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PubMed1997

13C Magic angle spinning NMR analysis and quantum chemical modeling of the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex in the carapace of the lobster Homarus gammarus.

Selective isotope enrichment, 13C magic angle spinning (MAS) NMR, and semiempirical quantum chemical modeling, have been used to analyze ligand-protein interactions associated with the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex from the carapace of the lobster Homarus gammarus. Spectra of alpha-crustacyanin were obtained after reconstitution with astaxanthins labeled with 13C at positions 4,4', 12,12', 13,13', or 20,20'. The data reveal substantial downfield shifts of 4.9 and 7.0 ppm at positions 12 and 12' in the complex, respectively. In contrast, at the 13 and 13' positions, small upfield shifts of 1.9 ppm were observed upon binding to the protein. These data are in line with previously obtained results for positions 14,14' (3.9 and 6.8 ppm downfield) and 15,15' (0.6 ppm upfield) and confirm the unequal perturbation of both halves after binding of the chromophore. However, these results also show that the main perturbation is of symmetrical origin, since the chemical shift differences exhibit a similar pattern in both halves of the astaxanthin molecule. A small downfield shift of 2.4 ppm was detected for the 4 and 4' positions. Finally, the 20,20' methyl groups are shifted 0.4 ppm upfield by the protein. The full data set provides convincing evidence that charge polarization is of importance for the bathochromic shift. The NMR shifts are compared with calculated charge densities for astaxanthin subjected to variations in protonation states of the ring-functional groups, as models of ligand-protein interactions. Taking into account the color shift and other available optical data, the current model for the mechanisms of interaction with the protein was refined. The results point toward a mechanism in which the astaxanthin is charged and subject to strong electrostatic polarizations originating from both keto groups, most likely a double protonation.

Animals↗
PubMed2006

Mechanistic aspects of proton chain transfer in the green fluorescent protein. Part II. A comparison of minimal quantum chemical models.

In this paper we report the results of extensive quantum chemical reaction pathway calculations for the electronic ground state of several different cluster models that mimic the proton chain transfer path within the green fluorescent protein (GFP). Our principal objective is to establish the robustness with respect to variations in the model of our recent mechanistic inferences for the ground state proton chain transfer [S. Wang and S. C. Smith, J. Phys. Chem. B, 2006, 110, 5084]. Additionally, comparison of our ground state results with the excited state proton transfer (ESPT) study by Vendrell et al. [O. Vendrell, R. Gelabert, M. Moreno and J. M. Lluch, J. Am. Chem. Soc., 2006, 128, 3564] leads to the conclusion that the mechanism of proton chain transfer may be expected to be analogous in ground and excited states, principally because in both cases the loss of the chromophore's phenolic proton contributes strongly to the reaction coordinate only late in the reaction path.

Computer Simulation↗
PubMed2000

Quantum chemical modeling (DFT) of active species on the V-W-O catalyst surface in various redox conditions

This study concerns quantum chemical modeling of water behaviour on V-W-O systems. It was undertaken in order to validate the hypothesis that the presence of W atoms on (001) surface of the crystalline vanadia-like species, facilitates low temperature water dissociation. Quantum chemical calculations were done with the use of modern electronic structure methodology, based on the density functional theory (DFT). The program package DMol of Molecular Simulations, was applied for the calculations. The calculations were performed for small clusters representing two adjacent metal sites, in pentacoordinated oxygen environment, analogous to bipiramidal clusters, introduced in description of the (001) layers of vanadium pentoxide.

Journal Article↗
PubMed1983

N,N-dibutylnitrosamine metabolism by rat liver S9 fraction and oxidation by chemical model systems.

Oxidative in vitro metabolism of N,N-dibutylnitrosamine (DBN) by 9000g supernatant fraction (S9 fraction) prepared from rat liver and oxidation of DBN by chemical model systems (Udenfriend and Fenton) were investigated. The products retaining the N-nitroso group of DBN were analyzed by gas-liquid chromatography. Incubation of DBN with the S9 fraction gave hydroxy derivatives of DBN at the omega, omega-1, and omega-2 positions, while the chemical reaction of DBN in the Udenfriend and the Fenton model systems afforded compounds with an oxo group at the same positions. In all cases, omega-1 oxidation was predominant, followed by omega and then by omega-2 oxidations, while omega and omega-1 oxidations were the principal metabolic pathways of DBN in vivo in the rat. The differences in the oxidative transformation of DBN among in vitro enzymatic, non-enzymatic and in vivo systems are discussed.

Animals↗
PubMedDate not supplied

Peroxylated and hydroxylated uroporphyrins: a study of their production in vitro in enzymic and chemical model systems.

In previous work certain hydroxylated and peroxylated derivatives of uroporphyrin (URO) have been isolated from the urine of patients suffering from porphyria. We have now investigated the mechanism of production of these oxygenated derivatives of URO, using both enzymic and chemical model systems and also the effect of exposure to light during reoxidation of uroporphyrinogen (URO'gen). When URO'gen was incubated with haemolysates, peaks with the same retention times as peroxyacetic acid URO, meso-hydroxy URO and beta-hydroxypropionic acid URO were all detected. The first of these was formed in sufficient amounts to allow its characterization by mass spectrometry. Under these conditions, peroxyacetic acid derivatives of heptacarboxylate and pentacarboxylate porphyrins could also be produced from the corresponding porphyrinogens, but no peroxylated product could be obtained from coproporphyrinogen (COPRO'gen, where no acetic acid side chains are present) or from the fully oxidized URO. Similar results were obtained on re-oxidation of URO'gen in the xanthine oxidase-xanthine system and in the presence of hydrogen peroxide/Fe-EDTA (ethylenediamine-tetraacetic acid) and here again no peroxylated product could be detected from either COPRO'gen or URO. Finally, formation of peroxyacetic acid URO could be demonstrated during photo-oxidation of URO'gen and this was followed by light-induced loss of both URO and its peroxylated derivative. It is concluded that the oxygenated derivatives arise from the action of reactive oxygen species on the porphyrinogens (rather than the porphyrins), with one of the acetic acid side chain serving as the preferential (or exclusive target) for peroxylation.

Chromatography, High Pressure Liquid↗
PubMed2006

A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: mixed basis set and ONIOM methods combined with a complete basis set extrapolation.

This article compares several quantum mechanical approaches to the computation of chemical shielding tensors in peptide fragments. First, we describe the effects of basis set quality up to the complete basis set (CBS) limit and level of theory (HF, MP2, and DFT) for four different atoms in trans N-methylacetamide. For both isotropic shielding and shielding anisotropy, the MP2 results in the CBS limit show the best agreement with experiment. The HF values show quite a different tendency to MP2, and even in the CBS limit they are far from experiment for not only the isotropic shielding of carbonyl carbon but also most shielding anisotropies. In most cases, the DFT values differ systematically from MP2, and small basis-set (double- or triple-zeta) results are often fortuitously in better agreement with the experiment than the CBS ones. Second, we compare the mixed basis set and ONIOM methods, combined with CBS extrapolation, for chemical shielding calculations at a DFT level using various model peptides. From the results, it is shown that the mixed basis set method provides better results than ONIOM, compared to CBS calculations using the nonpartitioned full systems. The information studied here will be useful in guiding the selection of proper quantum chemical models, which are in a tradeoff between accuracy and cost, for shielding studies of peptides and proteins.

Computer Simulation↗
PubMed1978

Limiting laws and counterion condensation in polyelectrolyte solutions. V. Further development of the chemical model.

Counterion binding to polyelectrolyte chains is formulated as a chemical reaction Mz (free) leads to Mz (bound). Expressions for the chemical potentials of free and bound counterions are set equal to obtain the reaction equilibrium. The results are equivalent to those in the previous paper of this series. An additional result obtained here is that a polyion holds its bound counterion layer with a strength on the order of 100 kcal/(mole cooperative unit). The method is then applied to the calculation of the polarizability along the chain due to the bound (condensed) counterions.

Electrolytes↗
PubMedDate not supplied

Ischemic-like change produced in canine heart by atractyloside: a chemical model.

Experiments were conducted in two canine models. Intracoronary infusion of atractyloside resulted in physiological, biochemical, and ultrastructural changes similar to those seen with ischemia. The fact that atractyloside, a specific inhibitor of adenine nucleotide translocase produces this change in vivo suggests that this inhibition in the key disturbance that initiates the metabolic derangements seen with ischemia. This chemical model seems to provide unique opportunities to study the possible factors that may reverse adenine nucleotide translocase inhibition and thus possibly prevent cell injury.

Animals↗
PubMed2003

Quantitative spin trapping and triplet quenching by radicals for in vivo studies. I. The chemical model.

In order to determine quantitatively the free radical content and its changes affected by additives using spin trapping under in vivo conditions, an approach is suggested carrying out experiments in a completely mixed open system (CMOS). Measurements have been carried out for a chemical oxidation process as a model system, and analysis of products and of the spin trap was extended by kinetic ESR spectrometry of the spin adducts. Since in a CMOS differential equations of accumulation of all species can be transformed into algebraic expressions using available rate constants for the formation of the spin adducts, corresponding concentrations of free radicals have been calculated. In addition, it has been established that triplet excited photosensitizers have a double effect: increasing the rate of initiation by decomposing hydroperoxide-type compounds and inhibiting the overall process by interactions with free radicals. Results indicate that by changing the "reaction vessel" the method can be applied for ex vivo and in vivo systems.

Benzene Derivatives↗
PubMed1997

Non-conventional modification of low density lipoproteins: chemical models for macrophage recognition of oxidized LDL.

To define the structural and chemical criteria governing recognition of oxidized LDL (oxLDL) by mouse peritoneal macrophages (MPM), we exposed LDL to novel chemical modification agents that induce defined neutralizing and non-neutralizing alterations of lysine as models for distinct apoB adducts present in oxLDL. We found some exceptions to the usual notion that neutralization of lysine positive charges is the principal determinant governing MPM recognition. In addition, competitive binding experiments using chemically modified 125I-LDL preparations revealed that, whereas some modifications engendered recognition principally by the classical scavenger receptor class A (SRA), as seen for acetylated LDL (acLDL), chemical models of advanced aldehydic modifications of LDL led instead to MPM uptake mainly by oxLDL receptors distinct from SRA.

Animals↗
PubMed1990

EQUIL: simulation and data analysis of binding reactions with arbitrary chemical models.

We have developed an algorithm for simulation and analysis of arbitrary chemical systems in equilibrium, with emphasis on ligand binding reactions. The program EQUIL can treat reactions involving multiple ligands, multiple binding sites, ternary complex models, allosteric effectors, competitive and noncompetitive binding, conformational changes, cooperativity, and generally any scheme that can be represented as a set of chemical equations. EQUIL is based on a general thermodynamic model of chemical equilibria; it does not involve nonlinear transformation of experimental data, but it does require the user to define the model of interaction between ligands and receptors by writing down the appropriate chemical reactions. EQUIL contains features of particular importance to ligand binding experiments: variable binding capacities, nonspecific binding, and the ability to simultaneously analyze data from different types of experiments. Furthermore, the simulation feature of EQUIL allows the user to investigate the feasibility of experiments that could possibly distinguish between different reaction models. We illustrate the use of this program on personal computers to analyze and simulate simple and complicated interactions between ligands and receptors.

Algorithms↗
PubMed2004

Is there a common chemical model for life in the universe?

A review of organic chemistry suggests that life, a chemical system capable of Darwinian evolution, may exist in a wide range of environments. These include non-aqueous solvent systems at low temperatures, or even supercritical dihydrogen-helium mixtures. The only absolute requirements may be a thermodynamic disequilibrium and temperatures consistent with chemical bonding. A solvent system, availability of elements such as carbon, hydrogen, oxygen and nitrogen, certain thermodynamic features of metabolic pathways, and the opportunity for isolation, may also define habitable environments. If we constrain life to water, more specific criteria can be proposed, including soluble metabolites, genetic materials with repeating charges, and a well defined temperature range.

Amino Acids↗
PubMed2006

Quantum chemical modelling of the rate determining step for oxygen reduction on quinones.

Two inner-sphere electrocatalytic channels for quinone-mediated reduction of molecular oxygen to form hydrogen peroxide have been addressed by means of density functional theory. Each of the channels comprises an initial rate determining chemical step and a subsequent electrochemical reduction step by which peroxide is produced. The reduction mechanism was determined for 9,10-anthraquinone and 9,10-phenanthrenequinone and the quantum chemical results are compared with experimental results. Two distinctly different structures were determined for the critical chemical step depending on whether the catalytic site is present as HQ* or Q*-. While a superoxo species is formed on HQ*, a van der Waals (vdW) type compound is formed on Q*-. It is shown that the Gibbs energy of activation for the semiquinone/oxygen reaction is largely determined by the entropy term. The results explain the experimentally observed pH dependence of the O2 reduction rate on quinone functionalised electrodes.

Computer Simulation↗
PubMed2006

A conceptual framework for predicting the toxicity of reactive chemicals: modeling soft electrophilicity.

Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point for modeling reactive toxicity is the applicability of the general rules of organic chemical reactions and the association of these reactions to cellular targets of importance in toxicology. The identification of plausible "molecular initiating events" based on covalent reactions with nucleophiles in proteins and DNA provides the unifying concept for a framework for reactive toxicity. This paper outlines the proposed framework for reactive toxicity. Empirical measures of the chemical reactivity of xenobiotics with a model nucleophile (thiol) are used to simulate the relative rates at which a reactive chemical is likely to bind irreversibly to cellular targets. These measures of intrinsic reactivity serve as correlates to a variety of toxic effects; what's more they appear to be more appropriate endpoints for QSAR modeling than the toxicity endpoints themselves.

Amino Acids↗