scholarly journals Infrared spectroscopic study of hydrogen bonding topologies in the smallest ice cube

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Gang Li ◽  
Yang-Yang Zhang ◽  
Qinming Li ◽  
Chong Wang ◽  
Yong Yu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Vacuum Ultraviolet ◽  
Structural Information ◽  
Distinct Species ◽  
Structural Motif ◽  
Infrared Spectroscopic Study ◽  
Hydrogen Bonding Interactions ◽  
Ice Cube ◽  
Vibrational Bands ◽  
Metastable Forms

Abstract The water octamer with its cubic structure consisting of six four-membered rings presents an excellent cluster system for unraveling the cooperative interactions driven by subtle changes in the hydrogen-bonding topology. Despite prediction of many distinct structures, it has not been possible to extract the structural information encoded in their vibrational spectra because this requires size-selectivity of the neutral clusters with sufficient resolution to identify the contributions of the different isomeric forms. Here we report the size-specific infrared spectra of the isolated cold, neutral water octamer using a scheme based on threshold photoionization using a tunable vacuum ultraviolet free electron laser. A plethora of sharp vibrational bands features are observed. Theoretical analysis of these patterns reveals the coexistence of five cubic isomers, including two with chirality. The relative energies of these structures are found to reflect topology-dependent, delocalized multi-center hydrogen-bonding interactions. These results demonstrate that even with a common structural motif, the degree of cooperativity among the hydrogen-bonding network creates a hierarchy of distinct species. The implications of these results on possible metastable forms of ice are speculated.

scholarly journals Infrared spectroscopic study of hydrogen bonding topologies in the water octamer: The smallest ice cube

2020 ◽  
Author(s):  
Gang Li ◽  
Yang-Yang Zhang ◽  
Qinming Li ◽  
Chong Wang ◽  
Yong Yu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Vacuum Ultraviolet ◽  
Structural Information ◽  
Distinct Species ◽  
Structural Motif ◽  
Infrared Spectroscopic Study ◽  
Ice Cube ◽  
Vibrational Bands ◽  
Metastable Forms ◽  
First Time

Abstract The water octamer, with its cubic structure consisting of six four-membered rings, presents an excellent system in which to unravel the cooperative interactions driven by subtle changes in the hydrogen-bonding topology. Although many distinct structures are calculated to exist, it has not been possible to extract the structural information encoded in their vibrational spectra because this requires size-selectivity of the neutral clusters with sufficient resolution to identify the contributions of the different isomeric forms. Here we report the size-specific infrared spectra of the isolated cold, neutral water octamer using a scheme based on threshold photoionization using a tunable vacuum ultraviolet free electron laser. A plethora of sharp vibrational bands features are observed for the first time. Theoretical analysis of these patterns reveals the coexistence of five cubic isomers, including two with chirality. The relative energies of these structures are found to reflect topology-dependent, delocalized multi-center hydrogen-bonding interactions. These results demonstrate that even with a common structural motif, the degree of cooperativity among the hydrogen-bonding network creates a hierarchy of distinct species. The implications of these results on possible metastable forms of ice are considered.

scholarly journals Infrared spectroscopy of neutral water clusters at finite temperature: Evidence for a noncyclic pentamer

2020 ◽  
Vol 117 (27) ◽  
pp. 15423-15428 ◽  
Author(s):  
Bingbing Zhang ◽  
Yong Yu ◽  
Yang-Yang Zhang ◽  
Shukang Jiang ◽  
Qinming Li ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectra ◽  
Liquid Water ◽  
Vacuum Ultraviolet ◽  
Water Clusters ◽  
Bulk Water ◽  
Infrared Spectroscopic Study ◽  
Stretching Vibration ◽  
Hydrogen Bonding Networks ◽  
Neutral Water

Infrared spectroscopic study of neutral water clusters is crucial to understanding of the hydrogen-bonding networks in liquid water and ice. Here we report infrared spectra of size-selected neutral water clusters, (H2O)n(n= 3−6), in the OH stretching vibration region, based on threshold photoionization using a tunable vacuum ultraviolet free-electron laser. Distinct OH stretch vibrational fundamentals observed in the 3,500−3,600-cm−1region of (H2O)5provide unique spectral signatures for the formation of a noncyclic pentamer, which coexists with the global-minimum cyclic structure previously identified in the gas phase. The main features of infrared spectra of the pentamer and hexamer, (H2O)n(n= 5 and 6), span the entire OH stretching band of liquid water, suggesting that they start to exhibit the richness and diversity of hydrogen-bonding networks in bulk water.

The dependence of thymine and thymidine Raman spectra on solvent

2004 ◽  
Vol 82 (6) ◽  
pp. 1092-1101 ◽  
Author(s):  
L Beyere ◽  
P Arboleda ◽  
V Monga ◽  
G R Loppnow
Keyword(s):  
Raman Spectroscopy ◽  
Hydrogen Bonding ◽  
Raman Spectra ◽  
Vibrational Modes ◽  
Frequency Shifts ◽  
Hydrogen Bonding Interactions ◽  
Lone Pairs ◽  
Vibrational Bands ◽  
Donor Numbers ◽  
Solvent Molecules

Recent work has focused on developing Raman spectroscopy as a noninvasive probe of DNA interactions with solvents, intercalants, proteins, and other ligands. Here, we report the Raman spectra of thymine in eight solvents and thymidine in nine solvents obtained with visible excitation. Raman spectra under acidic, neutral, and basic conditions were also obtained of both thymine and thymidine. Changes in both the frequencies and intensities of several of the vibrational bands in the 800–1800 cm–1 region are observed. No evidence of deprotonation in the different solvents is observed for either thymine or thymidine. Correlations of the observed frequency shifts of specific vibrational modes with characteristic properties of the solvent for both thymine and thymidine show a significant correlation with acceptor and donor numbers, measures of the hydrogen-bonding ability of the solvent, in both thymine and thymidine. These results are interpreted in terms of hydrogen-bonding interactions between the N-H protons of the thymine base and lone pairs of electrons on the solvent molecules and between the solvent hydrogens and lone pairs on C=O sites. The solvent-dependent intensity in vibrational bands of thymine between 1500 and 1800 cm–1 indicates a strong interaction between thymine and solvent at the C=O and N-H sites that leads to separation of the C=O stretches from the C=C stretch. The intensity variations with solvent were much smaller for thymidine than for thymine, perhaps as a result of replacing the N1 proton by the sugar. These results suggest that Raman spectroscopy is uniquely sensitive to specific interactions of thymine and thymidine with their environment.Key words: Raman spectroscopy, thymine, thymidine, solvent effects, hydrogen bonding.

Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes

2020 ◽  
Vol 17 (2) ◽  
pp. 233-247
Author(s):  
Krishna A. Gajjar ◽  
Anuradha K. Gajjar
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Docking Studies ◽  
Structural Motif ◽  
Roc Curve Analysis ◽  
Ligand Complex ◽  
Discovery Studio ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Pharmacophore Models

Background: Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. Methods: DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening active and inactive datasets, GH scoring and ROC curve analysis. The best model was exposed as a 3D query to screen the hits from databases like GLASS (GPCR-Ligand Association), GPCR SARfari and Mini-Maybridge. Various filters were applied to retrieve the hit molecules having good drug-like properties. A known protein structure of hGPR40 (pdb: 4PHU) having TAK-875 as ligand complex was used to perform the molecular docking studies; using SYBYL-X 1.2 software. Results and Conclusion: Clustering both the models gave RMSD of 0.89. Therefore, the present approach explored the maximum features by combining both ligand and structure based pharmacophore models. A common structural motif as identified in combiphore for GPR40 modulation consists of the para-substituted phenyl propionic acid scaffold. Therefore, the combiphore approach, whereby maximum structural information (from both ligand and biological protein) is explored, gives maximum insights into the plausible protein-ligand interactions and provides potential lead candidates as exemplified in this study.

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

scholarly journals Circular linkage of intramolecular multi-hydrogen bonding frameworks through nucleophilic substitutions of β-dicarbonyls onto cyanuric chloride and subsequent tautomerisation

RSC Advances ◽  
2020 ◽  
Vol 10 (64) ◽  
pp. 39033-39036
Author(s):  
Ayano Awatani ◽  
Masaaki Suzuki
Keyword(s):  
Hydrogen Bonding ◽  
Cyanuric Chloride ◽  
Nucleophilic Substitutions ◽  
Hydrogen Bonding Interactions ◽  
Triazine Derivatives

Triply β-dicarbonyl-embedded 1,3,5-triazine derivatives result in formation of circular linkage of resonance-assisted hydrogen bonding interactions, which can be regarded as well-delocalized resonance hybrids.

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