Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts

2021 ◽  
Author(s):  
Biswajit Sahariah ◽  
Bani Kanta Sarma
Keyword(s):  
Noncovalent Interactions ◽  
Polyproline Ii

Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽  
2021 ◽  
Author(s):  
Viktor N. Serezhkin ◽  
Anton V. Savchenkov
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Noncovalent Interactions ◽  
Organic Molecular Crystal ◽  
Universal Approach ◽  
Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

2020 ◽  
Author(s):  
Radu Talmazan ◽  
Klaus R. Liedl ◽  
Bernhard Kräutler ◽  
Maren Podewitz
Keyword(s):  
Noncovalent Interactions ◽  
Interaction Model ◽  
Alder Reaction ◽  
Diels Alder ◽  
Stacking Interactions ◽  
Pi Stacking ◽  
Diels Alder Reaction ◽  
Double Decker ◽  
Anthracene Molecule ◽  
New Strategies

We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented 'inverted sandwich' structure. Hence, it sheds light on new strategies to design functional fullerene based materials.<br>

The X40x10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation

2017 ◽  
Author(s):  
Manoj Kumar Kesharwani ◽  
Nitai Sylvetsky ◽  
Debashree Manna ◽  
Jan M.L. Martin
Keyword(s):  
Dissociation Energy ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Coupled Cluster ◽  
Dissociation Energies ◽  
Iodine Species ◽  
Explicitly Correlated ◽  
High Level ◽  
Cluster Methods ◽  
Small Separation

<p>We have re-evaluated the X40x10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)–MP2 “high-level corrections” (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies, and turns out to be more important for noncovalent interactions than is generally realized. As in previous studies, we find that the most efficient way to obtain HLCs is to combine (T) from conventional CCSD(T) calculations with explicitly correlated CCSD-F12–MP2-F12 differences.</p>

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

Recent Developments in Azole Compounds as Antitubercular Agent

2019 ◽  
Vol 16 (3) ◽  
pp. 290-306
Author(s):  
Rina Das ◽  
Gyati S. Asthana ◽  
Krishan A. Suri ◽  
Dinesh Mehta ◽  
Abhay Asthana
Keyword(s):  
Therapeutic Agent ◽  
Current Problem ◽  
Noncovalent Interactions ◽  
Drug Resistant ◽  
Antitubercular Drugs ◽  
Chemistry Research ◽  
Improper Use ◽  
Recent Developments ◽  
Important Direction ◽  
Tuberculosis Therapy

Tuberculosis (TB) is a global health disaster and is a wide-reaching hitch. The improper use of antibiotics in chemotherapy of TB patients led to the current problem of tuberculosis therapy which gives rise to Multi-Drug Resistant (MDR) strains. Nitrogen heterocycles including azole compounds are an important class of therapeutic agent with electron-rich property. Azole-based derivatives easily bind with the enzymes and receptors in organisms through noncovalent interactions, thereby possessing various applications in medicinal chemistry. Research on azoles derivatives have been expansively carried out and have become one of the extremely active area in recent years and the progress is quite rapid. A genuine attempt to review chemistry of azoles and to describe various azole-based compounds synthesized in the last two decades having promising antitubercular potential is described in the present article. It is hopeful that azole compounds may continue to serve as an important direction for the exploitation of azole-based antitubercular drugs with better curative effect, lower toxicity, less side effects, especially fewer resistances and so on.

Organocatalyzed Heterocyclic Transformations In Green Media: A Review

2020 ◽  
Vol 07 ◽  
Author(s):  
Neslihan Demirbas ◽  
Ahmet Demirbas
Keyword(s):  
Hydrogen Bonding ◽  
Phase Transfer ◽  
Noncovalent Interactions ◽  
Binding Capacity ◽  
Chemical Transformations ◽  
Organic Transformations ◽  
Phase Transfer Catalysts ◽  
Waste Production ◽  
Synthetic Methodologies ◽  
Organocatalytic Reactions

Background: Since the discovery of metal-free catalysts or organocatalysts about twenty years ago, a number of small molecules with different structures have been using to accelerate organic transformations. With the development of environmental awareness, in order to obtain highly privileged scaffolds, scientists have directed their studies towards the synthetic methodologies which minimize or preferably eliminate the formation of waste, avoid from toxic solvents and reagents and use renewable starting materials as far as possible. Methods: In this connection, the organocatalytic reactions providing efficiency and selectivity for most of case have become an endless topic in organic chemistry since several advantages from both practical and environmental standpoints. Organocatalysts supplying transformation of reactants into products with the least possible waste production have been serving to the concept of green chemistry. Results and Conclusion: Organocatalysts have been classified on the basis of their binding capacity to the substrate with covalently or noncovalent interactions involving hydrogen bonding and electrostatic interaction. Diverse types of small organic compounds including proline and its derivatives, phase-transfer catalysts, (thio)urease, phosphoric acids, sulfones, N-oxides, guanidines, cinchona derivatives, aminoindanol and amino acids have been utilized as hydrogen bonding organocatalysts in different chemical transformations.

NMR Techniques for the Investigation of Solvation Phenomena and Noncovalent Interactions

ChemInform ◽  
2006 ◽  
Vol 37 (23) ◽  
Author(s):  
Alessandro Bagno ◽  
Federico Rastrelli ◽  
Giacomo Saielli
Keyword(s):  
Noncovalent Interactions ◽  
Nmr Techniques

scholarly journals The phenoxyl group-modulated interplay of cation–π and σ-type interactions in the alkali metal series

2020 ◽  
Vol 22 (46) ◽  
pp. 27105-27120
Author(s):  
Giacomo Prampolini ◽  
Marco d'Ischia ◽  
Alessandro Ferretti
Keyword(s):  
Alkali Metal ◽  
Noncovalent Interactions ◽  
Metal Cations ◽  
Alkali Metal Cations ◽  
Striking Effect

An extensive exploration of the interaction PESs of phenol and catechol complexes with alkali metal cations reveals a striking effect of –OH substitution on the balance between cation-π and σ-type noncovalent interactions.

scholarly journals A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

2021 ◽  
Vol 61 (2) ◽  
pp. 795-809
Author(s):  
Erna K. Wieduwilt ◽  
Jean-Charles Boisson ◽  
Giancarlo Terraneo ◽  
Eric Hénon ◽  
Alessandro Genoni
Keyword(s):  
Molecular Orbital ◽  
Noncovalent Interactions ◽  
Biological Systems ◽  
Gradient Model
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