Search results for "molecular model"

Limulus polyphemus Hemocyanin: 10 Å Cryo-EM Structure, Sequence Analysis, Molecular Modelling and Rigid-body Fitting Reveal the Interfaces Between th…

2007

Abstract The blue copper protein hemocyanin from the horseshoe crab Limulus polyphemus is among the largest respiratory proteins found in nature (3.5 MDa) and exhibits a highly cooperative oxygen binding. Its 48 subunits are arranged as eight hexamers (1×6mers) that form the native 8×6mer in a nested hierarchy of 2×6mers and 4×6mers. This quaternary structure is established by eight subunit types (termed I, IIA, II, IIIA, IIIB, IV, V, and VI), of which only type II has been sequenced. Crystal structures of the 1×6mer are available, but for the 8×6mer only a 40 A 3D reconstruction exists. Consequently, the structural parameters of the 8×6mer are not firmly established, and the molecular inte…

Design, Synthesis, and Evaluation of New Tripeptides as COX-2 Inhibitors

2013

Cyclooxygenase (COX) is a key enzyme in the biosynthetic pathway leading to the formation of prostaglandins, which are mediators of inflammation. It exists mainly in two isoforms COX-1 and COX-2. The conventional nonsteroidal anti-inflammatory drugs (NSAIDs) have gastrointestinal side effects because they inhibit both isoforms. Recent data demonstrate that the overexpression of these enzymes, and in particular of cyclooxygenases-2, promotes multiple events involved in tumorigenesis; in addition, numerous studies show that the inhibition of cyclooxygenases-2 can delay or prevent certain forms of cancer. Agents that inhibit COX-2 while sparing COX-1 represent a new attractive therapeutic deve…

Monte Carlo simulations of the periodically forced autocatalyticA+B→2Breaction

2000

The one-parameter autocatalytic Lotka-like model, which exhibits self-organized oscillations, is considered on a two-dimensional lattice, using Monte Carlo computer simulations. Despite the simplicity of the model, periodic modulation of the only control parameter drives the system through a sequence of frequency locking, quasiperiodic, and resonance behavior.

Crossover scaling in semidilute polymer solutions: a Monte Carlo test

1991

On the impact of side methyl groups on the structure and vibrational properties of β-carotenoids. The case of butadiene and isoprene

2021

Abstract Theoretical consideration about the impact of methyl groups on the structure and vibrational properties of β-carotenoids, using medium size molecules of trans-butadiene and trans-isoprene, are reported. Density functional theory (DFT) calculations with correlation-consistent and polarization-consistent basis sets were applied to trans-1,3-butadiene and trans-isoprene as the smallest building bricks of β-carotenoids. Their structure and harmonic vibrations were estimated in the complete basis set limit (CBS) using the non-linear least square fit. Optimized geometries and harmonic frequencies, obtained with B3LYP and BLYP density functionals and large basis sets, were favorably repro…

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 …

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.

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…

DNA minor groove binders: an overview on molecular modeling and QSAR approaches

2007

Molecular recognition of DNA by small molecules and proteins is a fundamental problem in structural biology and drug design. Understanding of recognition in both sequence-selective and sequence neutral ways at the level of successful prediction of binding modes and site selectivity will be instrumental for improvements in the design and synthesis of new molecules as potent and selective gene-regulatory drugs. Minor groove is the target of a large number of non-covalent binding agents. DNA binding with specific sequences, mostly AT, takes place by means of a combination of directed hydrogen bonding to base pair edges, van der Waals interactions with the minor groove walls and generalized ele…