scholarly journals Communication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework

2016 ◽  
Vol 145 (24) ◽  
pp. 241101 ◽  
Author(s):  
Xiaofei Liu ◽  
Jan Hermann ◽  
Alexandre Tkatchenko
Keyword(s):  
Structure Stability ◽  
Many Body ◽  
Non Covalent Interactions ◽  
Covalent Interactions

scholarly journals On the Proton-Bound Noble Gas Dimers (Ng-H-Ng)+ and (Ng-H-Ng')+ (Ng, Ng'= He-Xe): Relationships betweenStructure, Stability, and Bonding Character

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1305
Author(s):  
Stefano Borocci ◽  
Felice Grandinetti ◽  
Nico Sanna
Keyword(s):  
Theoretical Calculations ◽  
Noble Gas ◽  
Structure Stability ◽  
Covalent Bonds ◽  
Dissociation Energies ◽  
Non Covalent Interactions ◽  
The Difference ◽  
Noble Gas Dimers ◽  
Covalent Interactions ◽  
Cluster Level

The structure, stability, and bonding character of fifteen (Ng-H-Ng)+ and (Ng-H-Ng')+ (Ng, Ng' = He-Xe) compounds were explored by theoretical calculations performed at the coupled cluster level of theory. The nature of the stabilizing interactions was, in particular, assayed using a method recently proposed by the authors to classify the chemical bonds involving the noble-gas atoms. The bond distances and dissociation energies of the investigated ions fall in rather large intervals, and follow regular periodic trends, clearly referable to the difference between the proton affinity (PA) of the various Ng and Ng'. These variations are nicely correlated with the bonding situation of the (Ng-H-Ng)+ and (Ng-H-Ng')+. The Ng-H and Ng'-H contacts range, in fact, between strong covalent bonds to weak, non-covalent interactions, and their regular variability clearly illustrates the peculiar capability of the noble gases to undergo interactions covering the entire spectrum of the chemical bond.

scholarly journals Structural and functional impact of non- synonymous SNPs in the CST complex subunit TEN1: Structural genomics approach

2018 ◽  
Author(s):  
Mohd. Amir ◽  
Vijay Kumar ◽  
Taj Mohammad ◽  
Ravins Dohare ◽  
Md. Tabish Rehman ◽  
...  
Keyword(s):  
Structural Changes ◽  
Computational Prediction ◽  
Structure Stability ◽  
Helix 12 ◽  
Functional Consequences ◽  
Non Covalent Interactions ◽  
Telomere Homeostasis ◽  
And Function ◽  
Blue Print ◽  
Covalent Interactions

TEN1 protein is a key component of CST complex, implicated in maintaining the telomere homeostasis, and provide stability to the eukaryotic genome. Mutations in TEN1 gene have higher chances of deleterious impact; thus, interpreting the number of mutations and their consequential impact on the structure, stability and function is essentially important. Here, we have investigated the structural and functional consequences of nsSNPs in the TEN1 gene. A wide array of sequence- and structure-based computational prediction tools were employed to identify the effects of 78 nsSNPs on the structure and function of TEN1 protein and deleterious nsSNPs were identified. These deleterious or destabilizing nsSNPs are scattered throughout the structure of TEN1. However, major mutations were observed in the α1-helix (12-16) and β5-strand (88-96). We further observed that mutations at C-terminal region were have higher tendency to form aggregate. In-depth structural analysis of these mutations reveals that the pathogenecity of these mutations are driven mainly through larger structural changes because of alterations in non-covalent interactions. This work provides a blue print to pinpoint the possible consequences of pathogenic mutations in the CST complex subunit TEN1.

scholarly journals Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Mohd. Amir ◽  
Vijay Kumar ◽  
Taj Mohammad ◽  
Ravins Dohare ◽  
Md. Tabish Rehman ◽  
...  
Keyword(s):  
Structural Changes ◽  
Computational Prediction ◽  
Structure Stability ◽  
Prediction Tools ◽  
Helix 12 ◽  
Functional Consequences ◽  
Non Covalent Interactions ◽  
Telomere Homeostasis ◽  
And Function ◽  
Covalent Interactions

Abstract TEN1 protein is a key component of CST complex, implicated in maintaining the telomere homeostasis, and provides stability to the eukaryotic genome. Mutations in TEN1 gene have higher chances of deleterious impact; thus, interpreting the number of mutations and their consequential impact on the structure, stability, and function is essentially important. Here, we have investigated the structural and functional consequences of nsSNPs in the TEN1 gene. A wide array of sequence- and structure-based computational prediction tools were employed to identify the effects of 78 nsSNPs on the structure and function of TEN1 protein and to identify the deleterious nsSNPs. These deleterious or destabilizing nsSNPs are scattered throughout the structure of TEN1. However, major mutations were observed in the α1-helix (12–16 residues) and β5-strand (88–96 residues). We further observed that mutations at the C-terminal region were having higher tendency to form aggregate. In-depth structural analysis of these mutations reveals that the pathogenicity of these mutations are driven mainly through larger structural changes because of alterations in non-covalent interactions. This work provides a blueprint to pinpoint the possible consequences of pathogenic mutations in the CST complex subunit TEN1.

scholarly journals Concerning the Role of σ-Hole in Non-Covalent Interactions: Insights from the Study of the Complexes of ArBeO with Simple Ligands

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4477
Author(s):  
Stefano Borocci ◽  
Felice Grandinetti ◽  
Nico Sanna
Keyword(s):  
Molecular Electrostatic Potential ◽  
Noble Gas ◽  
Coupled Cluster ◽  
Structure Stability ◽  
Chemical Bonds ◽  
Cluster Calculations ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Coupled Cluster Calculations

The structure, stability, and bonding character of some exemplary LAr and L-ArBeO (L = He, Ne, Ar, N2, CO, F2, Cl2, ClF, HF, HCl, NH3) were investigated by MP2 and coupled-cluster calculations, and by symmetry-adapted perturbation theory. The nature of the stabilizing interactions was also assayed by the method recently proposed by the authors to classify the chemical bonds in noble-gas compounds. The comparative analysis of the LAr and L-ArBeOunraveled geometric and bonding effects peculiarly related to the σ-hole at the Ar atom of ArBeO, including the major stabilizing/destabilizing role of the electrostatic interactionensuing from the negative/positive molecular electrostatic potential of L at the contact zone with ArBeO. The role of the inductive and dispersive components was also assayed, making itpossible to discernthe factors governing the transition from the (mainly) dispersive domain of the LAr, to the σ-hole domain of the L-ArBeO. Our conclusions could be valid for various types of non-covalent interactions, especially those involving σ-holes of respectable strength such as thoseoccurring in ArBeO.

NON COVALENT INTERACTIONS IN LARGE DIAMONDOID DIMERS IN THE GAS PHASE - A MICROWAVE STUDY

2017 ◽  
Author(s):  
Cristobal Perez ◽  
Melanie Schnell ◽  
Peter Schreiner ◽  
Norbert Mitzel ◽  
Yury Vishnevskiy ◽  
...  
Keyword(s):  
Gas Phase ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

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