On the gas phase hydrogen bond complexes between formic acid and hydroperoxyl radical. A theoretical study

We present a systematic study on the gas-phase hydrogen-bonded complexes formed between formic acid and hydroperoxyl radical, which has been carried out by using B3LYP and CCSD(T) theoretical approaches in connection with the 6-311+G(2df,2p) basis set. For all complexes we have employed the AIM theory by Bader and the NBO partition scheme by Weinhold to analyze the bonding features. We have found 17 stationary points, and 11 of them present a cyclic structure. Their computed stabilities vary from 0.3 to 11.3 kcal/mol, depending on several factors, such as involvement in the hydrogen bond interaction, the geometrical constraints, and the possible concurrence of further effects such as resonance-assisted hydrogen bonds or inductive effects. In addition, three stationary points correspond to transition structures involving a double proton-transfer process whose features are also analyzed.     

Cooperative interaction of hydrogen bonds in proton exchange between the bases of nucleic acids

The tautomeric equilibrium in the H-bonded pair guanine-cytosine was studied by the semiempirical MNDO/HB quantum-chemical method. It was shown that hydration of the bases leads to an appreciable reduction of the activation barrier in the synchronous exchange of protons between the bases. Desolvation of the active center of the polymerase reduces the probability of error in the synthesis of the complementary chain of the nucleic acid by 10⁶ times. Deprotonation of the phosphate groups of the nucleotides destabilizes the transition state in proton exchange. The genetic information is conserved as a result of the formation of nucleoprotein complexes with an ionic bond between the phosphate residue of the saccharophosphate skeleton of the nucleic acid and an amino (imino) group of the protein.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1828–1832, August, 1991.     

Substituent effects on two-center three-electron bonds and hydrogen bonds involving unsaturated organic functional groups and an ammonia radical cation--the resonance contribution

A theoretical investigation of the substituent effects on the two-center, three-electron (2c-3e) bond involved between unsaturated functional groups and an amine nitrogen is presented. The competitive hydrogen-bonded complexes are also studied. In both cases, the bond energies are found to be in the range of 20-30 kcal mol(-1). The variation of these energies is discussed with respect to the electron-donating effect of the substitutents, as well as with respect to the alpha-bonded atom of the organic functional group (O, S, NH). For the 2c-3e bonds, the results are discussed on the basis of the differences of the ionization potential (delta IP) of the separated fragments and can be rationalized through the valence bond theory. For the hydrogen bonds, the substituent influence is discussed by using the differences of the proton affinities (delta PA) of the substrates. The resonating nature of the hydrogen bond in these cationic systems is investigated and is found to account for most of the binding energy. Marcus theory is compared with the proposed resonating model.     

C-F...H-C hydrogen bonds in ribonucleic acids

We report the synthesis of 1'-deoxy-1'-(benzimidazol-1-yl)-beta-D-ribofuranose 7 and 1'-deoxy-1'-phenyl-beta-D-ribofuranose 2. With these two ribonucleoside analogues we have a set of nine different RNA building blocks in hand, which are isostere to the natural bases. Now it is possible to investigate their duplex stabilizing forces. These forces are hydrogen bonds, base stacking, and solvation. The phosphoramidites of all building blocks were incorporated into a 12mer RNA, and the resulting RNA duplexes were investigated by UV- and CD-spectroscopy. We found that some of the RNA analogues are universal bases. The best universal bases with the lowest destabilization and the smallest discrimination between the natural bases are 1 (B) and 9 (E). On the basis of UV measurements we determined the melting points and the thermodynamic data. We were able to show that there are no hydrogen bonds between the natural bases and the RNA analogues. From thermodynamic data we calculated the contributions for base stacking and solvation of all modified building blocks. Comparison of calculated and measured data of double modified base pairs in 12mer RNA duplexes showed a further duplex stabilizing force in base pairs containing fluorine atoms at the Watson-Crick binding site. This stabilizing force can be defined as C-F.H-C hydrogen bond as is observed in crystal structures of 1'-deoxy-1'-(4-fluorophenyl)-beta-D-ribofuranose.     

Structure of hydrogen tetroxide in gas phase and in aqueous environments: relationship to the hydroperoxyl radical self-reaction

Structural Chemistry - Hydrogen polyoxides are important species in atmospheric chemistry, advanced oxidation processes for wastewater treatment, and biological processes, among other fields....     

Modeling protein-protein interactions through alanine-amide hydrogen bonds

The hydrogen-bonded complexes formed between alanine and formamide and between alanine and N-methylformamide have been completely investigated in the present study using ab initio molecular orbital theory (MP2) and density functional theory (B3LYP) using aug-cc-pVDZ basis set. Geometry optimization and vibrational frequency calculations have been carried out for isolated and hydrogen-bonded systems. The stabilization energies (?E_BSSE) suggest that alanine-N-methylformamide complexes are more stable than alanine-formamide complexes. The tendency of N-H of amide to act as hydrogen bond (HB) donor is found to be much better in relative to the N-H of amino group of alanine. The study suggests that the tendency of carbonyl oxygen of amide to act as HB acceptor towards various sites of alanine decreases in the order O–H?>?N–H?>?C–H. The results are corroborated by natural bond orbital (NBO) analysis, Bader’s theory of atoms in molecules (AIM) and molecular electrostatic potential (MEP) studies. The blue and red shifts in the stretching frequencies of HB donors X-H (X?=?O, N, C) have also been analysed.     

Mechanism for the gas-phase reaction between formaldehyde and hydroperoxyl radical. A theoretical study

We present a high-level theoretical study on the gas-phase reaction between formaldehyde and hydroperoxyl radical carried out using the DFT-B3LYP, QCISD, and CCSD(T) theoretical approaches in connection with the 6-311+G(d,p), 6-311+G(2df,2p), and aug-cc-pVTZ basis sets. The most favorable reaction path begins with the formation of a pre-reactive complex and produces the peroxy radical CH(2)(OO)OH in a process that is computed to be exothermic by 16.8 kcal/mol. This reaction involves a process in which the oxygen terminal of the HO(2) moiety adds to the carbon of formaldehyde, and, simultaneously, the hydrogen of the hydroperoxyl group is transferred to the oxygen of the carbonyl in a proton-coupled electron-transfer mechanism. Our calculations show that this transition state lies below the sum of the energy of the reactants, and we computed a rate constant at 300 K of 9.29 x 10(-14) cm(3) molecule(-1) s(-1), which is in good agreement with the experimental results. Also of interest in combustion chemistry, we studied the hydrogen abstraction process by HO(2), the result of which is the formation of HCO + H(2)O(2). We found two reaction paths with activation enthalpies close to 12 kcal/mol. For this process, we computed a rate constant of 1.48 x 10(-16) cm(3) molecule(-1) s(-1) at 700 K, which also agrees quite well with experimental results.     

Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases

A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.     

Probing the nature of three-centered hydrogen bonds in minor-groove ligand-DNA interactions: the contribution of fluorine hydrogen bonds to complex stability

Double-stranded DNA sequences have been prepared in which single atoms (the O2-carbonyls of selected thymines) have been replaced by fluorine or methyl. To maintain normal Watson-Crick hydrogen bonding with the complementary purines, these analogue derivatives have been prepared as C-nucleosides. The O2-carbonyls of interest for this study are those involved in a bifurcated (or three-centered) hydrogen bond with the minor groove binding ligand 4',6-diamidino-2-phenylindole (DAPI). TM studies of the duplexes illustrate that the DNA duplexes are destabilized when fluorine or methyl replaces one or both of the minor groove O2-carbonyls, which can in part be explained by changes in minor groove hydration. In the presence of DAPI, most of the duplexes exhibit an increased TM due to the presence of DAPI bound in the minor groove. The extent of helix overstabilization negatively correlates with the presence of one or both methyl groups in the minor groove, suggesting that ligand binding is weakened in the presence of the non-carbonyl functional groups. The presence of single fluorine appears to promote helix stabilization, and native-like stabilization occurs when both fluorines are present. KD values quantitate binding effects between DAPI and the native and analogue sequences. Sequences with one or both methyl groups exhibit very poor binding with DAPI, while those containing a single fluorine behave essentially like native carbonyl-containing sequences. With both fluorines present, KD values were observed to increase by a moderate 3-fold at 100 mM NaCl and somewhat more at 200 mM NaCl. Binding affinities with both methyl groups present were 500-1000-fold weaker than native. The results suggest that organofluorines can function as hydrogen-bond acceptors, at least in the bifurcated interaction that contributes to minor groove binding by DAPI.     

Unique hydrogen bonds between 9-anthracenyl hydrogen and anions

Unique hydrogen bonds of the 9-H of anthracene moieties in hosts 1 and 2 with fluoride and pyrophosphate ions were observed on the basis of the (1)H NMR experiments. Furthermore, hosts 1 and 2 act as a colorimetric sensor and a fluorescent chemosensor for the recognition of fluoride ion, respectively.     

Comparative study of weak interactions in molecular crystals: H-H bonds vs hydrogen bonds

The crystal structures of tetraphenylphosphonium squarate, bianthrone, and bis(benzophenone)azine are shown to contain a variety of C-H(delta+)...(delta+)H-C interactions, as well as a variety of C-H...O and C-H...C(pi) interactions. Each of these molecules possesses interactions that can possibly be characterized as either H-H bonds or weak hydrogen bonds based on the first four criteria proposed by Koch and Popelier. These interactions have been completely characterized topologically after the multipole refinement of the structures. It appears that weak interactions of the form C-H(delta+)...(delta+)H-C possess certain correlations between the various properties of the electron density at the bond critical points. The coexistence of the three types of interactions makes it possible to establish similarities and differences in the correlations of these weak interactions. This all leads to a better understanding of H-H interactions and how they fit into the hierarchy of weak interactions.     

Imino- and aminomethylphenylboronic acids: stabilizing effect of hydrogen bonds

ortho-Iminomethylphenylboronic acids were synthesized from the reaction of 2-formyl–phenylboronic acid with primary aromatic amines. Reduction of these compounds yielded the corresponding aminomethylphenylboronic acids. For both types of the compounds, the crystal structure was determined by single crystal X-ray diffraction method. Hydrogen-bonded dimers with an additional intramolecular B–O–H…N hydrogen bond have been observed. Calculations at MP2/6–31+G** level proved that the most stable form is that with the above-mentioned intramolecular hydrogen bond while the form with dative N→B bond is less favoured. Since the calculated energy difference is small, the competition between possible forms was analyzed in terms of substituent effect stabilization energy (SESE). In the case of p-iminomethylphenylboronic acid, both hydroxyl groups are engaged in intermolecular O–H…O interactions resulting in a supramolecular ribbon motif.     

Utilizing hydrogen bonds and halogen-halogen interactions in the design of uranyl hybrid materials

Reactions of the uranyl cation (UO(2)(2+)) with 4-halopyridinium ions (X = Cl, Br, I) in high halide media (X' = Cl, Br) have produced six novel compounds, the structures of which have been determined by single crystal X-ray diffraction (XRD). The compounds can be divided into two categories based on the different modes of hydrogen bonding and halogen-halogen interactions present in the crystal structures, with one group showing approximately Type I halogen-halogen interactions and the second showing Type II. Presented is a discussion of the relative strengths of the interactions as a function of halogen size.     

The gas-phase hydrogen-bonded complex between ozone and hydroperoxyl radical. A theoretical study

We report a theoretical study on the gas-phase hydrogen-bonded complexes formed between ozone and hydroperoxyl radical, which are of interest in atmospheric chemistry. We have employed CASSCF, CASPT2, QCISD, and CCSD(T) theoretical approaches employing 6-311+G(2df,2p) and aug-cc-pVTZ basis sets, and we have found three complexes whose stabilities are computed to be 2.02, 1.19, and 1.34 kcal/mol, respectively, at 0 K. In addition, we have also found three transition states connecting these complexes that lie below the energy of the separate reactants. To help for possible experimental identification of these hydrogen-bonded complexes, we report also the computed harmonic vibrational frequencies along with the frequency shifts of the complexes, relative to the monomers, and the computed rotational constants.     

Analysis of complexes pairing hydroperoxyl radical with peroxyformic acid

Ab initio quantum calculations are used to analyze the binding of complexes pairing OOH with HOOCHO. Six minima are located on the potential energy surface, all of cyclic geometry. Of particular interest are the OH...O and CH...O H-bonds that arise in the complexes and the manner in which these interactions influence the internal properties of the subunits. The analysis is complicated by the presence of an intramolecular H-bond in the unperturbed HOOCHO molecule, which must be broken in order to form the pair of intermolecular H-bonds that are responsible for the binding in the most stable complex. The CH bond of HOOCHO is contracted, and its stretching frequency undergoes a blue shift, when this group participates in a H-bond.