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.

Polymorphs and pseudopolymorphs of N,N′-dithiobisphthalimide

2002 ◽  
Vol 58 (2) ◽  
pp. 289-299 ◽  
Author(s):  
Dorcas M. M. Farrell ◽  
Christopher Glidewell ◽  
John N. Low ◽  
Janet M. S. Skakle ◽  
Choudhury M. Zakaria
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Solvent Free ◽  
Stacking Interactions ◽  
Rotation Axes ◽  
Π Stacking ◽  
Wide Range ◽  
Unit Cells ◽  
Solvent Molecules

N,N′-Dithiobisphthalimide, C16H8N2O4S2 (I), forms a wide range of polymorphs and solvates (pseudopolymorphs). When (I) is crystallized from methanol it yields a solvent-free polymorph (4), in Pna21 with Z′ = 1, in which the molecules are linked into chains by a single C—H...O hydrogen bond: crystallization from either acetonitrile or dimethylformamide produces a monoclinic polymorph (5), in P21/c with Z′ = 2, also solvent-free, in which the molecules are linked into molecular ladders. Nitromethane forms a monosolvate, C16H8N2O4S2·CH3NO2 (6), in P21/c with Z′ = 1, in which the solvent molecules are linked to the molecules of (I) not only via a conventional C—H...O hydrogen bond but also via a polarized multicentre interaction involving all three C—H bonds of the solvent molecule. Chlorobenzene forms a precise hemisolvate, C16H8N2O4S2·0.5C6H5Cl (7), in P{\bar 1 } with Z′ = 1, while ethylbenzene forms an approximate hemisolvate 2C16H8N2O4S2·0.913C6H5C2H5·0.087H2O (8), in P21/c with eight molecules of (I) per unit cell. In both solvates the molecules of (I) are linked, in (7) by π...π stacking interactions augmented by weak C—H...O hydrogen bonds and in (8) by stronger C—H...O hydrogen bonds: the solvent molecules lie in isolated cavities, disordered across inversion centres in (7) and fully ordered in general positions in (8). Crystallization of (I) either from tetrahydrofuran or from wet tert-butanol yields isomorphous solvates (9) and (10), respectively, in C2/c with Z′ = 0.5, in which molecules of (I) lie across twofold rotation axes and are linked by π...π stacking interactions and very weak C—H...O hydrogen bonds, forming a framework enclosing continuous channels: highly disordered solvent molecules lie within these channels. p-Xylene and toluene form isomorphous hemisolvates (11) and (12) with unit cells metrically very similar to those of (9) and (10), but in P21/n with Z′ = 1: in these two solvates the molecules of (I) are linked into a framework by very short C—H...O hydrogen bonds; the solvent molecules lie within continuous channels, but they are localized across inversion centres so that the toluene is disordered across an inversion centre.

scholarly journals Investigation of the nature of hydrogen bonds in 3,5-dimethylpyrazole

2020 ◽  
Vol 61 (1) ◽  
pp. 9-13
Author(s):  
Tatiana G. Volkova ◽  
◽  
Konstantin A. Chicherin ◽  
Irina O. Talanova ◽  
◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Self Organization ◽  
Supramolecular Systems ◽  
Acceptor Interaction ◽  
Covalent Interaction ◽  
Wide Range ◽  
Main Motive ◽  
Donor Acceptor ◽  
Hydrogen Bound

Compounds containing a pyrazole fragment in their structure are part of many medicines and have a wide range of bioactivity (for example, antimicrobial, anti-tuberculosis, etc.), and are also successfully used for the development of various synthetic anti-tumor agents. Interest in them is also caused by the presence of hydrogen bonds, which are the main motive for self-organization of molecules. A theoretical study of the nature of hydrogen bonds in various hydrogen-bound motifs in 3,5-dimethylpyrazole was performed using the DFT/B3LYP/6-31G(d,p) method. The results obtained indicate the possible existence of dimeric, trimeric, and tetrameric cyclic forms. Geometric and energy parameters of hydrogen bonds N-H...N are determined and the energies of donor-acceptor interaction in possible forms of self-organization of the molecules of the studied compound are calculated. It has been established that the hydrogen bond (H-bond) is the result of the interaction of a hybrid unshielded pair of a nitrogen atom of one molecule and a loosening natural orbital between the nitrogen atoms of one molecule and the hydrogen of another molecule (σ* N-H). The formation of the binding σ-orbital of the H-bond indicates the predominance of covalent interaction in the hydrogen bond. The study and analysis of the results showed that the formation of supramolecular systems of 3,5-dimethylpyrazole most likely structures are trimers and tetramers.

Reactions between arylhydrazinium chlorides and 2-chloroquinoline-3-carbaldehydes: molecular and supramolecular structures of a hydrazone, a 4,9-dihydro-1H-pyrazolo[3,4-b]quinoline and two 1H-pyrazolo[3,4-b]quinolines

2016 ◽  
Vol 72 (9) ◽  
pp. 670-678 ◽  
Author(s):  
Tholappanavara H. Suresha Kumara ◽  
Gopalpur Nagendrappa ◽  
Nanjappa Chandrika ◽  
Haliwana B. V. Sowmya ◽  
Manpreet Kaur ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Biological Activities ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Compound I ◽  
Space Group ◽  
Π Stacking ◽  
Wide Range ◽  
A Chain

Hydrazone derivatives exhibit a wide range of biological activities, while pyrazolo[3,4-b]quinoline derivatives, on the other hand, exhibit both antimicrobial and antiviral activity, so that all new derivatives in these chemical classes are potentially of value. Dry grinding of a mixture of 2-chloroquinoline-3-carbaldehyde and 4-methylphenylhydrazinium chloride gives (E)-1-[(2-chloroquinolin-3-yl)methylidene]-2-(4-methylphenyl)hydrazine, C17H14ClN3, (I), while the same regents in methanol in the presence of sodium cyanoborohydride give 1-(4-methylphenyl)-4,9-dihydro-1H-pyrazolo[3,4-b]quinoline, C17H15N3, (II). The reactions between phenylhydrazinium chloride and either 2-chloroquinoline-3-carbaldehyde or 2-chloro-6-methylquinoline-3-carbaldehyde give, respectively, 1-phenyl-1H-pyrazolo[3,4-b]quinoline, C16H11N3, (III), which crystallizes in the space groupPbcnas a nonmerohedral twin havingZ′ = 3, or 6-methyl-1-phenyl-1H-pyrazolo[3,4-b]quinoline, C17H13N3, (IV), which crystallizes in the space groupR\overline{3}. The molecules of compound (I) are linked into sheets by a combination of N—H...N and C—H...π(arene) hydrogen bonds, and the molecules of compound (II) are linked by a combination of N—H...N and C—H...π(arene) hydrogen bonds to form a chain of rings. In the structure of compound (III), one of the three independent molecules forms chains generated by C—H...π(arene) hydrogen bonds, with a second type of molecule linked to the chains by a second C—H...π(arene) hydrogen bond and the third type of molecule linked to the chain by multiple π–π stacking interactions. A single C—H...π(arene) hydrogen bond links the molecules of compound (IV) into cyclic centrosymmetric hexamers having \overline{3} (S6) symmetry, which are themselves linked into a three-dimensional array by π–π stacking interactions.

Resonance-Induced Hydrogen Bonding at Sulfur Acceptors in R 1 R 2C=S and R 1CS2 − Systems

1997 ◽  
Vol 53 (4) ◽  
pp. 680-695 ◽  
Author(s):  
F. H. Allen ◽  
C. M. Bird ◽  
R. S. Rowland ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Bond Formation ◽  
Lone Pair ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Coordination Numbers ◽  
Wide Range

The hydrogen-bond acceptor ability of sulfur in C=S systems has been investigated using crystallographic data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. The R1R2C=S bond lengths span a wide range, from 1.58 Å in pure thiones (R 1 = R 2 = Csp 3) to 1.75 Å in thioureido species (R 1 = R 2 = N) and in dithioates —CS^{-}_2. The frequency of hydrogen-bond formation at =S increases from 4.8% for C=S > 1.63 Å to more than 70% for C=S > 1.70 Å in uncharged species. The effective electronegativity of S is increased by conjugative interactions between C=S and the lone pairs of one or more N substituents (R 1 R 2): a clear example of resonance-induced hydrogen bonding. More than 80% of S in —CS^{-}_2 accept hydrogen bonds. C=S...H—N,O bonds are shown to be significantly weaker than their C=O...H—N,O analogues by (a) comparing mean S...H and O...H distances (taking account of the differing non-bonded sizes of S and O and using neutron-normalized H positions) and (b) comparing frequencies of hydrogen-bond formation in `competitive' environments, i.e. in structures containing both C=S and C=O acceptors. The directional properties and hydrogen-bond coordination numbers of C=S and C=O acceptors have also been compared. There is evidence for lone-pair directionality in both systems, but =S is more likely (17% of cases) than =O (4%) to accept more than two hydrogen bonds. Ab initio calculations of residual atomic charges and electrostatic potentials reinforce the crystallographic observations.

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.

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.

scholarly journals Hydrogen bonding and DNA: 66-year retrospective (briefly)

2020 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Double Helix ◽  
Density Functional Method ◽  
Point Mutations ◽  
Functional Method ◽  
Wide Range ◽  
Functional Features ◽  
Hydrogen Bonded

Background: As Yu.P. Blagoi, the memory of who is dedicated to this work, once said: "The molecular structure of DNA — the famous double helix — is stabilized by water molecules and metal ions". The central, key interaction that determines both the double-helix structure of DNA and its functioning (the genetic code, replication, mutagenesis) is hydrogen-bonded interaction. Objectives: Demonstration of the diverse manifestations of the hydrogen bond in the structure and functioning of DNA. Materials and Methods: A computer simulation based on the density functional method was used. Results: This paper identifies a wide range of hydrogen-bonded interactions that determine key aspects of both DNA structures and functional features related to heredity (replication, mutagenesis). Conclusions: The preopeness of DNA base pairs with an embedded water molecule on the exterior hydrogen bond create more favorable conditions for proton transitions between bases along the central hydrogen bond. In this case, the hydrogen bonds of the bases to a lesser extent hinder the transition of the proton due to the smaller electrostatic repulsion (due to a larger distance) between them. Therefore, the preopened pairs are likely to form tautomeric forms of nucleic acid bases and to originate a probable mechanism for the formation of point mutations in DNA. At the same time, the central hydrogen bonds with the imino groups of bases in pairs remain intact.

Elasticity and Strength of Beta-Sheet Protein Materials: Geometric Confinement and Size Effects

2009 ◽  
Author(s):  
Sinan Keten ◽  
Markus J. Buehler
Keyword(s):  
Fracture Mechanics ◽  
Hydrogen Bonds ◽  
Protein Domains ◽  
Shear Loading ◽  
Beta Sheets ◽  
Elastic Behavior ◽  
Optimal Size ◽  
Entropic Elasticity ◽  
Strength Limit ◽  
Geometric Confinement

Elasticity and strength of proteins influence their biological functions. Under external forces, many proteins exhibit entropic elasticity with a characteristic stiffening elastic behavior and unravel due to the rupture of interstrand H-bonds. 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 protein domains at vanishing rates [1, 2]. Our analysis predicts that individual protein domains stabilized only by hydrogen bonds cannot exhibit rupture forces larger than 100–300 pN in the asymptotic quasi-static limit. This result explains earlier experimental and computational observations that suggest such a universal, asymptotic strength limit at vanishing pulling rates. We show that the rupture strength of H-bond assemblies in beta-sheets is governed by geometric confinement effects, suggesting that clusters of at most 3–4 H-bonds break concurrently, even under uniform shear loading of a much larger number of H-bonds. These strength, elasticity and size effect predictions all agree well with recent experimental findings and proteomics data. Our model confirms that fracture mechanics concepts, previously primarily applied to macroscale fracture phenomena, can also be directly applied at nanoscale, to be used for describing failure mechanisms in protein materials. Our strength and optimal size predictions lead to a key hypothesis: confined H-bond clusters are prevalent in alpha helices, beta-sheets and beta-solenoids, perhaps as an evolutionary design principle that derives from generic mechanical properties of the fundamental building blocks of life.

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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