scholarly journals Evidence of sulfur centered hydrogen bond with sulfur atoms as a donor in aromatic thiols and aliphatic thiols on complexation with water using quantum mechanical methods

2021 ◽  
Author(s):  
Arnav Paul ◽  
Renjith Thomas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Decomposition Analysis ◽  
Nbo Analysis ◽  
Energy Decomposition Analysis ◽  
Mechanical Methods ◽  
Aromatic Thiols ◽  
Density Delocalization ◽  
Aliphatic Thiols ◽  
Triple Excitation

It has been more than a century since the discovery of hydrogen bonds, but the knowledge about its impact on day to day life of people is getting enhanced even now. It has a pivotal role in the stabilization of various biomolecules and subsequent bioactivity. Sulfur cantered hydrogen bond (SCHB), which is a weak interaction, has attracted the attention of many scientists in the last few decades. In this work, we report the nature of the SCHB between aliphatic/aromatic thiols and water. B3LYP-D3(BJ) with cc-pVTZ level was used for modeling the hydrogen bonded thiol-water complexes. Domain-based local pair natural orbitals coupled-cluster theory with single, double, and perturbative triple excitation DLPNO-CCSD(T) method was used for local energy decomposition analysis. QTAIM analysis helped to examine hydrogen bonds, weak non-covalent interactions, and the various electron density delocalization. Natural Bond Orbital (NBO) analysis explains the reason for the sulfur atom being the H-bond donor. Second-order perturbation energy from NBO findings supports the data obtained by LED and AIM calculations. Aromatic thiols form stronger hydrogen bonds than aliphatic thiols. The effect of substituents was also explored by studying aromatic systems with electron-withdrawing groups and donating groups. EDG substituted have more vital interaction, and EWG substituted thiols form stronger S-H…O hydrogen bonds.

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 Intramolecular Hydrogen Bond Energy and Its Decomposition—O–H∙∙∙O Interactions

Crystals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 5
Author(s):  
Sławomir J. Grabowski
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bond ◽  
Bond Energy ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Intermolecular Hydrogen Bonds ◽  
Hydrogen Bond Energy ◽  
Intramolecular Hydrogen

The method to calculate the energy of intramolecular hydrogen bond is proposed and tested for a sample of malonaldehyde and its fluorine derivatives; the corresponding calculations were performed at the ωB97XD/aug-cc-pVTZ level. This method based on relationships found for related intermolecular hydrogen bonds is compared with other approaches which may be applied to estimate the intramolecular hydrogen bond energy. Particularly, methods based on the comparison of the system that contains the intramolecular hydrogen bond compared with corresponding conformations where such interaction does not occur are discussed. The function-based energy decomposition analysis, FB-EDA, of the intramolecular hydrogen bonds is also proposed here.

scholarly journals Hydrogen bonds in molecular crystals alanine and tyrosine: NBO analysis

2020 ◽  
Vol 64 (10) ◽  
pp. 1-6
Author(s):  
Tatiana G. Volkova ◽  
◽  
Iroda Mamirjon kizi Abdukhalimova ◽  
Irina O. Talanova ◽  
◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Molecular Crystals ◽  
Dft Method ◽  
Nbo Analysis ◽  
Chemical Modeling ◽  
Theoretical Concepts ◽  
Oh Groups ◽  
The Third

At present, the theoretical concepts of the hydrogen bond (H-bond) in condensed media, for example, in living systems, biomolecules, are not fully solved. Quantum chemical modeling is used as one of the methods for studying the nature and determining the strength of the H-bond. In this paper, we continue to study the system of hydrogen bonds in molecular crystals of alanine and tyrosine. The dimers of these amino acids were modeled using the DFT method using the B97D functional with bases 6-31++G**. In the framework of NBO analysis, the stabilization energies of the formed hydrogen bond and the value of the transferred charge are calculated. It is shown that in alanine dimers, the main factor affecting the h-bond stabilization energy is the geometric parameters and, first of all, (N-H...O). The binding σ-orbital of the hydrogen bond is the result of the interaction of a hybrid NBO of the lone electron pairs of an oxygen atom and a loosening σ*-NBO N−H bond. The nature of bond formation in all three cases is the same, and the charge transfer value is greater than the value of the bond criterion, which indicates the presence of hydrogen bonds in all analyzed alanine systems. In tyrosine dimers, two H-bonds are formed that are similar in nature, as well as in geometric and energy parameters. The third H-bond is very weak, and the amount of charge transfer indicates its absence. The main interaction between the molecules in the third tyrosine dimer is the H-bond between the –СОО− and –OH groups. It was found that the scheme of formation of hydrogen bonds in molecular crystals of tyrosine is somewhat different from that of alanine.

scholarly journals Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences

2020 ◽  
Vol 22 (19) ◽  
pp. 10397-10411 ◽  
Author(s):  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Liquid Water ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Energy Decomposition ◽  
Bond Network ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.

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