Volume 227, Issue 6-7 -

Associates of 3 ' ,5 ' -O-TBDMS protected derivatives of the 2 ' -deoxy forms of the nucleosides adenosine, 6-N-methyl-adenosine and thymidine (henceforward simply addressed by their parents' names) and further model systems in dichloromethane and Freon (CDClF 2 /CDF 3 ) solutions are studied at low temperatures by 1 H NMR and FT-IR spectroscopy. N⋯N distances in hydrogen bonds are estimated from chemical shifts of protons in hydrogen bonds employing geometric and spectroscopic hydrogen bond correlations. These distances are in turn employed to derive N–H stretching frequencies from IR spectroscopic hydrogen bond correlations which may be compared to corresponding experimental results. Three isomeric hydrogen bonded dimers of thymidine are characterized in Freon solution at 120 K. Binary associates of thymidine and a series of pyridines are studied; estimated N⋯N distances in the range of 3.08 to 2.85 Å are qualitatively correlated to shifts of N–H stretching bands where in all cases considerable contributions are found in the spectral region below 3000 cm -1 . For adenosine, three isomeric binary associates with 4-nitrophenol are found allowing for an assessment of site-specific acceptor capabilities. In associates of thymidine and adenosine, Watson-Crick and Hoogsteen type 1:1 associates (estimated N⋯N distances of 2.85 and 2.90 Å) as well as 2:1 associates bearing only marginally longer H-bonds could be characterized. Two 1:1 associates between thymidine and 6-N-methyl-adenosine are described that are exclusively bonded via N–H⋯N bridges of about 2.97 and 3.08 Å for Watson-Crick and Hoogsteen sites, respectively, which leads to the conclusion that cooperative effects among coupled N–H⋯O and N–H⋯N hydrogen bonds in A-T base pairs are significant as formation of the N–H⋯O bond induces a contraction of around 0.15 Å in the neighboring N–H⋯N bond.

1 H and 19 F NMR spectroscopy, X-ray diffractometry and DFT computations have been used for investigating the interaction between the Lewis base pyridine and bis(pentafluorophenyl)borinic acid Ar 2 BOH ( 1 , Ar=C 6 F 5 ). Previous studies showed that the latter species in solution exists as an equilibrium mixture of the monomer ( 1 m ) and a cyclic trimer ( 1 t ), in variable ratios, and that the trimer is stabilized in the presence of Lewis bases, by the formation of strong 1 t ··· L hydrogen bonds. In the present case, upon addition of 0.33 equivalents of pyridine, low-temperature NMR spectra showed the formation of deprotonated 1 t (anion 3 ), strongly hydrogen-bonded to the pyridinium cation Hpy + . The presence of this cation was confirmed by the high value of 1 J HN (88 Hz). DFT computations confirmed the higher stability of the O - ···H–N + limit form over the neutral O–H···N one. Variable temperature NMR spectra showed that the Hpy + · 3 ion pair has high conformational freedom. At temperatures higher than 260 K, 3 underwent reversible partial fragmentation to give 1 m and the Lewis acid-base covalent adducts between pyridine and either 1 m ( 2 py ), or its anhydride ( 5 py ). The fragmentation was perfectly reversible on lowering the temperature. The adduct 2 py became the only species in solution in the presence of 1 equivalent of pyridine, showing that the Lewis basicity of pyridine plays the major role, at variance with what previously observed with other bases. Hydrogen bond interactions, however, promote the supramolecular organization of 2 py in the form of a cyclic tetramer, as revealed by X-ray single crystal diffractometric analysis. The formation of the deprotonated trimer 3 was previously observed in the reaction of 1 with 1,8-bis(dimethylamino)naphtalene (DMAN). However the stepwise dearylation processes, which were dominant in the reactions with DMAN, have a very marginal role in the reaction with pyridine, due to its lower Brønsted basicity. For Supplementary Material see online version. Supporting information available: details of the NMR spectroscopic characterization (Figs. S1–S4), computed chemical shifts (Table S1), details of the X-ray diffractometric analysis, and tables of geometrical parameters (Tables S2–S3).

The hydrogen bond pattern and the types of non-covalent interactions in the crystals of the 1:1 and 1:2 adducts of 2,4,6-trimethylpyridine and benzoic acids are studied using high-resolution X-ray diffraction. The geometries of the hydrogen bonds are estimated using a combined XRD/DFT approach that provides the geometrical parameters within the margin of error of neutron diffraction studies. The energies of the non-covalent interactions are estimated on the base of the experimental electron density distribution function. It is shown that the structures of the adducts are governed by the NOH and OHO hydrogen bonds. In turn, C-H...O contacts and stacking interactions define the packing of the adducts in the crystal. On the other hand, it is important to note that the latter interactions affect the competition of the former hydrogen bonds in some 1:2 adducts.

A T Si T dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the T Si T dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of T Si T duplexes with an antiparallel strand orientation.

Molecular orbital calculations were performed to estimate the 18 O/ 16 O and D/H isotopic reduced partition function ratios (RPFRs) of water molecules around chloride and sulfate ions. Cl - (H 2 O) n and SO 4 2- (H 2 O) n clusters with n up to 120 were considered as models of aqueous solution containing those anions. The calculations indicated that the decreasing order of the 18 O preference over 16 O in the primary hydration sphere is: (bulk water) > SO 4 2- > Cl - . That is, water molecules in the primary hydration spheres of those anions are expected to be depleted in the heavier isotope of oxygen relative to water molecules in bulk, and the degree of the depletion is larger for the chloride ion than for the sulfate ion. Similar tendency was also observed for the isotope preference of hydrogen. No such isotopic preference was observed either for oxygen or for hydrogen in the secondary and outer hydration spheres.

A systematic ab initio investigation has been carried out to determine the structures, binding energies, and spin-spin coupling constants of ternary complexes X:HBO:Z for X, Z= LiH, HNC, HF, HCN, HCl, ClF, and HBO. All complexes X:HBO:Z are linear with C ∞ v symmetry, except for HCl:HBO:Z and ClF:HBO:Z which have C s symmetry, thereby reflecting the structures of the corresponding X:HBO and HBO:Z complexes. Cooperative effects on energies are synergistic in all ternary complexes. The enhanced binding energies of complexes X:HBO:Z correlate with the binding energies of the X:HBO and HBO:Z complexes. Coupling constants 1 J(B-H) and 2h J(B-A) across B-H ···s A hydrogen bonds correlate with the B-A distance, and exhibit synergistic effects due to the presence of Z. 1h J(H-A) indicates that these bonds have little proton-shared character. Coupling constants across D-H ···s O hydrogen bonds, H-Li ···s O lithium bonds, and F-Cl ···s O halogen bonds are also sensitive to the synergistic effects arising from the presence of X. D-H ···s O hydrogen bonds in ternary complexes are traditional (normal) hydrogen bonds.

The structure of three simple pyrazole-4-carboxylic acids unsubstituted in position 1 (N H derivatives) 1 H -pyrazole-4-carboxylic acid ( 1 ), 3(5)-methyl-1 H -pyrazole-4-carboxylic acid ( 2 ) and 3,5-dimethyl-1 H -pyrazole-4-carboxylic acid ( 3 ) are discussed based on crystallographic results (two new structures) and solid-state NMR (CPMAS). Compounds 1 and 3 present polymorphism and one of the polymorphs of each compound shows solid-state proton transfer (SSPT). Compound 2 presents tautomerism that has been studied by NMR, both in the solid-state and in solution at low temperature.

Fluorescence and absorption spectral parameters of acridine have been studied in solution at room temperature in the presence of different proton donors aiming to inspect whether or not acridine can be used as a spectroscopic probe suitable to measure the geometry of hydrogen bonds under different conditions. It has been shown that the most appropriate spectral parameter is the position of fluorescence maximum that changes heavily upon a contraction of the N···H distance. Presumably, also the intensity of the maximum strongly depends on the hydrogen bond geometry. These two parameters can be used to establish two independent, mutually complementary correlations connecting the spectral manifestations and the geometry of hydrogen bond.

The interaction between various proton donors (indole, CF 3 CH 2 OH, (CF 3 ) 2 CHOH, (CF 3 ) 3 COH) and (NNC)PtH hydrido complex (NNC-H = 6-(1,1'-dimethylbenzyl)-2,2'-bipyridine) was investigated through low-temperature IR and NMR spectroscopy in combination with density functional theory calculations at the M06 level of theory. The experiment shows formation of very weak hydrogen bonded complexes ( Δ Hº HB ca. -1.0 kcal mol -1 ), which undergo subsequent proton transfer surprisingly easy. Computational analysis of the hydrogen bonded complexes geometry, electronic parameters (obtained by NBO and AIM analysis), and orbital interaction energies shows that all the complexes are better described as bonded to the metal atom. At that in case of weak alcohols (CH 3 OH, TFE) there is also the additional interaction with the hydride ligand. These computational results allow explaining the observed experimental trends and give the first example of hydrogen bonding to a metal atom in the presence of hydride ligand.

The interaction of hydrogen and deuterium with the Co(0001) surface has been studied in UHV between 90 and 500 K by means of LEED, temperature-programmed thermal desorption (TPD) and work function change (Δ Φ ) measurements. Hydrogen adsorbs spontaneously and dissociatively in two atomic binding states denoted as β 1 and β 2 with a high initial sticking probability. The adsorption energies E ( β 1 ) and E ( β 2 ) are 80 and 100 kJ/mol, respectively, if a first-order desorption kinetics is assumed (a second-order kinetic analysis yields unreasonably low values for both the desorption energies and frequency factors). At sufficiently low temperatures, the adsorbed H atoms form a faint (2 × 2) LEED superstructure, which is best developed after an exposure of ∼20 L. From the temperature dependence of the fractional-order beam intensity at different exposures we determine the critical temperature of the (2 × 2) phase as ∼ 243 ( ± 10) K. Similar to the H-on-Ni(111) system the existence range of the (2 × 2) phase in the temperature–coverage plane is asymmetric; i.e. , below the critical coverage Θ crit the respective long-range order has a higher range of stability than above Θ crit . By analogy with H/Ni(111), we assume a similar honeycomb H structure also for the H-on-Co(0001) system and suggest the critical coverage Θ crit to be 0.5, i.e. , half a monolayer of H atoms. The H-induced work function change is surprisingly small; it decreases, forms a shallow minimum of −18 meV after ∼20 L exposure around the optimum coverage of the (2 × 2) phase and reaches a saturation value of −10 meV. Our data are discussed and compared with previous work on H/Co(0001) and other close-packed transition metal surfaces, especially with the H-on-Ni(111) system.

The five-fold coordinated ruthenium (II) catalyst RuCl 2 (PPh 3 ) 3 is heterogenized on the surface of amine functionalized mesoporous silica material SBA-3 and studied by BET, XRD and 31 P CP-MAS solid-state NMR. The spectra indicate the replacement of one or two of the triphenyl-phosphine groups in the course of the grafting. To distinguish between both possibilities two-dimensional J-resolved 31 P MAS solid-state NMR combined with quantum chemical calculations is employed. The changes of the scalar coupling pattern between the neat catalyst and the immobilized catalyst suggest the replacement of two of the PPh 3 -groups by coordinative bonds to the amine-functions of the linker. DFT calculations reveal the absence of two chemically and magnetically equivalent phosphines and confirm the replacement of two PPh 3 -groups. This finding is similar to the results observed for the binding of the rhodium in the Wilkinson's catalyst, despite the different coordination of the metals (four-fold versus five-fold), the presence of two chlorine ligands and the different transition metal.

An analysis is presented of secondary deuterium isotope effects on 15 N and 13 C chemical shifts of the methylamine Schiff base of 4,6-dimethoxysalicylaldehyde. It is shown that for this compound existing as an equilibrium between an OH and a NH-form, the secondary isotope effects depend on the OH/NH ratio giving a function with a maximum and a minimum. Secondary deuterium isotope effects on 13 C and 15 N chemical shifts are compared in a broader range of compounds and the above trend is confirmed. Changes in the dielectric constants of the medium with temperature are found to be rather unimportant for the change in equilibrium. Equilibrium isotope effects on chemical shifts are shown to be important. The magnitudes of the isotope effects are correlated both to intrinsic and equilibrium isotope effects. The latter correlate to the shape of the two-potential well, the energy difference and the difference in chemical shifts of the two tautomers.

The complex spin order of hyperpolarized multispin systems giving rise to anomalous NMR spectral patterns that vary with the RF excitation angle is analyzed by decomposing its nutation behavior in a superposition of Fourier harmonics. The product operator formalism is applied to calculating the spectral contributions of the various mutual alignments of scalar coupled spins. Two cases are treated, namely systems exhibiting only differences in population of their spin states and systems showing in addition zero-quantum coherences between states, a situation often seen at hyperpolarization. After deriving the general solution a number of representative examples are discussed in detail. The theoretical treatment is applied to analyzing the spin order observed in a hyperpolarized two-spin system that is prepared in the singlet state by para-hydrogen induced polarization.

The mechanism of the phase transition of supercooled water to ice I h at −36 ºC is discussed on a molecular level. The structure of liquid water is described by the interstitial model first proposed by Samoilov. It is consistent with the results of X-Ray and neutron scattering and the experimental results on the diverse properties of liquid water. In order to illustrate our reflections several numerical calculations have been performed using exclusively experimental data. From the temperatur dependence of the nucleation rate the minimum number of water molecules, which constitute the critical germ, and the volume of the critical germ are determined. The occupation numbers of the regular tridymite lattice and the vacancies of the interstitial lattice are evaluated. The negative entropy of nucleation is discussed. It can be split in two contributions. They refer to the change of the statistics by the the transition from the protonucleus to the nucleus and the changes of the degrees of freedom of motion. Considering the simple model, the calculated value fits well to the experimental value of the nucleation entropy. The transition state, which is a key point in the classical nucleation theory, is discussed on a molecular level. It has a lifetime of 0.57 × 10 −12 s. The nucleation volume is of the order nm 3 . One can expect that in this small volume density fluctuations exist in which especially the molecules in interstitial positions are involved. They are rich in energy and easily moveable. Statistical calculations deliver the deviation ±5 from the average value 23 of the number of molecules at interstitial positions in the nucleation volume. Corresponding density fluctuations have been observed by Huang et al. by very fast measurements of small angle X-ray scattering.

In a previous publication by Kalish et al. (J. Phys. Chem. A 115 (2011) 4063) the existence of well defined small protonated water clusters in acetonitrile has been established by IR spectroscopy. Here we report on a 1 H NMR study of triflic acid, CF 3 SO 3 H, in acetonitrile-water solutions. Using NMR we are able to corroborate the general solvation scheme we have proposed for the hydrated proton in acetonitrile as a function of the molar ratio between the strong mineral acid and water, n = [H 2 O]/[acid]. According to this scheme, backed now by both IR absorption spectroscopy and NMR measurements, the very strong triflic acid completely dissociates in acetonitrile/water solutions to yield the aqueous proton and the triflate anion when n > 1. Furthermore, increasing n results in the proton solvated in increasingly larger water clusters formed within the acetonitrile solution. Clearly distinguishable by NMR are the smallest protonated water clusters, the protonated water monomer, H 3 + O, and the protonated water dimer, H 5 + O 2 , which dominate the solution for n = 1,2,3. For larger n the NMR study indicates the gradual increase of the average protonated water cluster size as a function of n while the proton inner solvation core more closely retaining the characteristics of a deformed protonated water dimer, (H 2 O-H + ⋯OH 2 ) s than that of the protonated water monomer (H 3 + O) s .

The rate constants of intramolecular double hydrogen transfer have been determined for of tert -butyl-substituted porphycenes: 2- tert -butyl-, 2,7-di- tert -butyl-, 2,7,12-tri- tert -butyl-, and 2,7,12,17-tetra- tert -butylporphycene using femtosecond pump-probe polarization spectroscopy. The rates increase monotonically with the number of substituents. As is the case for other porphycenes studied so far, the tautomerization becomes slower after excitation to the lowest excited singlet state. The potential for the trans-trans self-exchange reaction is symmetrical in di- and tetra- tert -butyl substituted derivatives, but not for the singly and triply substituted ones. Our studies enabled determination of the relative populations of nonequivalent tautomers and thus of the equilibrium constants in S 0 and S 1 states, as well as estimation of ground and excited state activation energies for the tautomerization process.