Hydrogen Bond Exchange Research Articles

Mechanism for the Transport of Ammonia within Carbamoyl Phosphate Synthetase Determined by Molecular Dynamics Simulations

Carbamoyl phosphate synthetase (CPS) is a member of the amidotransferase family of enzymes that uses the hydrolysis of glutamine as a localized source of ammonia for biosynthetic transformations. Molecular dynamics simulations for the transfer of ammonia and ammonium through a tunnel in the small subunit of CPS resulted in five successful trajectories for ammonia transfer, while ammonium was immobilized in a water pocket inside the small subunit of the heterodimeric protein. The observed molecular tunnel for ammonia transport is consistent with that suggested by earlier X-ray crystallography and site-directed mutation studies. His-353, Ser-47, and Lys-202, around the active site center in the small subunit, function cooperatively to deliver ammonia from the site of formation to the interface with the large subunit, via the exchange of hydrogen bonds with a critical water cluster within the tunnel. The NH 3 forms and breaks hydrogen bonds to Gly-292, Ser-35, Pro-358, Gly-293, and Thr-37 in a stepwise fashion "macroscopically" as it travels through the hydrophilic passage toward the subunit interface. The potential of mean force calculations along the ammonia transfer pathway indicates a low free-energy path for the translocation of ammonia with two barriers of 3.9 and 5.5 kcal/mol, respectively. These low free-energy barriers are consistent with the delivery of ammonia from the site of formation into a water reservoir toward the exit of the tunnel and migration through the hydrophilic leaving passage, respectively. The high overall free-energy barrier of 22.4 kcal/mol for the transport of ammonium additionally substantiates that the tunnel in the small subunit of CPS is not an ammonium but an ammonia channel.

Switching Binding Sites: Low-Temperature NMR Studies on Adenosine−Aspartic Acid Interactions

Low-temperature NMR experiments were performed on mixtures of adenine nucleosides and aspartic acid derivatives in a freonic solvent. By acquiring spectra at temperatures as low as 123 K, the regime of slow hydrogen bond exchange is reached and hydrogen-bonded complexes can be characterized in detail. With 2'-deoxyadenosine lacking a 2'-substituent, N-Boc-protected aspartic acid benzyl ester binds through its carboxylic acid side chain to the Watson-Crick site of the adenine base, forming a strong hydrogen bond with the proton located close to the center between the oxygen donor and adenine N1 nitrogen acceptor. However, in the case of 2'-O-silylated adenine ribofuranosides, noncovalent interactions of the 2'-substituent with protecting groups on the amino acid shift the binding mode toward a Hoogsteen geometry with only a moderately strong hydrogen bond involving adenine N7.

BSSE‐free hardness profiles of hydrogen bond exchange in the hydrogen fluoride dimer

AbstractHardness profiles are calculated for the hydrogen bond interchange in the hydrogen fluoride dimer; the study is carried out at the Hartree–Fock and second‐order Møller–Plesset (MP2) levels of theory with three different basis sets. The basis set superposition error (BSSE) is corrected by means of the chemical Hamiltonian approach (CHA). Uncorrected and BSSE‐corrected energy and hardness profiles are compared. Their analysis shows that hardness profiles do not lead to spurious minima as energy profiles do in various cases. The CHA methodology is shown to be valuable in the analysis of intermolecular interactions, with BSSE observed to carry smaller modifications on hardness profiles than on energy curves. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.

Chemical exchange 2D IR of hydrogen-bond making and breaking.

The involvement of chemical exchange in 2D IR heterodyne echo spectroscopy is characterized through the hydrogen-bond exchange between CH3OH and the CN of CH3CN. The exchange dynamics on the hydrogen-bond potential surfaces associated with different quantum states of the high-frequency CN stretching mode contributes to strong cross peaks between CN groups in two different chemical configurations and provides firm evidence of the hydrogen exchange between them. In analogy with NMR, the chemical exchange is seen in both slow and dynamic regimes. The relative magnitudes of the cross peaks at various population periods measure the picosecond regime time constants for H-bond transfer, whereas the temperature dependences indicate that the activation energy for the exchange from the H-bonded state to the free state is approximately 6.2 kJ.mol(-1). The results suggest that the hydrogen-bond dynamics is very similar in both vibrational quantum states of CN, suggesting that this stretching mode is not strongly coupled to the H-bond breaking reaction coordinate. The likely manifestations of chemical exchange in 2D IR experiments are discussed.

Role of Hydrogen Bonds in Controlling the Morphology of Self-Assembling Carbamate Systems

With a view to understand the role of hydrogen bonding in controlling the morphology of self-assembling carbamate systems, N-octadecylcarbamate dodecyl ester was blended individually with a low molecular weight polyethylene and two commercial clarifiers, namely Kemamide S and Kemamide E 180. The effect of blending on the morphology of this long chain carbamate was investigated using optical microscopy, differential scanning calorimetry, and X-ray diffraction. The crystal structure of the carbamate was not affected by the addition of polyethylene or Kemamide S. The heterogeneous nucleation of the carbamate by the polyethylene or Kemamide S resulted in the reduction of the spherulite size of the carbamate, but it did not improve the transparency of the sample due to phase separation. On the other hand, significant improvement of transparency was achieved when the carbamate was blended with Kemamide E 180. Blending reduced the crystallite and spherulite size, heat of fusion, and crystallinity. An exchange of hydrogen bonds between the carbamate and Kemamide E is indicated in the IR spectra, and this affects the packing of the alkyl chains of the carbamates. This heterogeneous blending shows similar effects on the morphology as was achieved by blending two homologous carbamates in our previous study (J. Phys. Chem. B 2003, 107, 8416).

NMR studies of solid state—solvent and H/D isotope effects on hydrogen bond geometries of 1:1 complexes of collidine with carboxylic acids

1H and 15N NMR spectra of 10 complexes exhibiting strong OHN hydrogen bonds formed by 15N-labeled collidine and different proton donors, partially deuterated in mobile proton sites, have been observed by low-temperature NMR spectroscopy using a low-freezing CDF 3/CDF 2Cl mixture as polar aprotic solvent. The following proton donors have been used: HCl, formic acid, acetic acid, various substituted benzoic acids and HBF 4. The slow hydrogen bond exchange regime could be reached below 140 K, which allowed us to resolve 15N signal splittings due to H/D isotopic substitution. The valence bond order model is used to link the observed NMR parameters to hydrogen bond geometries. The results are compared to those obtained previously [Magn. Reson. Chem. 39 (2001) S18] for the same complexes in the organic solids. The increase of the dielectric constant from the organic solids to the solution (30 at 130 K) leads to a change of the hydrogen bond geometries along the geometric correlation line towards the zwitterionic structures, where the proton is partially transferred from oxygen to nitrogen. Whereas the changes of spectroscopic and, hence, geometric parameters are small for the systems which are already zwitterionic in the solid state, large changes are observed for molecular complexes which exhibit almost a full proton transfer from oxygen to nitrogen in the polar liquid solvent.

Characterization of Fluxional Hydrogen-Bonded Complexes of Acetic Acid and Acetate by NMR: Geometries and Isotope and Solvent Effects

1H, (2)H, and (13)C NMR spectra of enriched CH(3)(13)COOH acid without and in the presence of tetra-n-butylammonium acetate have been measured around 110 K using a liquefied Freon mixture CDF(3)/CDF(2)Cl as a solvent, as a function of the deuterium fraction in the mobile proton sites. For comparison, spectra were also taken of the adduct CH(3)(13)COOH.SbCl(5) 1 and of CH(2)Cl(13)COOH under similar conditions, as well as of CH(3)(13)COOH and CH(3)(13)COO(-) dissolved in H(2)O and D(2)O at low and high pH at 298 K. The low temperatures employed allowed us to detect several well-known and novel hydrogen-bonded complexes in the slow hydrogen bond exchange regime and to determine chemical shifts and coupling constants as well as H/D isotope effects on chemical shifts from the fine structure of the corresponding signals. The measurements show that self-association of both carboxylic acids in Freon solution gives rise exclusively to the formation of cyclic dimers 2 and 3 exhibiting a rapid degenerate double proton transfer. For the first time, a two-bond coupling of the type (2)J(CH(3)COOH) between a hydrogen-bonded proton and the carboxylic carbon has been observed, which is slightly smaller than half of the value observed for 1. In addition, the (1)H and (2)H chemical shifts of the HH, HD, and the DD isotopologues of 2 and 3 have been determined as well as the corresponding HH/HD/DD isotope effects on the (13)C chemical shifts. Similar "primary", "vicinal", and "secondary" isotope effects were observed for the novel 2:1 complex "dihydrogen triacetate" 5 between acetic acid and acetate. Another novel species is the 3:1 complex "trihydrogen tetraacetate" 6, which was also characterized by a complex degenerate combined hydrogen bond- and proton-transfer process. For comparison, the results obtained previously for hydrogen diacetate 4 and hydrogen maleate 7 are discussed. Using an improved (1)H chemical shift-hydrogen bond geometry correlation, the chemical shift data are converted into hydrogen bond geometries. They indicate cooperative hydrogen bonds in the cyclic dimers; i.e., widening of a given hydrogen bond by H/D substitution also widens the other coupled hydrogen bond. By contrast, the hydrogen bonds in 5 are anticooperative. The measurements show that ionization shifts the (13)C signal of the carboxyl group to low field when the group is immersed in water, but to high field when it is embedded in a polar aprotic environment. This finding allows us to understand the unusual ionization shift of aspartate groups in the HIV-pepstatin complex observed by Smith, R.; Brereton, I. M.; Chai, R. Y.; Kent, S. B. H. Nature Struct. Biol. 1996, 3, 946. It is demonstrated that the Freon solvents used in this study are better environments for model studies of amino acid interactions than aqueous or protic environments. Finally, a novel correlation of the hydrogen bond geometries with the H/D isotope effects on the (13)C chemical shifts of carboxylic acid groups is proposed, which allows one to estimate the hydrogen bond geometries and protonation states of these groups. It is shown that absence of such an isotope effect is not only compatible with an isolated carboxylate group but also with the presence of a short and strong hydrogen bond.

Transition path sampling: rearrangement of cage water hexamer

Abstract The hydrogen bond exchange reaction of cage water hexamer has been investigated. With an aid of transition path sampling method, a transition state for this reaction has been found. The transition state ensemble has been investigated as a function of energy, and the distribution of the structures of sampled transition states is consistent with that obtained by other method. From the ab initio calculations, it has been confirmed to be a transition state with one imaginary frequency along the reaction coordinate. The most important structural parameters for the transition are retardation (increase of r a and O⋯O distance) and C 2 rotation of a water molecule. I obtained rate constants at temperatures ranging from 0 to 300 K considering quantum mechanical tunneling effect. At temperatures below 100 K, the tunneling effect is very important, while at high temperatures, the classical transition state theory approach gives reasonable data. Transition path sampling method is very useful to find transition states for many complicated chemical reactions in which we do not know about transition states or it is hard to find a transition state by quantum mechanical approaches.

Pyridine-15N A Mobile NMR Sensor for Surface Acidity and Surface Defects of Mesoporous Silica

The hydrogen bond interaction of pyridine with the silanol groups of the inner surfaces of MCM-41 and SBA-15 ordered mesoporous silica has been studied by a combination of solid-state NMR techniques. The pore diameters were varied between 3 and 4 nm for MCM-41 and between 7 and 9 nm for SBA-15. 1 H MAS experiments performed under magic angle spinning (MAS) conditions in the absence and the presence of pyridine-d 5 reveal that the large majority of silanol groups are located in the inner surfaces, isolated from each other but able to form hydrogen bonds with pyridine. On the other hand, low- and room-temperature 1 5 N CPMAS and MAS experiments (CP ≡ cross-polarization) performed on pyridine- 1 5 N show that at low concentrations all pyridine molecules are involved in hydrogen bonds with the surface silanol groups. In the presence of an excess of pyridine, a non-hydrogen-bonded pyridine phase is observed at 120 K in the slow hydrogen bond exchange regime and associates with an inner core phase. From these measurements, the number of pyridine molecules bound to the inner surfaces corresponding to the number of silanol groups could be determined to be n O H 3 nm - 2 for MCM-41 and 3.7 nm - 2 for SBA-15. At room temperature and low concentrations, the pyridine molecules jump rapidly between the hydrogen-bonded sites. In the presence of an excess of pyridine, the hydrogen-bonded binding sites are depleted as compared to low temperatures, leading to smaller apparent numbers n O H . Using a correlation established previously between the 1 5 N and 1 H chemical shifts and the NHO hydrogen bond geometries, as well as with the acidity of the proton donors, the distances in the pyridine-hydroxyl pairs were found to be about r H N = 1.68 A, r O H = 1.01 A, and r O N = 2.69 A. This geometry corresponds in the organic solid state to acids exhibiting in water a pK a of about 4. Roomtemperature 1 5 N experiments on static samples of pyridine- 1 5 N in MCM-41 at low coverage show a residual 1 5 N chemical shift anisotropy, indicating that the jumps of pyridine between different different silanol hydrogen bond sites is accompanied by an anisotropic reorientational diffusion. A quantitative analysis reveals that in this regime the rotation of pyridine around the molecular C 2 axis is suppressed even at room temperature, and that the angle between the Si-O axes and the OH axes of the isolated silanol groups is about 47°. These results are corroborated by 2 H NMR experiments performed on pyridine-4-d 1 . In contrast, in the case of SBA-15 with the larger pore diameters, the hydrogen bond jumps of pyridine are associated with an isotropic rotational diffusion, indicating a high degree of roughness of the inner surfaces. This finding is correlated with the finding by 2 9 Si CPMAS of a substantial amount of Si(OH) 2 groups in SBA-15. in contrast to the MCM-41 materials. The Si(OH) 2 groups are associated with surface defects, exhibiting not only silanol groups pointing into the pore center but also silanol groups pointing into other directions of space including the pore axes, leading to the isotropic surface diffusion. All results are used to develop molecular models for the inner surface structure of mesoporous silica which may be a basis for future simulations of the surfaces of mesoporous silica.

Low-temperature NMR studies of the structure and dynamics of a novel series of acid-base complexes of HF with collidine exhibiting scalar couplings across hydrogen bonds.

The low-temperature (1)H, (19)F, and (15)N NMR spectra of mixtures of collidine-(15)N (2,4,6-trimethylpyridine-(15)N, Col) with HF have been measured using CDF(3)/CDF(2)Cl as a solvent in the temperature range 94-170 K. Below 140 K, the slow proton and hydrogen bond exchange regime is reached where four hydrogen-bonded complexes between collidine and HF with the compositions 1:1, 2:3, 1:2, and 1:3 could be observed and assigned. For these complexes, chemical shifts and scalar coupling constants across the (19)F(1)H(19)F and (19)F(1)H(15)N hydrogen bridges have been measured which allowed us to determine the chemical composition of the complexes. The simplest complex, collidine hydrofluoride ColHF, is characterized at low temperatures by a structure intermediate between a molecular and a zwitterionic complex. Its NMR parameters depend strongly on temperature and the polarity of the solvent. The 2:3 complex [ColHFHCol](+)[FHF](-) is a contact ion pair. Collidinium hydrogen difluoride [ColH](+)[FHF](-) is an ionic salt exhibiting a strong hydrogen bond between collidinium and the [FHF](-) anion. In this complex, the anion [FHF](-) is subject to a fast reorientation rendering both fluorine atoms equivalent in the NMR time scale with an activation energy of about 5 kcal mol(-)(1) for the reorientation. Finally, collidinium dihydrogen trifluoride [ColH](+)[F(HF)(2)](-) is an ionic pair exhibiting one FHN and two FHF hydrogen bonds. Together with the [F(HF)(n)()](-) clusters studied previously (Shenderovich et al., Phys. Chem. Chem. Phys. 2002, 4, 5488), the new complexes represent an interesting model system where the evolution of scalar couplings between the heavy atoms and between the proton and the heavy atoms of hydrogen bonds can be studied. As in the related FHF case, we observe also for the FHN case a sign change of the coupling constant (1)J(FH) when the F.H distance is increased and the proton shifted to nitrogen. When the sign change occurs, that is, (1)J(FH) = 0, the heavy atom coupling constant (2)J(FN) remains very large, of the order of 95 Hz. Using the valence bond order model and hydrogen bond correlations, we describe the dependence of the hydrogen bond coupling constants, of hydrogen bond chemical shifts, and of some H/D isotope effects on the latter as a function of the hydrogen bond geometries.

15N-pyridine—a mobile NMR sensor for surface acidity and surface defects of mesoporous silica

experiments performed under magic angle spinning (MAS) conditions in the absence and the presence of pyridine-d5 reveal that the large majority of silanol groups are located in the inner surfaces, isolated from each other but able to form hydrogen bonds with pyridine. On the other hand, low- and room-temperature 15 N CPMAS and MAS experiments (CP cross-polarization) performed on pyridine- 15 N show that at low concentrations all pyridine molecules are involved in hydrogen bonds with the surface silanol groups. In the presence of an excess of pyridine, a non-hydrogen-bonded pyridine phase is observed at 120 K in the slow hydrogen bond exchange regime and associates with an inner core phase. From these measurements, the number of pyridine molecules bound to the inner surfaces corresponding to the number of silanol groups could be determined to be nOH 3n m -2 for MCM-41 and 3.7 nm -2 for SBA-15. At room temperature and low concentrations, the pyridine molecules jump rapidly between the hydrogen-bonded sites. In the presence of an excess of pyridine, the hydrogen-bonded binding sites are depleted as compared to low temperatures, leading to smaller apparent numbers nOH. Using a correlation established previously between the 15 N and 1 H chemical shifts and the NHO hydrogen bond geometries, as well as with the acidity of the proton donors, the distances in the pyridine-hydroxyl pairs were found to be about rHN ) 1.68 A,rOH ) 1.01 A, andrON ) 2.69 A. This geometry corresponds in the organic solid state to acids exhibiting in water a pKa of about 4. Roomtemperature 15 N experiments on static samples of pyridine- 15 N in MCM-41 at low coverage show a residual 15 N chemical shift anisotropy, indicating that the jumps of pyridine between different different silanol hydrogen bond sites is accompanied by an anisotropic reorientational diffusion. A quantitative analysis reveals that in this regime the rotation of pyridine around the molecular C2 axis is suppressed even at room temperature, and that the angle between the Si-O axes and the OH axes of the isolated silanol groups is about 47°. These results are corroborated by 2 H NMR experiments performed on pyridine-4-d1. In contrast, in the case of SBA-15 with the larger pore diameters, the hydrogen bond jumps of pyridine are associated with an isotropic rotational diffusion, indicating a high degree of roughness of the inner surfaces. This finding is correlated with the finding by 29 Si CPMAS of a substantial amount of Si(OH)2 groups in SBA-15, in contrast to the MCM-41 materials. The Si(OH)2 groups are associated with surface defects, exhibiting not only silanol groups pointing into the pore center but also silanol groups pointing into other directions of space including the pore axes, leading to the isotropic surface diffusion. All results are used to develop molecular models for the inner surface structure of mesoporous silica which may be a basis for future simulations of the surfaces of mesoporous silica.

Dimerization and solvent-assisted proton dislocation in the low-barrier hydrogen bond of a Mannich base: a low-temperature NMR study

Using low-temperature UV, 1H and 15N NMR spectroscopy, we studied the easily polarizable O—H··· NOδ−···H··· Nδ+O−··· H—N+ hydrogen bond of the labeled Mannich base[15N] 2-(N,N-diethylaminomethyl)-3,4,6-trichlorophenol (Cl3MB) dissolved in dichloromethane and in a 2 : 1 mixture of CDF3 and CDClF2. Whereas at high temperature the molecule is present as a monomer exhibiting an intramolecular hydrogen bond, at low temperature two different cyclic hydrogen-bonded dimers are formed which have been observed for the first time by NMR in the slow hydrogen bond exchange regime. The proton chemical shifts and the scalar 1H, 15N coupling constants indicate a quasi-symmetric low-barrier hydrogen bond in the monomer but polar O−··· H—N+ hydrogen bonds exhibiting a considerable charge separation in the case of the dimers. The thermodynamics of the association process were elucidated by UV and NMR spectroscopy. Interestingly, it was found that the addition of methanol does not change substantially the monomer–dimer equilibrium but leads to a considerable shift of the proton in the monomer towards the nitrogen atom. The effect is smaller but also observable for the dimers. In order to assign molecular structures to the observed species, DFT calculations were performed. They reveal a variety of both monomeric and dimeric conformations of Cl3MB exhibiting different hydrogen bond geometries. In particular, two monomeric conformations, bent and planar, were found which exhibit almost the same energy and two proton-transfer dimeric species of similar energy and different dipole moments. Copyright © 2001 John Wiley & Sons, Ltd.

Influence of the temperature-dependent dielectric constant on the H/D isotope effects on the NMR chemical shifts and the hydrogen bond geometry of the collidine-HF complex in CDF3/CDClF2 solution

The influence of solvent polarity on the properties of hydrogen-bonded 1 : 1 complexes of 2,4,6-trimethylpyridine-15N with HF and DF, labeled below as FHN and FDN, has been studied by multinuclear magnetic resonance spectroscopy in the slow hydrogen bond exchange regime reached below 190 K. Mixtures of CDF3/CDClF2 were employed as solvent, which is liquid down to 90 K. In order to evaluate their polarity, the static dielectric constants eo of the CHF3, CHClF2 and of the binary 1 : 1 mixture were measured from 160 K down to 90 K. A strong increase of eo from 14 at 190 K to 38 at 103 K is observed for the mixtures used in the NMR measurements. Upon cooling, i.e. increase of the dielectric constant, the NMR spectra indicate a gradual transformation of an asymmetric molecular complex FH···N to a quasi-symmetric complex Fδ−···H···Nδ+ and eventually to a more or less zwitterionic species F−···H N+. These changes are not only manifested in the scalar couplings J(1H,19F) and J(1H,15N) but also lead to characteristic primary and secondary H/D isotope effects on the chemical shifts of the hydrogen bonded nuclei. Whereas the primary isotope chemical shift effect pΔ(D/H) ≡ δ(F2HN) − δ(F1HN) = −0.2 ppm is negative at 190 K and in agreement with an asymmetric hydrogen bond in the molecular complex, it changes its sign when the temperature is lowered, goes through a maximum of +0.27 ppm at eo ≈ 22 and finally decreases again. The positive value of pΔ(D/H) is in agreement with D more confined to the hydrogen bond center compared with H, which constitutes a fingerprint of a quasi-symmetric hydrogen bond involving a single well potential for the proton motion. The quasi-symmetric complex is further characterized by the following NMR parameters, J(1H,19F) = 30 Hz, J(1H,15N) = −50 Hz, J(19F,15N) = −96 Hz, δ(F1HN) = 20.0 ppm, δ(19FHN) = −114.2 ppm, δ(FH15N) = −63.5 ppm, and the one-bond H/D-isotope effects δ(F2HN) − δ(F1HN) = +0.27 ppm, δ(19FDN) − δ(19FHN) = 1.4 ppm and δ(FD15N) − δ(FH15N) = −3.4 ppm. Copyright © 2001 John Wiley & Sons, Ltd.

Water: foldase activity in catalyzing polypeptide conformational rearrangements.

Polypeptide conformer interconversion in a low dielectric environment is shown to be highly dependent on water concentration. Water increases this rate by 10(3), apparently by catalyzing hydrogen bond exchange, and thereby presenting functional properties analogous to that of a foldase. This catalytic effect is demonstrated on the interconversion of a parallel gramicidin dimer into an antiparallel dimer. A Hill coefficient of 6.5 is observed, illustrating the highly cooperative nature of the process. Protein folding in nonpolar environs, such as the hydrophobic core of a protein or the hydrophobic domain of a lipid bilayer, may be contingent on and rate-limited by the scarcity of water.

Exploring zero-point energies and hydrogen bond geometries along proton transfer pathways by low-temperature NMR

We have followed by NMR the zero-point energy changes of the hydrogen bond proton in 1:1 acid-base complexes AHB triple bond {A—H···B <-–> Aδ-···H···Bδ+ <-–> A-···H—B+} as a function of the proton position between A and B. For this purpose, the isotopic fractionation factors K between the acid-base complexes AHB + Ph3COD···B –><- ADB + Ph3COH···B, where AH represents a variety of acids and B represents pyridine-15N, were measured around 110 K, using a 2:1 mixture of liquefied CDClF2-CDF3 as solvent. As under these conditions the slow hydrogen bond exchange regime is reached, the values of K could be obtained directly by integration of appropriate proton NMR signals. Using the valence-bond order concept established previously by crystallography, the fractionation factors and corresponding zero-point energy changes (ΔZPE) are related in a quantitative way to the hydrogen bond geometries, the 1H chemical shift of the hydrogen bond proton, and the pyridine-15N chemical shift. The K values are related in a quasi-linear way to the chemical shifts of the hydrogen bond proton, where the slope depends on whether the proton is closer to oxygen or nitrogen. In the region of the strongly hydrogen-bonded quasi-symmetric complexes, which are characterized by a strong hydrogen bond contraction, the variation of K is very small in spite of substantial proton displacements.Key words: NMR, isotopic fractionation, hydrogen bonding, acid-base complexes, proton transfer, geometric isotope effects.

Molecular dynamics of acetophenone and its derivatives investigated by femtosecond optical Kerr effect spectroscopy and depolarized low-frequency Raman scattering

We present the results of femtosecond optical heterodyne-detected optical Kerr effect spectroscopy (OHD-OKE) on acetophenone and its derivatives: o-hydroxybenzaldehyde, o-methylacetophenone, and o-hydroxyacetophenone. The depolarized Raman scattering spectra were also measured, and compared with the frequency-domain representations of the OHD-OKE data. An oscillatory motion, corresponding to an intramolecular vibrational Raman mode, is clearly detected in the OHD-OKE transient for each of these liquids. The slow orientational relaxation times of o-hydroxybenzaldehyde and o-hydroxyacetophenone imply the existence of strong intermolecular interactions induced by hydrogen bond exchange.

Exploring zero-point energies and hydrogen bond geometries along proton transfer pathways by low-temperature NMR

We have followed by NMR the zero-point energy changes of the hydrogen bond proton in 1:1 acid-base complexes AHB triple bond {A—H···B <-–> Aδ-···H···Bδ+ <-–> A-···H—B+} as a function of the proton position between A and B. For this purpose, the isotopic fractionation factors K between the acid-base complexes AHB + Ph3COD···B –><- ADB + Ph3COH···B, where AH represents a variety of acids and B represents pyridine-15N, were measured around 110 K, using a 2:1 mixture of liquefied CDClF2-CDF3 as solvent. As under these conditions the slow hydrogen bond exchange regime is reached, the values of K could be obtained directly by integration of appropriate proton NMR signals. Using the valence-bond order concept established previously by crystallography, the fractionation factors and corresponding zero-point energy changes (ΔZPE) are related in a quantitative way to the hydrogen bond geometries, the 1H chemical shift of the hydrogen bond proton, and the pyridine-15N chemical shift. The K values are related in a quasi-linear way to the chemical shifts of the hydrogen bond proton, where the slope depends on whether the proton is closer to oxygen or nitrogen. In the region of the strongly hydrogen-bonded quasi-symmetric complexes, which are characterized by a strong hydrogen bond contraction, the variation of K is very small in spite of substantial proton displacements.Key words: NMR, isotopic fractionation, hydrogen bonding, acid-base complexes, proton transfer, geometric isotope effects.

The structure of N-aminopyrazole in the solid state and in solution: an experimental and computational study

The title compound N-aminopyrazole (AMPZ) has been studied both theoretically and experimentally using abinitio methods, low-temperature X-ray crystallography, differential scanning calorimetry, IR spectroscopy, liquid state 1H NMR, broadband solid state 2H NMR and high resolution solid state 15N NMR spectroscopy, focussing on the structure and dynamics of the amino group and the characteristics of hydrogen bond (HB) association. The complete amino group rotation–inversion surface of AMPZ and, for comparison, also of the aniline monomer were calculated at the B3LYP/6-31G* level. The results indicate that monomeric AMPZ exhibits an s hybridized pyramidal amino group where the HH-distance vector is located perpendicular to the pyrazole ring and the hydrogen atoms bent towards the pyrazole ring nitrogen atom, i.e. with the lone electron pair anti to the latter. Both inversion at the nitrogen atom and the 180° rotation of the amino group lead to a metastable structure, where the inversion barrier is much larger than the rotational barrier. These results contrast with those obtained for aniline where the amino group is almost planar and subject to a degenerate 180° rotation. Further calculations of the hydrogen bonded cyclic AMPZ dimer indicate that hydrogen bond association does not substantially perturb the geometry of the amino group, where one of the amino group protons and the ring nitrogen atoms are involved in hydrogen bonding. The X-ray structure was determined at -173°C (100 K) on a monocrystal obtained by zone crystallization. DSC shows that on cooling, neat liquid AMPZ exhibits a solid–solid phase transition around -45°C to a low-temperature phase. In this phase AMPZ forms a weakly hydrogen bonded chain where the structure is similar to the one calculated for the monomer. Only one of the amino protons is involved in hydrogen bonding, where the NH stretch of the hydrogen bonded proton appears at 3197 cm-1 and of the non-hydrogen bonded proton at 3314 cm-1. Solid state 2H NMR spectroscopy of [ND2]AMPZ shows low-temperature structures with rigid ND vectors below and isotropically rotating vectors above the solid–solid phase transition. Hydrogen bond association was further studied by solid state 15N CPMAS (cross polarization magic angle spinning) NMR and by low-temperature liquid state 1H NMR of AMPZ specifically 15N labelled in the amino group. In contrast to the solid state, hydrogen bond exchange rendering the two amino group protons equivalent was found to be fast in the NMR timescale even at 100 K.

Hydrogen bonding, solvent exchange, and coupled proton and electron transfer in the oxidation and reduction of redox-active tyrosine Y(Z) in Mn-depleted core complexes of photosystem II.

The redox-active tyrosines, Y(Z) and Y(D), of Photosystem II are oxidized by P680+ to the neutral tyrosyl radical. This oxidation thus involves the transfer of the phenolic proton as well as an electron. It has recently been proposed that tyrosine Y(Z) might replace the lost proton by abstraction of a hydrogen atom or a proton from a water molecule bound to the manganese cluster, thereby increasing the driving force for water oxidation. To compare and contrast with the intact system, we examine here, in a simplified Mn-depleted PSII core complex, isolated from a site-directed mutant of Synechocystis PCC 6803 lacking Y(D), the role of proton transfer in the oxidation and reduction of Y(Z). We show how the oxidation and reduction rates for Y(Z), the deuterium isotope effect on these rates, and the Y(Z)* - Y(Z) difference spectra all depend on pH (from 5.5 to 9.5). This simplified system allows examination of electron-transfer processes over a broader range of pH than is possible with the intact system and with more tractable rates. The kinetic isotope effect for the oxidation of P680+ by Y(Z) is maximal at pH 7.0 (3.64). It decreases to lower pH as charge recombination, which shows no deuterium isotope, starts to become competitive with Y(Z) oxidation. To higher pH, Y(Z) becomes increasingly deprotonated to form the tyrosinate, the oxidation of which at pH 9.5 becomes extremely rapid (1260 ms(-1)) and no longer limited by proton transfer. These observations point to a mechanism for the oxidation of Y(Z) in which the tyrosinate is the species from which the electron occurs even at lower pH. The kinetics of oxidation of Y(Z) show elements of rate limitation by both proton and electron transfer, with the former dominating at low pH and the latter at high pH. The proton-transfer limitation of Y(Z) oxidation at low pH is best explained by a gated mechanism in which Y(Z) and the acceptor of the phenolic proton need to form an electron/proton-transfer competent complex in competition with other hydrogen-bonding interactions that each have with neighboring residues. In contrast, the reduction of Y(Z)* appears not to be limited by proton transfer between pH 5.5 and 9.5. We also compare, in Mn-depleted Synechocystis PSII core complexes, Y(Z) and Y(D) with respect to solvent accessibility by detection of the deuterium isotope effect for Y(Z) oxidation and by 2H ESEEM measurement of hydrogen-bond exchange. Upon incubation of H2O-prepared PSII core complexes in D2O, the phenolic proton of Y(Z) is exchanged for a deuterium in less than 2 min as opposed to a t(1/2) of about 9 h for Y(D). In addition, we show that Y(D)* is coordinated by two hydrogen bonds. Y(Z)* shows more disordered hydrogen bonding, reflecting inhomogeneity at the site. With 2H ESEEM modulation comparable to that of Y(D)*, Y(Z)* would appear to be coordinated by two hydrogen bonds in a significant fraction of the centers.