Search results for "molecular model"

New tyrosinase inhibitors selected by atomic linear indices-based classification models.

2005

In the present report, the use of the atom-based linear indices for finding functions that discriminate between the tyrosinase inhibitor compounds and inactive ones is presented. In this sense, discriminant models were applied and globally good classifications of 93.51% and 92.46% were observed for non-stochastic and stochastic linear indices best models, respectively, in the training set. The external prediction sets had accuracies of 91.67% and 89.44%. In addition, these fitted models were used in the screening of new cycloartane compounds isolated from herbal plants. A good behavior is shown between the theoretical and experimental results. These results provide a tool that can be used i…

Molecular modelling and QSAR in the discovery of HIV-1 integrase inhibitors

2007

The treatment regimens for the HIV-1 have mainly included reverse transcriptase or protease inhibitors but their long-term clinical utility is limited by severe side effects and viral drug resistance. A new attractive target for chemotherapeutic intervention can be the Integrase enzyme, that mediates the integration of HIV-1 DNA into a host chromosome, for which there is no known counterparts in the host cell. A number of derivatives have been found to inhibit IN in in vitro assays, but no successful drug based on them has emerged so far, although many compounds have been proposed. Moreover most of the inhibitors do not belong to a very precise structural class: this fact makes these compou…

Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.

2005

The TOpological MOlecular COMputer Design (TOMOCOMD-CARDD) approach has been introduced for the classification and design of antimicrobial agents using computer-aided molecular design. For this propose, atom, atom-type, and total quadratic indices have been generalized to codify chemical structure information. In this sense, stochastic quadratic indices have been introduced for the description of the molecular structure. These stochastic fingerprints are based on a simple model for the intramolecular movement of all valence-bond electrons. In this work, a complete data set containing 1006 antimicrobial agents is collected and presented. Two structure-based antibacterial activity classificat…

E-2-Benzylidenebenzocycloalkanones III. Studies on transmission of substituent effects on IR carbonyl stretching frequencies and 13C NMR chemical shi…

2004

Abstract Single substituent parameter and dual substituent parameter analysis was applied to study transmission of substituent effects on IR carbonyl stretching frequencies of E -2-(X-benzylidene)-1-indanones ( 3 ), -tetralones ( 4 ), and -benzosuberones ( 5 ). Similar analyses were performed for selected 13 C NMR chemical shifts of some E -2-(X-benzylidene)-1-indanones ( 3 ). For a better understanding of the results semiempirical and ab initio quantum chemical calculations were performed to determine the preferred geometry and to calculate the theoretical 13 C NMR chemical shifts of the selected compounds ( 3 ). The differences among the regression coefficients were discussed in terms of …

Blocking of an ion channel by a highly charged drug: Modeling the effects of applied voltage, electrolyte concentration, and drug concentration

2005

We present a simple physical model to estimate the blocked pore probability of an ion channel that can be blocked by a highly charged drug in solution. The model is inspired by recent experimental work on the blocking of the ${\mathrm{PA}}_{63}$ channel, involved in the anthrax toxin infection, by a highly charged drug [Karginov et al. PNAS 102, 15075 (2005)]. The drug binding to the pore is highly specific but the strong dependence of blocking on the applied voltage and electrolyte concentration suggests that long range electrostatic interactions are important. Since basic electrostatic concepts rather than detailed molecular models are considered, the microscopic details of the channel bl…

Applications of Molecular Modeling in the Study of Small Molecules (N2, O2, Rare Gas) Interactions with Complex Molecular Systems Like Zeolites and M…

1996

Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

2015

We have studied the alkaline hydrolysis of p-nitrophenylmethylphosphate (p-NPmP) in aqueous solution by means of polarizable continuum models and by hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods. The theoretical predictions of kinetic isotope effects (KIEs) are in very good agreement with the experimental data, confirming a concerted asynchronous molecular mechanism. In addition, comparison of high level DFT theory with semiempirical AM1/d Hamiltonian has allowed checking the reliability of the later to be used in modeling very large molecular models containing phosphorus atoms.

Polarographische Untersuchungen an monomeren und polymeren N-Chlorcarbonamiden

1979

The polarographic reduction of low molecular and high molecular N-chlorocarboxamides at the dropping mercury electrode proceeds in two one-electron-transfer steps, which are highly irreversible. In the case of the low molecular models 1 and 2 the reaction is diffusion-controlled, whereas in the case of the poly(N-chloroamide) 3 the reaction is adsorption-controlled. Reduction of several poly(N-chloroamide)s shows always two reduction waves with a distance of 0,5 V. There is, however, no relation between the polyamide-type and the position of the half-wave potentials. The polarographic reduction can be used as an analytical method for quantitative determination of N-chlorocarboxamide groups …

Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole

2015

A combined experimental and theoretical study has been performed on 9-benzyl-3,6-diiodo-9H-carbazole. Experimental X-ray (100.0 K) and room-temperature 13C NMR studies were supported by advanced density functional theory (DFT) calculations. The non relativistic structure optimization was performed and the 13C nuclear magnetic shieldings were predicted at the relativistic level of theory using the Zeroth Order Regular Approximation (ZORA). The changes in the benzene and pyrrole rings compared to the unsubstituted carbazole or the parent molecules were discussed in terms of aromaticity changes using the harmonic oscillator model of aromaticity (HOMA) and the nucleus independent chemical shift…

Experimental and theoretical study of possible correlation between the electrochemistry of canthin-6-one and the anti-proliferative activity against …

2015

Abstract This work presents an approach to study the performance of novel targets able to overcome cancer stem cell chemoresistance, based on the voltammetric data for microparticulate films of natural or synthetic alkaloids from the canthin-6-one series. A comparison of this voltammetric technique with conventional solution phase electrochemistry suggests the differences in the anti-proliferative activity of canthin-6-ones could be tentatively correlated to their different capacity to generate semiquinone radical anions. These data also match theoretical calculations.