Influence of N−H···O and C−H···O Hydrogen Bonds on the17O NMR Tensors in Crystalline Uracil:  Computational Study

2006 ◽  
Vol 110 (3) ◽  
pp. 1065-1071 ◽  
Author(s):  
Ramsey Ida ◽  
Maurice De Clerk ◽  
Gang Wu
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Nmr Tensors

Redshift or Adduct Stabilization—A Computational Study of Hydrogen Bonding in Adducts of Protonated Carboxylic Acids

2009 ◽  
Vol 15 (2) ◽  
pp. 239-248 ◽  
Author(s):  
Solveig Gaarn Olesen ◽  
Steen Hammerum
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Bond Strength ◽  
Bond Length ◽  
Carboxylic Acids ◽  
Computational Study ◽  
Proton Affinities ◽  
Oh Groups ◽  
Hydrogen Bond Strength ◽  
Length Changes

It is generally expected that the hydrogen bond strength in a D–H•••A adduct is predicted by the difference between the proton affinities (Δ PA) of D and A, measured by the adduct stabilization, and demonstrated by the infrared (IR) redshift of the D–H bond stretching vibrational frequency. These criteria do not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The Δ PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength.

scholarly journals Crystal structure, computational study and Hirshfeld surface analysis of ethyl (2S,3R)-3-(3-amino-1H-1,2,4-triazol-1-yl)-2-hydroxy-3-phenylpropanoate

2019 ◽  
Vol 75 (12) ◽  
pp. 1919-1924
Author(s):  
Abdelkader Ben Ali ◽  
Youness El Bakri ◽  
Chin-Hung Lai ◽  
Jihad Sebhaoui ◽  
Lhoussaine El Ghayati ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Gas Phase ◽  
Surface Analysis ◽  
Computational Study ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dft Methods ◽  
Important Interaction ◽  
The Mean ◽  
Title Molecule

In the title molecule, C13H16N4O3, the mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intramolecular C—H...O and C—H...π(ring) interactions. In the crystal, layers parallel to (101) are generated by O—H...N, N—H...O and N—H...N hydrogen bonds. The layers are connected by inversion-related pairs of C—H...O hydrogen bonds. The experimental molecular structure is close to the gas-phase geometry-optimized structure calculated by DFT methods. Hirshfeld surface analysis indicates that the most important interaction involving hydrogen in the title compound is the H...H contact. The contribution of the H...O, H...N, and H...H contacts are 13.6, 16.1, and 54.6%, respectively.

Molecular conformations and π-hydrogen bonds in anti- and syn-binuclear Rh(I) complexes of as-indacene-diide: a computational study

2005 ◽  
Vol 690 (2) ◽  
pp. 482-492 ◽  
Author(s):  
Laura Orian ◽  
Paolo Ganis ◽  
Saverio Santi ◽  
Alberto Ceccon
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Molecular Conformations

A computational study of the interactions between anthocyans and cyclodextrins

2020 ◽  
Vol 75 (11-12) ◽  
pp. 433-441
Author(s):  
Raluca Pop ◽  
Adina Căta ◽  
Mariana Nela Ștefănuț ◽  
Ioana Maria Carmen Ienașcu
Keyword(s):  
Hydrogen Bonds ◽  
Inclusion Complexes ◽  
Acidic Medium ◽  
Ph Value ◽  
Computational Study ◽  
Dependence Structure ◽  
Computational Techniques ◽  
Oh Groups ◽  
Alkaline Environment

AbstractThe interactions between six anthocyans (cyanidin-3-O-glucoside, delphinidin-3-O-glucoside, malvidin-3-O-glucoside, cyanidin-3-O-rutinoside, delphinidin-3-O-rutinoside, malvidin-3-O-rutinoside) and cyclodextrins were investigated by means of computational techniques. Four different structures of the aforementioned anthocyans were considered, as a result of the dependence structure – pH value (flavylium cations in acidic medium, hemiketals in neutral solutions and two tautomeric quinones in alkaline environment). The results outlined that the anthocyanidin-3-O-rutinoside are favored for the obtaining of inclusion complexes with the cyclodextrins, mostly due to the larger number of OH groups involved in the formation of hydrogen bonds. For all the four types of structures, best results have been obtained for β- and γ-cyclodextrins.

scholarly journals A cinnamaldehyde Schiff base ofS-(4-methylbenzyl) dithiocarbazate: crystal structure, Hirshfeld surface analysis and computational study

2017 ◽  
Vol 73 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Enis Nadia Md Yusof ◽  
Mohamed I. M. Tahir ◽  
Thahira B. S. A. Ravoof ◽  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Mirror Symmetry ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Benzyl Substituent

The title dithiocarbazate ester (I), C18H18N2S2[systematic name: (E)-4-methylbenzyl 2-[(E)-3-phenylallylidene]hydrazinecarbodithioate, comprises an almost planar central CN2S2residue [r.m.s. deviation = 0.0131 Å]. The methylene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the molecule approximates mirror symmetry with the 4-tolyl group bisected by the plane. The configuration about both double bonds in the N—N=C—C=C chain isE; the chain has an alltransconformation. In the crystal, eight-membered centrosymmetric thioamide synthons, {...HNCS}2, are formedviaN—H...S(thione) hydrogen bonds. Connections between the dimersviaC—H...π interactions lead to a three-dimensional architecture. A Hirshfeld surface analysis shows that (I) possesses an interaction profile similar to that of a closely related analogue with anS-bound benzyl substituent, (II). Computational chemistry indicates the dimeric species of (II) connectedviaN—H...S hydrogen bonds is about 0.94 kcal mol−1more stable than that in (I).

scholarly journals N,N′-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Helical Chain ◽  
Central Plane ◽  
Orthogonal Relationship ◽  
Hydrogen Bonding Interactions ◽  
Hirshfeld Surfaces ◽  
Methylene Groups ◽  
Layer Region ◽  
The Stability

The molecular structure of the title bis-pyridyl substituted diamide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methylene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intramolecular amide-N—H...O(carbonyl) hydrogen bonds are formed, each closing an S(5) loop. Supramolecular tapes are formed in the crystal via amide-N—H...O(carbonyl) hydrogen bonds and ten-membered {...HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water molecules via water-O—H...N(pyridyl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methylene-C—H...O(water) and methylene-C—H...π(pyridyl) interactions, give rise to a layer parallel to (10\overline{1}); the layers stack without directional interactions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding interactions, and to the significant influence of the water molecule of crystallization upon the molecular packing. The analysis also indicates the contribution of methylene-C—H...O(carbonyl) and pyridyl-C—H...C(carbonyl) contacts to the stability of the inter-layer region. The calculated interaction energies are consistent with importance of significant electrostatic attractions in the crystal.

scholarly journals Strong intramolecular hydrogen bonds and steric effects involving C═S groups: An NMR and computational study

2019 ◽  
Vol 58 (2) ◽  
pp. 154-162
Author(s):  
Rita S. Elias ◽  
Bahjat A. Saeed ◽  
Fadhil S. Kamounah ◽  
Fritz Duus ◽  
Poul Erik Hansen
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Steric Effects ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Efficient SO2Capture through Multiple Chalcogen Bonds, Sulfur-Centered Hydrogen Bonds and S•••π Interactions: A Computational Study

2016 ◽  
Vol 1 (8) ◽  
pp. 1688-1694 ◽  
Author(s):  
Dipak Kumar Sahoo ◽  
V. Rao Mundlapati ◽  
Arun Anand Gagrai ◽  
Himansu S. Biswal
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Π Interactions
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