Search results for "conformation"
showing 10 items of 1414 documents
The Greenland shark Somniosus microcephalus—Hemoglobins and ligand-binding properties
2017
A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 +/- 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same a globin combined with two copies of three very similar beta subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology.…
Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study
2019
The adsorption of gas-phase pyruvic acid (CH3COCOOH) on hydroxylated silica particles has been investigated at 296 K using transmission Fourier transform infrared (FTIR) spectroscopy and theoretical simulations. Under dry conditions (<1% relative humidity, RH), both the trans-cis (Tc) and trans-trans (Tt) pyruvic acid conformers are observed on the surface as well as the (hydrogen bonded) pyruvic acid dimer. The detailed surface interactions were further understood through ab initio molecular dynamics simulations. Under higher relative humidity conditions (above 10% RH), adsorbed water competes for surface adsorption sites. Adsorbed water is also observed to change the relative populations …
MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor
2019
Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of thre…
Exotic SiO(2)H(2) Isomers: Theory and Experiment Working in Harmony.
2016
Replacing carbon with silicon can result in dramatic and unanticipated changes in isomeric stability, as the well-studied CO2H2 and the essentially unknown SiO2H2 systems illustrate. Guided by coupled-cluster calculations, three SiO2H2 isomers have been detected and spectroscopically characterized in a molecular beam discharge source using rotational spectroscopy. The cis,trans conformer of dihydroxysilylene HOSiOH, the ground-state isomer, and the high-energy, metastable dioxasilirane c-H2SiO2 are abundantly produced in a dilute SiH4/O2 electrical discharge, enabling precise structural determinations of both by a combination of isotopic measurements and calculated vibrational corrections. …
The substituent effect of π-electron delocalization in N-methylamino-nitropyridine derivatives: crystal structure and DFT calculations
2020
AbstractThe crystal and molecular structures of 3-(N-methylamino)-2-nitropyridine, 5-(N-methylamino)-2-nitropyridine and 2-(N-methylamino)-5-nitropyridine have been characterized by X-ray diffraction. To perform conformational analysis, the geometries of the compounds as well as their conformers and rotamers were optimized at the B3LYP/6-311++G(3df,3pd) level. The resulting data were used to analyze the π-electron delocalization effect in relation to the methylamino group rotation in ortho-, meta- and para-substitution positions. Quantitative aromaticity indices were calculated based on which we estimated the electronic structures of the analyzed compounds. The substituent effect of the met…
Structural Tuning and Conformational Stability of Aromatic Oligoamide Foldamers
2017
A series of aromatic oligoamide foldamers with two or three pyridine-2,6-dicarboxamide units as their main folding motifs and varying aromatic building blocks as linkers have been synthetized to study the effects of the structural variation on the folding properties and conformational stability. Crystallographic studies showed that in the solid state the central linker unit either elongates the helices and more open S-shaped conformations, compresses the helices to more compact conformations or acts as a rigid spacer separating the pyridine-2,6-dicarboxamide units, which for their part add the predictability of the conformational properties. Multidimensional NMR studies showed that, even in…
X-ray, conformation and electronic structures of 1-nitropyrrolidine
2016
Abstract The chemistry of pyrrolidine compounds has drawn much attention because of their biological activities. The crystal and molecular structure of 1-nitropyrrolidine (C4H8NNO2) at 150K, along with calculated structures (DFT and MP2), are reported herein. In the solid-state, the asymmetric part of the unit cell is composed of one quartermolecule at the position of two perpendicular mirror planes and the five-membered ring is disordered over a mirror plane, revealing the twisted conformation. Both geometries suggest slight sp3 hybridization of the amine nitrogen atom. The non-planar geometry suggests the lack of conjugation of the amine nitrogen lone pair with the nitro group, however th…
A Decade of Electrochemical Dehydrogenative C,C-Coupling of Aryls.
2019
The importance of sustainable and green synthetic protocols for the synthesis of fine chemicals has rapidly increased during the last decades in an effort to reduce the use of fossil fuels and other finite resources. The replacement of common reagents by electricity provides a cost- and atom-efficient, environmentally friendly, and inherently safe access to novel synthetic routes. The selective formation of carbon-carbon bonds between two distinct substrates is a crucial tool in organic chemistry. This fundamental transformation enables access to a broad variety of complex molecular architectures. In particular, the aryl-aryl bond formation has high significance for the preparation of organ…
Highly Stable Neutral and Positively Charged Dicarbollide Sandwich Complexes
2005
Novel sandwich metallacarboranes commo-[3,3'-Ni(8-SMe2-1,2-C2B9H10)2] (1), commo-[3,3'-Co(8-SMe2-1,2-C2B9H10)2]+ (2+), commo-[3,3'-Ru(8-SMe2-1,2-C2B9H10)2] (4) and commo-[3,3'-Fe(8-SMe2-1,2-C2B9H10)2] (5) have been prepared by reaction of [10-SMe2-7,8-nido-C2B9H10]- with NiCl2 x 6 H2O, CoCl2, [RuCl2(dmso)4] and [FeCl2(dppe)], respectively. Reduction of 2+ with metallic Zn leads to the neutral and isolable complex commo-[3,3'-Co(8-SMe2-1,2-C2B9H10)2] (3). Theoretical calculations using the ZINDO/1 semiempirical method show three energy minima for complexes 1-3 and 5 that agree with the presence of three different rotamers in solution at low temperature, while four relative energy minima have…
Phosphinotripeptidic Inhibitors of Leucylaminopeptidases
2021
Phosphinate pseudopeptide are analogs of peptides containing phosphinate moiety in a place of the amide bond. Due to this, the organophosphorus fragment resembles the tetrahedral transition state of the amide bond hydrolysis. Additionally, it is also capable of coordinating metal ions, for example, zinc or magnesium ions. These two properties of phosphinate pseudopeptides make them an ideal candidate for metal-related protease inhibitors. This research investigates the influence of additional residue in the P2 position on the inhibitory properties of phosphinopeptides. The synthetic strategy is proposed, based on retrosynthetic analysis. The N-C-P bond formation in the desired compounds is …