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At least 19 recordsLinked to original sources
PubMed1990

Theoretical study of electronic spectra and photophysics of uracil derivatives.

The changes that the UV absorption spectrum and the photophysics of uracil undergo under hydrogen substitution or deprotonation, were studied theoretically within the CS-INDO/CI scheme. First of all this method was tested on uracil. It was then used for the calculation of the electronic structure of excited states (Sn, Tn) of a large number of uracil derivatives (1-, 3- and 5-methyluracil; 1,3-, 1,5- and 3,5-dimethyluracil; 5-fluoro- and 5-chlorouracil), including some anions (1- and 3-methyluracil anion). The excited states were obtained in the singly-excited configuration interaction approximation (S-CI) and the correlation effects on (pi pi*) states were studied by including the most important doubly- and triply-excited configurations in the CI. The S-CI wavefunctions were used for the calculation of the most important electronic matrix elements for spin-orbit coupling. The photophysics of these compounds is discussed using Jablonski diagrams.

Models, Molecular↗
PubMed1987

Theoretical studies on oscillations in microtubule polymerization.

Oscillations in the polymerization of microtubules have been studied theoretically, using differential equations and (more realistically) Monte Carlo simulations. There is gross qualitative agreement between theory and experiment but a really satisfactory model has not been found as yet.

Microtubules↗
PubMed1989

The pharmacokinetics of volatile anesthetic agent elimination: a theoretical study.

The theoretical groundwork for a rate constant formulation of inhaled anesthetic elimination kinetics is discussed. In an effort to simulate recent experimental results a linear flow-limited five-compartment model was used comprising lung, vessel-rich tissue, muscle, nonvisceral fat, and an additional compartment, marrow-visceral fat whose functional existence recently has been experimentally demonstrated. Hypothetical but plausible parameters for the marrow-visceral fat compartment were used. The theoretically predicted values were in good agreement with experimental results suggesting that this model is appropriate for the elimination kinetics of agents that are not metabolized to any significant degree. Simple approximate expressions for the rate constants were also derived and were in reasonable agreement with experimental results. The model was also employed to clarify the effect of anesthetic duration on subsequent elimination kinetics.

Adipose Tissue↗
PubMed1990

Effects of transducer beam geometry and flow velocity profile on the Doppler power spectrum: a theoretical study.

A theoretical model is used to show how the Doppler spectrum for various axisymmetric velocity profiles is affected by beam misalignment and incomplete insonation. Results are presented for both circular and square beam geometries. Moreover, a closed-form expression is derived for the power spectral density received by an on-axis transducer with a Gaussian beam profile. It is shown that the error incurred in measuring the mean Doppler frequency with such a profile will generally be bounded by the results for the circular and square beam geometries. The effects of an ideal high-pass filter on the mean Doppler frequency and the backscattered Doppler power are examined. It is shown that such a filter can introduce large differences in the measured systolic to diastolic power ratios. Finally, theoretical expressions and results are presented for the spectral broadening index (SBI), normalized spectral variance (NSV), coefficient of kurtosis (CK), the coefficient of skewness (CS) as functions of the axisymmetric velocity profile shape assuming complete uniform insonation.

Blood Flow Velocity↗
PubMed1986

Theoretical study of inversions affecting human chromosomes.

A theoretical study of inversions affecting human chromosomes is proposed. Taking into consideration the number of bands and the fact that breaks occur at interfaces between bands, it is concluded that: 7.659 different pericentric inversions might be detected in a prometaphasic 802-band karyotype; this number decreases to 917 in a metaphasic 273-band karyotype; 8.607 and 862 different paracentric inversions might be detected in the same karyotypes respectively, but these results are likely to be overestimated. These theoretical data are used for showing that the pericentric inversions detected in human cytogenetic laboratories, are too frequently recurrent and are not distributed at random.

Chromosome Inversion↗
PubMed1990

A theoretical study of acriflavin-DNA binding.

A theoretical study of binding behaviour of acriflavin, a well-known mutagen, with DNA base pairs such as AT, GC, TA and CG has been performed using CNDO/2 method to compute net atomic charges and dipoles located at various centres in acriflavine as well as base pairs. Acriflavine-DNA base pair interactions have been evaluated using second order perturbation method with multicentered multipole approximation. Only minimum energy configurations have been reported. Results have been discussed with a view to obtain a comparative behaviour of other similar dyes like proflavine and acridine orange.

Acriflavine↗
PubMed1988

[Experimental simulation study on cerebral hemodynamics--Part 2: Bilateral severe internal carotid arterial stenosis and theoretical study].

Although cerebrovascular surgery, typically bypass procedure for example, is considered to change hemodynamics not only near the region but in remote sites, their quantitative speculation and evaluation are usually difficult because of mutually related multiple factors in a living body. One of the effective means is to stimulate expected operative procedures and resulting changes by use of a hydraulic vascular model. We have already reported the hemodynamics in bilateral moderate ICA stenosis and their changes after EC-IC bypass. In this research, vascular model of bilateral severe ICA stenosis has been manufactured with silicon and glass tubes. Peripheral vascular resistance (Rp) is so adjusted as to obtain an arterial flow of 180 ml/min at an intraluminal pressure of 60 mmHg. Four kinds of stenosis segments, Ra (2.59 mm in diameter), Rb (1.94 mm), Rc (1.12 mm) and Rd (0.84 mm) are prepared and used in the models. In addition, theoretical study was performed in an unilateral ICA stenosis to evaluate quantitatively and extensively the effects of stenosis and cut bypass flow on the ICA flow and bypass flow. The results obtained are as follows: 1. Under marked low flow conditions from 55% to 30% of normal value simulated in this study, collateral flow from the opposite ICA has reached the maximum and therefore its increase is no more expected against the advance of the stenosis. 2. Both increase of the hemispheric flow and decrease of the carotid flow were still observed after EC-IC bypass procedures.(ABSTRACT TRUNCATED AT 250 WORDS)

Carotid Artery Diseases↗
PubMed1977

Theoretical study of the hydration of B-DNA.

A theoretical study of the hydration of the B-form of DNA has been carried out using empirical potential energy functions. In the first stage the hydration scheme of a model compound representing the B-DNA has been determined and the results have been shown to agree to a large extent with those of refined ab initio SCF computations. In the second stage, the stabilization energy due to the presence of water in the first hydration shell was computed by considering the hydrated helix as a supermolecule. The computations indicate appreciable stabilization. The different components contributing to the overall stabilization are determined and analysed.

Binding Sites↗
PubMed1986

Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility.

A detailed theoretical study has been made for five antibiotics which all bind selectively to AT sequences in the minor groove of B-DNA: SN-18071, NSC-101327, distamycin-2, distamycin-3 and netropsin. The optimal complexes were found for systems in which the flexibility of DNA, as well as that of the antibiotics, was taken into account. Explicit, mobile counterions and a dielectric function modelling aqueous solution were also included. The binding geometries of the most strongly interacting antibiotics, distamycin-3 and netropsin, are compared in considerable detail and it is shown that notable differences exist between them. The results for netropsin are also discussed in the light of recent disagreements concerning its exact binding location within DNA.

Anti-Bacterial Agents↗
PubMed1975

Barrier to rotation and conformation of the NB2 group in cytosine and its derivatives. Part I. Theoretical study of cytosine.

A theoretical investigation of the conformation of the amino group in cytosine has been performed by the CNDO/2 and INDO methods. The results suggest that from the energetical point of view the conformation of the amino group is not stable in the course of rotation. It changes its hybridization from sp2-like in the planar case to sp3-like in the transition state. The physical basis of the barrier to rotation of this group around the C4-N7 bond are discussed. Some comments on the solvent dependence of the electronic absorption spectra of cytosine are presented.

Amines↗
PubMed1992

A theoretical study concerning the mode of interaction of the histamine H2-agonist dimaprit.

A theoretical study was performed to elucidate the mode of interaction of the histamine H2-agonist dimaprit with the histamine H2-receptor. For this purpose receptor mapping techniques, including ab initio energy calculations, geometry optimizations and molecular electrostatic potential calculations (MEPs), have been used. The characteristics of dimaprit were compared to those of histamine for which the points of interaction with the H2-receptor are known, as well as its bioactive conformation. In this comparative study two possible models for the interaction of dimaprit with the H2-receptor were considered. In one model the two nitrogen atoms of the isothiourea moiety of dimaprit play an essential role in the recognition of the ligand by the receptor and have the same function as the nitrogen atoms of the imidazole ring of histamine; in the second model this role is fulfilled by a sulphur and a nitrogen atom of the same isothiourea moiety. The comparison to histamine was based on geometrical resemblance as well as on similarity in MEPs. Also the conformational energy of dimaprit in the two interaction models was considered. Results of the investigations reveal that the isothiourea moiety of dimaprit most probably interacts with the histamine H2-receptor through the sulphur and nitrogen atom, the first atom acting as a proton acceptor and the second one as a proton donor. Subsequently, three analogues of dimaprit, namely SK&F 91487, SK&F 91488 and SK&F 92054, were studied. It was possible to explain their pharmacological behavior within the proposed model.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Simulation↗
PubMed1987

A theoretical study of the sequence specificity in binding of lexitropsins to B-DNA.

A theoretical study is presented on the binding to B-DNA of a series of lexitropsins, these ligands being netropsin derivatives in which one or both of the pyrrole rings have been replaced by imidazoles. The best complexes have been located by energy minimisation taking into account nucleic acid flexibility, ligand flexibility, explicit, mobile counterions and solvent dielectric effects. Calculations have been performed for two homopolymeric DNA receptor sequences, AT base sequence, which only decreases in the imidazole derivatives. These results emphasize the decisive role of the molecular electrostatic potential of the nucleic acid in determining the sequence selectivity of these ligands, as opposed to the postulated role of adenine C2 - pyrrole beta hydrogen contacts.

Base Sequence↗
PubMed1986

A theoretical study of the binding of phenothiazine derivatives to residues 82-93 of calmodulin.

A theoretical study was performed of the interaction of four phenothiazine derivatives, promethazine, promazine, trifluopromazine, and trifluoperazine, with a fragment (82-93) of calmodulin, held in the alpha-helical conformation. The computations were performed in the framework of the SIBFA 2 procedure (sum of interactions between fragments computed ab initio), which uses analytical formulas based on ab initio self-consistent field computations. The interaction energy is the sum of the intermolecular phenothiazine-oligopeptide interaction energy and of the separate intramolecular energy variations of the phenothiazine and of the side chains of the oligopeptide upon complex formation. The ordering of interaction energies of the four investigated phenothiazines parallels the ordering of their experimentally measured affinities for calmodulin, with a maximum affinity for trifluoperazine. The principal features of the trifluoperazine complex are a short hydrogen bond between the piperazinium proton and one anionic oxygen of Glu 87, and hydrophobic interactions between the piperazinium ring and Val 91 and between the methylene chain and Ala 88, together with partial insertion of the phenothiazine ring and the--CF3 substituent between Phe 89 and Phe 92.

Calmodulin↗
PubMed1985

Experimental and theoretical studies on Tl+ interactions with the cation-selective channel of the sarcoplasmic reticulum.

This paper presents an experimental study and a theoretical interpretation of the effects of thallous ion on the electrical properties of the cation-selective channel of the sarcoplasmic reticulum (SR channel). The properties of this channel in solutions which do not contain thallous ion are consistent with the predictions of Läuger's theory for singly occupied pores (P. Lüger, 1973, Biochim. Biophys. Acta 311:423-441). However, this theory does not account for SR channel properties in mixtures containing thallous ion. SR channel conductance is less than predicted in mixed salt solutions of thallium with either potassium or ammonium (J. Fox, 1983, Biochim. Biophys. Acta 736:241-245), yet is greater than expected in mixtures of lithium and thallium. In a simple single-ion pore, the ratio of the products of the single-salt binding constants and maximum conductances is equal to the permeability ratio calculated from zero-current potential experiments under near equilibrium conditions. This is not found for the SR channel when thallous ion is present. SR channel properties in the presence of thallous ion can, however, be explained by a model which postulates the existence of two external modulatory sites on the channel, without implying double-occupancy in the permeation pathway. When thallous ion is bound to a modulatory site the maximum conductance of the channel to all permeating ions is altered (thallous included). Two other models (a three-barrier, two-internal-site pore which allows multiple occupancy, and a pore with fluctuating barriers) are discussed, but are found to be unable to fit our conductance data at different concentrations.

Animals↗
PubMed1989

A theoretical study of the effect of optical properties in laser ablation of tissue.

The role of optical properties in the distribution of laser light and the resulting thermodynamic processes in biological tissue is studied from a theoretical perspective. Light distribution is modeled by a discrete ordinate method and heat transfer and ablation is modeled by an immobilized finite element method. The effect of parametric variation of absorption, scattering anisotropicity on the dynamics of the ablation process is examined. The manifestation of higher than the ablation threshold temperature in the subsurface tissue is observed and discussed. Results indicate significant differences in the ablation behavior which may have important clinical implications.

Hot Temperature↗
PubMed1992

A theoretical study of glucosamine synthase. II. Combined quantum and molecular mechanics simulation of sulfhydryl attack on the carboxyamide group.

Continuing our theoretical studies of glucosamine synthase catalysis, we have carried out MNDO and ab initio calculations of the first stage of the reaction, which involves the attack of a cysteine thiol group from the enzyme active site on the side chain carboxyamide group of glutamine, producing ammonia and thioester. The reactants were modelled by methyl mercaptate and acetamide, respectively. For two considered mechanisms of the reaction the energy surfaces were evaluated. Mechanism I, proposed by Chmara et al. (1985) involves the nucleophilic attack of a deprotonated thiol group on the carbonyl carbon atom. Mechanism II, postulated in our previous work (Tempczyk et al. 1989), assumes the concerted binding of the mercaptate sulphur to the carbonyl carbon and the sulfhydryl hydrogen to the amide nitrogen with simultaneous breaking of the S-H bond. The energy surface of mechanism I shows no minimum on the approach of the mercaptide anion towards the carbonyl carbon, which is also consistent with ab initio calculations in a 4-31 G basis set. Therefore, mechanism I seems to be unlikely. The same analysis of mechanism II shows that it leads to the desired products: methyl thioacetate and ammonia. The presence of a sulfhydryl hydrogen causes apparent pyramidicity of the amido nitrogen and lengthening of the C-N bond in the transition state, making conditions for the release of the ammonia molecule. The MNDO calculated energy barrier of the reaction is 50.1 kcal/mol and the approximate 4-31 G ab initio barrier (at the MNDO geometries of the substrate complex and the transition state) is 63 kcal/mol.(ABSTRACT TRUNCATED AT 250 WORDS)

Amides↗
PubMed1988

Theoretical study of the sequence selectivity of isolexins, isohelical DNA groove binding ligands. Proposal for the GC minor groove specific compounds.

A theoretical study is presented of complex formation between DNA fragments of different base sequences and isolexins, "isohelical base reading polymers", formed of heteroaromatic pentagonal rings joined by appropriate linkers. Extensive computations are performed for the isolexin composed of the furan-pyrrole-furan sequence. They involve charged ligands with propioamidinium groups at both ends as well as neutral molecules with terminal methyl, carbonyl and amino groups. Two different groups (C = O and NH) are used as linkers between the base reading moieties. The role of these elements on the binding preference of the ligands has been examined. The results show that the mere possibility of formation of hydrogen bonds between a ligand and the nucleic acid bases is not sufficient to ensure its binding specificity which is determined largely by the interplay of electrostatic factors. Thus the dicationic isolexins uniformly prefer AT sequences. For the neutral isolexins the nature of the groups forming the linkers is a major factor in defining the specificity, although these groups do not participate directly in the interaction with DNA. The C = O linkers favour binding to AT sequence while the N-H linkers permit preferential binding to the GAG sequence. Finally, for the first time in theoretical computations, a ligand is proposed which should bind preferentially to the minor groove of GC sequences: this ligand is a neutral isolexin composed of three furan rings linked by two N-H groups. This ligand is considered as an improvable prototype. Altogether the results presented open the path for the designing of minor groove ligands specific for any desirable DNA base sequence.

Base Sequence↗