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 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 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.

scholarly journals Structure, Infrared and Raman spectroscopic studies of the new Ba(NbV 0.5MIII0.5)(PO4)2 (MIII = Al, Cr, Fe, In) yavapaiite compounds ‘series

2019 ◽  
Vol 8 (5) ◽  
pp. 397-409
Author(s):  
Rachid Fakhreddine ◽  
Abderrahim Aatiq
Keyword(s):  
Structural Information ◽  
Rietveld Method ◽  
Spectroscopic Studies ◽  
Infrared Spectroscopic Study ◽  
Empirical Relationships ◽  
X Ray ◽  
Raman Spectroscopic ◽  
Air Atmosphere ◽  
Time Structures ◽  
First Time

Synthesis and structural study of the new Ba(NbV 0.50MIII 0.50)(PO4)2 (MIII = Al, Cr, Fe, In) phosphates, abbreviated as [BaNbM], were reported here for the first time. Structures of [BaNbM] compounds, obtained by solid-state reaction in air atmosphere, were determined at room temperature from X-ray powder diffraction using the Rietveld method. The four studied compoundsfeature the yavapaiite-type structure, with space group C2/m ( 3 C2h , N°12) and Z = 2. Their framework can be described as consisting of dense slabs of Nb(M)O6 octahedra and PO4 tetrahedra interconnected via corner-sharing, alternating along the c-axis with layers of Ba cations in ten-fold coordination. Raman and Infrared spectroscopic study were used to obtain further structural information about the nature of bonding in selected compositions. Assignments of Nb-O, M-O and P-O Raman and Infrared bands, in [BaNbM] compounds, were based on those already known in the literature for niobium and phosphates oxides. Some empirical relationships, connecting Raman stretching frequencies to the obtained Nb-O and P-O distance values, were also used for assignments of various Raman bands

Spider diversity in the Bukit Timah Nature Reserve, Singapore

2019 ◽  
Vol 71 ((suppl.1)) ◽  
pp. 209-243
Author(s):  
J.K.H. Koh ◽  
D.J. Court
Keyword(s):  
Nature Reserve ◽  
New Records ◽  
Secondary Forest ◽  
Distinct Species ◽  
Primary Forest ◽  
Preliminary Results ◽  
Vegetation Zones ◽  
Comprehensive Survey ◽  
Quantitative Analyses ◽  
First Time

This paper discusses the preliminary results of the first comprehensive survey of the spiders of the Bukit Timah Nature Reserve (BTNR) in Singapore. Two plots were established in each of the three zones of vegetation, viz., primary forest, old secondary forest, and maturing secondary forest. They were repeatedly sampled over an 18-month period. Sorting of the collection so far suggests that the three vegetation zones harbour rather different spider assemblages. Only ~9% of the total spider fauna recovered was shared by all three zones. The results have also yielded a preliminary picture of dominance, abundance and rarity. Although first intended to obtain a baseline for future quantitative analyses, the survey became a testing ground to modify and refine methodology so as to conduct future quantitative surveys with greater scientific rigour. Taxonomic work on the samples so far shows that the spiders in the BTNR span over 43 families, of which six families are listed for the first time in Singapore. The tally is summarised in an interim checklist of BTNR spiders. The checklist, with a total of 317 entries, shows that there are 158 described species of spiders in BTNR, of which 25 species are new records for Singapore. Another 159 morphospecies are provisionally recognised as distinct species, some of which may be new to science. Our observations during the survey have allowed us to provide a narrative of BTNR spider diversity against a backdrop of their microhabitat specialisation.

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.

Status of Family Fissidentaceae in Gujarat

2016 ◽  
Vol 1 (1) ◽  
Author(s):  
D.G. Shah ◽  
D.N. Mehta ◽  
R.V. Gujar
Keyword(s):  
Distinct Species ◽  
The State ◽  
The Other ◽  
Land Plants ◽  
Reproductive Structures ◽  
The Family ◽  
The Status ◽  
Vegetative Characters ◽  
First Time ◽  
Different Parts

Bryophytes are the second largest group of land plants and are also known as the amphibians of the plant kingdom. 67 species of bryophytes have been reported from select locations across the state of Gujrat. The status of family fissidentaceae which is a large moss family is being presented in this paper. Globally the family consists of 10 genera but only one genus, Fissidens Hedw. has been collected from Gujarat. Fissidens is characterized by a unique leaf structure and shows the presence of three distinct lamina, the dorsal, the ventral and the vaginant lamina. A total of 8 species of Fissidens have been reported from the state based on vegetative characters as no sporophyte stages were collected earlier. Species reported from the neighboring states also showed the absence of sporophytes. The identification of different species was difficult due to substantial overlap in vegetative characters. Hence a detailed study on the diversity of members of Fissidentaceae in Gujarat was carried out between November 2013 and February 2015. In present study 8 distinct species of Fissidens have been collected from different parts of the state. Three species Fissidens splachnobryoides Broth., Fissidens zollingerii Mont. and Fissidens curvato-involutus Dixon. have been identified while the other five are still to be identified. Fissidens zollingerii Mont. and Fissidens xiphoides M. Fleisch., which have been reported as distinct species are actually synonyms according to TROPICOS database. The presence of sexual reproductive structures and sporophytes for several Fissidens species are also being reported for the first time from the state.

Interaction of Gold Atom with Clusters of Water: Few Computational Mise-En-Scènes with Hydrogen Bonding Motif

2008 ◽  
Vol 73 (11) ◽  
pp. 1457-1474 ◽  
Author(s):  
Eugene S. Kryachko
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Computational Model ◽  
Photoelectron Spectroscopy ◽  
Water Clusters ◽  
Gold Atom ◽  
Proton Acceptor ◽  
Anion Photoelectron Spectroscopy ◽  
Relationship Of ◽  
First Time

The present work outlines the fair relationship of the computational model with the experiments on anion photoelectron spectroscopy for the gold-water complexes [Au(H2O)1≤n≤2]- that is established between the auride anion Au- and water monomer and dimer thanks to the nonconventional hydrogen bond where Au- casts as the nonconventional proton acceptor. This work also extends the computational model to the larger complexes [Au(H2O)3≤n≤5]- where gold considerably thwarts the shape of water clusters and even particularly breaks their conventional hydrogen bonding patterns. The fascinating phenomenon of the lavish proton acceptor character of Au- to form at least six hydrogen bonds with molecules of water is computationally unveiled in the present work for the first time.

Intramolecular hydrogen bonding guides a cationic amphiphilic organocatalyst to highly stereoselective aldol reactions in water

RSC Advances ◽  
2015 ◽  
Vol 5 (77) ◽  
pp. 62331-62335 ◽  
Author(s):  
Ángel M. Valdivielso ◽  
Alba Catot ◽  
Ignacio Alfonso ◽  
Ciril Jimeno
Keyword(s):  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bonding ◽  
Structural Motif ◽  
Aldol Reactions ◽  
Asymmetric Aldol ◽  
Neutral Ph ◽  
Intramolecular Hydrogen

A novel amphiphilic acylguanidine organocatalyst using intramolecular hydrogen bonding as a key structural motif is efficient for asymmetric aldol reactions of ketones in water at neutral pH.

Concomitant polymorphs of 1,3-bis(3-fluorophenyl)urea

2016 ◽  
Vol 72 (9) ◽  
pp. 692-696 ◽  
Author(s):  
Christina A. Capacci-Daniel ◽  
Jeffery A. Bertke ◽  
Shoaleh Dehghan ◽  
Rupa Hiremath-Darji ◽  
Jennifer A. Swift
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Structural Motif ◽  
Parallel Orientation ◽  
One Dimensional ◽  
Monoclinic Form ◽  
Engineering Studies ◽  
Hydrogen Bonded

Hydrogen bonding between urea functionalities is a common structural motif employed in crystal-engineering studies. Crystallization of 1,3-bis(3-fluorophenyl)urea, C13H10F2N2O, from many solvents yielded concomitant mixtures of at least two polymorphs. In the monoclinic form, one-dimensional chains of hydrogen-bonded urea molecules align in an antiparallel orientation, as is typical of many diphenylureas. In the orthorhombic form, one-dimensional chains of hydrogen-bonded urea molecules have a parallel orientation rarely observed in symmetrically substituted diphenylureas.

A Raman and infrared spectroscopic study of triethylenediamine (DABCO) and its protonated forms

1988 ◽  
Vol 66 (5) ◽  
pp. 1249-1257 ◽  
Author(s):  
David A. Guzonas ◽  
Donald E. Irish
Keyword(s):  
Raman Spectrum ◽  
Spectroscopic Study ◽  
Infrared Spectra ◽  
Infrared Spectroscopic Study ◽  
Protonated Forms ◽  
Infrared Spectroscopic ◽  
Vibrational Bands

The Raman and infrared spectra of DABCO have been measured as a function of the pH, and the vibrational bands of the two protonated forms of DABCO have been tabulated and assigned. The frequencies of several of the Raman bands were found to exhibit substantial shifts upon protonation, and the appearance of the Raman spectrum in the region between 900 and 1100 cm−1 in particular shows differences which can be used to differentiate between the three forms of DABCO. The values of the two pKa's were determined from the intensity versus pH plots for the three species.

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