scholarly journals Focal Point Evaluation of Energies for Tautomers and Isomers for 3-Hydroxy-2-Butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N)

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2623
Author(s):  
Zikri Altun ◽  
Erdi Bleda ◽  
Carl Trindle
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Focal Point ◽  
Noncovalent Interactions ◽  
Carbonyl Oxygen ◽  
Relative Strength ◽  
Basis Sets ◽  
Structural Variations ◽  
Internal Hydrogen ◽  
Correlation Consistent

The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH.

Carbon-13 nmr shifts and C—H coupling constants of deoxybenzoins and related acetophenones

1981 ◽  
Vol 59 (15) ◽  
pp. 2266-2282 ◽  
Author(s):  
Hem Chandra Jha ◽  
Fritz Zilliken ◽  
Werner Offermann ◽  
Eberhard Breitmaier
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shifts ◽  
Carbonyl Oxygen ◽  
Coupling Constants ◽  
Structural Variations ◽  
Naturally Occurring ◽  
Internal Hydrogen ◽  
Benzene Rings ◽  
Substitutional Saturation

13C Chemical shifts and resolved carbon–proton couplings of 39 deoxybenzoins and 11 acetophenones, most of which have naturally occurring substitution patterns, are assigned. Individual benzene rings turned out to have typical parameters not affected by structural variations in the rest of the molecule. Due to substitutional saturation, however, these benzenoid carbon shifts markedly deviate from increment additivity. A few trends of these deviations are described. Phenolic hydrogens, fixed between hydroxyl and carbonyl oxygen due to internal hydrogen bonding, are shown to give rise to additional carbon-splittings.

scholarly journals The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Noncovalent Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Mixed Ligand ◽  
Binding Energies ◽  
Zigzag Chain ◽  
X Ray ◽  
Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

scholarly journals Stabilization of N-, N,N-, N,N′-methylated and unsubstituted simple amidine salts by multifurcated hydrogen bonds

2006 ◽  
Vol 20 (4) ◽  
pp. 169-176 ◽  
Author(s):  
Jarosław Spychała
Keyword(s):  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Biological Properties ◽  
Carbonyl Oxygen ◽  
Relative Strength ◽  
Intramolecular Interactions ◽  
Covalent Bonds ◽  
Natural Isotopic Abundance

In the light of the usefulness of amidines in medicinal chemistry, this paper considers the effects on biological properties and chemical reactivities of organic molecules affected by intramolecular interactions. The study of chemical shifts has been an important source of information on the electronic structure of amidine salts and their ability to form non-covalent bonds with nucleic acids. The NMR and IR results demonstrate that hydrogen bonds are a force for promoting chemical reactions. The thymine O2 carbonyl oxygen in a close proximity to the amidinium cation does interact with the appropriately spaced amidinium NH donor moieties. The1H-15N 2D NMR (GHSQC and GHMBC) spectra with natural isotopic abundance of15N fully confirm the intramolecular character of the bonds. A rule able to estimate the relative strength of the new multifurcated hydrogen bonds is given. The appearance of the ΔδNHchemical shift differences near zero is due to the strong intramolecular interactions. The strength of the H-bond donation by acetamidines is reflected in the N–H dissociation/recombination process (positive charge shift has been invoked to explain other effects on benzamidines). The temperature dependence of chemical shift for the amidine NH protons in dimethyl sulfoxide solutions is herein discussed.

THEORETICAL STUDY OF THE HYDROGEN BOND CHARACTER BETWEEN THE FNO AND HO2 RADICAL

2010 ◽  
Vol 09 (05) ◽  
pp. 925-934 ◽  
Author(s):  
QIN HE ◽  
ZHI-FENG LI
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Theoretical Study ◽  
Basis Sets ◽  
Potential Density ◽  
Geometrical Characteristics ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonding Site ◽  
Ho2 Radical ◽  
Bond Character

The hydrogen-bonding characters between FNO and HO2 radical are studied systematically with the MPWB1K method and 6-311++G (d, p), aug-cc-PVDZ as well as aug-cc-PVTZ basis sets. The relevant geometrical characteristics, energy properties, and the characters of the intramolecular hydrogen bonds have been reported in this work. In addition, the changes of electrostatic potential density are presented for further understanding the nature of hydrogen bonds and the preference of F atom as the hydrogen-bonding site.

scholarly journals Crystal structures and hydrogen-bonding analysis of a series of benzamide complexes of zinc(II) chloride

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Elizabeth Tinapple ◽  
Sam Farrar ◽  
Dean H. Johnston
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Physical Properties ◽  
Crystal Structures ◽  
Organic Molecules ◽  
Inorganic Salt ◽  
Carbonyl Oxygen ◽  
Bonding Analysis ◽  
Amide Carbonyl ◽  
Improve Stability

Ionic co-crystals are co-crystals between organic molecules and inorganic salt coformers. Co-crystals of pharmaceuticals are of interest to help control polymorph formation and potentially improve stability and other physical properties. We describe the preparation, crystal structures, and hydrogen bonding of five different 2:1 benzamide or toluamide/zinc(II) chloride co-crystal salts, namely, bis(benzamide-κO)dichloridozinc(II), [ZnCl2(C7H7NO)2], dichloridobis(2-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(3-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(4-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], and dichloridobis(4-hydroxybenzamide-κO)zinc(II), [ZnCl2(C7H7NO2)2]. All of the complexes contain hydrogen bonds between the amide N—H group and the amide carbonyl oxygen atoms or the chlorine atoms, forming extended networks.

Statistical analysis of noncovalent interactions of anion groups in crystal structures. I. Hydrogen bonding of sulfate anions

1996 ◽  
Vol 52 (4) ◽  
pp. 677-684 ◽  
Author(s):  
L. Chertanova ◽  
C. Pascard
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Small Molecules ◽  
Crystal Structures ◽  
Noncovalent Interactions ◽  
Data Set ◽  
Hydrogen Bond Acceptor ◽  
Covalently Bonded ◽  
Different Types

The hydrogen-bond acceptor characteristics of sulfate dianions are analyzed in crystal structures of small molecules. For 85 anions, neither coordinated to metal ions nor covalently bonded, 697 hydrogen bonds are faund. Of these, 266 (38%) are the O...H—O type and 431 (62%) are the O...H—N type, proportions that correspond well to the stoichiometry of the compounds studied and indicate no preference for a particular donor. The analysis of the data set, after classifying the hydrogen bonds according to the different types of donors, shows that O...H—O bonds are more linear than O...H—N. The anion oxygen–acceptor function is characterized by multiple hydrogen bonding. Only in 56 cases does a sulfate oxygen participate in a single hydrogen bond. In most cases every sulfate oxygen is coordinated by two (187 cases) or three (89 cases) hydrogen bonds. For three H donors, the preferred coordination geometry of the sulfate oxygen is pyramidal. The most frequent coordination around a sulfate dianion is with eight to ten H donors. Thus, sulfate dianions can play a significant cohesive role in molecular aggregation.

scholarly journals Reconciling solvent effects on rotamer populations in carbohydrates — A joint MD and NMR analysis

2006 ◽  
Vol 84 (4) ◽  
pp. 569-579 ◽  
Author(s):  
Jorge Gonzalez-Outeiriño ◽  
Karl N Kirschner ◽  
Smita Thobhani ◽  
Robert J Woods
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Solvent Polarity ◽  
Local Environment ◽  
Dynamics Simulation ◽  
Hydrogen Bond Donor ◽  
Hydroxymethyl Group ◽  
Internal Hydrogen

The rotational preferences of the hydroxymethyl group in pyranosides is known to depend on the local environment, whether in solid, solution, or gas phase. By combining molecular dynamics (MD) simulations with NMR spectroscopy the rotational preferences for the ω angle in methyl 2,3-di-O-methyl-α-D-glucopyranoside (3) and methyl 2,3-di-O-methyl-α-D-galactopyranoside (6) in a variety of solvents, with polarities ranging from 80 to 2.3 D have been determined. The effects of solvent polarity on intramolecular hydrogen bonding have been identified and quantified. In water, the internal hydrogen bonding networks are disrupted by competition with hydrogen bonds to the solvent. When the internal hydrogen bonds are differentially disrupted, the rotamer populations associated with the ω angle may be altered. In the case of 3 in water, the preferential disruption of the interaction between HO6 and O4 destabilizes the tg rotamer, leading to the observed preference for gauche rotamers. Without the hydrogen bond enhancement offered by a low polarity environment, both 3 and 6 display rotamer populations that are consistent with expectations based on the minimization of repulsive intramolecular oxygen–oxygen interactions. In a low polarity environment, HO6 prefers to interact with O4, however, in water these interactions are markedly weakened, indicating that HO6 acts as a hydrogen bond donor to water.Key words: carbohydrate, rotamer, molecular dynamics simulation, MD, NMR.

On the Influence of Intra - and Inter-Molecular Hydrogen Bonding on the Excited State Lifetime of Indigo Dyes

1977 ◽  
Vol 32 (8) ◽  
pp. 876-878 ◽  
Author(s):  
W. Windhager ◽  
S. Schneider ◽  
F. Dörr
Keyword(s):  
Hydrogen Bonding ◽  
Excited State ◽  
Hydrogen Bonds ◽  
Molecular Hydrogen ◽  
Intramolecular Hydrogen Bonding ◽  
Excited State Lifetime ◽  
Internal Hydrogen ◽  
Solvent Molecules ◽  
Intramolecular Hydrogen ◽  
Indigo Dyes

Abstract It is shown that intramolecular hydrogen bonding can give rise to very fast nonradiative desactivation of the S1 -state of indigo dyes. In those derivatives, which lack the possibility of internal hydrogen bonds, hydrogen bonding to suitable solvent molecules can provide the channel for fast radiationless transitions. As a consequence, drastic effects on the S1 -state lifetime are observed both as a function of solvent and/or temperature.

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