The structure of microsolvated benzene derivatives and the role of aromatic substituents

Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene

IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).

Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters

Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.

AB INITIO AND DFT STUDY OF NON-COVALENT INTERACTIONS BETWEEN RARE GAS ATOMS AND AROMATIC RINGS

In this paper, the weak interaction between aromatic rings (ARs) and rare gas (Rg) atoms has been studied using ab initio calculation and density functional theory (DFT). The augmented Dunning basis sets were used, and the convergence test was performed up to aug-cc-pV5Z. Among the computationally feasible methods, ωB97XD performed the best for these non-covalent systems. NBO analysis was performed to investigate the nature of the Rg/AR interactions. In this type of weak interaction, the induced and instantaneous dipole and charge transfer character both contribute to the interaction energies and equilibrium distances.

Infrared predissociation of ternary cluster cations: the solvent effects on the branching ratio

Infrared (IR) predissociation of hydrogen-bonded ternary cluster ions such as aniline-water-ethanol (AWE(+)), aniline-water-isopropanol (AWP(+)), aniline-methanol-ethanol (AME(+)), aniline-water-pyrrole (AWPy(+)), and aniline-water-benzene (AWB(+)) was examined in the region of 2700-4000 cm(-1) to explore the key factors which determine the branching ratios in the concurrent unimolecular dissociation. The smaller solvent molecule was predominantly ejected when the binding energies of the two were not too different. On the other hand, when they were far off, the binding energy also acted significantly on the branching ratio. Besides, mode-selective IR predissociation was observed, while the selectivity was not quite distinct. The IR predissociation of ternary cluster ions bound via hydrogen bonding is considered to occur on a time scale much faster than intramolecular vibrational energy redistribution, which was proved by a statistical transition state theory.

Reactions within fluorobenzene-ammonia heterocluster ions: experiment and theory

Reactions occurring within gas phase fluorobenenze-ammonia heterocluster cations (FC(6)H(5)-(NH(3))(n=1-4)) have been studied through the use of a triple quadrupole mass spectrometer as well as employing density functional theory (DFT). Collision induced dissociation (CID) experiments were conducted in which mass selected cluster ions are accelerated into a cell containing argon gas and the resulting products then subsequently mass analyzed. Two dominate reaction channels are observed. The first is simple evaporative loss of neutral ammonia from the cluster ion. The second involves a substitution reaction occurring within the cluster ion to form the aniline cation, C(6)H(5)NH(2)(+), where the reactivity was found to vary as a function of cluster size. DFT calculations have been performed to both help analyze the structure and the reactivity of these cluster ions. Pronounced differences in activation energies were found that provide an explanation for the observed variation of reactivity as a function of cluster size. An ad hoc model based upon the Arrhenius equation was developed to fit both the experimental collision energy dependence of the reaction and the observed lowering of the reaction barrier to aniline formation as a function of cluster size.

Specific photodynamics in thymine clusters: the role of hydrogen bonding

A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.

What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller-Plesset second-order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K(+)/Cl(-) ion-pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion-pair [K(+)(H(2)O)(5)Cl(-)]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion-pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed.

Environment influences on the aromatic character of nucleobases and amino acids

Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤ 1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤ 1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues.