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.

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.

scholarly journals 2-(3-{(3R,4R)-4-Methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}oxetan-3-yl)acetonitrile monohydrate

2014 ◽  
Vol 70 (4) ◽  
pp. o382-o383
Author(s):  
Matthias Gehringer ◽  
Ellen Pfaffenrot ◽  
Peter R. W. E. F. Keck ◽  
Dieter Schollmeyer ◽  
Stefan A. Laufer
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Organic Molecules ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Chair Conformation ◽  
Pyrimidine Ring ◽  
Piperidine Ring ◽  
Water Molecules ◽  
Compound C

In the title compound, C18H24N6O·H2O, the piperidine ring adopts a chair conformation with an N—C—C—C torsion angle of 39.5 (5)° between thecis-related substituents. The pyrrole N—H group forms a water-mediated intermolecular hydrogen bond to one of the N atoms of the annelated pyrimidine ring. The water molecule connects two organic molecules and is disorderd over two positions (occupancies of 0.48 and 0.52). The crystal packing shows zigzag chains of alternating organic and water molecules running parallel to theaaxis.

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 (S,Z)-3-Phenyl-2-[(1,1,1-trichloro-7-methoxy-2,7-dioxohept-3-en-4-yl)amino]propanoic acid monohydrate

2014 ◽  
Vol 70 (2) ◽  
pp. o169-o170
Author(s):  
Alex Fabiani Claro Flores ◽  
Juliano Rosa de Menezes Vicenti ◽  
Lucas Pizzuti ◽  
Patrick Teixeira Campos
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Organic Molecule ◽  
Organic Molecules ◽  
Propanoic Acid ◽  
Water Molecules ◽  
Solvent Water ◽  
Compound C

In the title compound, C17H18Cl3NO5·H2O, intramolecular N—H...O and C—H...Cl hydrogen bonds formS(6) andS(5) ring motifs, respectively. The chiral organic molecule is connected to the solvent water molecule by a short O—H...O hydrogen bond. In the crystal, a weak C—H...Cl interaction connects the organic molecules along [100] while the water molecules act as bridges between the organic molecules in both the [100] and [010] directions, generating layers parallel to theabplane.

1-Carboxymethyl-3-methyl-1H-imidazol-3-ium chloride 2-(3-methyl-1H-imidazol-3-ium-1-yl)acetate monohydrate: a crystal stabilized by imidazolium zwitterions

2013 ◽  
Vol 69 (10) ◽  
pp. 1173-1176 ◽  
Author(s):  
Heng Zhang ◽  
Liangliang Chang ◽  
Na Wang ◽  
Xiaopeng Xuan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Chloride Ion ◽  
Water Molecules ◽  
Dimensional Chain ◽  
Acetate Monohydrate ◽  
One Dimensional ◽  
Compound C ◽  
Methylene Groups

The title compound, C6H9N2O2+·Cl−·C6H8N2O2·H2O, contains one 2-(3-methyl-1H-imidazol-3-ium-1-yl)acetate inner salt molecule, one 1-carboxymethyl-3-methyl-1H-imidazol-3-ium cation, one chloride ion and one water molecule. In the extended structure, chloride anions and water molecules are linkedviaO—H...Cl hydrogen bonds, forming an infinite one-dimensional chain. The chloride anions are also linked by two weak C—H...Cl interactions to neighbouring methylene groups and imidazole rings. Two imidazolium moieties form a homoconjugated cation through a strong and asymmetric O—H...O hydrogen bond of 2.472 (2) Å. The IR spectrum shows a continuous D-type absorption in the region below 1300 cm−1and is different to that of 1-carboxymethyl-3-methylimidazolium chloride [Xuan, Wang & Xue (2012).Spectrochim. Acta Part A,96, 436–443].

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.

Disorder of a Trigonally Planar Coordinated Water Molecule in Cobalt Sulfate Heptahydrate, CoSO4 · 7 D2O (Bieberite)+

1991 ◽  
Vol 46 (12) ◽  
pp. 1635-1640 ◽  
Author(s):  
Thomas Kellersohn ◽  
Robert G. Delaplane ◽  
Ivar Olovsson
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Lattice Water Molecule ◽  
Water Molecules ◽  
Ambient Conditions ◽  
Cobalt Sulfate ◽  
Sulfate Heptahydrate ◽  
Lattice Water ◽  
Coordinated Water ◽  
Average Position

Cobalt sulfate heptahydrate (d-14), CoSO4·7D2O, Mr = 294.99, monoclinic, P21/c, a = 1404.8(1), b = 649.41(6), c= 1092.5(2) pm, β = 105.232(8), V = 961.66·106 pm3, Z = 4, Dx = 2.073 Mg· m-3, λ(MoKa) = 71.073 pm, [(sin θ)/λ]max = 0.7035· 10-2 pm-1, μ = 20.26 cm-1, F(000) = 580, T = 298 K, R(F) = 0.0264 for 2339 observed unique reflections. CoSO4·7 D2O is shown to be isotypic to FeSO4· 7 H2O (Melanterite). The deuterated compound is stable at ambient conditions in contrast to the normal hydrate. Its structure is built up by [Co(D2O)6]2+ octahedra, SO42- tetrahedra, and “lattice” water molecules. One water molecule, which is almost exactly trigonally planar coordinated in its average position, exhibits a distinct oxygen disorder. The “lattice” water molecule accepts two strong hydrogen bonds and donates a linear and a bifurcated one. The hydrogen-bond lengths (O···O distances) are in the range 271-302 pm.

scholarly journals Water spines and networks in G-quadruplex structures

2020 ◽  
Author(s):  
Kevin Li ◽  
Liliya Yatsunyk ◽  
Stephen Neidle
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Water Molecule ◽  
Crystal Structures ◽  
Water Molecules ◽  
Nmr Structures ◽  
Loop Conformations ◽  
G Quadruplex ◽  
Guanine Base ◽  
Loop Regions

Abstract Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.

scholarly journals (E)-4-Bromo-5-methoxy-2-{[(2-methoxyphenyl)imino]methyl}phenol monohydrate

IUCrData ◽  
2017 ◽  
Vol 2 (12) ◽  
Author(s):  
Şehriman Atalay ◽  
Seda Nur Aygün ◽  
Seher Meral ◽  
Erbil Ağar
Keyword(s):  
Hydrogen Bond ◽  
Schiff Base ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Dihedral Angle ◽  
Schiff Bases ◽  
Water Molecules ◽  
Benzene Rings ◽  
Water Hydrogen

In the title Schiff base hydrate, C15H14BrNO3·H2O, the dihedral angle between the benzene rings is 0.9 (2)° and an intramolecular O—H...N hydrogen bond closes anS(6) ring. In the crystal, Ow—H...O (w = water) hydrogen bonds link the components into centrosymmetric tetramers (two Schiff bases and two water molecules). Weak C—H...Owinteractions consolidate the linking of the molecules within the tetramers. The O atom of the water molecule is disordered over two adjacent sites in a 0.73 (9):0.27 (9) ratio.

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