Determination of Chemical Reactivities of Oxytocin and Vasopressin Peptide Hormones Studied through Conceptual Density Functional Theory (CDFT) and Molecular Electron Density Theory (MEDT)

2021 ◽  
pp. 21-30
Author(s):  
Norma Flores-Holguin ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Density Functional ◽  
Peptide Hormones ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

scholarly journals Unveiling the Different Reactivity of Bent and Linear Three-Atom-Components Participating in [3 + 2] Cycloaddition Reactions

Organics ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 274-286
Author(s):  
Mar Ríos-Gutiérrez ◽  
Luis R. Domingo ◽  
Fatemeh Ghodsi
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Electron Density ◽  
Density Functional ◽  
Geometrical Parameters ◽  
Single Bond ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The reactivity of a series of pairs of bent and linear three-atom-component (B-TACs and L-TACs) participating in [3 + 2] cycloaddition (32CA) reactions towards ethylene and electrophilic dicyanoethylene (DCE) have been studied within the Molecular Electron Density Theory. While the pseudodiradical structure of B-TACs changes to that of pseudoradical or carbenoid L-TACs upon dehydrogenation, zwitterionic B-TACs remain unchanged. Conceptual Density Functional Theory (CDFT) indices characterize five of the nine TACs as strong nucleophiles participating in polar reactions towards electrophilic ethylenes. The activation energies of the 32CA reactions with electrophilic DCE range from 0.5 to 22.0 kcal·mol−1, being between 4.3 and 9.1 kcal·mol−1 lower than those with ethylene. In general, B-TACs are more reactive than their L-TAC counterparts. A change in the regioselectivity is found in these polar 32CA reactions; in general, while B-TACs are meta regioselective, L-TACs are ortho regioselective. The geometrical parameters of the transition state structures suggest that the formation of the single bond involving the most electrophilic carbon of DCE is more advanced. A change in the asynchronicity in the reactions involving B-TACs and L-TACs is also found.

Understanding the molecular mechanism of the stereoselective conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives

2021 ◽  
Author(s):  
Agnieszka Kącka-Zych ◽  
Radomir Jasinski
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanism ◽  
Electron Density ◽  
Density Functional ◽  
Dft Method ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

Conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives has been explored using Density Functional Theory (DFT) method within the context of the Molecular Electron Density Theory (MEDT) at the B97XD(PCM)/6-311G(d,p)...

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.

scholarly journals Understanding the Reactivity of C-Cyclopropyl-N-Methylnitrone Participating in [3+2] Cycloaddition Reactions Towards Styrene with a Molecular Electron Density Theory Perspective

2021 ◽  
Vol 65 (1) ◽  
Author(s):  
Haydar A. Mohammad-Salim
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Transition States ◽  
Free Energies ◽  
Conceptual Density Functional Theory ◽  
Covalent Bonds ◽  
Functional Theory ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory

Abstract. The [3+2] cycloaddition (32CA) reactions of C-cyclopropyl-N-methylnitrone 1 with styrene 2 have been studied within molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory. These zwitterionic type 32CA reactions occur through a one-step mechanism. The 32CA reactions undergo four stereo- and regioisomeric reaction paths to form four different products, 3, 4, 5 and 6.  Analysis of the conceptual density functional theory (CDFT) indices predict the global electronic flux from the strong nucleophilic nitrone 1 to the styrene 2. These 32CA reactions are endergonic with reactions Gibbs free energies between 2.83 and 7.39 kcal.mol-1 in the gas phase. The 32CA reaction leading to the formation of cycloadduct 3 presents the lowest activation enthalpy than the other paths due to a slightly increase in polar character evident from the global electron density transfer (GEDT) at the transition states and along the reaction path. The bonding evolution theory (BET) study suggests that these 32CA reactions occur through the coupling of pseudoradical centers and the formation of new C-C and C-O covalent bonds has not been started in the transition states.   Resumen.

scholarly journals Calculation of the Global and Local Conceptual DFT Indices for the Prediction of the Chemical Reactivity Properties of Papuamides A–F Marine Drugs

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3312 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Active Regions ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Global And Local

A well-behaved model chemistry previously validated for the study of the chemical reactivity of peptides was considered for the calculation of the molecular properties and structures of the Papuamide family of marine peptides. A methodology based on Conceptual Density Functional Theory (CDFT) was chosen for the determination of the reactivity descriptors. The molecular active sites were associated with the active regions of the molecules related to the nucleophilic and electrophilic Parr functions. Finally, the drug-likenesses and the bioactivity scores for the Papuamide peptides were predicted through a homology methodology relating them with the calculated reactivity descriptors, while other properties such as the pKas were determined following a methodology developed by our group.

Investigation of electron density changes at the onset of a chemical reaction using the state-specific dual descriptor from conceptual density functional theory

2015 ◽  
Vol 17 (14) ◽  
pp. 9359-9368 ◽  
Author(s):  
Frank De Proft ◽  
Valérian Forquet ◽  
Benjamin Ourri ◽  
Henry Chermette ◽  
Paul Geerlings ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Linear Combination ◽  
Electron Density ◽  
Chemical Reaction ◽  
Density Functional ◽  
The State ◽  
Dual Descriptor ◽  
Conceptual Density Functional Theory ◽  
Functional Theory

The electron density changes from reactants towards the transition state of a chemical reaction is expressed as a linear combination of the state-specific dual descriptors (SSDD) of the corresponding reactant complexes.

scholarly journals In Silico Pharmacokinetics, ADMET Study and Conceptual DFT Analysis of Two Plant Cyclopeptides Isolated From Rosaceae as a Computational Peptidology Approach

2021 ◽  
Vol 9 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Local Descriptors ◽  
Molecular Systems ◽  
Biological Targets ◽  
Global And Local

This research presents the outcomes of a computational determination of the chemical reactivity and bioactivity properties of two plant cyclopeptides isolated from Rosaceae through the consideration of Computational Peptidology (CP), a protocol employed previously in the research of similar molecular systems. CP allows the prediction of the global and local descriptors that are the integral foundations of Conceptual Density Functional Theory (CDFT) and which could help in getting in the understanding of the chemical reactivity properties of the two plant cyclopeptides under study, hoping that they could be related to their bioactivity. The methodology based on the Koopmans in DFT (KID) approach and the MN12SX/Def2TZVP/H2O model chemistry has been successfully validated. Various Chemoinformatics tools have been used to improve the process of virtual screening, thus identifying some additional properties of these two plant cyclopeptides connected to their ability to behave as potentially useful drugs. With the further objective of analyzing their bioactivity, the CP protocol is complemented with the estimation of some useful parameters related to pharmacokinetics, their predicted biological targets, and the Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) parameters related to the bioavailability of the two plant cyclopeptides under study are also reported.

scholarly journals Localizing electron density errors in density functional theory

2019 ◽  
Vol 21 (37) ◽  
pp. 20927-20938 ◽  
Author(s):  
Rubén Laplaza ◽  
Victor Polo ◽  
Julia Contreras-García
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Quantum Chemical ◽  
Density Functional ◽  
Electron Densities ◽  
Functional Theory ◽  
Chemical Topology ◽  
Molecular Electron ◽  
Quantum Chemical Topology

The accuracy of different density functional approximations is assessed through the use of quantum chemical topology on molecular electron densities.

scholarly journals Participation of Phosphorylated Analogues of Nitroethene in Diels–Alder Reactions with Anthracene: A Molecular Electron Density Theory Study and Mechanistic Aspect

Organics ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 36-48
Author(s):  
Agnieszka Kącka-Zych
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Diels Alder ◽  
Single Bond ◽  
Conceptual Density Functional Theory ◽  
Molecular Electron ◽  
Bet Analysis ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism

The structure and the contribution of the bis(2-chloroethyl) 2-nitro 1a and 2-bromo-2-nitroethenylphosphonates 1b with anthracene 2 in the Diels–Alder (DA) reactions have been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP functional together with 6-31G(d), 6-31+G(d) and 6-31+G(d,p) basic sets. Analysis of the Conceptual Density Functional Theory (CDFT) reactivity indices indicates that 1a and 1b can be classified as a strong electrophile and marginal nucleophile, while 2 is classified as a strong electrophile and strong nucleophile. The studied DA reactions take place through a one-step mechanism. A Bonding Evolution Theory (BET) of the one path associated with the DA reaction of 1a with 2 indicates that it is associated with non-concerted two-stage one-step mechanism. BET analysis shows that the first C2-C3 single bond is formed in Phase VI, while the second C1-C6 single bond is formed in the Phase VIII. The formation of both single bonds occurs through the merging of two C2 and C3, C1 and C6 pseudoradical centers, respectively.

scholarly journals A statistical thermodynamics view of electron density polarisation: application to chemical selectivity

2020 ◽  
Vol 22 (41) ◽  
pp. 23553-23562
Author(s):  
Frédéric Guégan ◽  
Vincent Tognetti ◽  
Jorge I. Martínez-Araya ◽  
Henry Chermette ◽  
Lynda Merzoud ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Heat Exchange ◽  
Electron Density ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Statistical Thermodynamics ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Effective Work ◽  
Chemical Selectivity

A fundamental link between conceptual density functional theory and statistical thermodynamics is herein drawn, showing that intermolecular electrostatic interactions can be understood in terms of effective work and heat exchange.

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