C[bond]H- - -O hydrogen bonds in beta-sheetlike networks: combined X-ray crystallography and high-pressure infrared study

Crystal structure of 1-butyl-3-{2-[(indan-5-yl)amino]-2-oxoeth-yl}-1H-imidazol-3-ium chloride

In the cation of the title mol-ecular salt, C18H24N3O+·Cl-, an intra-molecular C-H⋯O hydrogen bond stabilizes the almost coplanar orientation of the aromatic ring of the indane unit and the amide plane. In the crystal, the packing is dominated by inter-molecular C-H⋯Cl hydrogen-bonding inter-actions that result in the formation of slab-like structures propagating along [010]. The slabs are linked by weak C-H⋯O inter-actions, forming layers lying parallel to (100). The methyl-ene carbon atom of the indanyl substituent is disordered over two positions with a refined occupancy ratio of 0.84 (2):0.16 (2). The crystal studied was refined as a twin with matrix [1 0 0.9, 0 0, 0 0 ]; the resulting BASF value is 0.30.

The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals

Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.

Carbon-oxygen hydrogen bonding in biological structure and function

Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.

Investigation on the individual contributions of N-H...O=C and C-H...O=C interactions to the binding energies of beta-sheet models

In this article, the binding energies of 16 antiparallel and parallel beta-sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for beta-sheet models. Further comparisons suggest that the binding energy of the beta-sheet models might come mainly from dipole-dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole-dipole attractive and repulsive interactions are further obtained in this article. The total of N-H...H-N and C=O...O=C dipole-dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel beta-sheet models is estimated to be about 6.0 kcal/mol. The individual N-H...O=C dipole-dipole attractive interaction is predicted to be -6.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -5.2 +/- 0.6 kcal/mol in the parallel beta-sheet models. The individual C(alpha)-H...O=C attractive interaction is -1.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -1.5 +/- 0.2 kcal/mol in the parallel beta-sheet models. These values are important in understanding the interactions at protein-protein interfaces and developing a more accurate force field for peptides and proteins.

Stability of hydrogen-bonded supramolecular architecture under high pressure conditions: pressure-induced amorphization in melamine-boric acid adduct

The effects of high pressure on the structural stability of the melamine-boric acid adduct (C3N6H(6).2H3BO3, M.2B), a three-dimensional hydrogen-bonded supramolecular architecture, were studied by in situ synchrotron X-ray diffraction (XRD) and Raman spectroscopy. M.2B exhibited a high compressibility and a strong anisotropic compression, which can be explained by the layerlike crystal packing. Furthermore, evolution of XRD patterns and Raman spectra indicated that the M.2B crystal undergoes a reversible pressure-induced amorphization (PIA) at 18 GPa. The mechanism for the PIA was attributed to the competition between close packing and long-range order. Ab initio calculations were also performed to account for the behavior of hydrogen bonding under high pressure.

Infrared spectroscopy of hydrogen-bonded CHCl3-SO2 in the gas phase

A molecular association between chloroform and sulfur dioxide in the gas phase at room temperature was studied by Fourier transform infrared spectroscopy. Since the intensity of the CH-stretching fundamental vibration of monomer chloroform is very weak but much stronger upon complexation, a simple subtraction procedure isolated the CH-stretching vibration spectrum of the complex. The presence of a 1:1 complex was confirmed by two dilution series, where the monomer concentrations were varied. The molecular association manifested itself as a shift of the peak absorbance of the CH-stretching vibration of CHCl3-SO2 by +7 cm(-1) and of the CD-stretching vibration of CDCl3-SO2 by +5 cm(-1) to higher wave numbers compared to monomer chloroform, accompanied by a considerable broadening of the band contour. In agreement with previous ab initio calculations, this indicates a "blueshifting" or more appropriately, a "C-H contracting" hydrogen bond between chloroform and sulfur dioxide. An estimate of the complex concentration was made based on ab initio calculations for the integrated band strength and the measured spectrum. With this estimate, the equilibrium constant Kp (295 K)=0.014 (po=10(5) Pa) for the dimerization was calculated, providing one of the very few cases where the formation of a hydrogen-bonded gas phase complex at room temperature could be quantitatively studied by infrared spectroscopy.

Quantum-chemical study of CHCl3-SO2 association

CHCl(3)-SO(2) association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Moller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH...O hydrogen-bonded complex (DeltaE(0)=-8.73 kJmol) with a 2.4 A intermolecular H...O distance and two very weak van der Waals complexes (DeltaE(0)=-3.78 and -2.94 kJmol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency ("blueshift") of the CH-stretching vibration compared to the CHCl(3) monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance.

Evidence of Rotational Isomerism in 1-Butyl-3-methylimidazolium Halides: A Combined High-Pressure Infrared and Raman Spectroscopic Study

High-pressure methods were applied to investigate the rotational isomerism and the hydrogen-bonding structures of 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Conformation changes of the butyl chain were observed above a pressure of 0.3 GPa. Under ambient pressure, Raman spectra indicate that the more thermodynamically stable butyl structure of the cations is the gauche-anti (GA) and all-anti forms for 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Nevertheless, the high-pressure phases arise from the perturbed GA conformer. The imidazolium C-H bands of 1-butyl-3-methylimidazolium chloride display anomalous nonmonotonic pressure-induced frequency shifts. This discontinuity in the frequency shift is related to the modification of the imidazolium C-H---Cl- contacts upon compression. The alkyl C-H---Cl- interactions are suggested to be a compensatory mechanism to provide additional stability. Density-functional-theory-calculated results also support the high-pressure results that the methyl and butyl C-H groups are suitable proton donor sites for the GA conformer.

Effect of solvent upon CH...O hydrogen bonds with implications for protein folding

The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.

The methyl C–H blueshift in N,N-dimethylformamide-water mixtures probed by two-dimensional Fourier-transform infrared spectroscopy

Two-dimensional correlation spectroscopy was used to study the composition-dependent spectral variations of the CH-stretching bands of N,N-dimethylformamide (DMF)-water mixtures with X(DMF) ranging from 0.98 to 0.60. By a detailed correlation analysis of the spectral changes of the CH- and OH-stretching bands, it is found that the intensities of the CH and OH bands change in different ways when the water content is increased. It is also found that two different regions of the water content can be distinguished, in which the intensity changes have different signatures. A tentative explanation for how these phenomena might be related to structural changes in the mixture is proposed. The structural change of DMF induced by the water hydrogen bonded on the carbonyl group is supposed to be the possible origin of the methyl C-H blueshift instead of the direct C-H...O interactions before the hydrophobic hydration takes place.

Hydrogen Bond Stabilization in 1,3-Dimethylimidazolium Methyl Sulfate and 1-Butyl-3-Methylimidazolium Hexafluorophosphate Probed by High Pressure: The Role of Charge-Enhanced C−H···O Interactions in the Room-Temperature Ionic Liquid

The hydrogen bonding structures of room-temperature ionic liquids 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate have been studied by infrared spectroscopy. High-pressure infrared spectral profiles and theoretical calculations allow us to make a vibrational assignment of these compounds. The imidazolium C-H bands of 1,3-dimethylimidazolium methyl sulfate display anomalous non-monotonic pressure-induced frequency shifts. This discontinuity in frequency shift is related to enhanced C-H...O hydrogen bonding. This behavior is in contrast with the trend of blue shifts in frequency for the methyl C-H stretching mode at ca. 2960 cm(-1). Our results indicated that the imidazolium C-H groups are more favorable sites for hydrogen bonding than the methyl C-H groups in the pure 1,3-dimethylimidazolium methyl sulfate. Nevertheless, both methyl C-H and imidazolium C-H groups are favorable sites for C-H...O hydrogen bonding in a dilute 1,3-dimethylimidazolium methyl sulfate/D(2)O mixture. Hydrogen bond-like C-H...F interactions were observed between PF(6)(-) and H atoms on the alkyl side chains and imidazolium ring for 1-butyl-3-methylimidazolium hexafluorophosphate.

High-Pressure Raman Studies on Aqueous Protonated Thiazole: Presence of Charge-Enhanced C−H···O Hydrogen Bonds

Close interactions of the charge-enhanced C-H...O type have been analyzed both experimentally and computationally in the protonated thiazole-water system. The formation of a weak hydrogen bond was directly evidenced by a low-frequency shift of the hydrogen-bonded aromatic C-H stretch in the protonated thiazole moiety. For pure thiazole, the pressure dependence of the C-H bands yielded blue frequency shifts. The peak frequency of the aromatic C-H stretch band of protonated thiazole in a dilute D2O solution possesses an unusual nonmonotonic pressure dependence, which indicates enhanced C-H...O hydrogen-bond formation at high pressure. We performed density functional theory calculations to predict the frequency shift of the C-H stretching vibrations. The reorganization of the hydrogen-bonded network may be one of the factors to induce the blue frequency shift to the red frequency shift.

Stabilities of the C−H···O Bonded Complexes of the Haloforms HCClnF3-n (n = 0−3) with Dimethyl Ether, Oxirane, and Acetone: An Experimental and Theoretical Study

Complexation enthalpies of the complexes of the haloforms HCCl(n)F(3-)(n) (n = 0-3) with dimethyl ether, oxirane, and acetone have been determined in liquid krypton and/or liquid argon using infrared spectroscopy. The same quantities were derived starting from ab initio complexation energies, calculated at the MP2=FULL/aug-cc-VTZ level, and by correcting these energies for thermodynamic and solvent contributions. The two sets of data are compared and discussed.

Temperature-Dependent Photoelectron Spectroscopy of Methyl Benzoate Anions: Observation of Steric Effect in o-Methyl Benzoate

Temperature-dependent photoelectron spectra of benzoate anion (C6H5CO2(-)) and its three methyl-substituted isomers (o-, m-, p-CH3C6H4CO2(-)) have been obtained using a newly developed low-temperature photoelectron spectroscopy apparatus that features an electrospray source and a cryogenically controlled ion trap. Detachment channels due to removing electrons from the carboxylate group and benzene ring pi electrons were distinctly observed. Well-resolved vibrational structures were obtained in the lower binding energy region due to the OCO bending modes, except for o-CH3C6H4CO2(-), which yielded broad spectra even at the lowest ion trap temperature (18 K). Theoretical calculations revealed a large geometry change in the OCO angles between the anion and neutral ground states, consistent with the broad ground-state bands observed for all species. A strong steric effect was observed between the carboxylate and the methyl group in o-CH3C6H4CO2(-), such that the -CO2(-) group is pushed out of the plane of the benzene ring by approximately 25 degrees and its internal rotational barrier is significantly reduced. The low rotational barrier in o-CH3C6H4CO2(-), which makes it very difficult to be cooled vibrationally, and the strong coupling between the OCO bending and CO2 torsional modes yielded the broad PES spectra for this isomer. It is shown that there is no C-H...O hydrogen bond in o-CH3C6H4CO2(-), and the interaction between the carboxylate and methyl groups in this anion is found to be repulsive in nature.

Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.

Probing C–H⋯X hydrogen bonds in amide-functionalized imidazolium salts under high pressure

We have probed under high pressure the C-H hydrogen bonds formed by N,N(')-disubstituted imidazolium ions having PF(6) (-) and Br(-) counterions. High-pressure infrared spectral profiles, x-ray crystallographic analysis, and ab initio calculations allow us to make a vibrational assignment of these compounds. The appearance of a signal for the free-NH unit (or weakly bonded N-H...F unit) in the infrared spectrum of the PF(6) (-) salt indicates that conventional N-H...O and N-H...N hydrogen bonds do not fully dominate the packing. It is likely that the charge-enhanced C(2)-H...F interactions, combined with other weak hydrogen bonds, disturb the formation of N-H hydrogen bonds in the PF(6) (-) salt. This finding is consistent with the pressure-dependent results, which reveal that the C(2)-H...F interaction is enhanced upon increasing the pressure. In contrast to the PF(6) (-) salt, the imidazolium C-H bonds of the Br(-) salt have low sensitivity to high pressure. This finding suggests that the hydrogen bonding patterns are determined by the relative hydrogen bond acceptor strengths of the Br(-) and PF(6) (-) ions.

The PDZ2 Domain of Syntenin at Ultra-high Resolution: Bridging the Gap Between Macromolecular and Small Molecule Crystallography

The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 A resolution. The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and Rfree of 8.7%, making it the most precise crystallographic model of a protein molecule to date. The model reveals discrete disorder in several places in the molecule, and significant plasticity of the peptide bond, with some omega angles deviating by nearly 20 degrees from planarity. Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C-H...O type are clearly visible between the beta-strands. The study sets a new standard for high-resolution protein crystallography.