On the nature of hydrogen bonds: an overview on computational studies and a word about patterns

2007 ◽  
Vol 9 (22) ◽  
pp. 2782 ◽  
Author(s):  
Isabel Rozas
Keyword(s):  
Hydrogen Bonds ◽  
Computational Studies

Controlling the Conformation of Arylamides: Computational Studies of Intramolecular Hydrogen Bonds between Amides and Ethers or Thioethers

2004 ◽  
Vol 10 (20) ◽  
pp. 5008-5016 ◽  
Author(s):  
Robert J. Doerksen ◽  
Bin Chen ◽  
Dahui Liu ◽  
Gregory N. Tew ◽  
William F. DeGrado ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Computational Studies ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Asymptotic Strength Limit of Hydrogen Bond Assemblies in Proteins at Vanishing Pulling Rates

2007 ◽  
Vol 1062 ◽  
Author(s):  
Sinan Keten ◽  
Markus J. Buehler
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Computational Studies ◽  
Entropic Elasticity ◽  
Strength Limit ◽  
Wide Range ◽  
Peptide Hydrogen ◽  
Polypeptide Chains ◽  
Limiting Value ◽  
Intrinsic Strength

ABSTRACTExperimental and computational studies on mechanical unfolding of proteins suggest that rupture forces approach a limiting value of a few hundred pN at vanishing pulling velocities. We develop a fracture mechanics based theoretical framework that considers the free energy competition between entropic elasticity of polypeptide chains and rupture of peptide hydrogen bonds, which we use here to provide an explanation for the intrinsic strength limit of proteins. Our analysis predicts that individual protein domains stabilized by hydrogen bonds can not exhibit rupture forces larger than approximately ≈200 pN, regardless of the presence of a large number of hydrogen bonds. This result explains a wide range of experimental and computational observations.

scholarly journals Probing the conformation of a conserved glutamic acid within the Cl− pathway of a CLC H+/Cl− exchanger

2017 ◽  
Vol 149 (4) ◽  
pp. 523-529 ◽  
Author(s):  
Malvin Vien ◽  
Daniel Basilio ◽  
Lilia Leisle ◽  
Alessio Accardi
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Transport Proteins ◽  
Side Chain ◽  
Ion Binding ◽  
Computational Studies ◽  
Transport Models ◽  
Ions Transport ◽  
Selective Transport ◽  
Transport Cycle

The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H+/Cl− exchange. One of these states, in which Gluex occupies the central binding site (Scen) while Cl− ions fill the internal and external sites (Sint and Sext), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Gluex trapped in Scen between two Cl− ions. Transport by CLC-ec1 is reduced when [Cl−] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Gluex in Scen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl−] is abolished in the E148A mutant, in which the Gluex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Gluex can occupy Scen as well as the Sext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to Scen play a role in determining the equilibrium between these two conformations.

Secondary stereocontrolling interactions in chiral Brønsted acid catalysis: study of a Petasis–Ferrier-type rearrangement catalyzed by chiral phosphoric acids

2014 ◽  
Vol 5 (9) ◽  
pp. 3515-3523 ◽  
Author(s):  
Kyohei Kanomata ◽  
Yasunori Toda ◽  
Yukihiro Shibata ◽  
Masahiro Yamanaka ◽  
Seiji Tsuzuki ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Phosphoric Acid ◽  
Acid Catalysis ◽  
Computational Studies ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Chiral Phosphoric Acid ◽  
Acid Catalyzed ◽  
Chiral Bronsted Acid ◽  
Phosphoric Acids

Guided by computational studies, the involvement of non-classical C–H⋯O hydrogen bonds and π–π stacking interactions were found to be crucial for high stereocontrol in a chiral phosphoric acid-catalyzed reaction.

scholarly journals Crystal Structure, Spectroscopy, SEM Analysis, and Computational Studies of N-(1,3-Dioxoisoindolin-2yl)benzamide

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Hakan Bülbül ◽  
Yavuz Köysal ◽  
Necmi Dege ◽  
Sümeyye Gümüş ◽  
Erbil Ağar
Keyword(s):  
Crystal Structure ◽  
Ir Spectroscopy ◽  
Hydrogen Bonds ◽  
Theoretical Calculations ◽  
Sem Analysis ◽  
Monoclinic Space Group ◽  
Computational Studies ◽  
X Ray Diffraction ◽  
Ethanolic Solution ◽  
X Ray

The compound N-(1,3-dioxoisoindolin-2yl)benzamide, C15H10N2O3, was prepared by the heating of an ethanolic solution of 2-hydroxy-1H-isoindole-1,3(2H)-dione and 4-chloroaniline. The product was characterised using a combination of IR spectroscopy, SEM, and single crystal X-ray diffraction techniques. In addition to the experimental analysis, theoretical calculations were used to investigate the crystal structure in order to compare experimental and theoretical values. The X-ray diffraction analysis shows that the compound crystallises in the monoclinic space group P21/c with the geometric parameters of a=13.5324(11) Å, b=9.8982(8) Å, c=9.7080(8) Å, and β=95.425(6)°. The crystal structure is held together by a network of N-H⋯O hydrogen bonds involving the carboxamide group.

Cation⋯cation hydrogen bonds in synephrine salts: a typical interaction in an unusual environment

2019 ◽  
Vol 21 (37) ◽  
pp. 20647-20660 ◽  
Author(s):  
Sibananda G. Dash ◽  
Tejender S. Thakur
Keyword(s):  
Hydrogen Bonds ◽  
Computational Studies ◽  
Coulombic Repulsion ◽  
Cationic Species ◽  
Hydrogen Bonded

Computational studies of hydrogen-bonded cationic species observed in the synephrine salts point towards the stabilizing nature of hydrogen bonds and highlights their contribution in reducing destabilization caused by coulombic repulsion.

scholarly journals An unusually short intermolecular N—H...N hydrogen bond in crystals of the hemi-hydrochloride salt of 1-exo-acetamidopyrrolizidine

2020 ◽  
Vol 76 (1) ◽  
pp. 77-81
Author(s):  
Minakshi Bhardwaj ◽  
Qianxiang Ai ◽  
Sean R. Parkin ◽  
Robert B. Grossman
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Rotation Axis ◽  
Energy Difference ◽  
Membered Ring ◽  
Computational Studies ◽  
Data Set ◽  
Hydrochloride Salt ◽  
Twofold Axis ◽  
Unexpected Product

The title compound [systematic name: (1R*, 8S)-2-acetamidooctahydropyrrolizin-4-ium chloride–N-[(1R, 8S)-hexahydro-1H-pyrrolizin-2-yl)acetamide (1/1)], 2(C9H16N2O)·HCl or C9H17N2O+·Cl−·C9H16N2O, arose as an unexpected product when 1-exo-acetamidopyrrolizidine (AcAP; C9H16N2O) was dissolved in CHCl3. Within the AcAP pyrrolizidine group, the unsubstituted five-membered ring is disordered over two orientations in a 0.897 (5):0.103 (5) ratio. Two AcAP molecules related by a crystallographic twofold axis link to H+ and Cl− ions lying on the rotation axis, thereby forming N—H...N and N—H...Cl...H—N hydrogen bonds. The first of these has an unusually short N...N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N—H...N + N...H—N). Computational studies suggest that the disorder model is slightly more stable, but the energy difference is very small.

Competition between Hydrogen Bonds and Lewis Acid-Base Interactions in the Equilibria between Bis(pentafluorophenyl)borinic Acid and Pyridine: Insights from NMR, Diffractometric and Computational Studies

2013 ◽  
Vol 227 (6-7) ◽  
pp. 751-773 ◽  
Author(s):  
Daniela Maggioni ◽  
Tiziana Beringhelli ◽  
Guiseppe D' Alfonso ◽  
Maria Carlotta Malatesta ◽  
Pierluigi Mercandelli ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Lewis Acid ◽  
Computational Studies ◽  
Acid Base ◽  
Borinic Acid

Use of molecular overlap to predict intermolecular repulsion in N... H-O hydrogen bonds

1998 ◽  
Vol 95 (3) ◽  
pp. 525-537 ◽  
Author(s):  
I. NOBELI S. L. PRICE R. J. WHEATLEY
Keyword(s):  
Hydrogen Bonds
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