scholarly journals On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4196
Author(s):  
José Manuel Guevara-Vela ◽  
Miguel Gallegos ◽  
Mónica A. Valentín-Rodríguez ◽  
Aurora Costales ◽  
Tomás Rocha-Rinza ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Formation Energy ◽  
Function Analysis ◽  
Computational Cost ◽  
Intramolecular Interactions ◽  
Hydrogen Bond Interaction ◽  
Wave Function Analysis ◽  
The Relationship

Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely −F, −Cl, −Br, −CF3, −N(CH3)2, −OCH3, −NHCOCH3 on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions.

Excess volumes of an alcohol + 1,2-dichloroethane

1981 ◽  
Vol 59 (14) ◽  
pp. 2210-2211 ◽  
Author(s):  
Nettem V. Choudary ◽  
Puligundla R. Naidu
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binary Mixtures ◽  
Excess Volumes ◽  
Hydrogen Bond Interaction ◽  
Bond Interaction ◽  
Break Up ◽  
The Difference

Excess volumes for binary mixtures of 1,2-dichloroethane with n-propanol, n-butanol, n-pentanol, n-hexanol, n-heptanol, and n-octanol have been determined at 303.15 K. VE is positive over the whole range of composition in all the mixtures. However, it is noticed that the positive values of VE of mixtures of 1,2-dichloroethane with n-hexanol, n-heptanol, and n-octanol differ from those for the mixtures of 1,2-dichloroethane with corresponding alkanes. The difference has been explained in terms of the break up of hydrogen bonds, interstitial accommodation of 1,2-dichloroethane in alcohol aggregates, and possible hydrogen bond interaction of the type Cl … H—O between unlike molecules.

Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model

2009 ◽  
Vol 87 (12) ◽  
pp. 1738-1746 ◽  
Author(s):  
Ping Qian ◽  
Li-Nan Lu ◽  
Zhong-Zhi Yang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Potential Model ◽  
Lone Pair ◽  
Static Properties ◽  
Range Interaction ◽  
Hydrogen Bond Interaction ◽  
Lone Pair Electron ◽  
Dynamics Simulations

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

Different supramolecular architectures mediated by different weak interactions in the crystals of three N-aryl-2,5-dimethoxybenzenesulfonamides

2017 ◽  
Vol 73 (10) ◽  
pp. 833-844 ◽  
Author(s):  
K. Shakuntala ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
M. Abdoh
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Shape Index ◽  
Intramolecular Interactions ◽  
Molecular Conformations ◽  
Supramolecular Architectures ◽  
The Relationship

The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N-aryl-2,5-dimethoxybenzenesulfonamides, namely N-(2,3-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (I), N-(2,4-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (II), and N-(2,4-dimethylphenyl)-2,5-dimethoxybenzenesulfonamide, C16H19NO4S, (III), are described. The asymmetric unit of (I) consists of two symmetry-independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C—H...O interactions in (I), N—H...Cl and C—H...O interactions in (II), and C—H...O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C—H...O, C—H...Cl, C—H...π(aryl), π(aryl)–π(aryl) and Cl...Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The d norm and shape-index surfaces of (I)–(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H...H contacts, followed by H...O/O...H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N—H...O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N—H...O hydrogen bonds form either C(4) chain motifs or R 2 2(8) rings. Further comparison reveals that the characteristics of the N—H...O hydrogen-bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the benzenesulfonyl ring, with the nature and position of the substituents on the aniline ring exerting little effect. On the other hand, the crystal structures of (I)–(III) display several weak interactions other than the common N—H...O hydrogen bonds, resulting in supramolecular architectures varying from one- to three-dimensional depending on the nature and position of the substituents on the aniline ring.

scholarly journals Hydrogen bond simulation in molecular crystals of tyrosine

2019 ◽  
Vol 58 (6) ◽  
pp. 73-77
Author(s):  
Tatiana G. Volkova ◽  
◽  
Irina O. Talanova ◽  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Biologically Active ◽  
Model Systems ◽  
Significant Difference ◽  
Molecular Associate ◽  
Order Of Magnitude ◽  
Chemical Simulation

The problem of the study of hydrogen bonds in biomolecules and living systems is important. Among the drugs, doctors emphasize substances of natural origin involved in metabolic processes. Such compounds include amino acids, peptides, vitamins, enzymes, macro- and microelements, and other biologically active substances, many of which are capable of forming hydrogen bonds. Amino acids and their derivatives are drugs of metabolic pharmacotherapy, characterized by low toxicity and severity of side effects. They also have virtually no allergenic effect, which makes them promising for the creation of drugs or their modifications. The instability of the hydrogen bond can significantly affect the state of pharmaceutical drug containing, for example, amino acids, during their storage, transportation or technological processing. One of the methods for studying the nature and determining the strength of hydrogen bonds is quantum chemical simulation. The calculation of the interaction energy in the studied molecular associate and its decomposition have been carried out according to Morocuma’s method (HF/6-31G (PC GAMESS). The evaluation of such energy components as electrostatic, exchange repulsion, polarization, charge transfer, mixing is given. The main contribution to the interaction energy comes from the electrostatic component. All the studied models have the same distribution of the components of the interaction energy in order of magnitude. Significant difference in the interaction energy in two model systems was noted, that could be explained by different geometry of hydrogen bonds. The comparison of received data made it possible to conclude that there are three types of hydrogen bonds in the molecular tyrosine crystal, which differ from each other in energy and geometry.

scholarly journals Crystal structure of 3-benzyl-1-[(cyclohexylidene)amino]thiourea

2015 ◽  
Vol 71 (12) ◽  
pp. o933-o934
Author(s):  
Shaaban K. Mohamed ◽  
Joel T. Mague ◽  
Mehmet Akkurt ◽  
Alaa A. Hassan ◽  
Ahmed T. Abdel-Aziz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Title Compound ◽  
Chair Conformation ◽  
Hydrogen Bond Interaction ◽  
Compound C ◽  
Bond Interaction ◽  
Ring Motif

The conformation of the title compound, C14H19N3S, is partially determined by an intramolecular N—H...N hydrogen-bond interaction, although the N—H...N angle of 108° is quite small. The cyclohexylidene ring has a chair conformation and its mean plane is inclined to the benzene ring by 46.30 (8)°. In the crystal, molecules are linked by pairs of N—H...S hydrogen bonds, forming inversion dimers, with anR22(8) ring motif. The dimers are reinforced by pairs of C—H...S hydrogen bonds, and are linked by further weak C—H...S hydrogen bonds, forming chains propagating along [100].

Molecular insights into hydrogen bonds in polyurethane/hindered phenol hybrids: evolution and relationship with damping properties

2014 ◽  
Vol 2 (22) ◽  
pp. 8545-8556 ◽  
Author(s):  
Kangming Xu ◽  
Fengshun Zhang ◽  
Xianlong Zhang ◽  
Qiaoman Hu ◽  
Hong Wu ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Damping Properties ◽  
Property Variation ◽  
Damping Property ◽  
Hindered Phenol ◽  
The Relationship

By combining experiments and MD simulation, the relationship between hydrogen bond evolution and damping property variation of TPU was revealed.

scholarly journals Crystal structure of the 1,3,6,8-tetraazatricyclo[4.3.1.13,8]undecane (TATU)–4-nitrophenol (1/2) adduct: the role of anomeric effect in the formation of a second hydrogen-bond interaction

2015 ◽  
Vol 71 (11) ◽  
pp. 1356-1360 ◽  
Author(s):  
Augusto Rivera ◽  
Héctor Jairo Osorio ◽  
Juan Manuel Uribe ◽  
Jaime Ríos-Motta ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Normal Donor ◽  
Anomeric Effect ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Formation ◽  
Dimensional Network ◽  
Crystalline Adduct ◽  
Donor Acceptor

In the title ternary co-crystalline adduct, C7H14N4·2C6H5NO3, molecules are linked by two intermolecular O—H...N hydrogen bonds, forming a tricomponent aggregates in the asymmetric unit. The hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. In the title adduct, the two independent nitrophenol molecules are essentially planar, with maximum deviations of 0.0157 (13) and 0.0039 (13) Å. The dihedral angles between the planes of the nitro group and the attached benzene rings are 4.04 (17) and 5.79 (17)°. In the crystal, aggregates are connected by C—H...O hydrogen bonds, forming a supramolecular dimer enclosing anR66(32) ring motif. Additional C—H...O intermolecular hydrogen-bonding interactions form a second supramolecular inversion dimer with anR22(10) motif. These units are linkedviaC—H...O and C—H...N hydrogen bonds, forming a three-dimensional network.

Self-assembly of NH-pyrazoles via intermolecular N—H...N hydrogen bonds

1999 ◽  
Vol 55 (6) ◽  
pp. 985-993 ◽  
Author(s):  
Valerio Bertolasi ◽  
Paola Gilli ◽  
Valeria Ferretti ◽  
Gastone Gilli ◽  
Cristina Fernàndez-Castaño
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Self Assembly ◽  
Pyrazole Ring ◽  
Mean Value ◽  
Hydrogen Bond Interaction ◽  
Proton Disorder ◽  
Resonance Assisted Hydrogen Bond ◽  
Proton Sponges ◽  
Substituted Pyrazoles

The crystal structures of two NH-pyrazole derivatives forming intermolecular N—H...N hydrogen bonds are reported: 5-methyl-4-(3-methylpyrazol-5-yl)pyrazol-3-ol, C8H10N4O (P1), and 3-methyl-5-dihydro-1H-naphtho[1,2-d]pyrazole hemihydrochloride, C12H12N2.-C12H13N_{2}^{+}.Cl− (P2). 26 other structures are surveyed in order to obtain a deeper insight into the ways NH-pyrazoles self-assemble by means of intermolecular N—H...N hydrogen bonds in molecular crystals. A limited number of compounds form chains or dimers via homonuclear N+—H...N positive-charge-assisted hydrogen bonds, typical of proton sponges, which can be remarkably short [e.g. N...N 2.714 (3), N—H 1.09 (3), H...N 1.63 (3) Å, N—H...N 169 (3)° in (P2)]. Most pyrazoles, however, pack via neutral N—H...N bonds which are formally assisted by resonance (resonance-assisted hydrogen bond, RAHB) through the ...N=C—C=C—NH... iminoenamine fragment, contained in the ring, giving rise to dimers, trimers, tetramers and infinite chains of pyrazole molecules. Surprisingly, the resonance does not appear to shorten the N—H...N bond with respect to the accepted mean value N...N 2.97 (10) Å for non-resonant N—H...N bonds. It is shown that this is due to the internal π-delocalization of the pyrazole ring, which can be hardly increased by the hydrogen-bond interaction, except in symmetrically 3,5-substituted pyrazoles which display N...N distances as short as 2.82 Å, identical C—C and C—N distances in the two halves of the pyrazole molecule, and typical phenomena of N—H...N dynamical proton disorder, detectable by 15N-CP/MAS solid-state NMR.

scholarly journals Crystal structure of 5′′-(4-chlorobenzylidene)-4′-(4-chlorophenyl)-1′-methyltrispiro[acenapthylene-1,2′-pyrrolidine-3′,1′′-cyclohexane-3′′,2′′′-[1,3]dioxane]-2(1H),6′′-dione

2015 ◽  
Vol 71 (11) ◽  
pp. o814-o815 ◽  
Author(s):  
Kuppan Chandralekha ◽  
Deivasigamani Gavaskar ◽  
Adukamparai Rajukrishnan Sureshbabu ◽  
Srinivasakannan Lakshmi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ring System ◽  
Membered Ring ◽  
Boat Conformation ◽  
Pyrrolidine Ring ◽  
Hydrogen Bond Interaction ◽  
Compound C ◽  
Twist Conformation

In the title compound, C36H29Cl2NO4, two spiro links connect the methyl-substituted pyrrolidine ring to the acenaphthylene and cyclohexanone rings. The cyclohexanone ring is further connected to the dioxalane ring by a third spiro junction. The five-membered ring of the acenaphthylen-1-one ring system adopts a flattened envelope conformation, with the ketonic C atom as the flap, whereas the dioxalane and pyrrolidine rings each have a twist conformation. The cyclohexenone ring assumes a boat conformation. An intramolecular C—H...O hydrogen-bond interaction is present. In the crystal, molecules are linked by non-classical C—H...O hydrogen bonds, forming chains extending parallel to theaaxis.

Quantum-chemical study of N-methylacetamide and N,N-dimethylacetamide as models for peptidic bond in hydrogen-bond interaction with water, methanol and phenol

1983 ◽  
Vol 48 (11) ◽  
pp. 3214-3222 ◽  
Author(s):  
Milan Remko ◽  
Ivan Sekerka ◽  
Vladimír Frecer
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Geometry Optimization ◽  
Chemical Study ◽  
Hydrogen Bond Interaction ◽  
Proton Donors ◽  
Pcilo Method ◽  
Peptide Hydrogen

The PCILO quantum-chemical method with geometry optimization has been used to study rotation barriers of methyl groups in N-methylacetamide and N,N-dimethylacetamide. In all the cases studied, the eclipsed conformation have been found to be the most stable. Cis form of N-methylacetamide is less stable than the corresponding trans form by 2.0 kJ mol-1. Moreover, the PCILO method has been used to study linear n-mers (n = 4) of N-methylacetamide. On going from the dimer to tri- and tetramers, the hydrogen-bond energies have been found non-additive, and positive cooperativity has been observed. Finally, hydrogen-bond complexes have been studied which were formed by C=O groups of N-methylacetamide and N,N-dimethylacetamide with water, methanol or phenol as proton-donors. The said proton-donors have been found to act as breakers of inter-peptide hydrogen bonds N-H...O=C. The hydrogen bonds formed by methanol are somewhat stronger than those formed by water. In accordance with experiment, the strongest hydrogen bonds with the studied proton-acceptors are formed by phenol.

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