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PubMedDate not supplied

Molecular quantum similarity measures tuned 3D QSAR: an antitumoral family validation study.

In this work, a new methodology to construct a tuned QSAR model is presented, which is based on a convex set formalism. The present procedure continues previous 3D QSAR studies, performed using molecular quantum similarity measures (MQSM). With this new computational tool, the efficiency of MQSM applied to QSAR analysis is significantly improved. A reliable QSAR model is obtained using convex linear combinations of different kinds of MQSM, corresponding to different quantum-mechanical operators related to the quantum similarity integral. The active compounds studied here, as a case study, are a set of antitumor agents, the camptothecin molecule and analogues, and the property evaluated is the topoisomerase-I inhibition activity. Before performing a tuned QSAR analysis with this particular molecular set, a simple QSAR study for all the different possible types of MQSM is carried out. In addition, another application of MQSM is presented, to determine which method can be used to optimize molecular structures in order to reproduce experimental molecular geometries as well as possible.

Animals↗
PubMed1988

Molecular modelling in design of crop protection chemicals.

Specific examples from pesticide research are given which illustrate the types of analysis employed to design optimal inhibitors for a given receptor, based on the assumption that a congeneric series of compounds behave in a related mode in the biosystem. The examples illustrate the complementary role played by computational chemistry, X-ray crystallography and computer graphics and also raise questions as to the current limitations of existing molecular mechanics and quantum mechanics techniques.

Agriculture↗
PubMed1999

Noise power spectra of images from digital mammography detectors.

Noise characterization through estimation of the noise power spectrum (NPS) is a central component of the evaluation of digital x-ray systems. We begin with a brief review of the fundamentals of NPS theory and measurement, derive explicit expressions for calculation of the one- and two-dimensional (1D and 2D) NPS, and discuss some of the considerations and tradeoffs when these concepts are applied to digital systems. Measurements of the NPS of two detectors for digital mammography are presented to illustrate some of the implications of the choices available. For both systems, two-dimensional noise power spectra obtained over a range of input fluence exhibit pronounced asymmetry between the orthogonal frequency dimensions. The 2D spectra of both systems also demonstrate dominant structures both on and off the primary frequency axes indicative of periodic noise components. Although the two systems share many common noise characteristics, there are significant differences, including markedly different dark-noise magnitudes, differences in NPS shape as a function of both spatial frequency and exposure, and differences in the natures of the residual fixed pattern noise following flat fielding corrections. For low x-ray exposures, quantum noise-limited operation may be possible only at low spatial frequency. Depending on the method of obtaining the 1D NPS (i.e., synthetic slit scanning or slice extraction from the 2D NPS), on-axis periodic structures can be misleadingly smoothed or missed entirely. Our measurements indicate that for these systems, 1D spectra useful for the purpose of detective quantum efficiency calculation may be obtained from thin cuts through the central portion of the calculated 2D NPS. On the other hand, low-frequency spectral values do not converge to an asymptotic value with increasing slit length when 1D spectra are generated using the scanned synthetic slit method. Aliasing can contribute significantly to the digital NPS, especially near the Nyquist frequency. Calculation of the theoretical presampling NPS and explicit inclusion of aliased noise power shows good agreement with measured values.

Biophysics↗
PubMed2002

Computational approaches to the prediction of the blood-brain distribution.

This review attempts to summarise present knowledge related to the theoretical modelling of drug transport across the blood-brain barrier. Several computational protocols are described ranging from quantum mechanics-based approaches through molecular mechanics-related techniques to simple and fast procedures based on only the 2-D graph of the investigated structures. Amazingly, few descriptors have been shown to influence the derived relationships in a significant manner and a cornerstone in most of the described models are terms describing hydrogen bonding. A very quick quantitative assessment of the brain partitioning of a compound has also been devised using the following two rules: If N+O (the number of nitrogen and oxygen atoms) in a molecule is less than or equal to five, it has a high chance of entering the brain. The second rule predicts that if log P-(N+O) is positive then log BB is positive.

Algorithms↗
PubMed1991

Molecular structure and dynamics of cis(Z)-and trans(E)-flupenthixol and clopenthixol.

The three-dimensional structures and molecular electrostatic potentials of the cis(Z) and trans(E)-isomers of flupenthixol and clopenthixol were examined by computer graphics and molecular mechanical and quantum mechanical calculations, and their internal molecular motions were studied by molecular dynamics simulations in vacuo and in aqueous solution. The simulations demonstrated that both the side chains and the tricyclic ring systems of clopenthixol and flupenthixol are highly flexible. The angle between the two phenyl ring planes varied between 105 and 171 degrees during the simulations in solution. The electrostatic potentials around the 2-substituent were significantly more negative in the trans(E)-isomers than in the cis(Z)-isomers. The stronger negative potentials may weaken electrostatic receptor interactions and, thereby, cause the trans(E)-isomers to be less active than cis(Z)-isomers. Differences both in three-dimensional structure and in electronic structure may cause the difference in pharmacological activity between cis(Z)- and trans(E)-thioxanthenes.

Clopenthixol↗
PubMed1991

Three-dimensional structure and molecular dynamics of cis(Z)- and trans(E)-chlorprothixene.

cis(Z)-Chlorprothixene has antidopaminergic potency, while trans(E)-chlorprothixene is virtually inactive. In order to reveal the structural features causing the difference in activity, the three-dimensional molecular and electronic structures of cis(Z)- and trans(E)-chlorprothixene were examined by computer graphics and molecular mechanical and quantum mechanical calculations. The internal molecular motions of the isomers were studied by molecular dynamics simulations in vacuo and in aqueous solution. The cis(Z)-isomer had lower potential molecular energy than the trans(E)-isomer, mainly due to electrostatic interactions within the side-chain and between the dimethylamino group and the chlorine atom. During molecular dynamics simulations in aqueous solution, the side-chain of the trans(E)-isomer stayed closer to the central S-C axis of the ring system than did the side-chain of the cis(Z)-isomer. The molecular electrostatic potentials were significantly lower in the vicinity of the chlorine atom in the trans(E)- than in the cis(Z)-isomer. Differences in molecular electrostatic potentials and in three-dimensional structure are suggested to be the main reasons for the difference in pharmacological activities of cis(Z)- and trans(E)-chlorprothixene.

Chlorprothixene↗
PubMed1987

Nuclear magnetic resonance spectroscopic and computer-stimulated structural analyses of a heptapeptide sequence found around the N-glycosylation site of a proline-rich glycoprotein from human parotid saliva.

The proline-rich glycoprotein from human parotid saliva has a common heptapeptide sequence around four of six N-glycosylation sites (Maeda, N., H. S. Kim, E. A. Azen, and O. J. Smithies, 1985, J. Biol. Chem., 20:11123-11130). A synthetic model of the heptamer protein sequence, NH2-Q(1)-G(2)-G(3)-N(4)-Q(5)-S(6)-Q(7)-CONH2, was examined by nuclear magnetic resonance (NMR) spectroscopy and the ECEPP/2-VAO4A (Empirical Conformation Energy Program for Peptides) energy minimization computer algorithm (Scheraga, H. A., 1982, Quantum Chemistry Program Exchange, 454; Powell, M. J. D., 1964, Quantum Chemistry Program Exchange, 60). The NMR spectrum was almost completely assigned in dimethylsulfoxide-d6 (DMSO), and the amide chemical shift temperature dependence, phi dihedral angles, and chi 1 rotamer populations elucidated. These data indicated that a significant population of the heptamer could exist as a type I beta-turn [4----1 between Q(5) and G(2)] and/or a type II' beta-turn [4----1 between (Q)5 and G(2) and/or a gamma-turn [3----1 between Q(5) and G(3)] with the amino acid chi 1 torsion angles weighted toward the gauche- conformation. Starting from these three possible conformations, the ECEPP/2-VAO4A rigid geometry energy minimization program was used to find the localized predominant in vacuo structures of this heptapeptide sequence. The type II' beta-turn conformation best fits the data based on internuclear hydrogen-bonding distances, minimum potential energy considerations, and the NMR parameters.

Computer Simulation↗
PubMed1987

Osteoporosis: the state of the art in 1987: a review.

Osteoporosis affects approximately 15 to 20 million people in the United States and is the underlying cause of 1.3 million new fractures per year in people over age 45. The more common risk factors recognized in this disorder are older age, female sex, white race, physical inactivity, and early menopause. We now have available equipment which can measure bone density at various sites. These include single- and dual-photon densitometry, and single and dual quantitative computed tomography. These procedures are a quantum improvement over plain x-ray in the assessment of the severity of osteoporosis, but measurement at one site may not reflect the density at other sites. The value of these techniques in screening the general population for osteoporosis remains to be demonstrated. They are valuable when used to monitor patients longitudinally to assess the progression of disease and the effects of specific therapeutic regimens. There is no established effective therapy for osteoporosis so prevention is the goal. The effectiveness of different programs of physical activity in preventing bone loss and fractures is unknown but isotonic exercises three times a week for thirty minutes is recommended. There is general agreement that adequate calcium intake is important for maintenance of skeletal integrity, but there is no proof that a high dietary calcium alone will prevent osteoporosis. Estrogen therapy clearly prevents the accelerated bone loss which occurs in all white women at the time of menopause, but the question still remains who should be started on estrogens, and within what period of time after menopause are estrogens still useful in preventing postmenopausal bone loss, and for how long do we continue hormone therapy. Many questions are left to be answered but at least now osteoporosis is recognized as a major medical problem and much research is being done to answer the above questions.

Aged↗
PubMed2000

Stereoselectivity and chiral recognition in copper(I) olefin complexes with a chiral diamine

Trigonal copper(I) complexes of the chiral bidentate ligand (1S,2S)-N,N'-Bis-(mesitylmethyl)-1,2-diphenyl-1,2-ethanediamine ((S,S)-1) have been prepared with hydrocarbon olefins, as well as with allylic alcohols and ethers. The stereochemistry of the complexes has been investigated by 1H NMR spectroscopy and by combined quantum mechanics and molecular mechanics (QM/MM) computational methods. The coordinated chiral nitrogen atoms can display equal (R, R) or opposite (R, S) configuration, the latter being disfavored if steric hindrance is present above and below the coordination plane. Although the complexes exist as rapidly equilibrated mixtures of stereoisomers, one of these is often dominant, and prochiral olefins are coordinated with high enantioface selection. In addition, the [(S,S)-1]-Cu+ fragment selectively recognizes the R enantiomer of secondary allylic alcohols and ethers, as confirmed by the X-ray crystal structure analysis of the adduct with (R)-1-buten-3-ol. The reasons for the observed selectivities have been elucidated, and lead to some implications which are consistent with the enantioselection observed in catalytic cyclopropanation reactions promoted by copper complexes of the same ligand.

Journal Article↗
PubMed1992

On the suitability of semiempirical calculations as sources of force field parameters.

The suitability of Dewar's Hamiltonians as a source of bonded force field parameters is explored from the comparison analysis between up to 270 semiempirically derived force field parameters and experimentally derived values reported in some of the most popular force fields. From the statistical analysis of the results, some general conclusions about the semiempirical parametrization are formulated.

Mathematical Computing↗
PubMed1993

Fluorescence decay of DPH in lipid membranes: influence of the external refractive index.

The radiative decay rate of a fluorescent probe in an optically thin layer is known to depend on the orientation of the probe and on the refractive indices inside and outside the layer (W. Lukosz, Phys. Rev. B 22 (1980) 3030). Fluorescent probes in phospholipid bilayer membranes approximate such a system. The natural lifetime is expected to vary with the refractive index of the medium surrounding the bilayer. The lifetime variation with the refractive index depends on the orientation of the fluorescent probe. This can be used to retrieve the second-rank orientational order parameter, . The fluorescence decay of all-trans 1,6-diphenyl-1,3,5-hexatriene in L-alpha-dipalmitoyl-phosphatidylcholine large unilamellar vesicles (LUVs) was measured at a temperature well below that of the phase transition. The refractive index of the medium was varied by addition of glycerol or sucrose. The observed change of decay time with the refractive index followed the theoretical prediction. The value of the order parameter, , recovered is significantly lower than that obtained from fluorescence polarization data. Possible reasons for this disagreement are discussed.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2002

Descriptors, physical properties, and drug-likeness.

We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike.

Chemical Phenomena↗
PubMed1995

Synthesis and characterization of adducts of alachlor and 2-chloro-N-(2,6-diethylphenyl)acetamide with 2'-deoxyguanosine, thymidine, and their 3'-monophosphates.

Adducts of the preemergence herbicide 2-chloro-N-(methoxymethyl)-N-(2,6-diethylphenyl)-acetamide (alachlor) and 2-chloro-N-(2,6-diethylphenyl)acetamide (CDEPA) with 2'-deoxyguanosine, thymidine, 2'-deoxyguanosine 3'-monophosphate, and thymidine 3'-monophosphate have been synthesized and characterized. Under mildly basic conditions alachlor and CDEPA form N-1 adducts with 2'-deoxyguanosine and N-3 adducts with thymidine as a result of chlorine displacement. In addition, alachlor formed an N-7 adduct with 2'-deoxyguanosine, 7-[[(N-(methoxymethyl)-N-(2,6-diethylphenyl)carbamoyl]methyl]guani ne. N-1 adducts of alachlor and CDEPA with 2'-deoxyguanosine 3'-monophosphate and N-3 adducts with thymidine 3'-monophosphate are also described. In addition to spectroscopic data, structural proof included the dephosphorylation of each nucleotide adduct to its corresponding nucleoside adduct by nuclease P1. Alachlor and alachlor adducts but not CDEPA and CDEPA adducts exhibited rotational isomerism as evidenced by proton and 13C NMR studies. These rotamers were attributed to hindered rotation about the shortened N-carbonyl bond. Computational methods employing molecular mechanics and quantum mechanics were used to characterize the structures and energies of these rotamers to account for the patterns of duplicate NMR resonances observed.

Acetamides↗
PubMed2000

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities.

The alanine helix provides a model system for studying the energetics of interaction between water and the helical peptide group, a possible major factor in the energetics of protein folding. Helix formation is enthalpy-driven (-1.0 kcal/mol per residue). Experimental transfer data (vapor phase to aqueous) for amides give the enthalpy of interaction with water of the amide group as approximately -11.5 kcal/mol. The enthalpy of the helical peptide hydrogen bond, computed for the gas phase by quantum mechanics, is -4.9 kcal/mol. These numbers give an enthalpy deficit for helix formation of -7.6 kcal/mol. To study this problem, we calculate the electrostatic solvation free energy (ESF) of the peptide groups in the helical and beta-strand conformations, by using the delphi program and parse parameter set. Experimental data show that the ESF values of amides are almost entirely enthalpic. Two key results are: in the beta-strand conformation, the ESF value of an interior alanine peptide group is -7.9 kcal/mol, substantially less than that of N-methylacetamide (-12.2 kcal/mol), and the helical peptide group is solvated with an ESF of -2.5 kcal/mol. These results reduce the enthalpy deficit to -1.5 kcal/mol, and desolvation of peptide groups through partial burial in the random coil may account for the remainder. Mutant peptides in the helical conformation show ESF differences among nonpolar amino acids that are comparable to observed helix propensity differences, but the ESF differences in the random coil conformation still must be subtracted.

Alanine↗
PubMed2000

Decay and slowing down of the multiquanta Davydov-like solitons in molecular chains.

Dynamics and the stability of the multivibron solitons in molecular chains have been examined by means of the perturbation method based upon the inverse scattering transform. We demonstrate that due to the coupling with phonons the soliton radiates energy which causes its slowing down and gradual decay of its amplitude. It was shown that the soliton lifetime depends strongly on temperature and the values of the basic physical parameters of the system. On the basis of these results the possible role of the multivibron solitons in the intramolecular vibrational energy transfer has been critically assessed.

Energy Transfer↗
PubMed2000

Minimization methods for the one-particle dirac equation.

Taking into account relativistic effects in quantum chemistry is crucial for accurate computations involving heavy atoms. Standard numerical methods can deal with the problem of variational collapse and the appearance of spurious roots only in special cases. The goal of this Letter is to provide a general and robust method to compute particle bound states of the Dirac equation.

Journal Article↗
PubMed1992

Dynamic control of inositol 1,4,5-trisphosphate-induced Ca2+ release: a theoretical explanation for the quantal release of Ca2+.

A theoretical model has been elaborated in order to describe the kinetics of Ca2+ release induced by inositol 1,4,5-trisphosphate (IP3). The model is based on the existence of a key molecule that controls the interconversion of open and closed forms of the Ca2+ channel. The model can quantitatively explain the previously obtained experimental observations that showed that a continuous IP3 stimulus leads to a biphasic Ca2+ release and that successive IP3 additions provoke repetitive bursts of Ca2+ release. Other published interpretations of these observations are discussed.

Calcium↗
PubMed1993

Theoretical conformational analyses of endothelin-1 in vacuum, aqueous, and lipid environments.

Endothelin-1 (ET-1) is a flexible molecule capable of existing in multiple shapes (conformations) depending on the surrounding molecular solvation. The conformational diversity of ET-1 was studied in three solvation spheres (gas phase, aqueous, and membrane lipid) with the new evolving biotechnology of computational biomolecular simulation. Simulations were performed using a combination of molecular mechanics, molecular dynamics, and semiempirical quantum mechanics calculations in a RISC architecture large-scale computing environment. Marked differences between the gas phase "folded" conformation and the membrane lipid "extended" conformation were identified.

Chemical Phenomena↗