scholarly journals Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2148
Author(s):  
Irtaza Hassan ◽  
Federica Ferraro ◽  
Petra Imhof
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Carbonyl Group ◽  
Perfect Match ◽  
Hydration Shell ◽  
Interaction Strength ◽  
Bond Distance ◽  
Water Molecules ◽  
Carbonyl Groups ◽  
Bond State

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

scholarly journals 2,2′-Bipyridin-1-ium hemioxalate oxalic acid monohydrate

IUCrData ◽  
2018 ◽  
Vol 3 (8) ◽  
Author(s):  
Błażej Dziuk ◽  
Anna Jezuita
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Oxalic Acid ◽  
Water Molecule ◽  
Title Compound ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Compound C ◽  
Oxalic Acids

The asymmetric unit of the title compound, C10H9N2 +·0.5C2O4 2−·C2H2O4·H2O, consists of a 2,2′-bipyridinium cation, half an oxalate dianion, one oxalic acid and one water molecule. One N atom in 2,2′-bipyridine is unprotonated, while the second is protonated and forms an N—H...O hydrogen bond. In the crystal, the anions are connected with surrounding acid molecules and water molecules by strong near-linear O—H...O hydrogen bonds. The water molecules are located between the anions and oxalic acids; their O atoms participate as donors and acceptors, respectively, in O—H...O hydrogen bonds, which form sheets arranged parallel to the ac plane.

Prediction of Interaction of Citric Acid Modified Cellulose with Water Region Using Molecular Modelling Technique

2019 ◽  
Vol 797 ◽  
pp. 118-126
Author(s):  
Nornizar Anuar ◽  
Wan Nor Asyikin Wan Mohamed Daid ◽  
Sopiah Ambong Khalid ◽  
Sarifah Fauziah Syed Draman ◽  
Siti Rozaimah Sheikh Abdullah
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Water Molecule ◽  
Hydration Shell ◽  
Computational Technique ◽  
Water Molecules ◽  
Ferric Ion ◽  
Water Loading ◽  
Higher Temperature ◽  
Modified Cellulose

In this paper, chemically modified cellulose was used instead of cellulose as it offers higher adsorption capacities, great chemical strength and good resistance to heat. As part of Phyto-Adsorption Remediation Method, citric acid modified cellulose (CAMC) was used to treat ferric ion. However, there is a large possibility that CAMC molecule might interact with water molecule that contain hydrogen bond and hence pose as a competitor to ferric acid and reduces the efficiency of CAMC in ferric ion removal. Thus, the aim of this work is to identify the most stable hydrogen bond between CAMC and water, by using a computational technique. The interaction between the water molecules and CAMC was observed by varying the volume of water molecule with modified cellulose by an expansion in amorphous region. The simulation result shows that for water loading less than 20 molecules, the interaction between water molecules and CAMC is higher at temperature 311K, whilst for water loading higher than 20 molecules, the interaction weakens at higher temperature. This work proves that water molecules have the tendency to bind to carboxyl group of glucose, to oxygen of ester and to oxygen of anhydride acid of the CAMC molecule, which might pose a competition for ferric acid removal. The calculation of coordination number has shown that the number of atoms present in the first hydration shell (of radius < 2.5Å) is more as the temperature increases from 298K to 311K, which indicates that the adsorption is better at higher temperature. For hydration shell at radius >2.5Å, cell temperature is not significant to the number of atoms present.

3-(4-Oxocyclohexyl)propionic acid monohydrate: hydrogen bonding in the hydrate of a ζ-keto acid

2007 ◽  
Vol 63 (3) ◽  
pp. o1173-o1175
Author(s):  
Stephanie M. Witko ◽  
Mark Davison ◽  
Hugh W. Thompson ◽  
Roger A. Lalancette
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Carboxyl Group ◽  
Keto Acid ◽  
Carbonyl Groups ◽  
O 178 ◽  
Network Of Hydrogen Bonds

In the title crystal structure, C9H14O3·H2O, the water molecule accepts a hydrogen bond from the carboxyl group [O...O = 2.6004 (13) Å and O—H...O = 163°], while donating hydrogen bonds to the ketone [O...O = 2.8193 (14) Å and O—H...O = 178 (2)°] and the acid carbonyl groups [O...O = 2.8010 (14) Å and O—H...O = 174 (2)°]. This creates a network of hydrogen bonds confined within a continuous flat ribbon two molecules in width and extending in the [101] direction.

scholarly journals 2-(Trimethylazaniumyl)ethyl hydrogen phosphate (phosphocholine) monohydrate

2014 ◽  
Vol 70 (5) ◽  
pp. o549-o549
Author(s):  
Yohsuke Nikawa ◽  
Kyoko Fujita ◽  
Keiichi Noguchi ◽  
Hiroyuki Ohno
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Torsion Angle ◽  
Title Compound ◽  
Water Molecules ◽  
Zigzag Chain ◽  
Hydrogen Phosphate ◽  
Compound C ◽  
Phosphate Groups

In the crystal structure of the title compound, C5H14NO4P·H2O, the zwitterionic phosphocholine molecules are connected by an O—H...O hydrogen bond between the phosphate groups, forming a zigzag chain along theb-axis direction. The chains are further connected through O—H...O hydrogen bonds involving water molecules, forming a layer parallel to (101). Three and one C—H...O interactions are also observed in the layer and between the layers, respectively. The conformation of the N—C—C—O backbone isgauchewith a torsion angle of −75.8 (2)°

Infrared study of the interactions of acetone and siliceous surfaces

1969 ◽  
Vol 47 (14) ◽  
pp. 2545-2554 ◽  
Author(s):  
J. C. McManus ◽  
Yoshio Harano ◽  
M. J. D. Low
Keyword(s):  
Hydrogen Bonds ◽  
Carbonyl Group ◽  
Boron Atom ◽  
Porous Glass ◽  
Carbonyl Groups ◽  
Infrared Study ◽  
Oh Groups ◽  
Silica Surfaces ◽  
Surface Hydroxyls ◽  
Glass Surfaces

Adsorbed acetone is held to silica surfaces by hydrogen bonds between surface silanols and the acetone carbonyl groups. Acetone is adsorbed by this mechanism on porous glass surfaces but there is also some decomposition, as shown by the increase in surface B—OH groups and by formation of new C—H absorptions at 2984 and 2940 cm−1. Experiments with boron-impregnated silica indicated that the presence of boron in the porous glass can account for this decomposition process. Bands at 1660–1670 and 1650 cm−1, observed when acetone and acetone-d6, respectively, were adsorbed on either porous glass or boron-impregnated silica, are attributed to ν(C=O) of the carbonyl group coordinated with a surface boron atom. The surface hydroxyls of both silica and porous glass could exchange with the deuterium of acetone-d6 via a mechanism involving an enol intermediate.

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

2012 ◽  
Vol 68 (5) ◽  
pp. o209-o212 ◽  
Author(s):  
Barbara Wicher ◽  
Krystian Pyta ◽  
Piotr Przybylski ◽  
Ewa Tykarska ◽  
Maria Gdaniec
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Amide Group ◽  
Water Molecules ◽  
Acta Cryst ◽  
Oh Groups ◽  
Zwitterionic Form ◽  
The Family

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975).Acta Cryst.B31, 1454–1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol –OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C43H58N4O12·5H2O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O—H...O and N—H...N hydrogen bonds. Four of the symmetry-independent water molecules are arrangedviahydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interactviaO—H...O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

scholarly journals (E)-4-Methoxy-N′-[(6-methyl-4-oxo-4H-chromen-3-yl)methylidene]benzohydrazide monohydrate

2014 ◽  
Vol 70 (7) ◽  
pp. o784-o784 ◽  
Author(s):  
Yoshinobu Ishikawa ◽  
Kohzoh Watanabe
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Benzene Ring ◽  
Dihedral Angle ◽  
Dihedral Angles ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Solvent Water ◽  
Centroid Distance

In the title hydrate, C19H16N2O4·H2O, the 4H-chromen-4-one segment is slightly twisted, with a dihedral angle between the two six-membered rings of 3.30 (5)°. The dihedral angles between the plane of the pyranone ring and the hydrazide plane and between the planes of the pyranone ring and the benzene ring of thep-methoxybenzene unit are 26.69 (4) and 2.23 (3)°, respectively. The molecule is connected to the solvent water molecule by an N—H...O hydrogen bond. In the crystal, there are π–π stacking interactions between centrosymmetrically related pyranone rings [centroid–centroid distance = 3.5394 (9) Å], as well as bridges formed by the water moleculesviaO—H...O hydrogen bonds.

scholarly journals Crystal water as the molecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexahydrate

2018 ◽  
Vol 74 (4) ◽  
pp. 559-562
Author(s):  
L. Vella-Zarb ◽  
U. Baisch
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gallic Acid ◽  
Carbonyl Oxygen ◽  
Crystalline Solid ◽  
Water Molecules ◽  
Crystal Water ◽  
Classical Hydrogen Bond ◽  
Additional Hydrogen

The crystal structure of the hexahydrate co-crystal of gallic acid and caffeine, C7H6O5·3C8H10N4O2·6H2O or GAL3CAF·6H2O, is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water molecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the intermolecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two molecules is formed between the carboxylic oxygen of gallic acid and the carbonyl oxygen of caffeine with d(D...A) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

Solid-state and Calculated Electronic Structure of 4-Acetylpyrazole

2014 ◽  
Vol 69 (7) ◽  
pp. 839-843 ◽  
Author(s):  
Guido D. Frey ◽  
Wolfgang W. Schoeller ◽  
Eberhardt Herdtweck
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Electronic Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Carbonyl Group ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Ribbon Structure

The crystal structure of 1-(1H-pyrazol-4-yl)ethanone (commonly known as 4-acetylpyrazole; C5H6N2O) was determined from single-crystal X-ray data at 173 K: monoclinic, space group P21/n (no. 14), a = 3.865(1), b = 5.155(1), c = 26.105(8) Å, β = 91.13(1)°, V = 520.0(2) Å3 and Z = 4. The adjacent molecules assemble into a wave-like ribbon structure in the solid state, linked by strong intermolecular N-H...N hydrogen bonds between the pyrazole rings and a weak C-H...O=C hydrogen bond involving the carbonyl group. The ribbons are stacked in the solid state via weak π interactions between the pyrazole rings.

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