OC Hydrogen Bonds Research Articles

New Coordination Modes of an Oxime Ligand in a Triosmium Cluster. Stabilization by Intra- and Intermolecular C−H···O Hydrogen Bonds

Reaction of the hydroxyamine 7-chloro-4-(hydroxyamino)quinoline with the triosmium cluster Os3(CO)10(NCMe)2 gave the complex (μ-H)Os3(CO)10(μ2-η1-O-C9H6N2Cl) (3), in which a new mode of μ2-η1-O-oximato ligand bridged two osmium centers by an oxygen atom. This complex was slowly converted to (μ-H)Os3(CO)10(μ2-η2-ON-C9H6NCl) (4), where an aromatic C−H moiety in the μ2-η2-ON-oximatoquinoline group formed an unusual short intramolecular C−H···O−N hydrogen bond and an intermolecular C−H···OC hydrogen bond simultaneously. The formation of the intramolecular hydrogen bond may provide a stabilization effect for the generation of the η2-ON complex 4 and a driving force for the transformation of 3 to 4.

Selection of substituted benzaldehyde conformers by the cyclodextrin inclusion process: a Raman spectroscopic study

Raman spectra of benzaldehyde (B), 4-Methoxybenzaldehyde (4MeOB), 3-methoxybenzaldehyde (3MeOB), 3-methylbenzaldehyde (3MB) and 3-chlorobenzaldehyde (3CB) included in α-, β- and γ-cyclodextrins (α-, β- and γCD) were recorded. The effects of the inclusion process on the conformational isomerism and on the hydrogen bond interactions of the guests were studied by monitoring sensitive modes, such as the C O and CH stretching modes, among others. Overall, the spectral observations suggest that the inclusion in the small αCD cavity imposes structural restrictions on the guest not observed with the larger βCD and γCD. For the 4MeOB molecule, only the most stable form is included in αCD, whereas for 3CB, the most stable form is completely absent from the αCD complex. Clear evidence of hydrogen bonding interactions with the carbonyl oxygen atom was observed for the 4MeOB·αCD complex. In addition, the presence of a C—H···OC hydrogen bond in the B·αCD structure is suggested by the changes observed in the region of the CH stretching modes. Copyright © 2000 John Wiley & Sons, Ltd.

Role of α-Helix Conformation Cooperating with NH···S Hydrogen Bond in the Active Site of Cytochrome P-450 and Chloroperoxidase: Synthesis and Properties of [MIII(OEP)(Cys-Helical Peptide)] (M = Fe and Ga)

Heme-thiolate protein model complexes, [FeIII(OEP)(Ac-LcXAF-LLLLL-ALFL-OMe)] {OEP = octhaethylporphinato, X = Leu (1) and Pro (2)}, having α-helical structure were synthesized and characterized as P-450 and CPO models. The stable ligation of cysteinyl thiolate at the axial position of model complexes was established using MCD, UV−visible, 1H NMR, and ESI-MS. These results indicate that 1 and 2 possess high-spin 5-coordinated Fe(III) ions. The helical contents were examined by CD measurements in THF which revealed the contents of 1 and [GaIII(OEP)(Ac-LcLAF-LLLLL-ALFL-OMe)] (3) to be both 49%, though the thiolate anion (Et4N){Ac-LC(S-)LAF-LLLLL-ALFL-OMe} (5) has the value of 57%. Thus, the α-helical NH···OC hydrogen bond network is intercepted by the NH···S hydrogen bond between NH(Leu3) and Sγ(Cys2). However, the helical percentages of 2 (59%) and [GaIII(OEP)(Ac-LcPAF-LLLLL-ALFL-OMe)] (4) (57%) are similar to that of (Et4N){Ac-LC(S-)LAF-LLLLL-ALFL-OMe} (6) (52%). The NMR analysis of the solution structure ...

Indifference to Hydrogen Bonding in a Family of Secondary Amides

N−H stretch region IR spectroscopy has been used to probe the hydrogen bond-donating properties of six structurally related secondary amides in which the amide group is flanked by sterically bulky groups. For three of the compounds, solid state IR analysis reveals N−H stretch bands >3400 cm-1, which suggests the absence of intermolecular N−H--OC hydrogen bonds. Crystallographic data for these three amides confirm the absence of a standard N−H--OC interaction. For the other three amides, N−H stretch bands in the range 3370−3290 cm-1 suggest the occurrence of intermolecular N−H--OC hydrogen bonds in the solid state, but high quality crystals could not be grown. Steric hindrance to hydrogen bond donation by these amides is manifested in IR data obtained in DMSO: although this solvent is a strong hydrogen bond acceptor, N−H stretch bands are observed for both solvent-hydrogen bonded and non-hydrogen bonded amide groups. The amides described here and related compounds should be useful for calibrating spectros...

Active site of bacteriorhodopsin. FTIR and 1H NMR studies using a model molecule

We obtained the 2-N-methylaminoethylguanidine amide, 4, of Kemp's triacid(all-cis-1,3,5-trimethylcyclohexane 1,3,5-tricarboxylic acid) as a model substance for the active site of bacteriorhodopsin. Compound 4 was synthesised from Kemp's triacid triethyl ester, 1, in three reactions. Compound 4 and its complex with tetrabutylammonium 4-methylphenolate were studied by FTIR and 1H NMR spectroscopy in acetonitrile solutions. In the case of compound 4, two types of hydrogen bond are formed: one is the CO2H⋯N⇌CO–2⋯H+N bond. In this case, the donor is one of the two carboxylic acid groups, and the acceptor, the guanidine group. A double-minimum proton potential is present in this bond and therefore it exhibits large proton polarizability. The second NH⋯OC hydrogen bond formed between the protonated guanidine (proton donor group) and the carbonyl O atom of the other carboxylic group is asymmetrical. The proton is localised at the guanidine residue. If a phenolate molecule is added to the solution of compound 4, the situation changes dramatically. A PhOH⋯N⇌PhO–⋯H+N bond with large proton polarizability is formed between the phenolate and guanidine groups. The polarizable carboxylic acid–guanidine hydrogen bond is broken and the asymmetrical NH⋯O bond between guanidine and the O atoms of carboxylic acid becomes much stronger. The results obtained with the model are compared with those obtained earlier with bacteriorhodopsin.

Aggregation, hydrogen bonding and thermodynamic studies on tetrapeptide micelles

The temperature dependence of critical micelle concentration (c.m.c.), aggregation number, standard Gibbs energy change (ΔmG°), enthalpy change (ΔmH°) and entropy change (ΔmS°) of micelle formation, and proton chemical shifts of the TFA · Tyr-Gly-Phe-Ala-OBz peptide (TFA is trifluoroacetic acid) have been presented in the light of NH⋯OC hydrogen-bond formation and forces implicated in micellization. It has been found that the c.m.c. of the tetrapeptide increases with increase in temperature from 20 to 40 °C, whereas it decreases at temperatures above 40 °C. Moreover, the temperature dependence of the aggregation number, proton chemical shifts and thermodynamic results suggest that intramolecular H bonds are formed at temperatures in the range 20–40 °C (secondary level of structure) owing to hindrance of micelle formation, whereas above 40 °C the intramolecular H bonds of the peptide are broken as micellization increases which demonstrates a tertiary level of structure. It has also been found that the temperature of 40 °C appears very significant in that it is close to the temperature at which both the enthalpy and entropy of micellization change sign, which presumably relates to the opposing temperature dependences of hydrophobic and electrostatic interactions, the inverse temperature dependence of hydrophobic interactions, reflecting changes in water structure.

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

AbstractTwo conformers of protonated pyruvate, CH3C+(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the CCC plane have been studied using the ab initio SCF/3‐21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the CCOO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH3COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a CCOO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6‐311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone‐type isomer of protonated pyruvate, which contains a CCO ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3‐21G basis set. The most stable complex is predicted to occur between trans‐methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ⃛ OC hydrogen bond. © 1993 John Wiley & Sons, Inc.

Helical screw sense of peptide molecules. X-Ray diffraction structures of two oligopeptides with a single chiral centre

A crystal-state structural analysis of Z-L-Dap(pBrBz)-(Aib)2-NHMe and Z-L-Dab(pBrBz)-(Aib)2-NHMe has been performed by X-ray diffraction. Both peptides are folded into incipient 310 helices stabilized by two consecutive intramolecular N–H ⋯ OC hydrogen bonds of the C10 type (β-bends). While Z-L-Dap(pBrBz)-(Aib)2-NHMe gives rise to a left-handed helix, two independent molecules of opposite helical screw sense are observed in the crystals of Z-L-Dab(pBrBz)-(Aib)2-NHMe. The latter compound represents the first example of screw sense indifference shown in the crystal state by a peptide containing a single chiral Cα-trisubstituted α-amino acid residue.

Conformational feature of aureobasidin E, a new type of potent antifungal antibiotic

The crystal structure of aureobasidin E, a new type of potent antifungal antibiotic, revealed the molecular conformation stably held by three intramolecular NH ⋯ OC hydrogen bonds, showing a possible feature responsible for its biological activity.

ChemInform Abstract: β‐Diketone Interactions. Part 11. The Hydrogen‐Bonded Adduct 4,6‐Dimethylpyrimidin‐2‐one·Urea (DMP·U) from the Reaction of Pentane‐2,4‐dione and Urea

The X-ray crystal Structure of the adduct formed between 4,6-dimethylpyrimidin-2-one and urea (DMP·U) shoes a compact unit joined through two N–H ⋯ OC hydrogen bonds. One of these is remarkably short with RN ⋯ O 2.735 A(RH ⋯ O 1.705 A), and is believed to be among the shortest example of an NHO hydrogen bond between neutral molecules. Its hydrogen-bond energy, estimated from IR data, is ca. 75 kJ mol–1

Parallel zippers formed by alpha-helical peptide columns in crystals of Boc-Aib-Glu(OBzl)-Leu-Aib-Ala-Leu-Aib-Ala-Lys(Z)-Aib-OMe.

The crystal structure of the decapeptide Boc-Aib-Glu(OBzl)-Leu-Aib-Ala-Leu-Aib-Ala-Lys(Z)-Aib-OMe (where Aib is alpha-aminoisobutyryl, Boc is t-butoxycarbonyl, OBzl is benzyl ester, and Z is benzyloxycarbonyl) illustrates a parallel zipper arrangement of interacting helical peptide columns. Head-to-tail NH...OC hydrogen bonding extends the alpha-helices formed by the decapeptide into long columns in the crystal. An additional NH...OC hydrogen bond in the head-to-tail region, between the extended side chains of Glu(OBzl), residue 2 in one molecule, and Lys(Z), residue 9 in another molecule, forms a "double tooth" on the side of the column. These double teeth are repeated regularly on the helical columns with spaces of six residues between them (approximately 10 A). The double teeth on a pair of parallel columns (all carbonyl groups pointed in the same direction) interdigitate in a zipper motif. All contacts in the zipper portion are of the van der Waals type. The peptide, with formula C66H103N11O17.H2O, crystallizes in space group P2(1)2(1)2(1) with a = 10.677(4) A, b = 16.452(6) A, and c = 43.779(13) A; overall agreement R = 10.2% for 3527 observed reflections (magnitude of /F0/ greater than 3 sigma); resolution 0.9 A.

β-Diketone interactions. Part 11. The hydrogen-bonded adduct 4, 6-dimethylpyrimidin-2-one·urea (DMP·U) from the reaction of pentane-2,4-dione and urea

The X-ray crystal Structure of the adduct formed between 4,6-dimethylpyrimidin-2-one and urea (DMP·U) shoes a compact unit joined through two N–H ⋯ OC hydrogen bonds. One of these is remarkably short with RN ⋯ O 2.735 Å(RH ⋯ O 1.705 Å), and is believed to be among the shortest example of an NHO hydrogen bond between neutral molecules. Its hydrogen-bond energy, estimated from IR data, is ca. 75 kJ mol–1

The role of hydroxyproline in collagen folding: conformational energy calculations on oligopeptides containing proline and hydroxyproline.

AbstractWe have observed that the rate of folding of the enzymatically hydroxylated form of poly(Gly‐Pro‐Pro) into the triple‐helical conformation is considerably higher than that of the unhydroxylated polypeptide [R. K. Chopra and V. S. Ananthanarayanan (1982) Proc. Natl. Acad. Sci. USA 79, 7180–7184]. In this study, we examine a plausible kinetic pathway for triple‐helix formation by selecting peptide models for the unhydroxylated collagen molecule, and computing their conformational energies before and after proline hydroxylation. Starting with the available data on the preferred conformations of proline‐ and hydroxyproline‐containing peptide sequences, energy minimization was carried out on the following pairs of peptides: Gly‐Ala‐Pro‐Gly‐Ala and Gly‐Ala‐Hyp‐Gly‐Ala; Gly‐Pro‐Pro‐Gly‐Ala and Gly‐Pro‐Hyp‐Gly‐Ala; Gly‐Ala‐Pro‐Gly‐Ala‐Pro and Gly‐Ala‐Hyp‐Gly‐Ala‐Hyp. It was found that, with each pair of peptides, the energetically most favorable conformation (I) has an extended structure at the Gly‐Ala or Gly‐Pro segment and a β‐bend at the Pro‐Gly or Hyp‐Gly segment. In the Hyp‐containing peptides, this conformation is further stabilized by a (Hypi + 2)OH…OC(Glyi) hydrogen bond. Conformation I is lower in energy by about 6–13 kcal/mol of the peptide than the fully extended conformations that resemble the single collagen polypeptide chain and contain no intramolecular hydrogen bond. In contrast to the proline counterpart, the hydroxyproline‐containing peptides are found capable of adopting a partially extended conformation that does not contain the β‐bend but retains the (Hyp)OH…OC(Gly) hydrogen bond. The energy of this conformation is intermediate between conformation I and the fully extended conformation. The continuation of the β‐bend along the chain is restricted by stereochemical constraints that are more severe in the latter two pairs of peptides than in the first pair. Such a restriction may be considered to trigger the “unbending” of the minimum energy conformation leading to its straightening into the fully extended conformation; the latter, in turn, would lead to triple‐helix formation through favorable interchain interactions. We propose that the partially extended conformation in the Hyp‐containing peptides could serve as a kinetic intermediate on the way to forming the fully extended conformation. Because of the (Hypi + 2)OH…OC(Glyi) hydrogen bond, this conformation would also serve to lock the trans geometry at the Gly‐Ala(Pro) and Ala(Pro)‐Hyp peptide bonds, thereby enhancing the rate of their helix formation. A scheme for collagen folding in proposed on the basis of these results.

Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-A resolution.

The structure of troponin C has been refined at 2A resolution to an R value of 0.172 using a total of 8,100 reflections. Troponin C has an unusual dumbbell shape with only the two C-domain high affinity sites III and IV occupied with metals, while the pair of N-domain low affinity sites I and II are devoid of metals. The coordination of the Ca2+ approaches seven with the last glutamic acid residue in each site forming an asymmetric bidentate ligand. The flanking helices in the metal-bound EF hands are in similar orientation (both 113 degrees) while in the apo sites they are more obtuse (134 and 149 degrees). The EF hands of holo sites III and IV are similar while the apo sites I and II are less similar (rms for backbone atoms, 0.78 and 1.44). The half-loops of the 12-residue holo and apo sites show better agreement than the full loops themselves, suggesting a hinge motion at the midpoint of the loops. The long central helix is stabilized by electrostatic interactions and salt bridges between charged side chains spaced at 3 or 4 residues along the helix. A cluster of water molecules encircle the long helix and hydrogen bond to the backbone carbonyls. At the beginning of the B-helix, a water molecule is interposed at each of two consecutive backbone NH...OC hydrogen bonds. The terminal pair of helices A/D (apo) match with E/H (holo), and the internal pair of helices B/C (apo) match with F/G (holo). Thus, muscle contraction may be triggered by Ca2+ binding to loops I and II which results in a concerted rearrangement of residues in the loops, including the essential Gly at position 6 in each loop. This rearrangement than causes a reorientation of helices B and C along with the BC linker.

Crystal and molecular structure of the di-μ-hydroxo-dimolybdenum compound, [Mo(CO)2(OH)(C4H7)(3,5-diMepzH)]2•C6H6

The synthesis and X-ray crystal analysis of a hydroxy-bridged molybdenum dimer are described. Crystals of di-μ-hydroxo-bis [dicarbonyl(3,5-dimethylpyrazole)(η3-2-methylallyl)molybdenum(II)] benzene solvate are monoclinic, P21/c, a = 7.508(1), b = 20.747(1), c = 20.717(3) Å, β = 99.536(6)°, Z = 4. The structure was determined by Patterson and Fourier methods and refined by full-matrix least-squares procedures to R = 0.022 for 3197 observed reflections. The dimeric molecule contains two distorted Mo coordination octahedra sharing an OH … OH edge to form a central folded four-membered Mo(μ-OH)2Mo ring. The pyrazole ligands form bent N—H … O intramolecular hydrogen bonds to the bridging OH groups, and the other ligands occupy positions which result in approximate C2 molecular symmetry. Two sets of Mo—OH bonds differ significantly in length, 2.237(2) and 2.140(2) Å; other molecular dimensions are within expected ranges. Molecules are linked into chains along a by O—H … OC hydrogen bonds, and benzene solvate molecules are well defined.

Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 3(10)-helix, alpha-helix, and beta-bend ribbon.

Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-Ala-Aib-Pro-Aib-Pro-Phe-OMe (where Boc is t-butoxycarbonyl and Aib is alpha-aminoisobutyric acid), a synthetic apolar analog of the membrane-active fungal peptide antibiotic zervamycin IIA, crystallizes in space group P1 with Z = 1 and cell parameters a = 9.086 +/- 0.002 A, b = 10.410 +/- 0.002 A, c = 28.188 +/- 0.004 A, alpha = 86.13 +/- 0.01 degrees, beta = 87.90 +/- 0.01 degrees, and gamma = 89.27 +/- 0.01 degrees; overall agreement factor R = 7.3% for 7180 data (F0 greater than 3 sigma) and 0.91-A resolution. The peptide backbone makes a continuous spiral that begins as a 3(10)-helix at the N-terminus, changes to an alpha-helix for two turns, and ends in a spiral of three beta-bends in a ribbon. Each of the beta-bends contains a proline residue at one of the corners. The torsion angles phi i range from -51 degrees to -91 degrees (average value -64 degrees), and the torsion angles psi i range from -1 degree to -46 degrees (average value -31 degrees). There are 10 intramolecular NH...OC hydrogen bonds in the helix and two direct head-to-tail hydrogen bonds between successive molecules. Two H2O and two CH3OH solvent molecules fill additional space with appropriate hydrogen bonding in the head-to-tail region, and two additional H2O molecules form hydrogen bonds with carbonyl oxygens near the curve in the helix at Pro-10. Since there is only one peptide molecule per cell in space group P1, the molecules repeat only by translation, and consequently the helices pack parallel to each other.

Vibrational Properties of the peptide NH bond as a function of hydrogen-bond geometry: an ab initio study

The IR intensity and the harmonic force constant of the NH stretch mode in peptide NH⋯OC hydrogen bonds are studied as functions of the hydrogen-bond geometry using a model complex of N-methylacetamide and formamide the STO-3G basis set. Results on the equilibrium NH bond length and the energy are also reported. The variations of the properties with geometry are qualitatively as expected. Comparisons with relevant experimental data indicate that quantitative information may also be extracted from our results. The correlations among the properties are also discussed.

Picosecond relaxations in hydrated polyamide‐6 observed by millimeter‐wave spectroscopy

AbstractAbsorption measurements at millimeter‐wave frequencies (50–151 GHz) are reported for dried and hydrated polyamide‐6. The measurements were extended over the temperature range from liquid helium to room temperature using the oversized‐cavity technique. For dried polyamide‐6 (water content ≤ 0.5% w/w), a nearly linear increase with frequency and an exponential increase with temperature of the absorption coefficient is found between 50 and 300 K. This frequency and temperature dependence is described by relaxation processes in asymmetric double‐well potentials. The observed relaxation times are on a picosecond time scale, thus suggesting an assignment to the NH…OC hydrogen bonds and the adjacent peptide unit (OCNH). Hydration results in an increase of the absorption over the whole temperature and frequency range. This is attributed to the fact that the water of hydration is adsorbed in the neighborhood of the hydrogen bonds and changes their dynamical properties. This interpretation is supported by IR‐spectroscopic measurements of the shift of amide I and amide II after hydration.

Picosecond relaxations in hydrated lysozyme observed by mm-wave spectroscopy

Dielectric absorption measurements at mm-wave frequencies (50 GHz… 150 GHz) are reported for lysozyme at different hydration levels. The measurements were extended over the temperature range from liquid helium to room temperature using the untuned cavity technique. For dried lysozyme (water content ≤ 0.5%, w/w) a nearly linear increase with frequency and an exponential increase with temperature of the absorption coefficient is observed between 50 K and 300 K. This frequency and temperature dependence is described by relaxation processes in asymmetric double-well potentials with relaxation times in the picosecond range. Hydration yields a nearly frequency-independent contribution to the absorption, which arises only at temperatures above 120 K. The frequency independence indicates relaxation rates for the bound water that are small compared to mm-wave frequencies. Thereby the contribution of bound water can clearly be distinguished from the fast intrinsic processes. An assignment of these picosecond relaxations to the NH… OC hydrogen bond of the peptide backbone is suggested.

Relaxation processes on a picosecond time scale in hemoglobin and poly(L‐alanine) observed by millimeter‐wave spectroscopy

AbstractBroadband measurements of the millimeter‐wave and far‐ir absorption (10–104 GHz) of lyophilized hemoglobin are reported. Additionally, the absorption of poly(L‐alanine) and crystalline L‐alanine at 70 GHz was measured for comparison. All measurements were extended over the temperature range from liquid helium to room temperature. For the millimeter range, this was attained by using the novel oversized‐cavity technique. It was found that the millimeter‐wave absorption of the materials increased nearly exponentially with temperature and increased as ν1.2–ν2 with frequency. The far‐ir absorption of hemoglobin showed broadbands with almost no temperature dependence. The frequency and temperature dependence of the millimeter‐wave absorption is quantitatively described as due to three distinct relaxation processes on a picosecond time scale occurring in asymmetric double‐well potentials. These processes are most probably assigned to the NH ⃛OC hydrogen bonds of the peptide backbone.