scholarly journals Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

2016 ◽  
Vol 18 (29) ◽  
pp. 19746-19756 ◽  
Author(s):  
Suehiro Iwata ◽  
Dai Akase ◽  
Misako Aida ◽  
Sotiris S. Xantheas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Nearest Neighbor ◽  
Water Clusters ◽  
Hydrogen Donor ◽  
Donor And Acceptor ◽  
Bond Strengths

Comparison of the sum of the characteristic factors for some of the typical hydrogen donor and acceptor pairs with the CT term/kJ mol−1 (the upper value) and the O⋯O distance/in cubic (H2O)8.

Compressed hydrogen-bond effects in the pressure-frozen chloroacetic acid

2007 ◽  
Vol 63 (6) ◽  
pp. 896-902 ◽  
Author(s):  
Roman Gajda ◽  
Andrzej Katrusiak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Pressure Range ◽  
Chloroacetic Acid ◽  
Dichloroacetic Acid ◽  
Hydrogen Donor ◽  
Monoclinic Space Group ◽  
Space Group ◽  
Donor And Acceptor ◽  
Atom Position

The competing effects of squeezed OH...O bonds, destabilizing the H-atom position, and of displaced hydrogen donor and acceptor groups, favouring the ordered H-atom sites, have been tuned by pressure in the pressure-frozen dichloroacetic acid. Its structure has been determined at 0.1, 0.7, 0.9 and 1.4 GPa: in this pressure range the crystals are stable in the monoclinic space group P21/n. The molecules are O—H...O hydrogen bonded into dimers, which in turn interact via a unique pattern of halogen...halogen contacts. Between 0.1 and 1.4 GPa the OH...O bond is squeezed from 2.674 (13) to 2.632 (9) Å. Within the pressure range investigated the hydrogen bonds are squeezed and the shear displacement of the molecules compensate, and the H atoms remain ordered.

STRUCTURAL IMPLICATIONS OF O—H⋯O HYDROGEN BONDS IN INORGANIC CRYSTALS

2009 ◽  
Vol 23 (31n32) ◽  
pp. 3951-3958 ◽  
Author(s):  
FANGFANG ZHANG ◽  
DONGFENG XUE
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Spatial Frequency ◽  
Frequency Distribution ◽  
Structural Characteristics ◽  
Scatter Plot ◽  
Inorganic Crystal ◽  
Inorganic Crystals ◽  
Bond Strengths ◽  
Crystal Design

Structural characteristics of O — H ⋯ O hydrogen bonds in inorganic crystals were comprehensively investigated on the basis of a database study. It is shown that the multi-furcated hydrogen bonds are very common, therefore, the structures of hydrogen bonds in inorganic crystals are extremely flexible. The direction and distance preferences of hydrogen bonds were systematically analyzed through frequency distribution histograms and normalized spatial frequency distribution scatter plot. In addition, new bond valence parameters were proposed for O — H ⋯ O bonds in inorganic crystals fully taking into account the multi-furcated hydrogen bonds, which can be used to properly evaluate hydrogen bond strengths in inorganic crystals. The current work sheds some light on the usage of hydrogen bonds in inorganic crystal design.

C–H⋯S interaction exhibits all the characteristics of conventional hydrogen bonds

2020 ◽  
Vol 22 (31) ◽  
pp. 17482-17493 ◽  
Author(s):  
Sanat Ghosh ◽  
Pragya Chopra ◽  
Sanjay Wategaonkar
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant.

Universal prediction of intramolecular hydrogen bonds in organic crystals

2010 ◽  
Vol 66 (2) ◽  
pp. 237-252 ◽  
Author(s):  
Peter T. A. Galek ◽  
László Fábián ◽  
Frank H. Allen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Probability Model ◽  
Organic Crystals ◽  
Intramolecular Hydrogen Bonds ◽  
Donor And Acceptor ◽  
Universal Prediction ◽  
Structural Database ◽  
Chemical Descriptors ◽  
Intramolecular Hydrogen

A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB.

scholarly journals Defining the Bounds of Chemical Coupling Between Covalent and Hydrogen-bonds in Small Water Clusters

2021 ◽  
Author(s):  
Zi Li ◽  
Yong Yang ◽  
Xing Nie ◽  
Tianlv Xu ◽  
Steven Kirk ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Clusters ◽  
Covalent Bond ◽  
Covalent Bonds ◽  
Bond Path ◽  
Small Water ◽  
Chemical Coupling ◽  
Chemical Character ◽  
Sigma Bond

We seek to determine the two-way transfer of chemical character due to the coupling occurring between hydrogen-bonds and covalent-bonds known to account for the unusual strength of hydrogen-bonds in water. We have provided a vector-based quantification of the chemical character of uncoupled hydrogen-bonds and covalent-bonds and then determined the effects of two-way coupling consistent with the total local energy density H(rb) < 0 for hydrogen-bonds. We have calculated the precessions Kʹ of the eigenvectors around the bond-path for the Ehrenfest Force F(r) and compared with the corresponding QTAIM Kʹ. In doing so we explain why the Ehrenfest Force F(r) provides insights into the coupling between the hydrogen and covalent bonds whilst QTAIM cannot. Conditions for favorable transfer of electron momentum from the hydrogen atom of a sigma bond to the hydrogen-bond are found, with excellent agreement with the hydrogen-bond BCP and covalent-bond BCP separations providing the theoretical bounds for coupling.

scholarly journals The crystal structures of three disordered 2-substituted benzimidazole esters

2021 ◽  
Vol 77 (5) ◽  
pp. 473-479
Author(s):  
Chayanna Harish Chinthal ◽  
Hemmige S. Yathirajan ◽  
Nagaraja Manju ◽  
Balakrishna Kalluraya ◽  
Sabine Foro ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Stacking Interaction ◽  
Π Stacking ◽  
Donor And Acceptor ◽  
Π Stacking Interaction ◽  
Related Compounds

The crystal structures of three benzimidazole esters containing aryl or heterocyclic substituents at position 2 are reported, and all three exhibit disorder of molecular entities. In ethyl 1-methyl-2-[4-(prop-2-ynoxy)phenyl]-1H-benzimidazole-5-carboxylate, C20H18N2O3, (I), the prop-2-yn-1-oxyphenyl unit is disordered over two sets of atomic sites having effectively equal occupancies, 0.506 (5) and 0.494 (5). The propyl substituent in ethyl 1-propyl-2-(pyren-1-yl)-1H-benzimidazole-5-carboxylate, C29H24N2O2, (II), is disordered over two sets of atomic sites having occupancies 0.601 (8) and 0.399 (8), and the ester unit in ethyl 1-methyl-2-(5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1H-benzimidazole-5-carboxylate, C21H19ClN4O2 (III), is disordered over two sets of atomic sites having occupancies 0.645 (7) and 0.355 (7). In each of the C—H...π(arene) hydrogen bonds in (I), the donor and acceptor form parts of different disorder components, so that no continuous aggregation is possible. The molecules of (II) are linked by a single C—H...O hydrogen bond into C(10) chains, which are linked into sheets by a π–π stacking interaction, whereas those of (III) are just linked into C(13) chains, again by a single C—H...O hydrogen bond. Comparisons are made with the structures of some related compounds.

scholarly journals DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

2020 ◽  
Author(s):  
Maria Izabel Muniz ◽  
Hershel Lackey ◽  
Jennifer Heemstra ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Stacking Interactions ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Mesoscopic Modeling ◽  
Bond Strengths ◽  
Purine Pyrimidine

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.

scholarly journals Effective prediction of short hydrogen bonds in proteins via machine learning method

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Shengmin Zhou ◽  
Yuanhao Liu ◽  
Sijian Wang ◽  
Lu Wang
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Protein Structures ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Donor And Acceptor ◽  
Wide Range ◽  
Short Hydrogen Bonds

AbstractShort hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.

Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers

2017 ◽  
Vol 19 (36) ◽  
pp. 24866-24878 ◽  
Author(s):  
Christopher Copeland ◽  
Omkaran Menon ◽  
D. Majumdar ◽  
Szczepan Roszak ◽  
Jerzy Leszczynski
Keyword(s):  
Hydrogen Bond ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
High Frequency ◽  
Low Frequency ◽  
Weakly Interacting ◽  
Bond Strengths ◽  
High Frequency Modes

Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer.

A New Hydrogen-Bonding Motif with Constituents Bearing Donor and Acceptor Sites 7 Å Apart

2005 ◽  
Vol 60 (7) ◽  
pp. 758-762 ◽  
Author(s):  
Katja Heinze ◽  
Anja Reinhart
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Hydrogen Donor ◽  
Para Position ◽  
Hydrogen Acceptor ◽  
Aryl Ring ◽  
Donor And Acceptor ◽  
Pyrrole Nitrogen

Aryl substituted dipyrromethanes [di(pyrrol-2-yl)-phenyl-methanes] with hydrogen acceptor substituents R in para position of the aryl ring [R = CO2Me, CO2H, CONH(iPr) and NH2] located 7 Å apart from the hydrogen donor pyrrole nitrogen atom are shown to self-assemble in the solid state via hydrogen bonds to form rings or chains.

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