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
2021 ◽  
pp. 1-8
Author(s):  
Azadeh Jafari Rad ◽  
Maryam Abbasi ◽  
Bahareh Zohrevand

This work was performed regarding the importance of iron (Fe) chelation for biological systems. This goal was investigated by assistance of a model of thiocytosine (TC) for participating in Fe-chelation processes. First, formations of tautomeric conformations were investigated to explore existence of possible structures of TC. Next, Fe-chelation processes were examined for all four obtained tautomers of TC. The results indicated that thiol tautomers could be seen at higher stability than thio tautomers, in which one of such thiol tautomers yielded the strongest Fe-chelation process to build FeTC3 model. As a consequence, parallel to the results of original TC tautomers, Fe-chelated models were found to be achievable for meaningful chelation processes or sensing the existence of Fe in media. Examining molecular orbital features could help for sensing purposes. The results of this work were obtained by performing density functional theory (DFT) calculations proposing TC compounds suitable for Fe-chelation purposes.


1994 ◽  
Vol 346 ◽  
Author(s):  
Larry L. Hench

ABSTRACTMany biological systems have evolved means of controlling the architecture of inorganic-organic composites at a nanometer scale. The principles of biochemistry and materials science underlying the potential use of biochemical processing to develop new molecularly tailored materials are discussed, with emphasis on:methods of stereochemical control of the organic-inorganic interface,genetic and enzymic control of biosynthesis and biomineralization,molecular orbital modelling of bio organic-inorganic interfaces,barriers and limitations of biomimetic and hierarchical processing,examples of unique materials made with biochemical processing.needs and potential applications in human prostheses.


Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2742 ◽  
Author(s):  
Ephrath Solel ◽  
Sebastian Kozuch

Tetrel bonds are noncovalent interactions formed by tetrel atoms (as σ-hole carriers) with a Lewis base. Here, we present a computational and molecular orbital study on the effect of the geometry of the substituents around the tetrel atom on the σ-hole and on the binding strengths. We show that changing the angles between substituents can dramatically increase bond strength. In addition, our findings suggest that the established Sn > Ge > Si order of binding strength can be changed in sufficiently distorted molecules due to the enhancement of the charge transfer component, making silicon the strongest tetrel donor.


2019 ◽  
Vol 43 (39) ◽  
pp. 15498-15512 ◽  
Author(s):  
Hans-Jörg Schneider

Quantification of noncovalent interactions is the key for the understanding of binding mechanisms, of biological systems, for the design of drugs, their delivery and for the design of receptors for separations, sensors, actuators, or smart materials.


Molecular Orbital Calculations for Biological Systems is a hands-on guide to computational quantum chemistry and its applications in organic chemistry, biochemistry, and molecular biology. With improvements in software, molecular modeling techniques are now becoming widely available; they are increasingly used to complement experimental results, saving significant amounts of lab time. Common applications include pharmaceutical research and development; for example, ab initio and semi-empirical methods are playing important roles in peptide investigations and in drug design. The opening chapters provide an introduction for the non-quantum chemist to the basic quantum chemistry methods, ab initio, semi-empirical, and density functionals, as well as to one of the main families of computer programs, the Gaussian series. The second part then describes current research which applies quantum chemistry methods to such biological systems as amino acids, peptides, and anti-cancer drugs. Throughout the authors seek to encourage biochemists to discover aspects of their own research which might benefit from computational work. They also show that the methods are accessible to researchers from a wide range of mathematical backgrounds. Combining concise introductions with practical advice, this volume will be an invaluable tool for research on biological systems.


Author(s):  
Henry S. Slayter

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.


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