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PubMed1991

Development of a conformational search strategy for flexible ligands: a study of the potent mu-selective opioid analgesic fentanyl.

An extensive conformational search of the potent opioid analgesic, fentanyl, was performed using the semiempirical quantum mechanical method AM1 and the CHARMm potential energy function. A combination of two procedures was used to search the conformational space for fentanyl, which included nested dihedral scans, geometry optimization and molecular dynamics simulation at different temperatures. In addition, the effect of a continuum solvent environment was taken into account by use of appropriate values for the dielectric constant in the CHARMm computations. The results of the conformational search allowed the determination of the probable conformation of fentanyl in polar and nonpolar solvents and of three candidate conformers for its bioactive form.

Fentanyl↗
PubMed1992

Theoretical framework for the interpretation of STM images of adsorbates.

A theoretical formalism for the interpretation of STM images of adsorbates is developed by approaching the calculation of the observed current as a transport problem in quantum statistical mechanics. The STM configuration is treated as a system of three groups of states--the substrate, the adsorbate and the tip--in contact with a thermal reservoir, with which it exchanges energy. A new definition of current is introduced, and shown to be related to that given in the traditional transfer Hamiltonian approach. The transport instrument used for the description is the stochastic Liouville equation, known to have the advantage of allowing the incorporation of thermal effects as well as arbitrary degree of coherence in the quantum transport. Some preliminary calculations of STM images of simple adsorbate models are presented.

Computer Simulation↗
PubMed1979

[Image properties of computer tomography. III. Measurements on homogenous materials. Relationship of attenuation and scatter to various parameters (author's transl)].

The present paper investigates the variations due to various parameters on the image of homogeneous materials as obtained with the Somatom CT scanner. Sugar solutions were used with concentrations equivalent to the absorption values of soft tissues. Because of quantum noise, attentuation at various points is not uniform, but is distributed in a Gaussian manner round a mean value. Using the Evaluskop it was possible to determine the degree of scatter. It was shown that, with increasing density of the material, the scatter increased and that this can be reduced by subjecting the tomogram to a smoothing process. It was further shown how the scatter depends on various parameters, such as thickness and dose. The amount of scatter in a tomogram is important in determining the density gradation which can be a achieved.

Absorptiometry, Photon↗
PubMed1982

Statistical contrast enhancement of subtraction images for radiographic caries diagnosis.

The effects of the nonlinear contrast-enhancement technique are examined in terms of diagnostic performance obtainable from subtracted dental radiographs for a variety of simulated exposures. Conventional bitewing radiographs of patients known to be free of caries were digitized by means of a computer interfaced with a conventional television camera. The resulting images were duplicated and stored in the computer. Radiolucencies similar in appearance to interproximal caries were simulated analytically in one set of the images. Reference images were superimposed spatially and subtracted from their counterparts containing the induced interproximal lesions after simulating the effects of quantum limited exposure on both sets. This was done for each separate image element independently by replacing original gray levels in each image with levels determined by a Poisson random deviate. The resulting difference images were contrast enhanced by a method which first smooths out local variations in gray level and then reassigns gray-level values in a way determined by the observed second-order spatial statistics. To aid in localization, these images were then again subtracted from the original noise-degraded pictures without lesions, rendering images similar to conventional radiographs but contrast enhanced. Observer performance by means of these enhanced images was compared with that produced from unenhanced-lesion-containing controls. The results suggest that enhancement increases the certainty with which diagnosis can be made and, further, that diagnostic accuracy can be improved in severely degraded images which simulate the effects of reduced levels of exposure.

Computers↗
PubMed1985

A comparative quantum chemical study of methyl acetate and S-methyl thioacetate. Toward an understanding of the biochemical reactivity of esters of coenzyme A.

The electronic structures of methyl acetate and S-methyl thioacetate and the corresponding anions have been investigated using the INDO-MO method. Equilibrium geometries, gas-phase anion proton affinities and barriers to internal rotation have been computed. Analysis of the effect of the d-type functions on sulfur on the static and dynamic properties of the thioester and its anion reveal no role for (p-d) pi conjugative effects. The results of this work indicate that the unique properties of thioester, and hence esters of coenzyme A, may be attributed to the lack of resonance, rather than to a sulfur d-orbital expansion.

Acetates↗
PubMedDate not supplied

Epoxide ring opening and related reactivities of cyclopenta polycyclic aromatic hydrocarbons: quantum mechanical studies.

A series of 13 cyclopenta polycyclic aromatic hydrocarbons have been studied using quantum mechanical methods. The three-dimensional molecular structure of each carbocation that might result from the opening of a protonated epoxide ring formed between the carbon atoms completing the cyclopenta ring was computed with AM1. AM1 and ab initio calculations, using a split valence basis set, were then used to predict the direction of ring opening and obtain information about the reactivity of the carbocation. These calculations have shown that for all carbocations studied the cationic charge is well distributed throughout the molecule. The largest CH group charges are approximately 0.3 electron. If the protonated epoxide ring can open so that the nominal charge is on a CH group that is attached to the central ring of an anthracenic core, that carbocation will be greatly favored. For carbocations of this type, the unoccupied alpha' position (the CH group opposite the position of attachment to the anthracenic core) has as much or more of the cation charge as the nominally charged CH position. The group charges, and other properties related to electrostatic reactivity, clearly favor addition of nucleophiles at the unoccupied alpha' position over addition at the nominally charged position. However, when the addition of small nucleophiles at both of these positions is modeled for two such examples, the results favor addition at the nominally charged position in one case and are equivocal in the other case. The group charges and other reactivities considered characterize the electrostatic part of the interaction.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗
PubMed1991

Digital image analysis of radio-opacities in the paranasal sinuses using computed radiography.

A computed radiograph system (Toshiba, model TCR-201) was used to investigate the digital image analysis of radio-opacity of the paranasal sinuses. The results of the preliminary phantom examination for evaluating the exposure technique indicated that the tube voltage should be kept constant. By using conventional radiographic images and tomographic images of normals and cases of sinusitis, the quantum values (Q-values), Q-value profiles, and Q-value histograms of radio-opacities in the paranasal sinuses were assessed statistically. Findings demonstrated that radio-opacities in the paranasal sinuses could be evaluated quantitatively by these digital image analyses.

Computer Systems↗
PubMed1992

Applications of molecular physics 'biotechnology' to the rational design of an improved phenytoin analogue.

This study exploits molecular physics, in conjunction with a large scale computing environment, as a tool for understanding the clinical phenomenology of phenytoin (PHT) toxicology at a molecular level and for employing this understanding in an attempt to design improved drugs. The application of molecular physics techniques, such as quantum mechanics and molecular force field calculations, to the process of rational anticonvulsant drug design remains virtually unexplored. A 3-step strategy for applying these techniques to the design of an improved PHT molecule is presented. Step 1 employs quantitative structure-activity relationship calculations on 80 PHT analogues to ascertain the portion of the PHT molecule necessary for bioactivity (i.e. the 'bioactive face' of PHT); the N3-C4(O)-C5-R fragment of PHT was identified as the bioactive face. Step 2 employs molecular modelling studies to determine the portion of the PHT molecule necessary for the teratogenic, mutagenic and connective tissue toxicities of PHT (i.e. the 'biotoxic face'); the C2(O)-N3 fragment of PHT was identified as the biotoxic face. Step 3 experiments design an 'improved' PHT analogue, which maintains the bioactive face while eliminating the integrity of the biotoxic face; 2-deoxy-5,5-diphenylhydantoin was designed and synthesized as the improved PHT analogue. This compound had biological activity equivalent to PHT, but was unable to bind to nucleic acids or to chelate metals involved in connective tissue metabolism.

Biotechnology↗
PubMed1984

Conformational analysis of the antiulcer drug pirenzepine. X-ray investigations, molecular mechanics and quantum mechanical calculations and comparisons with structurally or pharmacologically related compounds.

The crystal structures of the antiulcer drug 5,11-dihydro-11-[(4-methyl-1-piperazinyl) acetyl]-6H-pyrido[2,3-b] [1,4]benzodiazepin-6-one dihydrochloride (pirenzepine dihydrochloride, L-S 519 CL 2, Gastrozepin) and its monoprotonated form (pirenzepine monohydrochloride, L-S 519 CL) were determined by X-ray analysis. Molecular mechanics (MMPI) and semiempirical quantum chemical (MNDO) calculations showed that the calculated minimum energy conformations of the tricycle and of the exocyclic amide group are in agreement with the crystal structures. The conformational energies of pirenzepine as a function of four important torsional angles were calculated using different semiempirical quantum chemical methods with the CNDO/2 (complete neglect of differential overlap)-, MNDO (modified neglect of diatomic overlap)- and PCILO (perturbative configuration interaction using localized orbitals)-approximations. The conformation of one local energy minimum corresponds closely to the crystal structure of pirenzepine monohydrochloride. This conformation has a spatial arrangement which is analogous to a single consistent conformation known from the literature of 24 anticholinergic agents determined from their crystal structures by a computer graphics analysis. On the other hand there are no structural relationships of any low energy conformation of pirenzepine to conformations of other classes of tricyclic compounds which could rationalize their antidepressant, neuroleptic or antihistaminic activity. This finding explains the absence of any central effect of pirenzepine following intracerebral application. The computational elucidation of the conformational requirements for the interaction with the muscarinic receptors may be helpful for the interpretation of the selectivity of pirenzepine within the muscarinic system.

Antidepressive Agents, Tricyclic↗
PubMed1993

Use of intracellular Ca2+ stores from rat basophilic leukemia cells to study the molecular mechanism leading to quantal Ca2+ release by inositol 1,4,5-trisphosphate.

Quantal Ca2+ release is a novel motif for the mediation of signal transduction in which the amplitude of a biological response following multiple stepwise increases in agonist concentration is retained. The release of Ca2+ from permeabilized cells in response to the second messenger inositol 1,4,5-trisphosphate (InsP3) proceeds in this fashion. The mechanisms leading to quantal Ca2+ release are unknown. InsP3 releases 50-90% of the Ca2+ sequestered within the intracellular stores of mammalian cells permeabilized with saponin. However, preparation of microsomes results in the loss of this sensitivity. In this report, functionally intact intracellular Ca2+ stores were isolated from rat basophilic leukemia (RBL) cells by osmotic lysis followed by differential and sucrose density gradient centrifugation. From this preparation, 64% of the stored Ca2+ is released by InsP3. We demonstrate that quantal Ca2+ release is retained by isolated Ca2+ stores and is identical to that observed in permeabilized cells. Addition of a subsaturating (28 nM) concentration of InsP3 to permeabilized cells at 37 degrees C results in the release of only a small fraction of the sequestered Ca2+. When the cells are cooled to 11 degrees C, the remaining Ca2+ is rapidly released. Hence, the mechanism leading to the quantal nature of Ca2+ release is reversible and is thus not likely to be the result of a covalent modification of the channel protein or of the Ca2+ store.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1990

A practical procedure for the determination of electrostatic charges of large molecules.

A practical procedure for the precise determination of electrostatic charges, which are evaluated by fitting the rigorous quantum mechanical molecular electrostatic potential to a monopole-monopole expression, is presented. The proposal of this procedure arises from the study of the minimum requirements necessary to obtain reliable electrostatic charges. Such a study is focused on: (i) the dependence of the electrostatic charges on the set of points where the quantum mechanical and the monopole-monopole molecular electrostatic potentials are fitted; thus, both the influence of the number of points and their distribution in layers located out of the van der Waals radii of the atoms are examined, and (ii) the reliability of the use of fractional models for the evaluation of electrostatic charges of large molecules. Results point out that the optimum number of points is defined by a density of points ranging from 0.45 to 0.60 points/A2 when four layers (separated by 0.2 A) are considered. Nevertheless, the use of only two layers (separated by 0.4 A) for large molecules is recommended, thus enabling one to obtain reliable charges at a reduced computational cost. Moreover, results justify the use of fractional models for the determination of electrostatic charges of extremely large molecules, even when aromatic structures exist.

Adenosine↗
PubMed1993

Is the mind-body interface microscopic?

This paper puts forward the hypothesis that consciousness might be linked to matter in a way which is more sophisticated than the traditional macroscopic Cartesian hypothesis suggests. Advances in the biophysics of the nervous system, not only on the level of its macroscopic functioning but also on the level of individual ion channels, have made the question of 'how finely' consciousness is tied to matter and its dynamics more important. Quantum mechanics limits the attainable resolution and puts into doubt the idea of an infinitely fine-woven attachment. A recent approach to physics rekindles such a rationalist hope. 'Endophysics' focuses on the global implications of microscopic computer simulations of chemical and biophysical processes. A complete 'artificial universe' can be set up in the computer. It produces non-classical and nonlocal effects inside--on the 'interface' that exists between an internal observer ('fluid neuron') and the rest of the world. This interface is finer than any brain property to which the status of the mind-body interface has been attributed hitherto. A new class of experiments becomes possible in the artificial world and, by analogy, in the real world. Magnetic resonance imaging experiments, routinely performed under open-loop conditions, can be repeated under psychophysical (closed-loop) conditions--in search for microscopically induced changes in the perceived and measured structure of the world.

Biophysics↗
PubMed1993

Determination of spin-5/2 quadrupolar coupling with two-pulse sequences.

The density matrix of a spin-5/2 system excited by two in-phase pulses separated by a delay tau 2 is calculated from the equilibrium state to the end of the second pulse. The interaction involved throughout the computation is the first-order quadrupolar interaction. Consequently, the results are valid for any ratio of the quadrupolar coupling to the amplitude of the radio-frequency pulse. It is shown that single- and multi-quantum coherences developed during the first pulse are detected at the end of the second pulse through single-quantum coherences. Other two-pulse sequences with various phase cyclings as well as the rotary echo sequence are also discussed and illustrated with the nuclei 27Al in a single crystal of corundum Al2O3.

Magnetic Resonance Spectroscopy↗
PubMedDate not supplied

Application of information theory to the assessment of computed tomography.

The imaging process has two fundamental stages: detection and display. The detection stage can be quantified rigourously using Shannon's information theory. This requires the contrast scale (CS), modulation transfer function (MTF), and noise power spectrum [N(f)] to be combined into a signal-to-noise ratio (SNR). This results in two fundamental summary figures of merit: the density of noise equivalent quanta (NEQ) in the image and the information bandwidth integral (IBWI). These algorithm-independent measures are used to quantify the recording stage. The display stage is less well understood since it couples to an external observer. Several types of decision makers are treated. Examples are drawn from first and second generation CT, demonstrating that thye are nearly quantum limited for large signals, indicating how their algorithms are matched or mismatched to the geometry, and calculating the contrast-detail diagrams for those decision makers.

Data Display↗
PubMed1989

Consequences of stochastic release of neurotransmitters for network computation in the central nervous system.

Neuronal membrane potentials vary continuously due largely to background synaptic noise produced by ongoing discharges in their presynaptic afferents and shaped by probabilistic factors of transmitter release. We investigated how the random activity of an identified population of interneurons with known release properties influences the performance of central cells. In stochastic models such as thermodynamic ones, the probabilistic input-output function of a formal neuron is sigmoid, having its maximal slope inversely related to a variable called "temperature." Our results indicate that, for a biological neuron, the probability that given excitatory input signals reach threshold is also sigmoid, allowing definition of a temperature that is proportional to the mean number of quanta comprising noise and can be modified by activity in the presynaptic network, a notion which could be included in neural models. By introducing uncertainty to the input-output relation of central neurons, synaptic noise could be a critical determinant of neuronal computational systems, allowing assemblies of cells to undergo continuous transitions between states.

Animals↗
PubMed1975

[Advances in the clinical application of quantum and electron irradiation (author's transl)].

The technical perequisites for irradiation with fast electrons and high-energy photons are described in the introduction and the physical and biological development of megavoltage therapy is discussed. The role of exact treatment planning is mentioned and new developments avising from introduction of ultrasound and computer-dosimetry are demonstrated. Finally, emphasis is placed on the progress actieved with modern radiotherapeutic in the treatment of tumours in certain selected clinical fields, which appear suited to the application of electron- and photon-beam therapy. Further improvement in therapeutic results is expected with the introduction of chemotherapeutic agents, radiation sensitizers and combined surgical-radiotherapeutic biological methods. The importance of collaboration amongst various suspecialities engaged in oncology is stressed.

Antineoplastic Agents↗
PubMed1993

NMR chemical shifts and structure refinement in proteins.

Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is reproduced (overall r.m.s.d. = 1.4 ppm) using 'optimized' protein structures, corrected for bond-length/bond-angle errors, and rovibrational effects.

Alanine↗