Topological aspects of chemical reactivity. On the similarity of molecular structures

1987 ◽  
Vol 52 (3) ◽  
pp. 555-562 ◽  
Author(s):  
Robert Ponec
Keyword(s):  
Electron Density ◽  
Chemical Reactions ◽  
Chemical Reactivity ◽  
Similarity Index ◽  
Molecular Structures ◽  
Similarity Criteria ◽  
Topological Similarity

A topological similarity index is introduced, allowing to characterize quantitatively the extent of reorganization of electron density in the course of chemical reactions. The possible application of this new index for the description and the classification of chemical reactions is discussed on the basis of certain analogy of similarity criteria with the so-called least-motion principle.

Topological aspects of chemical reactivity. On the possible use of similarity index in characterizing the transition state structure in concerted pericyclic reactions

1987 ◽  
Vol 52 (6) ◽  
pp. 1375-1385
Author(s):  
Robert Ponec
Keyword(s):  
Transition State ◽  
Chemical Reactivity ◽  
Transition States ◽  
Similarity Index ◽  
Pericyclic Reactions ◽  
State Structure ◽  
Transition State Structure ◽  
Topological Similarity

The use of the topological similarity index as a simple means for classification and characterization of the structure of the transition states in concerted pericyclic reactions is discussed. The suggested formulation makes it possible to bring a quantitative aspects into the empirical Dewar's classification of transition states in terms of aromaticity and/or antiaromaticity.

scholarly journals Unveiling the Different Chemical Reactivity of Diphenyl Nitrilimine and Phenyl Nitrile Oxide in [3+2] Cycloaddition Reactions with (R)-Carvone through the Molecular Electron Density Theory

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1085 ◽  
Author(s):  
Mar Ríos-Gutiérrez ◽  
Luis R. Domingo ◽  
M’hamed Esseffar ◽  
Ali Oubella ◽  
My Youssef Ait Itto
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
Nitrile Oxide ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The [3+2] cycloaddition (32CA) reactions of diphenyl nitrilimine and phenyl nitrile oxide with (R)-carvone have been studied within the Molecular Electron Density Theory (MEDT). Electron localisation function (ELF) analysis of these three-atom-components (TACs) permits its characterisation as carbenoid and zwitterionic TACs, thus having a different reactivity. The analysis of the conceptual Density Functional Theory (DFT) indices accounts for the very low polar character of these 32CA reactions, while analysis of the DFT energies accounts for the opposite chemoselectivity experimentally observed. Topological analysis of the ELF along the single bond formation makes it possible to characterise the mechanisms of these 32CA reactions as cb- and zw-type. The present MEDT study supports the proposed classification of 32CA reactions into pdr-, pmr-, cb- and zw-type, thus asserting MEDT as the theory able to explain chemical reactivity in Organic Chemistry.

Topological aspects of chemical reactivity. Valency changes in the course of chemical reactions

1987 ◽  
Vol 52 (11) ◽  
pp. 2603-2612 ◽  
Author(s):  
Robert Ponec
Keyword(s):  
Electron Density ◽  
Chemical Reactions ◽  
Chemical Treatment ◽  
Quantum Chemical ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
Topological Description

The Jug and Gopinathan approach to the use of valency changes for the characterization of chemical reactions is generalized by incorporating it into the framework of the recently proposed topological description of chemical reactivity in terms of the overlap determinant method. The conclusions of the simple topological analysis agree with the results of the direct quantum chemical treatment, indicating thus that the overlap determinant method depicts correctly the principal features of the electron density reorganization occuring during the chemical reactions.

Topological Aspects of Chemical Reactivity. Electron Correlation in the Course of Chemical Reactions

1993 ◽  
Vol 58 (8) ◽  
pp. 1751-1760 ◽  
Author(s):  
Robert Ponec ◽  
Martin Strnad
Keyword(s):  
Chemical Reactions ◽  
Electron Correlation ◽  
Energy Barrier ◽  
Chemical Reactivity ◽  
Similarity Index ◽  
Pericyclic Reactions ◽  
Correlation Effects ◽  
Transient Species

The second order similarity index gRP, which has been proposed recently as a new means for a qualitative characterization of correlation effects in chemical reactivity, was generalized by incorporation into a topological model of the overlap determinant method. The resulting approach, which provides information about the variation of electron correlation during chemical reactions, was applied to the investigation of several selected pericyclic reactions. Consistent with what can be expected, the role of electron correlation was found to be the most critical for transition states of other transient species near the top of the energy barrier. The systematic differences in the extent of electron correlation between allowed and forbidden reactions are also discussed.

Topological aspects of chemical reactivity. Correlation diagrams and overlap determinant method

1986 ◽  
Vol 51 (9) ◽  
pp. 1834-1842 ◽  
Author(s):  
Robert Ponec
Keyword(s):  
Chemical Reactions ◽  
Chemical Reactivity ◽  
Alternative Means

The recently proposed overlap determinant method is applied as an alternative means of construction of correlation diagrams. In comparison with existing techniques the main advantage of the proposed formalism lies above all in its universality allowing the unified classification of all types of chemical reactions.

scholarly journals Discovery of novel chemical reactions by deep generative recurrent neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
William Bort ◽  
Igor I. Baskin ◽  
Timur Gimadiev ◽  
Artem Mukanov ◽  
Ramil Nugmanov ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Short Term Memory ◽  
De Novo ◽  
Molecular Structures ◽  
Topographic Map ◽  
Short Term ◽  
Suzuki Reactions ◽  
Class A ◽  
Latent Space ◽  
Long Short Term Memory

AbstractThe “creativity” of Artificial Intelligence (AI) in terms of generating de novo molecular structures opened a novel paradigm in compound design, weaknesses (stability & feasibility issues of such structures) notwithstanding. Here we show that “creative” AI may be as successfully taught to enumerate novel chemical reactions that are stoichiometrically coherent. Furthermore, when coupled to reaction space cartography, de novo reaction design may be focused on the desired reaction class. A sequence-to-sequence autoencoder with bidirectional Long Short-Term Memory layers was trained on on-purpose developed “SMILES/CGR” strings, encoding reactions of the USPTO database. The autoencoder latent space was visualized on a generative topographic map. Novel latent space points were sampled around a map area populated by Suzuki reactions and decoded to corresponding reactions. These can be critically analyzed by the expert, cleaned of irrelevant functional groups and eventually experimentally attempted, herewith enlarging the synthetic purpose of popular synthetic pathways.

Epitaxy and Chemical Reactions During Thin Film Formation from Low Energy Ions New Kinetic Pathways, New Phases and New Properties

1991 ◽  
Vol 236 ◽  
Author(s):  
Nicole Herbots ◽  
O.C. Hellman ◽  
O. Vancauwenberghe
Keyword(s):  
Thin Film ◽  
Chemical Reactions ◽  
Degrees Of Freedom ◽  
Film Growth ◽  
Film Formation ◽  
Chemical Reactivity ◽  
Ion Beam ◽  
Low Energy ◽  
Low Energy Ions ◽  
Beam Deposition

AbstractThree important effects of low energy direct Ion Beam Deposition (IBD) are the athermal incorporation of material into a substrate, the enhancement of atomic mobility in the subsurface, and the modification of growth kinetics it creates. All lead to a significant lowering of the temperature necessary to induce epitaxial growth and chemical reactions. The fundamental understanding and new applications of low temperature kinetics induced by low energy ions in thin film growth and surface processing of semiconductors are reviewed. It is shown that the mechanism of IBD growth can be understood and computed quantitatively using a simple model including ion induced defect generation and sputtering, elastic recombination, thermal diffusion, chemical reactivity, and desorption The energy, temperature and dose dependence of growth rate, epitaxy, and chemical reaction during IBD is found to be controlled by the net recombination rate of interstitials at the surface in the case of epitaxy and unreacted films, and by the balance between ion beam decomposition and phase formation induced by ion beam generated defects in the case of compound thin films. Recent systematic experiments on the formation of oxides and nitrides on Si, Ge/Si(100), heteroepitaxial SixGe1−x/Si(100) and GaAs(100) illustrate applications of this mechanism using IBD in the form of Ion Beam Nitridation (IBN), Ion Beam Oxidation (IBO) and Combined Ion and Molecular beam Deposition (CIMD). It is shown that these techniques enable (1) the formation of conventional phases in conditions never used before, (2) the control and creation of properties via new degrees of freedom such as ion energy and lowered substrate temperatures, and (3) the formation of new metastable heterostructures that cannot be grown by pure thermal means.

scholarly journals FOUR-PARTICLE ANYON EXCITON: BOSON APPROXIMATION

1995 ◽  
Vol 09 (02) ◽  
pp. 123-133 ◽  
Author(s):  
M. E. Portnoi ◽  
E. I. Rashba
Keyword(s):  
Angular Momentum ◽  
Electron Density ◽  
Ground State ◽  
Hypergeometric Functions ◽  
Energy Levels ◽  
Confluent Hypergeometric Functions ◽  
Full Symmetry ◽  
Hole Confinement ◽  
Boson Approximation

A theory of anyon excitons consisting of a valence hole and three quasielectrons with electric charges –e/3 is presented. A full symmetry classification of the k = 0 states is given, where k is the exciton momentum. The energy levels of these states are expressed by quadratures of confluent hypergeometric functions. It is shown that the angular momentum L of the exciton ground state depends on the distance between the electron and hole confinement planes and takes the values L = 3n, where n is an integer. With increasing k the electron density shows a spectacular splitting on bundles. At first a single anyon splits off of the two-anyon core, and finally all anyons become separated.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

2021 ◽  
Vol 21 ◽  
Author(s):  
Prajakta U. Kulkarni ◽  
Harshil Shah ◽  
Vivek K. Vyas
Keyword(s):  
Quantum Mechanics ◽  
Drug Design ◽  
Molecular Mechanics ◽  
Chemical Reactions ◽  
Classical Mechanics ◽  
Molecular Structures ◽  
Protein Crystal ◽  
Structure Based Drug Design ◽  
Structure And Property ◽  
Qsar Models

: Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

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