Description of ?-Conjugation Effects by Means of Torsional Energy Profiles

ChemInform ◽  
2005 ◽  
Vol 36 (19) ◽  
Author(s):  
J. C. Sancho-Garcia ◽  
A. J. Perez-Jimenez
Keyword(s):  
Energy Profiles ◽  
Torsional Energy

scholarly journals Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

2021 ◽  
Author(s):  
Amanuel Wolde-Kidan ◽  
Anna Herrmann ◽  
Albert Prause ◽  
Michael Gradzielski ◽  
Rainer Haag ◽  
...  
Keyword(s):  
Free Energy ◽  
Time Resolved ◽  
Energy Profiles ◽  
Penetration Data ◽  
Free Energy Profiles

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

scholarly journals Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors

2021 ◽  
Vol 22 (14) ◽  
pp. 7637
Author(s):  
Liliya T. Sahharova ◽  
Evgeniy G. Gordeev ◽  
Dmitry B. Eremin ◽  
Valentine P. Ananikov
Keyword(s):  
Uv Light ◽  
Computational Design ◽  
Energy Profiles ◽  
Vinyl Sulfides ◽  
Tunable Sensors ◽  
Radical Generation ◽  
Metal Catalyzed ◽  
Dynamics Simulations ◽  
Simulations And Modeling ◽  
Insight Into

The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals—alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions.

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

scholarly journals On the Effects of Doping on the Catalytic Performance of (La,Sr)CoO3. A DFT Study of CO Oxidation

Catalysts ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 312 ◽  
Author(s):  
Antonella Glisenti ◽  
Andrea Vittadini
Keyword(s):  
Catalytic Activity ◽  
Co Oxidation ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Formation Energy ◽  
Oxygen Vacancies ◽  
Catalytic Performance ◽  
Energy Profiles ◽  
High Concentrations ◽  
3D Impurities

The effects of modifying the composition of LaCoO3 on the catalytic activity are predicted by density functional calculations. Partially replacing La by Sr ions has benefical effects, causing a lowering of the formation energy of O vacancies. In contrast to that, doping at the Co site is less effective, as only 3d impurities heavier than Co are able to stabilize vacancies at high concentrations. The comparison of the energy profiles for CO oxidation of undoped and of Ni-, Cu-m and Zn-doped (La,Sr)CoO3(100) surface shows that Cu is most effective. However, the effects are less spectacular than in the SrTiO3 case, due to the different energetics for the formation of oxygen vacancies in the two hosts.

scholarly journals Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

Reactions of the ambident super-electrophile series: the 2-(nitroaryl)-4,6-dinitrobenzotriazole 1-oxides with isopropoxide ion. Pathways of decomposition of the anionic σ-adducts

1994 ◽  
Vol 72 (1) ◽  
pp. 218-226 ◽  
Author(s):  
Julian M. Dust ◽  
Erwin Buncel
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Magnetic Resonance Spectroscopy ◽  
Nuclear Magnetic Resonance Spectroscopy ◽  
Adduct Formation ◽  
Resonance Spectroscopy ◽  
Energy Profiles ◽  
Meisenheimer Complexes ◽  
Bond Scission ◽  
Relative Selectivity

To elucidate the reactivity of super-electrophiles such as 4,6-dinitrobenzofuroxan as compared to normal electrophiles such as 1,3,5-trinitrobenzene, reaction of isopropoxide ion (iPrO−) with a series of ambident super-electrophiles was studied by 400 MHz 1H nuclear magnetic resonance spectroscopy. The 2-(nitroaryl)-4,6-dinitrobenzotriazole 1-oxides, 1–3, possess both a super-electrophilic (C-7) site and a normal electrophilic (C-1′) site. Nucleophiles can demonstrate selectivity for attack at C-7, which leads to formation of persistent anionic σ-adducts (Meisenheimer complexes), as compared to C-1′, which leads to N-2:C-1′ bond scission. The most reactive substrate, 2-(2′,4′,6′-trinitrophenyl)-4,6-dinitrobenzotriazole 1-oxide (Pi-DNBT, 1) was found to be the least selective substrate in C-7 adduct formation, while 2-(2′,4′-dinitrophenyl)- and 2-(4′-nitrophenyl)-4,6-dinitrobenzotriazole 1-oxides (DNP-DNBT, 2, and NP-DNBT, 3, respectively) showed increasing selectivity towards iPrO−, in turn. These results are discussed on the basis of overall selectivity for C-7 adduct formation and the relative selectivity of iPrO− as compared to methoxide and tert-butoxide ions. The conclusions are illustrated using comparative energy profiles. In terms of pathways for decomposition of the adducts, the C-7 adducts decompose via dissociation back to substrate and nucleophile and, thence, through C-1′ adduct formation to the scission products. However, for 1, the C-7 adduct 1a has now been found to decompose to 7-isopropyl-2-picryldinitrobenzotriazole, 1c. The possible mechanism of this formal internal redox will be discussed.

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