Internal Hydrogen Bond Research Articles

2-Phenyl-2-(pyridin-2-yl)hexahydropyrimidine

The title compound, C15H17N3, was prepared by reaction of benzoyl­pyridine and hexahydropyrimidine. The 1,3-diazinane ring adopts a chair conformation with one N—H group axial and the other equatorial. The axial N—H group participates in very weak hydrogen bonding to the lone pair of electrons of the N atom with the equatorial H atom producing a very weakly hydrogen-bonded dimer. The pyridine N atom accepts an inter­nal hydrogen bond from the equatorial H atom. The phenyl ring adopts an equatorial position while the pyridine ring is axial. The phenyl ring exhibits a slight twist (ca 25°) relative to the hexahydropyrimidine ring. The pyridine ring stacks with symmetry-related pyridine rings.

Receptor activity and conformational analysis of 5′-halogenated resiniferatoxin analogs as TRPV1 ligands

A series of 5′-halogenated resiniferatoxin analogs have been investigated in order to examine the effect of halogenation in the A-region on their binding and the functional pattern of agonism/antagonism for rat TRPV1 heterologously expressed in Chinese hamster ovary cells. Halogenation at the 5-position in the A-region of RTX and of 4-amino RTX shifted the agonism of parent compounds toward antagonism. The extent of antagonism was greater as the size of the halogen increased (I>Br>Cl>F) while the binding affinities were similar, as previously observed for our potent agonists. In this series, 5-bromo-4-amino RTX (39) showed very potent antagonism with Ki (ant)=2.81nM, which was thus 4.5-fold more potent than 5′-iodo RTX, previously reported as a potent TRPV1 antagonist. Molecular modeling analyses with selected agonists and the corresponding halogenated antagonists revealed a striking conformational difference. The 3-methoxy of the A-region in the agonists remained free to interact with the receptor whereas in the case of the antagonists, the compounds assumed a bent conformation, permitting the 3-methoxy to instead form an internal hydrogen bond with the C4-hydroxyl of the diterpene.

A New Strategy to Photoactivate Green Fluorescent Protein

Photoactivatable fluorescent proteins have become an important addition to the set of molecular probes used to understand cellular function. Known as “molecular highlighters”, their fluorescence is switched on by irradiation, thereby enabling non-invasive tracking of protein trafficking and dynamics. They are also the basis for the imaging technique called photoactivated light microscopy (PALM) in which multiple emitted photons are observed from individual active fluorophores which are sequentially activated from a large pool of inactive proteins and then photobleached. By locating the center of the point spread function for these emitted photons, it is possible to determine the location of the active fluorophore at better resolution than the theoretical diffraction limit. Previous green fluorescent protein (GFP) mutants exhibiting photomodulatory behavior have been reported including Kaede and KikGR whose emission wavelength change irreversibly, Dronpa whose fluorescence can be reversibly activated with light, and photoactivatable GFP (paGFP), whose excitation wavelength can be irreversibly changed with light. For Kaede, KikGR, and Dronpa, the precise three-dimensional structure of the fluorophore must be preserved to maintain photoswitching behavior. In paGFP, the shift in excitation wavelength is mediated by a light dependent decarboxylation of Glu222. The loss of this carboxy group is believed to cause reorientation of an internal hydrogen bond network, which changes the protonation state of the fluorophore and leads to an irreversible shift in the excitation maximum from 397 nm to 475 nm. This mechanism of GFP photoactivation requires the preservation of active-site residues His203, His148, Ser205, and Glu222. Unfortunately, the sequence restrictions necessary to maintain photomodulatory behavior are not always compatible with the mutations necessary to produce other fluorescent protein variants including YFP and RFP. In addition, Kaede, KikGR, and paGFP exist in two forms with differing excitation and emission wavelengths, precluding the simultaneous use of these wavelengths for other purposes. To address these problems, we have developed a general strategy for photoactivating GFP based upon nonnatural amino acid mutagenesis with the photocaged tyrosine analogue o-nitrobenzyl-O-tyrosine (ONBY). Replacing the fluorophore tyrosine 66 with ONBY yields a GFP molecule that is non-fluorescent as observed for other onitrobenzyl appended fluorophores including fluoresceine, Texas Red, and quantum dots. An earlier nonnatural variant of GFP was produced using a similar strategy, however, the high pre-irradiation background fluorescence and low protein yield made this unsuitable for use as a molecular marker. Fast, time-resolved UV/Vis spectroscopy measurements indicate that the fluorescence quenching likely occurs through photo-induced electron transfer (PET). Irradiation at 365 nm is sufficient to remove the o-nitrobenzyl

Crystallographic Characterization of 12-Helical Secondary Structure in β-Peptides Containing Side Chain Groups

Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.

X-ray Crystal Structures of Monomeric and Dimeric Peptide Inhibitors in Complex with the Human Neonatal Fc Receptor, FcRn

The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 A resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.

Infrared study of glycolaldehyde isolated in parahydrogen matrix

The infrared spectrum of glycolaldehyde sugar model in solid parahydrogen is reported and interpreted in the light of ab initio anharmonic frequency calculations. The advantages of parahydrogen lead to a simplification of its infrared spectroscopy compared to other conventional matrices. Surprisingly, the sugar molecule is found to display an unexpected large bandwidth compared to the smaller organic molecules studied in parahydrogen so far. Among them, only glycolaldehyde possesses an internal hydrogen-bond. Band broadening in glycolaldehyde is interpreted as originating mainly from the presence of the hydrogen-bond and to a lesser extent from clustering with oH(2) impurities.

ChemInform Abstract: Conformational Energies of 2-Fluoroethanol and 2-Fluoroacetaldehyde Enol: Strength of the Internal Hydrogen Bond

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ChemInform Abstract: Excitation Spectra of 2,5-Dihydroxy-p-benzoquinone Monomer and Hydrates.

The fluorescence excitation spectrum of the lowest allowed singlet–singlet transition of jet‐cooled 2,5‐dihydroxy‐p‐benzoquinone is reported. The transition is assigned as S3←S0, 1Bu←1Ag, π*←π and the 0–0 band origin is at 275.55 nm. Twenty vibrational levels, which include half of the Ag fundamentals, are assigned for the S3 state. The observed laser‐induced fluorescence transitions are structureless peaks with bandwidths that depend on the intensity of the excitation laser. No spectral multiplets attributable to intramolecular tunneling were observed. Deuterium isotope shifts of the 0–0 transition are +21 cm−1 per internal hydrogen bond. The 0–0 transitions of hydrate isotopomers with hydration shifts of only +11 cm−1 per water molecule are reported.

Communication: Energetics of reaction pathways for reactions of ethenol with the hydroxyl radical: The importance of internal hydrogen bonding at the transition state

We find high multireference character for abstraction of H from the OH group of ethenol (also called vinyl alcohol); therefore we adopt a multireference approach to calculate barrier heights for the various possible reaction channels of OH+C(2)H(3)OH. The relative barrier heights of ten possible saddle points for reaction of OH with ethenol are predicted by multireference Møller-Plesset perturbation theory with active spaces based on correlated participating orbitals (CPOs) and CPO plus a correlated pi orbital (CPO+pi). Six barrier heights for abstracting H from a C-H bond range from 3.1 to 7.7 kcal/mol, two barrier heights for abstracting H from an O-H bond are both 6.0 kcal/mol, and two barrier heights for OH addition to the double bond are -1.8 and -2.8 kcal/mol. Thus we expect abstraction at high-temperature and addition at low temperature. The factor that determines which H is most favorable to abstract is an internal hydrogen bond that constitutes part of a six-membered ring at one of the abstraction saddle points; the hydrogen bond contributes about 3 kcal/mol stabilization.

The Discovery of Pyridone and Pyridazone Heterocycles as γ-Secretase Modulators.

A series of novel pyridazone and pyridone compounds as γ-secretase modulators were discovered. Starting from the initial lead, structure-activity relationship studies were carried out in which an internal hydrogen bond was introduced to conformationally fix the side chain, and compounds with improved in vitro Aβ42 inhibition activity and good Aβtotal/Aβ42 selectivity were quickly discovered. Compound 35 displayed very good in vitro activity and excellent selectivity with good in vivo efficacy in both CRND8 mouse and nontransgenic rat models. This compound displayed a good overall profile in terms of rat pharmacokinetics and ancillary profile. No abnormal behavior and side effects were observed in all of the studies.

Nanomechanics of Ankyrin-R Repeats Probed by AFM and SMD Simulations

Ankyrin (ANK) repeats, identified in thousands of proteins, are composed of pairs of antiparallel alpha-helices that stack on top of each other and form super-helical spiral domains with suggestive spring-like properties, whose primary function is to mediate specific protein-protein interactions. For example, ankyrin-R links the anion exchanger in the erythrocyte membrane to the membrane skeleton and contains 24 ANK repeats that form a spiral domain. Ankyrin-R stabilizes the erythrocyte membrane and mutations in ANK repeats are documented in hereditary spherocytosis (HS), the life-threatening human anemia. Since repeats 13 to 24 (D34) of Ankyrin R are especially active in binding interactions and are subjected to the HS mutations, therefore the mechanical properties of this region of ankyrin-R are of the utmost importance. Although the conserved residues in each ankyrin repeat generate nearly identical helix-helix-loop structures, the exact positions and numbers of internal hydrogen-bonds, salt bridges and hydrophobic residue packing between repeats vary along the D34 domain and this variation is expected to modulate the elasticity, mechanical stability and mechanical unfolding/refolding properties of D34. We probed these properties of D34 directly by means of AFM-based single molecule force spectroscopy and by Steered Molecular Dynamics (SMD) simulations. By mapping the AFM force spectroscopy data onto the SMD-determined behavior of the internal network of H-bonds and salts bridges, we propose a model of the complex mechanical unfolding and refolding patterns of ANK repeats in D34.

Differential reactivity of thiophene-2-carboxylic and thiophene-3-carboxylic acids

In the course of investigating the propensity of aromatic acids to react with selected nucleophiles, we came across an interesting difference in yields for two structurally similar thiophene carboxylic acids. Given that these yields were consistent across more than 40 repetitions for each structure, we felt that the difference was real, and worth exploration. To extract the potential steric and electronic origins of such differences, we employed both DFT B3LYP/6-31G* and HF/6-311+G** levels of theory to evaluate structures and energetics. Two somewhat different pictures emerge of the origin of the differences between the carboxylic acids and their individual conformations. In particular, Hartree-Fock calculations with the larger 6-311+G** basis set, which includes multiple diffuse functions, show a profound difference in the delocalization of the LUMO, relative to the DFT method which, expectedly, provides a more localized picture of the contributions to the LUMO. For each of the conformers, the molecular electrostatic potential and the ionization potential (ESP and IP, respectively), together with charge distributions, dipole moments and orbital energies have been explored. A potential explanation for the somewhat more reactive character of the thiophene-2-carboxylic acid appears to arise from the presence of a conformer which has an internal hydrogen bond to the thiophene sulfur, which, in turn, polarizes the acid function significantly relative to other conformers, and optimizes the angle of attack of the nucleophile.

The Kinetic Effect of Internal Hydrogen Bonds on Proton-Coupled Electron Transfer from Phenols: A Theoretical Analysis with Modeling of Experimental Data

Proton-coupled electron transfer (PCET) was studied in two biomimetic covalently linked Ru(bpy)(3)-tyrosine complexes with the phenolic proton hydrogen-bonded to an internal carboxylate group. The phenolic group is either a salicylic acid (o-hydroxybenzoic acid, SA) or an o-hydroxyphenyl-acetic acid (PA), where the former gives a resonance-assisted hydrogen bond. Transient absorption data allowed direct determination of the rate constant for these intramolecular, bidirectional, and concerted PCET (CEP) reactions, as a function of temperature and H/D isotope. We found, unexpectedly, that the hydrogen bond in SA is in fact weaker than the hydrogen bond in the complex with PA, which forced us to reassess an earlier hypothesis that the proton coupling term for CEP with SA is increased by a stronger hydrogen bond. Consequently, the kinetic data was modeled numerically using a quantum mechanical rate expression. Sufficient experimentally determined observables were available to give robust and well-determined parameter values. This analysis, coupled with DFT/B3LYP and MP2 calculations and MD simulations, gave a detailed insight into the parameters that control the CEP reactions, and the effect of internal hydrogen bonds. We observed that a model with a static proton-tunneling distance is unable to describe the reaction correctly, requiring unrealistic values for the equilibrium proton-tunneling distances. Instead, when promoting vibrations that modulate the proton donor-acceptor distance were included, satisfactory fits to the experimental data were obtained, with parameter values that agree with DFT calculations and MD simulations. According to these results, it is in fact the weaker hydrogen bond of SA which increases the proton coupling. The inner reorganization energy of the phenolic groups is a significant factor contributing to the CEP barriers, but this is reduced by the hydrogen bonds to 0.35 and 0.50 eV for the two complexes. The promoting vibrations increase the rate of CEP by over 2 orders of magnitude, and dramatically reduce the kinetic isotope effect from ca. 40 for the static case to a modest value of 2-3.

Substituent effects on the thermodynamic stability of imines formed from glycine and aromatic aldehydes: implications for the catalytic activity of pyridoxal-5'-phosphate.

Equilibrium constants for addition of glycine to substituted benzaldehydes to form the corresponding imines and pK(a)'s for ionization of the iminium ions were determined by (1)H NMR analysis in D(2)O. The introduction of a phenoxide anion substituent into the aromatic ring of benzaldehyde leads to a substantial increase in the pK(a) of the iminium ion from 6.3 to 10.2 for p-hydroxybenzaldehyde and to 12.1 for salicylaldehyde. An analysis of the differential effect of ortho- versus para-substitution shows that the iminium ion to salicylaldehyde is stabilized by an intramolecular hydrogen bond in aqueous solution, with an estimated energy ca. 3 kcal/mol larger than can be accounted for by a simple electrostatic interaction. A comparison of the o-O(-) substituent effect on the acidity of the iminium ions of glycine to benzaldehyde and 4-pyridine-carboxaldehyde provides evidence for the existence of an internal hydrogen bond of similar strength in pyridoxal 5'-phosphate (PLP) iminium ions in water. The effects of other ring substituents on the stability of PLP iminium ions are discussed.

Bilirubin Chemistry and Metabolism; Harmful and Protective Aspects

Unconjugated bilirubin (UCB), the principal mammalian bile pigment, is the end product of heme catabolism. Both belong to the superfamily of tetrapyrrolic compounds that serve multiple biological functions in animals and plants. Its six internal hydrogen bonds give UCB a unique structure responsible for its physico-chemical properties and biological effects. Like many weakly-polar, poorly-soluble compounds, UCB is transported in blood tightly bound to albumin, with less than 0.01% of total bilirubin circulating in an unbound form (free bilirubin, Bf). This fraction governs the diffusion of UCB into tissues, and therefore Bf is responsible for both its beneficial and toxic effects on cells. Although, UCB was long thought to be a non-functional waste product, recent studies have shown that the antioxidant effects of mildly elevated serum bilirubin levels, as well as activation of heme oxygenase, may protect against diseases associated with oxidative stress, such as atherosclerosis. By contrast, markedly elevated serum UCB levels may cause severe neurological damage, especially in neonates. The regulation of cellular UCB content, by its conjugation, oxidation, and export, are, therefore of paramount importance to cellular health.

Energetics and Vibrational Analysis of Methyl Salicylate Isomers

Energetics and vibrational analysis study of six isomers of methyl salicylate in their singlet ground state and first excited triple state is put forward in this work at the density functional theory level and large basis sets. The ketoB isomer is the lowest energy isomer, followed by its rotamer ketoA. For both ketoB and ketoA their enolized tautomers are found to be stable as well as their open forms that lack the internal hydrogen bond. The calculated vibrational spectra are in excellent agreement with IR experiments of methyl salicylate in the vapor phase. It is demonstrated that solvent effects have a weak influence on the stability of these isomers. The ionization reaction from ketoB to ketoA shows a high barrier of 0.67 eV ensuring that thermal and chemical equilibria yield systems containing mostly the ketoB isomer at normal conditions.

A Single α‐Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge

Walking the carbon bridge to helix stabilization: α-Helix mimetics have been synthesized that contain an ethylene linkage in place of an (i,i+4) hydrogen bond (see structure). The smallest unit possible, a modified pentapeptide, shows the characteristic features of a helix (see CD spectrum). Incorporation of this carbon bridge into a peptide represents the first example of replacement of an internal backbone hydrogen bond.

A Single α‐Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge

A Single α‐Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge

Thermochemical Properties and Contribution Groups for Ketene Dimers and Related Structures from Theoretical Calculations

This research's main goals were to analyze ketene dimers' relative stability and expand group additivity value (GAV) methodology for estimating the thermochemical properties of high-weight ketene polymers (up to tetramers). The CBS-Q multilevel procedure and statistical thermodynamics were used for calculating the thermochemical properties of 20 cyclic structures, such as diketenes, cyclobutane-1,3-diones, cyclobut-2-enones and pyran-4-ones, as well as 57 acyclic base compounds organized into five groups. According to theoretical heat of formation predictions, diketene was found to be thermodynamically favored over cyclobutane-1,3-dione and its enol-tautomeric form (3-hydroxycyclobut-2-enone). This result did not agree with old combustion experiments. 3-Hydroxycyclobut-2-enone was found to be the least stable dimer and its reported experimental detection in solution may have been due to solvent effects. Substituted diketenes had lower stability than substituted cyclobutane-1,3-diones with an increased number of methyl substituents, suggesting that cyclobutane-1,3-dione type dimers are the major products because of thermodynamic control of alkylketene dimerization. Missing GAVs for the ketene dimers and related structures were calculated through linear regression on the 57 acyclic base compounds. Corrections for non next neighbor interactions (such as gauche, eclipses, and internal hydrogen bond) were needed for obtaining a highly accurate and precise regression model. To the best of our knowledge, the hydrogen bond correction for GAV methodology is the first reported in the literature; this correction was correlated to MP2/6-31Gdagger and HF/6-31Gdagger derived geometries to facilitate its application. GAVs assessed by the linear regression model were able to reproduce acyclic compounds' theoretical thermochemical properties and experimental heat of formation for acetylacetone. Ring formation and substituent position corrections were calculated by consecutively replacing the GAVs regarding the 20 cyclic structures' thermochemical properties.

Influence of temperature and crown ether complex formation on the charge partitioning between z and c fragments formed after electron capture by small peptide dications

Electron capture by peptide dications results in N–C α bond cleavage to give c + and z or c and z + fragments. In this work we have investigated how crown ether (18-crown-6 = CE) complex formation and a change in the internal energy affect the charge division between the z and c fragments. Both complex formation and a high temperature have the effect of breaking internal ionic hydrogen bonds. The crown ether complex also lowers the probability of internal proton transfer between the two fragments, and reduces the recombination energy of the charged group it targets. The systems under study were doubly protonated di- and tripeptides, [AK+2H] 2+, [AR+2H] 2+, [KK+2H] 2+ and [GHK+2H] 2+ (A = alanine, K = lysine, R = arginine, G = glycine and H = histidine). For crown ether complexes the formation of z + ions was always preferred over c + ions. In the case of [GHK+2H] 2+, the bare ion dissociated into z 2 + + c 1 and z 1 + c 2 + from cleavage of the first and second N–C α bond, respectively, whereas z 1 + fragment ions had higher yield than c 2 + for [GHK+2H] 2+(CE). The internal energy of the ions was changed by storing them in a 22-pole ion trap in which they were equilibrated to a temperature between −60 and 90 °C in collisions with helium gas. The average internal energy increased by about 0.4 eV from the lowest to the highest temperature for the dipeptides and 0.6 eV for the tripeptide. More fragmentation occurred at the higher temperature, as observed by an increase in the formation of b + and y + ions after breakage of the peptide bond of vibrationally hot even-electron cations and from secondary reactions of z + radical cations within the time window of the experiment. However, the z + to c + partitioning was not found to depend significantly on temperature in the measured range. In addition the decay of [GHK+H] +/[GHK+2H] + and [AK+H] + formed after electron capture by [GHK+2H] 2+ and [AK+2H] 2+ was found to occur on a microsecond to millisecond timescale. The data are well described by a power-law decay, which implies that the internal energy distribution is broad after electron capture and/or hydrogen loss.