The H-bond motif found in this system exhibits the same connectivity by strong hydrogen bonds N-H(+)[dot dot dot]O(-) and O-H[dot dot dot]O as that in the CyPy/(TCA)(2) complex predicted by DFT calculation. Certain discrepancies are observed in C-H[dot dot dot]O connectivity only. The networks of H-bonds in both assemblies differ from those usually pictured for 1 : 2 base/carboxylic acid complexes in the literature.

An o-Iminothioquinone: Its Cycloaddition To Produce an Indologlycoside and Its Self-Dimerization To Form a Dithio-Diazocycloctane, the Structure Assignment of Which Is Based on the DFT Prediction of Its IR Spectrum

An unusual heterodiene, an indolothiono quinone, undergoes cycloaddition with a glycal to form an indole-N-glycoside. A novel dimer of the indolothionoquinone is assigned its structure on the basis of a match between its predicted and observed IR spectrum.