Search results for "molecular model"

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage

2022

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomi…

Ligand-based discovery of novel trypanosomicidal drug-like compounds: In silico identification and experimental support

2010

Abstract Two-dimensional bond-based linear indices and linear discriminant analysis are used in this report to perform a quantitative structure–activity relationship study to identify new trypanosomicidal compounds. A database with 143 anti-trypanosomal and 297 compounds having other clinical uses, are utilized to develop the theoretical models. The best discriminant models computed using bond-based linear indices provides accuracies greater than 90 for both training and test sets. Our models identify as anti-trypanosomals five out of nine compounds of a set of already-synthesized substances. The in vitro anti-trypanosomal activity of this set against epimastigote forms of Trypanosoma cruzi…

Influence of solvents on conformation of dehydropeptides

2013

Abstract Structural investigations of dehydropeptides containing (Z)-dehydrophenylalanine in solvents characterized by different polarity are discussed. The conformational analysis are based on spectroscopic methods (NMR, CD), molecular modeling techniques and in case of the tripeptide, ab initio methods. The results of temperature experiment indicate, that the only conformation of the investigated hexapeptide 3 is stabilized by intramolecular hydrogen bonds. Depending on the length of the peptide chain, the polarity of solvent influences on arrangement of the side chain of the amino acids or of the main chain of the peptide.

Preparation and structural studies on the tBu2Sn(IV) complexes with aromatic mono- and dicarboxylic acids containing hetero {N} donor atom

2004

Nine complexes of 'Bu2Sn(IV)(2+) were obtained in the solid state with ligands containing -COOH group(s) and aromatic (N) donor atom. The binding sites of the ligands were identified by FT-IR spectroscopic measurements. It was found that in most cases the -COO- groups are co-ordinated in monodentate manner. Nevertheless, in some of our complexes, the -COO- group forms bridges between two central {Sn} atoms resulting in the formation of an oligomeric structure, a motif that is characteristic only to the nicotinate compound. These pieces of information and the rationalisation of the experimental Sn-119 Mossbauer nuclear quadrupole splittings, Delta, - according to the point charge model forma…

Structural investigation of four-centre photopolymerisation of bis-phthalamic bis-chalcone derivative in the crystalline state

1997

By combining the results obtained from an electron diffraction tilting series with solid state NMR and powder X-ray diffraction, it was possible to determine the unit cell parameters and space group of BPABC crystals grown from DMAA solution both before and after irradiation. Subsequently semi-empirical quantum mechanical and packing energy calculations led to a model structure which agreed well with all the electron diffraction data and thus provided insight into the cross-linking mechanism. © 1997 John Wiley & Sons Ltd.

Most of the field/inductive substituent effect works through the bonds

2019

AbstractAn application of the quantum chemical modeling allowed to investigate the nature of the field/inductive substituent effect (SE). For this purpose, series of X-tert-butyl···tert-butane (TTX) complexes (where X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) were studied. A starting distance between central carbon atoms in substituted and unsubstituted fragments of TTX, dC1–C4, was the same as the distance C1–C4 in X-substituted bicyclo[2.2.2]octane (BCO), where the SE acts both via bonds and via space. A strength of interaction between substituted and unsubstituted components of TTX was described by deformation and interaction energies. The substituent …

Monte Carlo simulation of DNA electrophoresis

1989

This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.

Metal-atom impact on the self-assembly of cup-and-ball metalloporphyrin–fullerene conjugates

2014

International audience; A fullerene ammonium derivative has been combined with different metalloporphyrin–crown ether receptors to generate very stable supramolecules. The combination of fullerene–porphyrin and ammonium–crown ether interactions leads to a strong chelate effect as evidenced by a high effective molarity (3.16 M). The different parameters influencing the stability of the supramolecular ensembles, in particular the nature of the metal in the porphyrin moiety, have been rationalized with the help of theoretical calculations thus providing new insights into fullerene–porphyrin interactions.

Double chained naphthalenes as G4 binders

2014

Modeling 21Ne NMR parameters for carbon nanosystems

2013

The potential of nuclear magnetic resonance (NMR) technique in probing the structure of porous systems including carbon nanostructures filled with inert gases is analysed theoretically using accurate calculations of neon (21Ne) nuclear magnetic shieldings. The CBS estimates of 21Ne NMR parameters were performed for single atom, its dimer and neon interacting with acetylene, ethylene and 1,3-cyclopentadiene. Several levels of theory including restricted Hartree-Fock (RHF), Møller-Plesset perturbation theory to the second order (MP2), density functional theory (DFT) with van Voorhis and Scuseria's t-dependent gradient-corrected correlation functional (VSXC), coupled cluster with single and do…