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PubMed1991

Prediction of the reactivities of cyclopenta-polynuclear aromatic hydrocarbons by quantum mechanical methods.

1. The direction of epoxide ring opening may be predicted using the techniques of theoretical chemistry by comparing the computed total energy of the two possible carbocations formed. 2. To predict the direction of epoxide ring opening and the potential binding of aceanthrylene 1,2-epoxide to biopolymers, quantum mechanical calculations were performed on the two potential hydroxy carbocations. 3. The 2-hydroxy carbocation (II) was favoured over the 1-hydroxy carbocation by 11.8 kcal/mol. Molecule II had more positive charge at the meso carbon group than at the nominally charged 1 position. Both the lowest unoccupied molecular orbital and the molecular electrostatic potential confirm this result, and indicate the possibility of unusual adducts to biopolymers. 4. Similar calculations on the equivalent epoxides of acenaphthylene and acephenanthrylene do not show the same results. 5. Modelling the addition products of II with small nucleophiles indicates that these unusual addition products do not form, and that the interaction is controlled by electronic effects and not electrostatic effects. 6. The calculations on acephenanthrylene demonstrate the importance of including the hydroxyl group when making predictions relative to epoxide ring opening. 7. Molecular descriptors are surrogates for the interaction of that molecule with an often unknown biological target. In cases where molecular descriptors are used without information about the target, small quantitative differences may not be appropriate discriminators.

Chemical Phenomena↗
PubMed1991

Medical informatics--an Australian perspective.

Computers, like the X-ray and stethoscope can be seen as clinical tools, that provide physicians with improved expertise in solving patient management problems. As tools they enable us to extend our clinical information base, and they also provide facilities that improve the delivery of the health care we provide. Automation (computerisation) in the health domain will cause the computer to become a more integral part of health care management and delivery before the start of the next century. To understand how the computer assists those who deliver and manage health care, it is important to be aware of its functional capabilities and how we can use them in medical practice. The rapid technological advances in computers over the last two decades has had both beneficial and counterproductive effects on the implementation of effective computer applications in the delivery of health care. For example, in the 1990s the computer hobbyist is able to make an investment of less than $10,000 on computer hardware that will match or exceed the technological capacities of machines of the 1960s. These rapid technological advances, which have produced a quantum leap in our ability to store and process information, have tended to make us overlook the need for effective computer programmes which will meet the needs of patient care. As the 1990s begin, those delivering health care (eg, physicians, nurses, pharmacists, administrators ...) need to become more involved in directing the effective implementation of computer applications that will provide the tools for improved information management, knowledge processing, and ultimately better patient care.

Australia↗
PubMed1986

One- and two-dimensional NMR spectral analysis of the consequences of single amino acid replacements in proteins.

The traditional approach of using homologous sequences to elucidate the role of specific amino acid residues in protein structure and function becomes more meaningful as the number of differences is minimized, with the limit being alteration of a single residue. For small proteins in solution, NMR spectroscopy offers a means of obtaining detailed information about each residue and its response to a given change in the protein sequence. Extraction of this information has been aided by recent progress in spectrometer technology (higher magnetic fields, more sensitive signal detection, more sophisticated computers) and experimental strategies (new NMR pulse sequences including multiple-quantum and two-dimensional NMR methods). The set of avian ovomucoid third domains, which consists of the third domain proper plus a short leader (connecting peptide) and has a maximum of 56 amino acid residues, offers an attractive system for developing experimental methods for investigating sequence-structure and structure-function relationships in proteins. Our NMR results provide examples of sequence effects on pKa' values, average conformation, and internal motion of amino acid side chains.

Amino Acid Sequence↗
PubMed1977

Photochemical transformation of the DDT and methoxychlor degradation products, DDE and DMDE, by sunlight.

DDE and DMDE, degradation products of the pesticides DDT and methoxychlor, rapidly undergo an unusual photoisomerization in solution when exposed to sunlight. The isomerization involves the exchange of a vinyl chlorine and an ortho aromatic hydrogen. Other photoproducts identified were corresponding benzophenones and 1,1-diaryl-2-chloroethylenes. Quantum yields for the reactions were measured and then used to compute sunlight photolysis half-lives for DMDE and DDE. Although both compounds absorb only the short-wavelength ultraviolet component of sunlight, their photolysis was found to be surprisingly rapid. During summer at latitude 40 degrees N, the photolysis half-lives near the surface of a water body are one hour and one day for dissolved DMDE and DDE, respectively. Photolysis of the DDE photoisomers is about an order of magnitude slower than that of DDE, suggesting that they may accumulate under environmental conditions. The DDE photoisomers photocyclize to form chlorinated dibenzofulvene and dichlorofluorenone. Neither DDE nor its photoisomers photoreact in solution to form PCB's. The environmental significance of these results is discussed, and its is suggested that the persistence of DDE in inland surface waters may be related to its tendency to sorb onto sediments and biota where not light is present.

Dichlorodiphenyl Dichloroethylene↗
PubMed2025

Enzymatic Anti-Baldwin Ring-Closure Cascade for Fused Bicyclic Ether Formation.

Pyrenulic acids are cytotoxic polyketides isolated from the ascomycete Pyrenula sp. derived from Vietnamese lichen that are characterized by complex fused cyclic core structures. Genome sequencing, in silico sequence analysis, and RT-PCR studies identified the pyrenulic acid (pya) biosynthetic gene cluster. Based on a functional analysis of the enzymes by expression of each gene in a heterologous host using Aspergillus nidulans, we discovered two cytochrome P450s PyaJ and PyaG that effect epoxidation and hydroxylation of the alkyl chain terminal, respectively, and an α/β hydrolase PyaF that constructs a 6- and 7-membered fused bicyclic diether skeleton by catalyzing successive epoxide ring-opening 6-endo and 7-endo cyclization reactions. To elucidate the detailed mechanism of pyrenulic acid formation, we obtained PyaF as a recombinant enzyme and performed an in vitro experiment, which confirmed catalysis by PyaF of the cyclization reaction. In addition, we performed alignment analysis of PyaF with α/β hydrolases with known functions, as well as an in-depth computational study. In-depth computational analyses of the cyclization reaction pathways with density functional theory quantum mechanics and detailed characterization of PyaF by Chai-1-based protein structure modeling with molecular dynamics simulations and site-specific mutagenesis predicted the active amino acid residues of this serine α/β hydrolase to be an unusual catalytic serine tetrad involving Ser170, Asn342, Asp314, and His169, with Tyr255 and His284 acting as general bases to facilitate opening of the epoxides. Our study provides insight into how regioselectivity of enzymatic anti-Baldwin epoxide ring-opening cascades for the formation of a fused cyclic ether structure is controlled.

Cyclization↗
PubMedDate not supplied

Fast Fourier digital quantum mottle analysis with application to rare earth intensifying screen systems.

The advent of fast Fourier techniques has greatly facilitated the digital analysis of noise power spectra (Wiener spectra) by circumventing the need for the autocorrelation function. We are now able to Fourier analyze film data at about the same rate the microdensitometer-computer system can collect it (1000 points/sec). The new technique has been applied to the analysis of the quantum mottle of several rare earth intensifying screen systems confirming earlier estimates from our pilot studies that such screens are capable of reducing exposure by a factor of about 2 with imaging parameters comparable to those of conventional calcium tungstate systems.

Calcium↗
PubMed1986

Hydrophobic and ionic hydration phenomena.

Computer simulation offers an increasing opportunity to examine the details of solvation structure for well-defined solution models. One can characterize idealized models that exemplify specific aspects of solution behavior or those that realistically model systems experimentally difficult to access. As an example from the first category, results are presented for the aqueous solvation structure and solvent hydrogen bonding in the presence of a small apolar solute, and these are contrasted with the quite different behavior observed for a large apolar surface. As an example from the second category, structural results are presented for hydration of an excess electron in bulk water. These latter results, obtained via recent path integral simulation methods, manifest significant solvent structural disruption compared to the case of a simple ion, due to the irregular and fluctuating shape of the quantum solute.

Chemical Phenomena↗
PubMed1991

Interaction energy studies on antibiotics nucleoside analogs 2-azaadenine.

The 2-azaadenine antibiotic is known to be a potent cytotoxic nucleoside analog. Evaluation of the interaction energy of this molecule with nucleic acid bases and base pairs has been performed using a quantum-mechanical perturbation technique. Both in-plane and stacking energies have been computed. These energy values along with their sites of association have been compared with the standard energy values and spatial positions for the nucleic acid bases during transcription. The results have been examined in the light of their biological significance.

Adenine↗
PubMed1989

Computer modelling: future directions.

Recent developments in computing and in the theory of simulation have extended greatly the successes of the modelling of ionic crystals pioneered by Mott and Littleton. This has changed the way in which computer experiments are brought to bear on an increasing range of solid-state phenomena. Yet applied science creates new demands, both in the form of new types of system and in terms of the complexity and subtlety of what is studied. The author's brief survey looks at some of the successes and gaps from interfaces and catalysts to neurotransmitters and from superconductors to slags.

Computer Simulation↗
PubMed1992

Base compositional structure of genomes.

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.

Escherichia coli↗
PubMed1992

The structure and properties of liquid water: recent theoretical advances.

Computer simulations of water, and of water in the neighborhood of biological materials, are now commonplace. However, from the molecular physicist's viewpoint existing models of water/water, water/solute, and water/substrate interactions are incorrect and potentially misleading. Almost all existing simulations of biological interest assume that the molecules are rigid, or at least that the bonds do not vibrate. In this paper we review recent advances in the theory of water interactions, emphasizing the need to construct potential energy surfaces that include vibrational degrees of freedom.

Computer Simulation↗