Tests for aromaticity applied to the pentalenoquinones — A computational study

2001 ◽  
Vol 79 (10) ◽  
pp. 1492-1504
Author(s):  
C Delamere ◽  
C Jakins ◽  
E Lewars
Keyword(s):  
Computational Study ◽  
Single Point ◽  
Resonance Energy ◽  
Dft Method ◽  
Diels Alder ◽  
Chemical Hardness ◽  
Bond Orders ◽  
Resonance Energies ◽  
Ring Opening Reactions ◽  
Nics Calculations

Criteria for aromaticity and antiaromaticity were applied to the four pentalenoquinones, 1,2-, 1,5-, 1,4-, and 1,6-pentalenoquinone, i.e., bicyclo[3.3.0]octa-4,6,8-triene-2,3-dione (7a), bicyclo[3.3.0]octa-3,5,8-triene-2,7-dione (7b), bicyclo[3.3.0]octa-1(5),3,7-triene-2,6-dione (7c), and bicyclo[3.3.0]octa-1(5),3,6-triene-2,8-dione (7d). Geometry optimizations and frequency calculations were done with the pBP/DN* DFT method as implemented in Spartan, and single-point HF/3-21G calculations to obtain Löwdin bond orders (Spartan), as well as HF/6-31G* NICS calculations (Gaussian 98) were also carried out. Geometries and bond orders, chemical hardness, and NICS values gave no definite indication of aromatic or antiaromatic character. However, homodesmotic ring-opening reactions to give acyclic analogues indicated that 7a and 7b are nonaromatic (resonance energies –11 and 5 kJ mol–1) while 7c and 7d are antiaromatic (resonance energies –83 and –54 kJ mol–1). The resonance energies were obtained with the aid of an estimate of the strain energy of the molecules 7 (86 kJ mol–1) by a novel extrapolation procedure on hydropentalenes. Calculated pBP/DN* activation energies for Diels–Alder reactions with ethyne and ethene placed 7a and 7b in an "unreactive" class similar to 1,3-butadiene and fulvene, and 7c and 7d in a "reactive" class, similar to cyclopentadienone.Key words: aromaticity, pentalenoquinones, DFT, hardness, NICS, homodesmotic, resonance energy, bicyclo[3.3.0]octatrienediones.

On the generation of oxirene and dimethyloxirene by retro-Diels–Alder reactions, and reactions of dimethyloxirene: a computational study

2002 ◽  
Vol 80 (1) ◽  
pp. 94-105 ◽  
Author(s):  
C Delamere ◽  
C Jakins ◽  
E Lewars
Keyword(s):  
Transition State ◽  
Ring Opening ◽  
Computational Study ◽  
Single Point ◽  
Diels Alder ◽  
Reaction Energy ◽  
One Step ◽  
Reaction Energies ◽  
Level 1 ◽  
Late Transition

The isomerization of oxirene (oxacyclopropene) (1) to ketene, dimethyloxirene (7) to dimethylketene via the oxo carbene ("ketocarbene"), and the retro-Diels–Alder extrusion of oxirene and dimethyloxirene from their formal adducts (9 and 24, respectively) with benzene were studied computationally. All species were optimized at the MP2(fc)/6–31G(df,p) level; the species involving 1 were also subjected to MP2(fc)/6–31G(df,p) frequency and single-point CCSD(T)/6–31G(df,p) calculations. At the CCSD(T)/6–31G(df,p)//MP2(fc)/6–31G(df,p) level 1 isomerized to ketene in one step with a barrier of 2.8 kJ mol–1 and a reaction energy of –320.6 kJ mol–1. The extrusion of 1 from 9 had a late transition state and activation and reaction energies of 264.2 and 214.2 kJ mol–1, respectively, cf. cyclopropene extrusion from its adduct (192.3 and 95.9 kJ mol–1), indicating an antiaromatic destabilization energy of 214.2 – 95.9 = 118 kJ mol–1 for 1. The carbene 8 from ring-opening of 7 lay 10.9 kJ mol–1 above 7 (CCSD(T)/6–31G(df,p)//MP2(fc)/6–31G(df,p)), but the transition state could not be found; 8 isomerized to dimethylketene (252.7 kJ mol–1 below 7) with a barrier of 16.4 kJ mol–1, and to s-(Z)- and s-(E)-butenone with barriers of 28.5 and 35.4 kJ mol–1, respectively. The UV (TDDFT, B3P86/6–311++G**//MP2(fc)/6–31G(df,p)) spectra of 1 and 7 were calculated. Discrepancies were seen between the calculated IR spectra of 7 (bis(trifluoromethyl)oxirene) and perfluoro ethyl methyloxirene, and those attributed to these species in earlier matrix-isolation work. Key words: oxirene, dimethyloxirene, ab initio, retro-Diels–Alder, Diels–Alder.

A Comprehensive Computational Study on OCH+-Rg (Rg = He, Ne, Ar, Kr, Xe) Complexes

2003 ◽  
Vol 68 (3) ◽  
pp. 489-508 ◽  
Author(s):  
Yinghong Sheng ◽  
Jerzy Leszczynski
Keyword(s):  
Computational Study ◽  
Relativistic Effects ◽  
Dft Method ◽  
Basis Set ◽  
Rare Gas ◽  
Geometrical Parameters ◽  
Minor Effect ◽  
Dissociation Energies ◽  
Equilibrium Geometries

The equilibrium geometries, harmonic vibrational frenquencies, and the dissociation energies of the OCH+-Rg (Rg = He, Ne, Ar, Kr, and Xe) complexes were calculated at the DFT, MP2, MP4, CCSD, and CCSD(T) levels of theory. In the lighter OCH+-Rg (Rg = He, Ne, Ar) rare gas complexes, the DFT and MP4 methods tend to produce longer Rg-H+ distance than the CCSD(T) level value, and the CCSD-calculated Rg-H+ bond lengths are slightly shorter. DFT method is not reliable to study weak interaction in the OCH+-He and OCH+-Ne complexes. A qualitative result can be obtained for OCH+-Ar complex by using the DFT method; however, a higher-level method using a larger basis set is required for the quantitative predictions. For heavier atom (Kr, Xe)-containing complexes, only the CCSD method predicted longer Rg-H+ distance than that obtained at the CCSD(T) level. The DFT method can be applied to obtain the semiquantitative results. The relativistic effects are expected to have minor effect on the geometrical parameters, the H+-C stretching mode, and the dissociation energy. However, the dissociation energies are sensitive to the quality of the basis set. The nature of interaction between the OCH+ ion and Rg atoms was also analyzed in terms of the interaction energy components.

On the Mechanism of Au‐catalyzed Enynamide‐Yne Dehydro‐Diels‐Alder Reactions: An Experimental and Computational Study

2021 ◽  
Author(s):  
David Fabian León Rayo ◽  
Young J. Hong ◽  
Dominic Campeau ◽  
Dean J. Tantillo ◽  
Fabien Gagosz
Keyword(s):  
Computational Study ◽  
Diels Alder

Controlling fluorescence resonance energy transfer of donor–acceptor dyes by Diels–Alder dynamic covalent bonds

2021 ◽  
Vol 57 (26) ◽  
pp. 3275-3278
Author(s):  
Yanhui Cui ◽  
Fen Li ◽  
Xin Zhang
Keyword(s):  
Energy Transfer ◽  
Fluorescence Resonance Energy Transfer ◽  
Aromatic Amine ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Diels Alder ◽  
Covalent Bonds ◽  
Donor Acceptor ◽  
Fluorescence Resonance ◽  
Mutual Conversion

Two new dyes, consisting of an aromatic amine donor and dansyl acceptor connected by Diels–Alder bonds, display a switchable energy transfer. Dynamic covalent properties enable the mutual conversion of the two dyes by maleimide exchanges.

Quantum-Chemical Ab Initio Calculations on Inda- and Thallabenzene (C5H5In and C5H5Tl) and their Structural Isomers η5-C5H5In and η5-C5H5Tl

2018 ◽  
Vol 71 (3) ◽  
pp. 102
Author(s):  
Emma Persoon ◽  
Yuekui Wang ◽  
Gerhard Raabe
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Density Functional ◽  
Single Point ◽  
Normal Modes ◽  
Dft Method ◽  
Basis Sets ◽  
Triplet States ◽  
Structural Isomers ◽  
Td Dft

Quantum-chemical ab initio, time-independent, as well as time-dependent density functional theory (TD-DFT) calculations were performed on the so far elusive heterocycles inda- and thallabenzene (C5H5In and C5H5Tl), employing several different methods (MP2, CISD, CCSD, CCSD(T), BD, BD(T), QCISD, QCISD(T), CASSCF, DFT/B3LYP), effective core potentials, and different basis sets. While calculations on the MP2 level predict the ground states of the title compounds to be singlets with the first triplet states between 13 and 15 kcal mol−1 higher in energy, single point calculations with the QCISD(T), CCSD(T), and BD(T) methods at CCSD-optimized structures result in energy differences between the singlet and the triplet states in the range between 0.3 and 2.1 kcal mol−1 in favour of the triplet states. According to a CASSCF(8,8) calculation the triplets are also more stable by about 2.5–2.9 kcal mol−1. Calculations were also performed for the C5v-symmetric η5 structural isomers (cyclopentadienylindium, CpIn, and cyclopentadienylthallium, CpTl, Cp = C5H5) of the title compounds. At the highest level of theory employed in this study, C5H5In is between 79 and 88 kcal mol−1 higher in energy than CpIn, while this energy difference is even larger for thallabenzene where C5H5Tl is energetically between 94 and 102 kcal mol−1 above CpTl. In addition we report on the UV/vis spectra calculated with a TD-DFT method as well as on the spectra of the normal modes of C5H5In and C5H5Tl. Both types of spectra might facilitate identification of the title compounds eventually formed in photolysis or pyrolysis experiments.

scholarly journals Stepwise or concerted? DFT study on the mechanism of ionic Diels-Alder reaction of chromanes

2016 ◽  
Vol 81 (1) ◽  
pp. 67-80 ◽  
Author(s):  
Mina Haghdadi ◽  
Mousavi Soghra ◽  
Hassan Ghasemnejad
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Theoretical Method ◽  
Dft Method ◽  
Alder Reaction ◽  
Diels Alder ◽  
Computational Method ◽  
Diels Alder Reaction ◽  
Styrene Derivatives

The stepwise and concerted Ionic Diels-Alder reaction between phenyl (pyridin-2-ylmethylene) oxonium and styrene derivatives are explored using theoretical method. The results support using computational method via persistent intermediates. The DFT method was essential to reproduce a reasonable potential energy surface for these challenging systems.

Computational Study of Adsorption Effects of Karanjin Drug Over Carbon Nanotube (C56H16) as Factor of Drug Delivery System — A Quantum Chemical Approach

NANO ◽  
2021 ◽  
pp. 2150106
Author(s):  
Anoop Kumar Pandey ◽  
Vijay Singh ◽  
Apoorva Dwivedi
Keyword(s):  
Drug Delivery ◽  
Carbon Nanotube ◽  
Gas Phase ◽  
Drug Delivery System ◽  
Delivery System ◽  
Quantum Chemical ◽  
Density Functional ◽  
Computational Study ◽  
Chemical Hardness ◽  
Adsorption Effect

Karanjin, phytochemical from Pongamia pinnata is reported to be effective against HIV that causes AIDS in humans, however, the delivery of this therapeutic molecule still needs improvement. Hence, this study provides a better understanding of the nonbonded interaction between an anti-HIV drug karanjin and carbon nanotube (CNT) (C56H16). The electronic structure and interaction properties of the molecule karanjin over the surface of CNT were theoretically studied in the gas phase by DFT/B3LYP/6-31G ([Formula: see text]) level of theory for the first time. The UV–Vis spectra and transitions of the karanjin drug, CNT (C56H16) and complex CNT (C-56)/karanjin in gas phase have been calculated by time-dependent density functional theory (TDDFT) for the investigation of adsorption effect. To support our hypothesis, we have performed quantum chemical analysis for CNT (C56H16)/karanjin in water and DMSO solvent. In this process, this CNT (C-56)/karanjin complex enters into affected cell in liquid medium. After that, the drug delivery system CNT (C-56) unloads karanjin at the affected site. The binding character interactive species have been determined by NBO and AIM analysis. The frontier orbital HOMO–LUMO gap, chemical softness, chemical hardness have also been calculated to understand its complete chemical properties. The outcomes from our interaction of drug karanjin with CNT (C56H16) will be instrumental for better drug delivery potential in the upcoming future.

Identification of Allosteric Fingerprints of Alpha-Synuclein Aggregates in Matrix Metalloprotease-1 and Substrate-Specific Virtual Screening with Single Molecule Insights

2021 ◽  
Author(s):  
Sumaer Kamboj ◽  
Chase Harms ◽  
Derek Wright ◽  
Anthony Nash ◽  
Lokender Kumar ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Single Molecule ◽  
Conformational Changes ◽  
Single Point ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Alpha Synuclein ◽  
Matrix Metalloproteases ◽  
Single Point Mutation ◽  
Mmp Inhibitor

Abstract Alpha-synuclein (aSyn) has implications in pathological protein aggregations in neurodegeneration. Matrix metalloproteases (MMPs) are broad-spectrum proteases and cleave aSyn, leading to aggregation. Previously, we showed that allosteric communications between the two domains of MMP1 on collagen fibril and fibrin depend on substrates, activity, and ligands. Here we report quantification of allostery using single molecule measurements of MMP1 dynamics on aSyn-induced aggregates by calculating Forster Resonance Energy Transfer (FRET) between two dyes attached to the catalytic and hemopexin domains of MMP1. The two domains of MMP1 prefer open conformations that are inhibited by a single point mutation E219Q of MMP1 and tetracycline, an MMP inhibitor. A two-state Poisson process describes the interdomain dynamics, where the two states and kinetic rates of interconversion between them are obtained from histograms and autocorrelations of FRET values. Since a crystal structure of aSyn-bound MMP1 is not available, we performed molecular docking of MMP1 with aSyn using ClusPro. We simulated MMP1 dynamics using different docking poses and matched the experimental and simulated interdomain dynamics to identify an appropriate pose. We used experimentally validated simulations to define conformational changes at the catalytic site and identify allosteric residues in the hemopexin domain having strong correlations with the catalytic motif residues. We defined Shannon entropy to quantify MMP1 dynamics. We performed virtual screening against a site on selected aSyn-MMP1 binding poses and showed that lead molecules differ between free MMP1 and substrate-bound MMP1. Also, identifying aSyn-specific allosteric residues in MMP1 enabled further selection of lead molecules. In other words, virtual screening needs to take substrates into account for substrate-specific control of MMP1 activity. Molecular understanding of interactions between MMP1 and aSyn-induced aggregates may open up the possibility of degrading aggregates by targeting MMPs.

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