Search results for "Isomerization"

High vibrational overtone excitation‐induced conformational isomerization of glycolic acid in solid argon matrix

2018

‘Maya chemistry’ of organic–inorganic hybrid materials: isomerization, cyclicization and redox tuning of organic dyes attached to porous silicates

2013

[EN] Association of indigo and lapachol dyes to aluminosilicate clays yields polyfunctional organic – inorganic hybrid materials forming Maya Blue-like systems. Upon partial removing of clay's zeolitic water by moderate thermal treatment, abundant isomerization, cyclicization and oxidation reactions occur defining a‘ Maya chemistry whose complexity could explain the versatile use of such materials in the pre-Columbian cultures and permits the preparation of polyfunctional materials potentially usable for therapeutic and catalytic purposes.

UV‐Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes

2019

Red-light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large-scale secondary and tertiary changes which follow small-scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore-binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemi…

Thecis-transisomerization ofN-methyl-α,β-dehydroamino acids

2012

Dehydroamino acids with the methylated N-terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis-trans isomerization of the N-terminal tertiary amide group of diamides: Ac-(Z)-Δ(Me)Abu-NHMe (1), Ac-(Z)-Δ(Me)Phe-NHMe (2), Ac-(E)-Δ(Me)Phe-NHMe (3), Ac-Δ(Me)Ala-NHMe (4), and Ac-(Me)Ala-NHMe (5). The compounds were analyzed in the solid state by an X-ray crystallography (1-3), and in the solution by FTIR (MeCN and CHCl(3) ) and NMR (DMSO-d6 and CDCl(3) ) methods (1-5). In the solid state, the studied compounds adopt the cis configuration of N-terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1-…

Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase

2009

4-Oxalocrotonate tautomerase enzyme (4-OT) catalyzes the isomerization of 2-oxo-4-hexenedioate to 2-oxo-3-hexenedioate. The chemical process involves two proton transfers, one from a carbon of the substrate to the nitrogen of Pro1 and another from this nitrogen atom to a different carbon of the substrate. In this paper the isomerization has been studied using the combined quantum mechanical and molecular mechanical (QM/MM) method with a dual-level treatment of the quantum subsystem employing the MPW1BK density functional as the higher level. Exploration of the potential energy surface shows that the process is stepwise, with a stable intermediate state corresponding to the deprotonated subs…

Density Functional Theory Study of the Trans-Trans-Cis (TTC)→Trans-Trans-Trans (TTT) Isomerization of a Photochromic Spiropyran Merocyanine

2008

Density Functional Theory (DFT) calculations have been performed on the TTC→TTT isomerization reaction of the open forms of the 1',3'-dihydro-8-bromo-6-nitro- 1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-(2H)indole (8-Br-6-nitro-BIPS) system. The calculations were carried out in vacuo and in methylene chloride solution at different temperatures. Results are compared with the available experimental values of free energy difference and activation energy in solution.

3-(2-Pyridyl)-[1,2,3]triazolo[1,5-a]pyridines. An experimental and theoretical (DFT) study of the ring-chain isomerization

2005

An experimental (1H NMR) and theoretical (DFT) study of the ring-chain-ring isomerization of 3-(2-pyridyl)-[1,2,3]triazolo[1,5-a]pyrid-7-yl derivatives (A) into 6-{[1,2,3]triazolo[1,5-a]pyrid-3-yl}-2-pyridyl derivatives (B) has been carried out. Based on the calculations, a mechanism of several steps will be proposed. The experimental results as well as the calculations lead to the conclusion that the A-B ratio depends on the electronic properties of the substituents. © The Royal Society of Chemistry 2005.

Origins of fluorescence in evolved bacteriophytochromes

2014

Use of fluorescent proteins to study in vivo processes in mammals requires near-infrared (NIR) biomarkers that exploit the ability of light in this range to penetrate tissue. Bacteriophytochromes (BphPs) are photoreceptors that couple absorbance of NIR light to photoisomerization, protein conformational changes, and signal transduction. BphPs have been engineered to form NIR fluorophores, including IFP1.4, Wi-Phy, and the iRFP series, initially by replacement of Asp-207 by His. This position was suggestive because its main chain carbonyl is within hydrogen-bonding distance to pyrrole ring nitrogens of the biliverdin chromophore, thus potentially functioning as a crucial transient proton sin…

Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching.

2009

Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pock…

Chemistry and Photochemistry of 2,6-Bis(2-hydroxybenzilidene)cyclohexanone. An Example of a Compound Following the Anthocyanins Network of Chemical R…

2014

The kinetics and thermodynamics of the 2,6-bis(2-hydroxybenzilidene)cyclohexanone chemical reactions network was studied at different pH values using NMR, UV-vis, continuous irradiation, and flash photolysis. The chemical behavior of the system partially resembles anthocyanins and their analogue compounds. 2,6-Bis(2-hydroxybenzilidene)cyclohexanone exhibits a slow color change from yellow to red styrylflavylium under extreme acidic conditions. The rate constant for this process (5 × 10(-5) s(-1)) is pH independent and controlled by the cis-trans isomerization barrier. However, the interesting feature is the appearance of the colorless compound, 7,8-dihydro-6H-chromeno[3,2-d]xanthene, isolat…