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PubMed1996

Neural networks as a tool for compact representation of ab initio molecular potential energy surfaces.

Ab initio quantum chemical calculations of molecular properties such as, e.g., torsional potential energies, require massive computational effort even for moderately sized molecules, if basis sets with a reasonable quality are employed. Using ab initio data on conformational properties of the cofactor (6R,1'R,2'S)-5,6,7,8-tetrahydrobiopterin, we demonstrate that error backpropagation networks can be established that efficiently approximate complicated functional relationships such as torsional potential energy surfaces of a flexible molecule. Our pilot simulations suggest that properly trained neural networks might provide an extremely compact storage medium for quantum chemically obtained information. Moreover, they are outstandingly comfortable tools when it comes to making use of the stored information. One possible application is demonstrated, namely, computation of relaxed torsional energy surfaces.

Biopterins↗
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↗
PubMed1993

13C n.m.r. isotopomer and computer-simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes.

13C double-quantum filtered correlation spectroscopy (DQF-COSY) provides a novel method for the detection of reactions involving carbon-bond scissions. We report the use of this technique to investigate isotopic exchange reactions of the non-oxidative pentose phosphate pathway in human erythrocytes. These exchange reactions resulted in the formation of a range of isotopic isomers (isotopomers) of glucose 6-phosphate after incubation of a mixture of universally 13C-labelled and unlabelled glucose 6-phosphate with fructose 1,6-bisphosphate and haemolysates. These isotopomers were detected in the coupling patterns of cross-peaks within the DQF-COSY spectrum of the deproteinized sample. A computer model which fully describes the reactions of the non-oxidative pentose phosphate pathway in human erythrocytes has previously been constructed and tested with 31P n.m.r. time-course data in our laboratory. This model was refined using 13C n.m.r. time-course data and extended to include the range of isotopomers which may be formed experimentally by the reactions of the non-oxidative pentose phosphate pathway. The isotopomer ratios obtained experimentally from the DQF-COSY spectrum were consistent with simulations generated by this model.

Carbon Isotopes↗
PubMed1996

Signal-to-noise ratio and detective quantum efficiency analysis of optically coupled CCD mammography imaging systems.

RATIONALE AND OBJECTIVES: Design considerations for x-ray systems with optically coupled charge-coupled devices require an understanding of the characteristics of cascaded multistage imaging chains. Performance evaluations rely on accurate analyses of signal-to-noise ratio, noise power spectrum, and detective quantum efficiency. METHODS: Theoretic models of signal-to-noise ratio, noise power spectrum, and detective quantum efficiency were extended to analyze the optically coupled charge-coupled device and other electronic x-ray imaging systems. The descriptions of how to measure or compute these parameters are provided. RESULTS: The results of our quantitative analysis illustrate that x-ray quantum-noise limitation can be obtained without an image intensifier by using a low additive noise charge-coupled device. CONCLUSION: This theoretic model and experimental method provide a useful tool for developing optoelectronic x-ray imaging systems for digital mammography and other radiologic procedures.

Female↗
PubMed1996

Selected new developments in computational chemistry.

Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry.

Chemical Phenomena↗
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↗
PubMed1995

Discriminating D1 and D2 agonists with a hydrophobic similarity index.

Currently, methods for calculating molecular similarity indices have been developed for comparing steric, charge density, and molecular electrostatic potential (MEP) properties. Much of the existing technology may, however, be applied to the quantitative comparison of molecular hydrophobicities. In this article we present an empirical hydrophobic similarity index. We utilize atomic hydrophobic parameters derived from a quantum mechanical semiempirical wavefunction. Hydrophobicity at points on a grid is computed with a recently introduced "molecular lipophilicity potential." The overlap of pairs of molecules is calculated with the metric introduced by Carbó. This approach is applied to a case in which steric and electrostatic criteria have already been shown to be inadequate in rationalizing selectivity, namely, requirements for recognition at the dopamine D1 and D2 receptors. We demonstrate that, for a set of dopamine agonists, D1 ligands show higher similarity in this property that D2 analogs. This indicator of similarity is more successful at accounting for D1 selectivity than previous methods.

8-Hydroxy-2-(di-n-propylamino)tetralin↗
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↗
PubMed1996

Lipoprotein changes in relation to body mass index in Native American adolescents.

In view of their known high incidence of noninsulin dependent diabetes (NIDDM), we sought to determine whether Native American (Plains Indian) children and adolescents show evidence of risk factors for both NIDDM and cardiovascular disease. Children and adolescents between the ages of 4 and 19 y were recruited, and field days were organized for data collection, which included height, weight [to compute body mass index (BMI)], waist and hip circumference, family histories, quantum of Native American ancestry, and blood sampling for fasting lipids, apolipoproteins, insulin, and glucose. BMI increased with age in boys and girls and tended to be higher than in Caucasian children. The difference was significant in 5-9-y-old (p < 0.05) and 10-14-y-old (p < 0.05) boys and 10-14-y-old girls (p < 0.001). Ten- to 14-y-old girls in the highest quartile for BMI had higher triglyceride levels (p < 0.05) and lower HDL cholesterol (p < 0.001) when compared with those in the lower quartiles. In contrast, 15-19 y olds in the highest quartile for BMI had higher cholesterol, LDL cholesterol, and apolipoprotein B (p < 0.001). The mean fasting insulin levels were not related to BMI. The data suggest that, within this Plains Indian population, obesity associated with elevated lipid levels tends to begin at an early age in Native American children. Insulin levels do not appear to be related to BMI, a putative index of adiposity, in this population of children known to be prone to NIDDM in adult life.

Adolescent↗
PubMed1996

Glycine and GABA receptors: molecular mechanisms controlling chloride ion flux.

We have been able to show that the three clearly identified atoms common to the inhibitory neurotransmitters glycine and GABA, that we previously hypothesized to serve as attachment points at the glycinergic and gabanergic receptor, can indeed interact through both electrostatic and hydrogen bonding to several amino acids, which have been identified in molecular biological investigations as both present and critical in the physiological functioning of key polypeptides common to these inhibitory receptors. In addition, amino acids also involved in stabilizing the interaction between the antagonists strychnine and R5135 at the glycinergic and gabanergic receptors, respectively, have been shown to fit our complex model. We identify in detail molecular mechanisms to explain how glycine and GABA initiate chloride ion movement from extraneuronal fluid in the synaptic cleft to intraneuronal volume. In addition, we also identify the molecular mechanisms involved in the blocking of chloride ion movement by strychnine at the glycinergic receptor and by R5135 at the gabanergic receptor. We also present two computer-generated color prints, one for the glycine receptor and one for the GABA receptor, which show the quantum mechanically geometry optimized complex formed between receptor side chains, i.e., the part of the amino acids in the polypeptide that interacts with the zwitterionic inhibitory neurotransmitters. These computer-generated color figures also show a) the important electrostatic and hydrogen bonding in these interactions, b) a van der Waals model of this complex to illustrate that no steric repulsions exist, and c) the molecular electrostatic potential energy map showing the electrostatic potentials of neurotransmitter bound to the receptor model. Finally, we show with computer calculations that the pseudo-rings, formed between the positive quanidinium group in arginine and one of the oxygen atoms in the carboxyl group in both glycine or GABA, result in a positive planar region which appears to be involved in a charge-transfer complex with aromatic benzene groups in amino acids such as phenylalanine and tryosine.

Androstanes↗
PubMed1993

Reproduction of correct electrostatic field by charges and dipoles on a closed surface.

A general algorithm based on the Green function theorem has been developed to correctly reproduce electrostatic fields inside a closed space by point charges and point dipoles on the surface surrounding the space. For actual computations, limited numbers of point charges, including charge pairs replacing point dipoles, are enough to approximate the inner fields. As examples, reaction fields were reproduced by the current surface charges and dipoles for the dielectric models, where a monopole, dipole, or quadrupole was individually set at the center in a vacuum sphere surrounded by high dielectric continuum. The potentials due to those reaction fields agree well with the analytical ones. As an application of this method to the analysis of the electronic structure of the active site of a protein, a combination of the continuum dielectric model and ab initio molecular orbital calculation was carried out. Other applications to molecular dynamics and quantum mechanical calculations are also discussed.

Algorithms↗
PubMed1994

Integration of graph theory and quantum chemistry for structure-activity relationships.

The objective of this article is to outline both graph-theoretically based and quantum chemically based structural indices of potential use in quantitative structure activity correlations. We consider graph-theoretical indices such as the connectivity index, topological index, Wiener index and molecular ID indices. Several structural and geometry-dependent indices can be derived from semiempirical and ab initio quantum calculations based on the charge densities, overlap matrices, frontier orbitals, molecular hardness, free valence, density matrices, quantum spectral difference indices, quantum spectral indices and bond matrices. Finally, the use of electrostatic potentials and charge densities for the prediction of reactive sites will be discussed.

Butadienes↗
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↗
PubMed1993

Modeling the anticancer action of some retinoid compounds by making use of the OASIS method.

The powerful OASIS (optimized approach based on structural indices set) approach is applied to the anticancer activity of a series of vitamin A analogs. The best three- and four-variable models obtained via the OASIS technique have correlation coefficients of 0.973 vs. 0.990 and standard deviations s2 = 0.11 and 0.05, respectively. The models incorporate the hydrophobicity factor log P, two geometric parameters (topological indices and/or 3-D steric ones), and the molecular dipole moment. For a set of 15 compounds studied here, the activity measured by ED50 was well correlated by models with approximately equal contribution of the through cell membrane transport and the geometric drug-receptor correspondence while weak nonspecific electronic interaction was also found to play some role. Comparison to previous treatments of this data is given and extension to larger sets is discussed.

Antineoplastic Agents↗