Hydrogen bond

About: Hydrogen bond is a research topic. Over the lifetime, 57701 publications have been published within this topic receiving 1306326 citations.

Anion−Aromatic Bonding: A Case for Anion Recognition by π-Acidic Rings

Abstract: The basis for unprecedented noncovalent bonding between anions and the aryl centroid of electron-deficient aromatic rings has been demonstrated by an ab initio study of the interaction between 1,3,5-triazine and the fluoride, chloride, and azide ion at the MP2 level of theory. Minima are also located corresponding to C[bond]H...X(-) hydrogen bonding, reactive complexes for nucleophilic attack on the triazine ring, and pi-stacking interactions (with azide). Trifluoro-1,3,5-triazine also participates in aryl centroid complexation and forms nucleophilic reactive complexes with anions. This novel mode of bonding suggests the development of new cyclophane-type receptors for the recognition of anions.

Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution.

Abstract: Photoisomerization of the retinal of bacteriorhodopsin initiates a cyclic reaction in which a proton is translocated across the membrane. Studies of this protein promise a better understanding of how ion pumps function. Together with a large amount of spectroscopic and mutational data, the atomic structure of bacteriorhodopsin, determined in the last decade at increasing resolutions, has suggested plausible but often contradictory mechanisms. X-ray diffraction of bacteriorhodopsin crystals grown in cubic lipid phase revealed unexpected two-fold symmetries that indicate merohedral twinning along the crystallographic c axis. The structure, refined to 2.3 angstroms taking this twinning into account, is different from earlier models, including that most recently reported. One of the carboxyl oxygen atoms of the proton acceptor Asp85 is connected to the proton donor, the retinal Schiff base, through a hydrogen-bonded water and forms a second hydrogen bond with another water. The other carboxyl oxygen atom of Asp85 accepts a hydrogen bond from Thr89. This structure forms the active site. The nearby Arg82 is the center of a network of numerous hydrogen-bonded residues and an ordered water molecule. This network defines the pathway of the proton from the buried Schiff base to the extracellular surface.

Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy

Abstract: The far-infrared dielectric function of a wide range of organic molecules is dominated by vibrations involving a substantial fraction of the atoms forming the molecule and motion associated with intermolecular hydrogen bond vibrations. Due to their collective nature such modes are highly sensitive to the intra- and intermolecular structure and thus provide a unique fingerprint of the conformational state of the molecule and effects of its environment. We demonstrate the use of terahertz time-domain spectroscopy (THz-TDS) for recording the far-infrared (0.5-4.0 THz) dielectric function of the four nucleobases and corresponding nucleosides forming the building blocks of deoxyribose nucleic acid (DNA). We observe numerous distinct spectral features with large differences between the molecules in both frequency-dependent absorption coefficient and index of refraction. Assisted by results from density-functional calculations we interpret the origin of the observed resonances as vibrations of hydrogen bonds between the molecules.

Understanding the Behavior of Halogens as Hydrogen Bond Acceptors

Abstract: The similarities and differences between the behavior of carbon-bound and terminal metal-bound halogens and halide ions as potential hydrogen bond acceptors has been extensively investigated through examination of many thousands of interactions present in crystal structures. Halogens in each of these environments are found to engage in hydrogen bonding, and geometric preferences for these interactions have been established. Notably, typical H···X−M angles are markedly different for X = F than for X = Cl, Br, I. Furthermore, there are significant parallels between the behavior of moderately strong hydrogen bond acceptors X−M and the much weaker acceptors X−C. The underlying reasons for the observed geometric preferences have been established by ab initio molecular orbital calculations using suitable model systems. The results are presented within the context of their potential applications in crystal engineering and supramolecular chemistry, including relevance to nucleation in halogenated solvents. The br...

Early Time Hydrogen-Bonding Dynamics of Photoexcited Coumarin 102 in Hydrogen-Donating Solvents: Theoretical Study

Abstract: To study the early time hydrogen-bonding dynamics of chromophore in hydrogen-donating solvents upon photoexcitation, the infrared spectra of the hydrogen-bonded solute-solvent complexes in electronically excited states have been calculated using the time-dependent density functional theory (TDDFT) method. The hydrogen-bonding dynamics in electronically excited states can be widely monitored by the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds. In this study, we have demonstrated that the intermolecular hydrogen bonds between coumarin 102 (C102) and hydrogen-donating solvents are strengthened in the early time of photoexcitation to the electronically excited state by theoretically monitoring the stretching modes of C=O and H-O groups. This is significantly contrasted with the ultrafast hydrogen bond cleavage taking place within a 200-fs time scale upon electronic excitation, proposed in many femtosecond time-resolved vibrational spectroscopy experiments. The transient hydrogen bond strengthening behaviors in excited states of chromophores in hydrogen-donating solvents, which we have demonstrated here for the first time, may take place widely in many other systems in solution and are very important to explain the fluorescence-quenching phenomena associated with some radiationless deactivation processes, for example, the ultrafast solute-solvent intermolecular electron transfer and the internal conversion process from the fluorescent state to the ground state.