Solvent effects on the molecular stability,intramolecular hydrogen bond,and π-electron delocalization in the simple RAHB systems with different donors and acceptors: a quantum chemical study

Structural Chemistry - In the present study, solvent effects on the molecular stability, intramolecular hydrogen bond (IMHB), and π-electron delocalization (π-ED) in some of the simple...     

When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction.

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.     

In situ 19F NMR spectroscopy study of enzymatic transglycosylation reactions using α-d-aldohexopyranosyl fluorides as donors and acceptors

The use of ¹⁹F NMR spectroscopy to study the kinetics of the self-condensation reaction of α-d-aldohexopyranosyl fluorides catalysed by α-glycosidases is described. The corresponding fluorinated disaccharides thus synthesised present separate individual fluorine resonances allowing the integration of each species. This method looks particularly useful to help in the choice of donor in enzymatic transglycosylation reactions since the self-condensation reaction always remains in competition with the condensation reaction (reaction of the donor with acceptors other than itself).     

Quantum dots as simultaneous acceptors and donors in time-gated Förster resonance energy transfer relays: characterization and biosensing

The unique photophysical properties of semiconductor quantum dot (QD) bioconjugates offer many advantages for active sensing, imaging, and optical diagnostics. In particular, QDs have been widely adopted as either donors or acceptors in F?rster resonance energy transfer (FRET)-based assays and biosensors. Here, we expand their utility by demonstrating that QDs can function in a simultaneous role as acceptors and donors within time-gated FRET relays. To achieve this configuration, the QD was used as a central nanoplatform and coassembled with peptides or oligonucleotides that were labeled with either a long lifetime luminescent terbium(III) complex (Tb) or a fluorescent dye, Alexa Fluor 647 (A647). Within the FRET relay, the QD served as a critical intermediary where (1) an excited-state Tb donor transferred energy to the ground-state QD following a suitable microsecond delay and (2) the QD subsequently transferred that energy to an A647 acceptor. A detailed photophysical analysis was undertaken for each step of the FRET relay. The assembly of increasing ratios of Tb/QD was found to linearly increase the magnitude of the FRET-sensitized time-gated QD photoluminescence intensity. Importantly, the Tb was found to sensitize the subsequent QD-A647 donor-acceptor FRET pair without significantly affecting the intrinsic energy transfer efficiency within the second step in the relay. The utility of incorporating QDs into this type of time-gated energy transfer configuration was demonstrated in prototypical bioassays for monitoring protease activity and nucleic acid hybridization; the latter included a dual target format where each orthogonal FRET step transduced a separate binding event. Potential benefits of this time-gated FRET approach include: eliminating background fluorescence, accessing two approximately independent FRET mechanisms in a single QD-bioconjugate, and multiplexed biosensing based on spectrotemporal resolution of QD-FRET without requiring multiple colors of QD.     

Lewis acids as α-directing additives in glycosylations by using 2,3-O-carbonate-protected glucose and galactose thioglycoside donors based on preactivation protocol

Catalytic or stoichiometric amounts of Lewis acids were found to be very effective α-directing additives in the stereoselective glycosylations of diverse 2,3-O-carbonate-protected glucose and galactose thioglycoside donors by preactivation protocol. The poor stereoselectivities of 4,6-di-O-acetyl-2,3-O-carbonate protected thioglycoside donors in glycosyl coupling reactions were greatly improved, and excellent α-stereoselectivities were achieved by the addition of 0.2 equiv of BF(3)·OEt(2). On the other hand, the β-selectivities of 4,6-di-O-benzyl-2,3-O-carbonate-protected thioglucoside donor toward glycosylations were reversed completely to the α-selectivities by the use of 1 equiv of SnCl(4), making the stereoselectivity controllable. Furthermore, the poor stereoselectivities of 4,6-di-O-benzyl-2,3-O-carbonate-protected thiogalactoside donor in glycosylations were also improved by using SnCl(4) as additive.     

Constrained α/γ-peptides: a new stable extended structure in solution without any hydrogen bond and characterized by a four-fold symmetry

Small α/γ-peptides alternating α-aminoisobutyric acid and cyclic γ-amino acid residues are described. NMR studies together with restrained simulated annealing revealed that an extended backbone conformation largely dominates in solution for as short as 4-residues long oligomers. This new fold type is devoid of any hydrogen bond and characterized by a four-fold symmetry.     

Vibronic coupling and intramolecular dynamics of pyrene as revealed by the S0→S2 excitation spectrum in a supersonic jet

The fluorescence excitation spectrum of pyrene obtained in a supersonic jet for the S₀→S₂ transition shows a complicated structure due to the interaction of discrete levels of S₂ with the quasi-continuous levels belonging to S₁. The intensity distribution pattern in this region has been evaluated from quantum-mechanically calculated quantities, such as the vibronic coupling integrals, and Franck-Condon factors deduced from independent experiments. The dynamics in pyrene following excitation into S₂ are discussed.     

Porpholactams and chlorolactams: replacement of a β,β'-double bond in meso-tetraphenyl-porphyrin and -chlorin by a lactam moiety

Reaction of meso-tetraphenylporpholactone with hydrazine converts the lactone moiety to an N-aminolactam. It also reduces the opposite pyrrolic moiety of both the starting material and the N-aminolactam, generating chlorin-like chlorolactone and N-aminochlorolactam, respectively. Reductive N-N cleavage of the N-aminoporpholactam generates the parent porpholactam.     

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol⁻¹. This value increases by ca. 1 kcal mol⁻¹ on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol⁻¹ depending on the structure of the β-diketone in question.     

A piezo-resonator as a detector of α- and β-alanine in aqueous solutions

The results of analysis of aqueous solutions of α- and β-alanine using a piezo-resonator are presented. Analytical signals from analytes were found to significantly differ from each other, which is connected with the peculiarities of the piezo-resonator operation in the solution as a viscosimetric rather than a mass-sensitive device.     

Hydrogen bonding interactions in α-substituted cinnamic acid ester derivatives studied by FT–IR spectroscopy and calculations

Intermolecular hydrogen bonding interactions in stereoisomeric α-substituted cinnamic acid methyl esters (methyl 2,3-diphenylpropenoate, methyl 2-phenyl-3-(2′-methoxyphenyl)-propenoate, methyl 2-(2′-methoxyphenyl)-3-phenylpropenoate and methyl-2,3-bis(2′-methoxyphenyl)-propenoate) were studied by FT–IR spectroscopy and model calculations at the semi-empirical quantum chemical level of theory. Intermolecular hydrogen bonds of C–H…O types were found to be general in the solid state, but rare in solution. In this hydrogen bond the carbon may be part of either aromatic ring or the olefinic bond. The hydrogen bond acceptor may be the carbonyl oxygen or the oxygen in the methoxy substituent. Modeling helped in determining probable hydrogen bonding sites and their positions and provided with approximate geometric parameters (bond lengths and angles). Pointing out differences between the stereoisomers was also possible.     

Small heterocyclics as hydrogen bond acceptors and donors: the case of the C2H3XS···NH3 complexes (X = H, F and CH3)

B3LYP/6-311++G(d,p) calculations were employed in order to examine the molecular parameters of the C₂H₃XS···NH₃ heterocyclic hydrogen-bonded complexes with X = H, F and CH₃. Intermolecular criteria were taken into account when studying the formation of these hydrogen-bonded complexes, such as geometry analysis, charge density quantification and interpretation of the harmonic vibrational spectrum, in which case the appearance of red-shift and blue-shift effects was discussed. It was assumed from the outset that many hydrogen bond types may exist in these systems, and these were investigated using the results of topological integrations from the quantum theory of atoms in molecules (QTAIM) and intermolecular charge transfer calculations using the ChelpG scheme. The proton donor/acceptor behavior of C₂H₃XS was interpreted in terms of hydrogen bond energies, whose values were corrected using the basis sets superposition error (BSSE) and zero point energy (ZPE). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Adsorbate-adsorbent and adsorbate-adsorbate interactions in CO overlayers adsorbed on α-Cr203 as investigated by infrared spectroscopy

CO is adsorbed at 298 K only on the (0001) faces of polycrystaltine αCr₂0₃ with the appearance of a single i.r. peak whose frequency shifts from 2185 (θ ≈ 0) to 2170 cm^-1 (θ_max). This shift is due to the building up of adsorbate-adsorbate interactions (dynamic and static). The dipole--dipole (dynamic) interaction has been measured by means of the diluted isotopic method and can be explained in terms of CO oscillators adsorbed on identical sites and with their axes parallel. This suggests that the (0001) face is fiat and that the Cr³⁺-CO bond, although mainly σ in character, has some participation of the d-π^* orbitals, The adsorption of CO causes distinct perturbations in the i.r, spectrum of the α-Cr₂O₃ (intensity erosions in the multiphonon and fundamental regions): this is ascribed to changes in the anharmonieity and force constants ofsurface vibrations. Attempts to detect the Me-CO stretching and bending vibrations in the low frequency range of the spectrum (700--200 cm ^-1) have been unsuccessful; the reasons for this negative result are discussed.     

Cofactor composition and function of a H2-sensing regulatory hydrogenase as revealed by M?ssbauer and EPR spectroscopy

The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H₂ and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O₂ and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron–sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe–4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H₂ leads to reduction of two of the [4Fe–4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe–4S] center in ‘proximal’ position to the [NiFe] center. In the two different active site redox states, the low-spin Fe^II exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H₂-sensing regulatory hydrogenases.