scholarly journals Molecular interactions of amyloid nanofibrils with biological aggregation modifiers: implications for cytotoxicity mechanisms and biomaterial design

2017 ◽  
Vol 7 (4) ◽  
pp. 20160160 ◽  
Author(s):  
Durga Dharmadana ◽  
Nicholas P. Reynolds ◽  
Charlotte E. Conn ◽  
Céline Valéry
Keyword(s):  
Molecular Interactions ◽  
Lipid Membranes ◽  
Reaction Pathway ◽  
Third Party ◽  
Final Word ◽  
Nucleated Polymerization ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Functional Amyloids ◽  
Covalent Interactions

Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, either molecules or surfaces. Specifically, in the biological context, different classes of biomolecules are known to act as catalysts, inhibitors or modifiers of the generic protein fibrillization process. The biological aggregation modifiers reviewed here include lipid membranes of varying composition, glycosaminoglycans and metal ions, with a final word on xenobiotic compounds. The corresponding molecular interactions are critically analysed and placed in the context of the mechanisms of cytotoxicity of the amyloids involved in diverse pathologies and the non-toxicity of functional amyloids (at least towards their biological host). Finally, the utilization of this knowledge towards the design of bio-inspired and biocompatible nanomaterials is explored.

scholarly journals Tunable aziridinium ylide reactivity: non-covalent interactions enable divergent product outcomes

2021 ◽  
Author(s):  
Kate Nicastri ◽  
Soren Zappia ◽  
Jared Pratt ◽  
Julia Duncan ◽  
Ilia Guzei ◽  
...  
Keyword(s):  
Chemical Space ◽  
Steric Effects ◽  
Computational Studies ◽  
Rapid Preparation ◽  
Rotational Barriers ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Further Development ◽  
Covalent Interactions

Methods for rapid preparation of densely functionalized and stereochemically complex N-heterocyclic scaffolds are in demand for exploring potential new bioactive chemical space. This work describes experimental and computational studies to better understand the features of aziridinium ylides as intermediates for the synthesis of highly substituted dehydromorpholines. The development of this chemistry has enabled the extension of aziridinium ylide chemistry to the concomitant formation of both a C–N and a C–O bond in a manner that preserves the stereochemical information embedded in the substrate. The chemistry is tolerant of a wide range of functionalities that can be employed for DNA-encoded library (DEL) synthesis to prepare diverse libraries of heterocycles with potential bioactivity. In addition, we have uncovered several key insights that describe the importance of steric effects, rotational barriers around the C–N bond of the aziridinium ylide, and non-covalent interactions (NCIs) on the ultimate reaction outcome. These critical insights will assist in the further development of this chemistry to generate novel and complex N-heterocycles that will further expand complex amine chemical space.

scholarly journals A IMPORTÂNCIA DAS CUMARINAS PARA A QUÍMICA MEDICINAL E O DESENVOLVIMENTO DE COMPOSTOS BIOATIVOS NOS ÚLTIMOS ANOS

Química Nova ◽  
2020 ◽  
Author(s):  
Daiana Franco ◽  
Thiago Pereira ◽  
Felipe Vitorio ◽  
Nathalia Nadur ◽  
Renata Lacerda ◽  
...  
Keyword(s):  
Chemical Space ◽  
Biological Activities ◽  
Research Projects ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Iupac Nomenclature ◽  
Living Organisms ◽  
Coumarin Compounds ◽  
New Treatments ◽  
Covalent Interactions

Coumarins are natural products characterized as 2H-chromen-2-one, according to IUPAC nomenclature, largely distributed in plants, as well as, in species of fungi and bacteria. Nowadays, many synthetic procedures allow the discovery of coumarins with expanded chemical space. The ability to exert non-covalent interactions with many enzymes an receptors in living organisms lead the coumarins to exhibit a wide range of biological activities and applications. Then, this manuscript provides an overview of the use of coumarin compounds in medicinal chemistry in treating many diseases. Important examples of the last years have been selected concerning the activities of coumarins as anticoagulant, anticancer, antioxidant, antiviral, antidiabetics, anti-inflammatory, antibacterial, antifungal, and anti-neurodegenerative agents. Thus, this work aims at contributing to the development of new rational research projects searching for new treatments and bioactive compounds for many pathologies using coumarin derivatives.

Non-Covalent Interactions Atlas Benchmark Data Sets: Hydrogen Bonding

2019 ◽  
Author(s):  
Jan Řezáč
Keyword(s):  
Hydrogen Bonding ◽  
Basis Sets ◽  
Data Sets ◽  
Neutral Systems ◽  
Benchmark Data ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Dissociation Curves ◽  
New Generation ◽  
Covalent Interactions

The Non-Covalent Interactions Atlas project (www.nciatlas.org) aims to cover a wide range of non-covalent interactions with a new generation of benchmark data sets. This paper presents the first two data sets focused on hydrogen bonding: HB375, featuring neutral systems, and IHB100 for ionic H-bonds. Both data sets are complemented by ten-point dissociation curves (HB375x10, IHB100x10). The interaction energies are extrapolated to the CCSD(T)/CBS limit from calculations in large basis sets. The paper also summarizes the design principles that will be used to construct the subsequent data sets in the series. The testing of DFT-D methods on the HB375 set has revealed interesting, previously unnoticed issues. The application of the new data to the testing and parameterization of semiempirical QM methods is also discussed.

SUPPRESSION OF CHROMOPHORE AGGREGATION IN AMORPHOUS POLYMERIC MATERIALS: TOWARDS MORE EFFICIENT PHOTORESPONSIVE BEHAVIOR

2010 ◽  
Vol 19 (01) ◽  
pp. 57-73 ◽  
Author(s):  
ARRI PRIIMAGI ◽  
MATTI KAIVOLA ◽  
MATTI VIRKKI ◽  
FRANCISCO J. RODRÍGUEZ ◽  
MARTTI KAURANEN
Keyword(s):  
Phase Separation ◽  
System Performance ◽  
Polymeric Materials ◽  
Optical Performance ◽  
Polymer Backbone ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Optical Phenomena ◽  
Potential Impact ◽  
Covalent Interactions

We give an overview of our recent work on improving the optical performance of polymeric materials via supramolecular concepts, i.e., by making use of spontaneous non-covalent interactions between the chromophores and the polymer backbone. More precisely, we show that the aggregation of dipolar chromophores in amorphous polymeric materials can be controlled by simply choosing a proper polymer matrix. This approach has a potential impact in a wide range of optical phenomena where chromophore aggregation or phase separation sets a limit to the system performance.

Non-Covalent Interactions Atlas Benchmark Data Sets: Hydrogen Bonding

2019 ◽  
Author(s):  
Jan Řezáč
Keyword(s):  
Hydrogen Bonding ◽  
Basis Sets ◽  
Data Sets ◽  
Neutral Systems ◽  
Benchmark Data ◽  
Wide Range ◽  
Non Covalent Interactions ◽  
Dissociation Curves ◽  
New Generation ◽  
Covalent Interactions

The Non-Covalent Interactions Atlas project (www.nciatlas.org) aims to cover a wide range of non-covalent interactions with a new generation of benchmark data sets. This paper presents the first two data sets focused on hydrogen bonding: HB375, featuring neutral systems, and IHB100 for ionic H-bonds. Both data sets are complemented by ten-point dissociation curves (HB375x10, IHB100x10). The interaction energies are extrapolated to the CCSD(T)/CBS limit from calculations in large basis sets. The paper also summarizes the design principles that will be used to construct the subsequent data sets in the series. The testing of DFT-D methods on the HB375 set has revealed interesting, previously unnoticed issues. The application of the new data to the testing and parameterization of semiempirical QM methods is also discussed.

Non-Covalent interaction between Ionic liquid (1-ethyl-3-methylimidazolium chloride-aluminum chloride) and pure alcohols

2021 ◽  
Vol 11 ◽  
Author(s):  
Samir Das ◽  
Paramita Karmakar ◽  
Deepak Ekka ◽  
Nirmala Deenadayalu ◽  
Mahendra Nath Roy
Keyword(s):  
Ionic Liquid ◽  
Physicochemical Properties ◽  
Molecular Interactions ◽  
Aluminum Chloride ◽  
Binary Systems ◽  
Primary Alcohol ◽  
Intermolecular Forces ◽  
Molar Refraction ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Background: The non-covalent molecular interactions of 1-Ethyl-3-methylimidazolium chloride-aluminum chloride and pure alcohols attract attention in the industry, academic and research. Chemists, engineers, designers, and some researchers are much interested in the accessibility of its trustworthy databases. Objective: 1-Ethyl-3-methylimidazolium chloride-aluminum chloride is interacting with pure alcohols with non-covalent interactions. Physicochemical properties with their convincing data interpreting the interactions occurring there. Mehtods: For that limiting apparent molar volume, molar refraction, and limiting apparent molar isentropic compressibility of the binary systems viz., ([EMIm]Cl/AlCl3) +methanol, ([EMIm]Cl/AlCl3) +ethanol, ([EMIm]Cl/AlCl3) +1-propanol, and ([EMIm]Cl/AlCl3)+1-butanol have been calculated using physicochemical properties i.e.,. density, refractive index, and speed of sound, respectively, within the temperature range T=293.15K-318.15K (with the interval of 5K). Results: The ionic liquid strongly interacts with 1-butanol (106ϕ_v^o=874.52 m3 mol-1, 106•RM = 211.13 m3 mol-1, and 10-11•ϕ_k^o= -0.10 m3 mol-1 Pa-1, 108•((〖∂ϕ〗_E^o)⁄∂T)_p = 1.52 m3 mol-1 K-2) than other chosen primary alcohol at a higher temperature (318.15K). Among individual ions, the 106•ϕ_(V(ion))^o is higher for 〖AlCl_(4 )〗^-(522.96 m3 mol-1) than [EMIm]^+(351.56 m3 mol-1) at high temperature (318.15K) in 1-butanol. Conclusion: The molecular interactions occurring between the ionic liquid and solvent molecules are due to the structure-making capacity that causes by intermolecular forces and non-covalent interactions. Where, the 1-butanol strongly interact with ionic liquids. In beween the ions, the anaion interaction is greater than cation to solvents.

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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