Search results for "Biochem"

Fundamentals on the Molecular Mechanism of Action of Antimicrobial Peptides

2019

Abstract Antimicrobial peptides (AMPs) are produced by several organisms as their first line of defense. Constituted by amino acids, they may present different mechanisms of action. The antimicrobial activity can be used by the peptide-producing organism itself, as innate immune strategy, or in the industry, applying as natural source preservatives. Understanding the possibilities of the operation of these compounds is a prerequisite for the development of effective uses, as well as for the establishment of combinations, which can even expand their applications considering the possibilities of genetic manipulations. Thus, the objective of this article is to review the basic principles of AM…

Ab initio multi-reference perturbation theory calculations of the ground and low-lying electronic states of the KRb molecule

2016

The potential energy curves of the low-lying electronic states correlating up to the limit K(4p) + Rb(5s) of KRb molecule have been calculated using the multi-reference perturbation theory method at the CASSCF/ XMCQDPT2 level of theory without and with spin–orbit coupling. The calculated parameters of the ground X 1 R + state are in the best agreement among all previously performed ab initio calculations for the KRb molecule. The calculated vibrational intervals of the ground electronic term of the 39 K 85 Rb molecule describe the experiment with the accuracy within ±1 cm ?1 . The calculated intensities of the 2 1 R + (v 0 = 3, J 0 = 26) ? X 1 R + (v 00 = 0...24, J 00 = 25, 27) transitions …

Structural, electronic and energetic effects in heterocyclic fluorene derivatives fused with a fulvene unit

2019

Abstract A set of 36 heterocyclic (B, N and O) fluorene (C) derivatives fused in nine ways with fulvene ring have been analyzed by means of different local aromaticity criteria. Molecular geometry of analyzed compounds were optimized at B3LYP/6-311++G(2d,2p) level of theory. The evaluation of the local aromaticity has been carried out through the use of the geometry-based harmonic oscillator model of aromaticity (HOMA) and the magnetism-based zz‐component of the nucleus independent chemical shifts calculated 1 A above the ring center (NICS1zz) indices as well as one aromaticity index derived from the Quantum Theory Atoms in Molecules (QTAIM), i.e. the para-delocalization index (PDI). Additi…

Hydrogen bonding interaction of N5H with water: A first principle calculations

2019

Abstract The cyclopentazol (N5H) and its anion counterpart (N5–) have been studied extensively over the years and detected in the gas phase as well as in solution recently. In the present investigation, an attempt has been made to understand the interaction with water molecule using first principle calculations. Nature of interactions have been studied using both energy decomposition analysis and atoms in molecule (AIM) theory calculations. Further, the strength of non-covalent interactions were analysed using IGMplots.

Quasi-RRHO approximation and DFT study for understanding the mechanism and kinetics of nitration reaction of benzonitrile with nitronium ion

2021

Abstract The nitration reaction of benzonitrile with nitronium cation, NO2+, has been studied within the Molecular Electron Density Theory at the MN15-L/aug-cc-pVTZ level of theory. For this electrophilic aromatic substitution (EAS) reaction, three regioisomeric reaction paths have been studied. Quasi-RRHO approximation was applied to consider the vibrational contribution to entropy and correct the Gibbs free energy profile of the reaction in the solvent phase. Benzonitrile is less nucleophilically activated than benzene due to the presence of the electron-withdrawing CN group the meta position is the more favorable reaction path of this EAS reaction. The analysis of ELF and AIM demonstrate…

Steering the excited state dynamics of a photoactive yellow protein chromophore analogue with external electric fields

2014

Abstract The first excited state of the Photoactive Yellow Protein chromophore exhibits a strong charge transfer character and the dipole moments of the excited and ground states differ significantly. Furthermore, the excited state charge distribution changes during the isomerization of this chromophore. These observations suggest that external electric fields can be used to control photo-isomerization, providing a new concept for developing photochromic devices, such as e-paper or optical memory. To test this idea, we performed excited state dynamics simulations and static calculations of a PYP chromophore analogue (pCK − ) in an external electric field. By adjusting direction and strength…

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…

The Challenges of Air Protection and Control

2016

Sensitive Assays by Nucleophile-Induced Rearrangement of Photoactivated Diarylethenes.

2018

Upon light-induced isomerization, diarylethenes (DAEs) equipped with reactive aldehyde moieties rearrange selectively in the presence of amines, accompanied by decoloration. In a comprehensive study, the probe structure was optimized with regard to its inherent reactivity in the nucleophile-triggered rearrangement reaction. Detailed structure−reactivity relationships could be derived, in particular with regard to the type of integrated (het)aryl moieties as well as the location of the formyl residue, and the probes’ intrinsic reactivity with primary and secondary amines was optimized. Utilizing an ancillary base, the initially formed rearrangement product can engage in a subsequent catalyti…

Oxidovanadium(V) amine bisphenolates as epoxidation, sulfoxidation and catechol oxidation catalysts

2017

Air-stable oxidovanadium(V) complexes with tetradentate amine bisphenolate ligands were made by the reaction of VOSO4·xH2O and ligand precursors in MeOH solutions. Isolated compounds were studied as catechol oxidase models as well as catalysts for epoxidation and sulfoxidation reactions. All compounds can catalyse such oxidation reactions without notable structure-activity correlations. The 51V NMR studies indicate that the complexes turn to the number of different species during the catalytic experiments. peerReviewed