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PubMed1992

Molecular structure and antiaggregating activity of the potent local anaesthetic (-)-4-[2-hydroxy-3-(N-isopropylamino)-propoxyimino]-cis-carane .

The molecular structure of (-)-4-[-2-hydroxy-3-(N-isopropylamino)- propoxyimino]-cis-carane (C16H30O2N2.HCl), a recently synthesized potent local anaesthetic, including the absolute configuration at 4 chirality centres was determined using X-ray diffraction method. The substance crystallizes in diastereoisomeric form in lowest symmetry (triclinic P1 space group). Determined intermolecular close contacts between chlorine atoms and nitrogen and hydroxyl oxygen are the main determinants of crystal packing. In the crystalline state nitrogen of the isopropylamine group has quaternary coordination. The influence of the title compound on blood platelets aggregation induced by adenosine diphosphate was studied. The results of parallel tests conducted for lidocaine and bupivacaine show that the antiaggregating activity of the title compound is much stronger. This property could be attributed to the monoterpene part of its molecule, in analogy to the observed cyclic adenosine monophosphate inhibitory action of forskolin (diterpene).

Adenosine Diphosphate↗
PubMedDate not supplied

Investigation and modification of molecular structures with the nanoManipulator.

The nanoManipulator system adds a virtual reality interface to an atomic force microscope (AFM), thus providing a tool that enables the user not only to image but also to manipulate nanometer-sized molecular structures. As the AFM tip scans the surface of these structures, the tip-sample interaction forces are monitored, which in turn provide information about the frictional, mechanical, and topological properties of the sample. Computer graphics are used to reconstruct the surface for the user, with color or contours overlaid to indicate additional data sets. Moreover, by means of a force-feedback pen, which is connected to the scanning tip via software, the user can touch the surface under investigation to feel it and to manipulate objects on it. This system has been used to investigate carbon nanotubes, fibrin, DNA, adenovirus, and tobacco mosaic virus. Nanotubes have been bent, translated, and rotated to understand their mechanical properties and to investigate friction on the molecular level. AFM lithography is being combined with the nanoManipulator to investigate the electromechanical properties of carbon nanotubes. The rupture forces of fibrin and DNA have been measured. This article discusses how some of the graphics and interface features of the nanoManipulator made these novel investigations possible. Visitors have used the system to examine chromosomes, bacterial pili fibers, and nanochain aggregates (NCAs). Investigators are invited to apply to use the system as described on the web at http:@www.cs.unc.edu/Research/nano/doc/biovis it.html.

Adenoviridae↗
PubMed2001

Mitomycin antitumor compounds. Part 1. CD studies on their molecular structure.

The UV-Vis and circular dichroism (CD) spectra of several mitomycin antitumor compounds and some of their derivatives were analyzed in order to attribute the proper assignment to their electronic transitions. The lowest energy pi-->pi* transition was found to depend on the effect of the auxochromic group in the aromatic ring, whereas the three n-->pi* transitions, present at around 240, 400 and 560 nm, are related to the C(9)==O of the carbamoyl group and to the C(8)==O and the C(5)==O of the quinone, respectively. The chirality of the C(9) is responsible for the sign of the Cotton effect (CE) at around 240 nm, whereas the substituents of the chromophore for mitosane derivatives and the conformation of the carbamoyloxymethyl group at C(9) determine the CE sign of the (1)A-->(1)L(b) transition. When the aziridine ring was opened and mitosenes derivatives were obtained, CD spectra did not differ significantly among the compounds and the bands associated to the different transitions had similar Cotton effect. Our findings suggest that the differences in the CD spectra, observed between mitosanes and mitosenes, are probably related to the more rigid molecular structure of the mitosene derivatives and the different conformations in solution of the C(9) side chain.

Antibiotics, Antineoplastic↗
PubMed1990

Molecular structure of opiate alkaloids. IV. Structure of two thioniamorphinans.

(I) S(equatorial)-Allyl-3-hydroxy-17-thioniamorphinan perchlorate, C19H25OS+.C1O4-, Mr = 400.91, monoclinic, P2(1)/n, a = 9.4171 (8), b = 10.7425 (10), c = 19.096 (2) A, beta = 95.666 (7) degrees, V = 1922.4 (3) A3, Z = 4, Dx = 1.385 Mg m-3, lambda (Mo K alpha) = 0.70930 A, mu = 0.33 mm-1, F(000) = 847.92, room temperature, final R = 0.052 for 1742 observed reflections. (II) S(axial)-Allyl-3-hydroxy-17-thioniamorphinan perchlorate, C19H25OS+.C1O4-, Mr = 400.91, monoclinic, P2(1), a = 8.4554 (10), b = 11.658 (3), c = 9.5831 (21) A, beta = 95.620 (10) degrees, V = 940.1 (3) A 3, Z = 2, Dx = 1.416 Mg m-3, lambda (Mo K alpha) = 0.70930 A, mu = 0.33 mm-1, F(000) = 423.96, room temperature, final R = 0.054 for 1015 observed reflections. The molecular structures of (I) and (II) are differentiated only by the orientation of the S-allyl substituent: the S-allyl group is equatorial in (I) and axial in (II). It has been shown that the activities as potent and selective blockers of kappa opioid receptors (kappa 2 subtype) are to be attributed to the alpha-thiamorphinan isomer (I). The inactive compound (II) is the beta-isomer. The fused ring systems are almost identical in the two molecules.

Alkaloids↗
PubMed2003

Data mining for seeking accurate quantitative relationship between molecular structure and GC retention indices of alkanes by projection pursuit.

Primary data mining on alkanes for seeking accurate quantitative relationship between molecular structure and retention indices of gas chromatography is developed in this paper. Based on the results obtained from projection pursuit (PP), a new variable named class distance variable, which essentially describes the branching structure of the alkanes, is proposed. With the help of the new variable, both fitting and prediction accuracy of the regression model can be dramatically improved. The results obtained in this work show that the technique of PP developed in statistics is a quite promising tool for seeking accurate quantitative structure-activity relationship (QSAR) and/or quantitative structure-property relationship (QSPR) researches.

Journal Article↗
PubMed2003

New Rh(I) and Rh(III) bisimidazol-2-ylidene complexes: synthesis, reactivity, and molecular structures.

New chelate bis-heterocyclic-carbene complexes of Rh(I) and Rh(III) have been obtained and fully characterized. The molecular structures of the new species have been determined. The synthesis of the compounds starts from the bisimidazolium precursors, which are deprotonated with NEt(3) under mild reaction conditions, leading to coordination to the Rh complex. The Rh(III) compounds are generated from Rh(I) and [Rh(II)](2) species, although there is no apparent oxidizing agent in the reaction media.

Journal Article↗
PubMed1993

Crystal and molecular structure and in vitro antiproliferative and antitumor activity of two organotin (IV) carbohydrate compounds.

3-C-[(Triphenylstannyl)methyl]-1,2:5,6-di-O-isopropylidene-alpha-D -allofuranose (Ph3SnCH2 carbohydrate) and 3-C-(triphenylstannyl)-1,2:5,6-di-O-isopropylidene-alpha-D-allo furanose (Ph3Sn carbohydrate) were studied by diffraction methods, space groups P2(1)2(1)2(1), a = 6.073 (1), b = 13.091 (3), c = 37.739 (13) and a = 8.3219 (9), b = 11.876 (1), c = 29.575 (5) A, respectively; both compounds have distorted tetrahedral coordination. The biological study of these compounds along with Ph3SnCl shows the following: (a) With respect to their capacity to interfere with DNA, RNA, and protein synthesis of isolated fastly proliferating thymocytes, the triphenyltin carbohydrates are less active than Ph3SnCl. Protein synthesis was found to be most sensitive with an IC50 value of approximately 0.3 microM for Ph3SnCl, 3 microM for Ph3Sn-carbohydrate, and greater than 5 microM for Ph3SnCH2-carbohydrate; (b) The in vitro activity toward the mouse tumor cell lines MOPC315, P815, SL2, and L1210, which was also performed for Bu2SnCl2, also showed that the two triphenyltin carbohydrates were less effective than Ph3SnCl. From these results it is concluded that in vitro these Sn-C bonded triphenyltin carbohydrates are less active than Ph3SnCl. Ph3Sn carbohydrate is more active than Ph3SnCH2 carbohydrate, and this may be related with the long Sn-C (of the carbohydrate moiety) bond distance (2.225 (8) A) for the former compound. This compound shows a biological activity which is in contrast to the normal inactivity of tetraorganotins and is the first active member of this family whose molecular structure is reported.

Animals↗
PubMed1992

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers.

The crystal and molecular structure of d(CGUA'CG)2 (where A' is 2-aminoadenine) has been determined and refined to an R factor of 13.8% for data 8.0-1.3 A. The structure is very similar to the original Z-DNA structures with the sequence d(CGCGCG)2 [Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A., & Wang, A. H.-J. (1989) J. Biol. Chem. 264, 7921] and shows that the substitution of 2-aminoadenine-uracil base pairs in the two central steps is consistent with Z-DNA formation. In addition, we show how waters mediating intermolecular interactions may help to explain the ZI-ZII conformational pattern found in many Z-DNA structures.

2-Aminopurine↗
PubMedDate not supplied

Spectroscopic QSAR methods and self-organizing molecular field analysis for relating molecular structure and estrogenic activity.

The performance of three "spectroscopic" quantitative structure-activity relationship (QSAR) methods (eigenvalue (EVA), electronic eigenvalue (EEVA), and comparative spectra analysis (CoSA)) for relating molecular structure and estrogenic activity are critically evaluated. The methods were tested with respect to the relative binding affinities (RBA) of a diverse set of 36 estrogens previously examined in detail by the comparative molecular field analysis method. The CoSA method with (13)C chemical shifts appears to provide a predictive QSAR model for this data set. EEVA (i.e., molecular orbital energy in this context) is a borderline case, whereas the performances of EVA (i.e., vibrational normal mode) and CoSA with (1)H shifts are substandard and only semiquantitative. The CoSA method with (13)C chemical shifts provides an alternative and supplement to conventional 3D QSAR methods for rationalizing and predicting the estrogenic activity of molecules. If CoSA is to be applied to large data sets, however, it is desirable that the chemical shifts are available from common databases or, alternatively, that they can be estimated with sufficient accuracy using fast prediction schemes. Calculations of NMR chemical shifts by quantum mechanical methods, as in this case study, seem to be too time-consuming at this moment, but the situation is changing rapidly. An inherent shortcoming common to all spectroscopic QSAR methods is that they cannot take the chirality of molecules into account, at least as formulated at present. Moreover, the symmetry of molecules may cause additional problems. There are three pairs of enantiomers and nine symmetric (C(2) or C(2)(v)) molecules present in the data set, so that the predictive ability of full 3D QSAR methods is expected to be better than that of spectroscopic methods. This is demonstrated with SOMFA (self-organizing molecular field analysis). In general, the use of external test sets with randomized data is encouraged as a validation tool in QSAR studies.

Journal Article↗
PubMed2004

Molecular structure and function of the glycine receptor chloride channel.

The glycine receptor chloride channel (GlyR) is a member of the nicotinic acetylcholine receptor family of ligand-gated ion channels. Functional receptors of this family comprise five subunits and are important targets for neuroactive drugs. The GlyR is best known for mediating inhibitory neurotransmission in the spinal cord and brain stem, although recent evidence suggests it may also have other physiological roles, including excitatory neurotransmission in embryonic neurons. To date, four alpha-subunits (alpha1 to alpha4) and one beta-subunit have been identified. The differential expression of subunits underlies a diversity in GlyR pharmacology. A developmental switch from alpha2 to alpha1beta is completed by around postnatal day 20 in the rat. The beta-subunit is responsible for anchoring GlyRs to the subsynaptic cytoskeleton via the cytoplasmic protein gephyrin. The last few years have seen a surge in interest in these receptors. Consequently, a wealth of information has recently emerged concerning GlyR molecular structure and function. Most of the information has been obtained from homomeric alpha1 GlyRs, with the roles of the other subunits receiving relatively little attention. Heritable mutations to human GlyR genes give rise to a rare neurological disorder, hyperekplexia (or startle disease). Similar syndromes also occur in other species. A rapidly growing list of compounds has been shown to exert potent modulatory effects on this receptor. Since GlyRs are involved in motor reflex circuits of the spinal cord and provide inhibitory synapses onto pain sensory neurons, these agents may provide lead compounds for the development of muscle relaxant and peripheral analgesic drugs.

Animals↗
PubMed2003

Decoding of complex isothermal chromatograms recovered from space missions. Identification of molecular structure.

A chemometric approach, based on the study of the autocovariance function, is described to study isothermal GC chromatograms of multicomponent mixtures: isothermal GC analysis is the method of choice in space missions since it is, to date, the only method compatible with flight constraints. Isothermal GC chromatograms look inhomogeneous and disordered with peak density decreasing at higher retention times: a time axis transformation is proposed to make retention an homogeneous process so that CH2 addition in terms of an homologous series yields a constant retention increment. The time axis is transformed into a new scale based on the retention times of n-alkanes, as they are the basis of the universal Kovats indices procedure. The order introduced into the chromatogram by retention time linearization can be simply singled out by the experimental autocorrelation function (EACF) plot: if constant inter-distances are repeated in different regions of the chromatogram, well-shaped peaks are evident in the EACF plot. By comparison, with a standard mixture it is possible to identify peaks diagnostic of specific molecular structures: study of the EACF plot provides information on sample chemical composition. The procedure was applied to standard mixtures containing compounds representative of the planetary atmospheres that will be investigated in the near future: in particular, those related to Titan's atmosphere (Cassini-Huygens mission) and cometary's nucleus (Rosetta mission). The employed experimental conditions simulated those applied to GC instruments installed on space probes and landers in space missions. The method was applied to two specific investigations related to space research, i.e., a comparison of retention selectivity of different GC columns and identification of the chemical composition of an unknown mixture.

Chromatography, Gas↗
PubMed2000

Molecular structural analysis of HPRT mutations induced by thermal and epithermal neutrons in Chinese hamster ovary cells.

Chinese hamster ovary (CHO) cells were exposed to thermal and epithermal neutrons, and the occurrence of mutations at the HPRT locus was investigated. The Kyoto University Research Reactor (KUR), which has been improved for use in neutron capture therapy, was the neutron source. Neutron energy spectra ranging from nearly pure thermal to epithermal can be chosen using the spectrum shifters and thermal neutron filters. To determine mutant frequency and cell survival, cells were irradiated with thermal and epithermal neutrons under three conditions: thermal neutron mode, mixed mode with thermal and epithermal neutrons, and epithermal neutron mode. The mutagenicity was different among the three irradiation modes, with the epithermal neutrons showing a mutation frequency about 5-fold that of the thermal neutrons and about 1.5-fold that of the mixed mode. In the thermal neutron and mixed mode, boron did not significantly increase the frequency of the mutants at the same dose. Therefore, the effect of boron as used in boron neutron capture therapy (BNCT) is quantitatively minimal in terms of mutation induction. Over 300 independent neutron-induced mutant clones were isolated from 12 experiments. The molecular structure of HPRT mutations was determined by analysis of all nine exons by multiplex polymerase chain reaction. In the thermal neutron and mixed modes, total and partial deletions were dominant and the fraction of total deletions was increased in the presence of boron. In the epithermal neutron mode, more than half of the mutations observed were total deletions. Our results suggest that there are clear differences between thermal and epithermal neutron beams in their mutagenicity and in the structural pattern of the mutants that they induce. Mapping of deletion breakpoints of 173 partial-deletion mutants showed that regions of introns 3-4, 7/8-9 and 9-0 are sensitive to the induction of mutants by neutron irradiation.

Animals↗
PubMed2004

Molecular structure of 2,2,4,4,6,6-hexamethyl-1,3,5-trimethylenecyclohexane as determined by gas-phase electron diffraction.

The molecular structure of 2,2,4,4,6,6-hexamethyl-1,3,5-trimethylenecyclohexane has been determined in the gas phase at a nozzle tip temperature of 340 K. The electron diffraction data were found to be consistent with a model where the cyclohexane ring adopts a distorted twist-boat conformation. The averaged geometrical parameters (r(g) and 90 degree angle (alpha)) obtained from least squares analysis are r(C=C) = 1.346(4) A, r(C-C)(ring) = 1.537(1) A, r(C-C)(Me) = 1.543(1) A, 90 degree angle C(6)C(1)C(2) = 117.5(11) degrees, 90 degree angle C(1)C(2)C(3) = 113.1(12) degrees, and 90 degree angle MeCMe = 108.2(13) degrees. The experimental results are consistent with the results from HF/6-311G(d) and MP2/6-311G(d) calculations where the distorted twist-boat form is found to be lower in energy than the chair form by 9.85 and 10.7 kcal/mol, respectively.

Journal Article↗
PubMed2006

Tailored coupled cluster singles and doubles method applied to calculations on molecular structure and harmonic vibrational frequencies of ozone.

To assess the separation of dynamic and nondynamic correlations and orbital choice, we calculate the molecular structure and harmonic vibrational frequencies of ozone with the recently developed tailored coupled cluster singles and doubles method (TCCSD). We employ the Hartree-Fock and complete active space (CAS) self-consistent field (SCF) orbitals to perform TCCSD calculations. When using the Hartree-Fock orbitals, it is difficult to reproduce the experimental vibrational frequency of the asymmetric stretching mode. On the other hand, the TCCSD based on the CASSCF orbitals in a correlation consistent polarized valence triple zeta basis yields excellent results with the two symmetric vibrations differing from the experimental harmonic values by 2 cm(-1) and the asymmetric vibration differing by 9 cm(-1).

Journal Article↗
PubMed1988

The molecular structure of indium oxine.

The radiopharmaceutical use of [111In]oxine for radiolabeling of blood products has recently met with FDA approval. The molecular structure of tris(8-quinolinolato) indium(III), "indium oxine", was determined by x-ray crystallography using a single yellow crystal grown from ethanol solution. The structural study reveals an asymmetric pseudo-octahedral N3O3 metal coordination sphere with meridional stereochemistry. This asymmetry is not detected in solution by proton NMR spectroscopy at room temperature; however, at -90 degrees C spectroscopic changes suggest slowing of a fluxional process. The molecule unexpectedly crystallized with a molecule of ethanol hydrogen-bonded to an oxygen atom of one of the oxine ligands, suggesting that hydrogen-bonding will play a role in the solvation of this complex in protic solvents.

Chemical Phenomena↗
PubMed1980

Proton nuclear magnetic resonance study of the electronic and molecular structure of the heme crevice in horseradish peroxidase.

High field proton nuclear magnetic resonance spectroscopy was used to investigate the electronic and molecular structure of the ferric heme in the resting state of horseradish peroxidase. Deuterium labeling of selected positions of hemin and deuterohemin which were subsequently reconstituted into apo-horseradish peroxidase yielded hyperfine shift patterns for the prosthetic group which are consistent with a ferric porphyrin exhibiting appreciable S = 3/2 character in a quantum mixed spin state. All resolved resonances with significant hyperfine shifts can be accounted for by the porphyrin and a proximal histidyl imidazole, although a sixth ligand from the protein cannot be definitely eliminated. The extremely slow exchange rate with bulk water of the proximal histidyl imidazole exchangeable proton and the absence of deviations from Curie behavior for the porphyrin vinyl and propionic acid proton hyperfine shifts indicate a buried heme crevice which is more rigid than in metmyoglobin. The observation of significant deviations from Curie behavior of the proximal histidyl imidazole exchangeable proton in horseradish peroxidase but not in metmyoglobins is suggested to arise from strong hydrogen bonding between the coordinated imidazole and some unspecified protein acceptor residue in the former protein.

Heme↗
PubMed1999

Design of peptides with alpha,beta-dehydro-residues: synthesis, and crystal and molecular structure of a 3(10)-helical tetrapeptide Boc-L-Val-deltaPhe-deltaPhe-L-Ile-OCH3.

The peptide Boc-L-Val-deltaPhe-deltaPhe-L-Ile-OCH3 was synthesized using the azlactone method in the solution phase, and its crystal and molecular structures were determined by X-ray diffraction. Single crystals were grown by slow evaporation from solution in methanol at 25 degrees C. The crystals belong to an orthorhombic space group P2(1)2(1)2(1) with a = 12.882(7) A, b = 15.430(5) A, c = 18.330(5) A and Z = 4. The structure was determined by direct methods and refined by a least-squares procedure to an R-value of 0.073. The peptide adopts a right-handed 3(10)-helical conformation with backbone torsion angles: phi1 = 56.0(6)degrees, psi1 = -38.0(6)degrees, phi2 = -53.8(6)degrees, psi2 = 23.6(6)degrees, phi3 = -82.9(6)degrees, psi3 = -10.6(7)degrees, phi4 = 124.9(5)degrees. All the peptide bonds are trans. The conformation is stabilized by intramolecular 4-->1 hydrogen bonds involving Boc carbonyl oxygen and NH of deltaPhe3 and CO of Val1 and NH of Ile4. It is noteworthy that the two other chemically very similar peptides: Boc-Val-deltaPhe-deltaPhe-Ala-OCH3 (i) and Boc-Val-deltaPhe-deltaPhe-Val-OCH3 (ii) with differences only at the fourth position have been found to adopt folded conformations with two overlapping beta-turns of types II and III', respectively, whereas the present peptide adopts two overlapping beta-turns of type III. Thus the introduction of Ile at fourth position in a sequence Val-deltaPhe-deltaPhe-X results in the formation of a 3(10)-helix. The crystal structure is stabilized by intermolecular hydrogen bonds involving NH of Val1 and carbonyl oxygen of a symmetry related (-x, y - 1/2, 1/2 + z) deltaPhe2 and NH of deltaPhe2 with carbonyl oxygen of a symmetry related (x, y1/2, 1/2 + z) Ile4. This gives rise to long columns of helical molecules linked head to tail running along [010] direction.

Amino Acids↗
PubMed2000

Gas-phase molecular structures of third row transition-metal hexafluorides WF6, ReF6, OsF6, IrF6, and PtF6. An electron-diffraction and ab initio study.

The molecular structures of WF6, ReF6, OsF6, IrF6, and PtF6 have been measured by electron diffraction from the gases, the last from both PtF6 itself and from a vapor assumed to consist of a mixture of O2 and PtF6 obtained by heating the salt O2PtF6. For models of Oh symmetry the bond lengths in the first three members of the series are essentially identical, but the Ir-F and Pt-F bonds are respectively about 0.01 and 0.02 A longer. Models of D4h symmetry were also tested for ReF6, OsF6, and IrF6 in which operation of the Jahn-Teller effect is thought possible. For these models the same trend was seen in the average bond-length values. The effect of three-atom multiple scattering was also investigated, and experimental estimates of the effects of vibrational averaging ("shrinkage") on the distances were obtained. Normal-coordinate analyses based on the observed wavenumbers yielded stretching force constants consistent with the usual inverse bond-length/force-constant relationship. Ab initio molecular orbital optimizations of the molecules constrained to Oh symmetry were carried out at several levels of theory and basis-set size. Less extensive optimizations of ReF6, OsF6, and IrF6 with D4h symmetry were also carried out. The best overall agreement with both the experimental values and the distance trend for Oh symmetry was obtained with the Hay-Wadt (n+1)VDZ basis on the metals and the aug-cc-pVTZ on the fluorines at the MP2 level, but these bases with B3P86 and B3PW91 density functional theory were nearly as good and with B3LYP only slightly worse. The D4h structures for ReF6, OsF6, and IrF6 with the cited bases at the B3P86 level were slightly more stable (respectively 0.8, 2.6, and 1.4 kcal/mol) with the axial bonds shorter by about 0.04 A in ReF6 and 0.07 A in OsF6, but about 0.05 A longer in IrF6. The significance of these values is uncertain. The experimental bond lengths (rg/A) with estimated 2sigma uncertainties for the models of Oh symmetry are W-F = 1.829(2), Re-F = 1.829(2), Os-F = 1.828(2), Ir-F = 1.839(2), and Pt-F = 1.852(2); the Pt-F value from the O2PtF6 sample was 1.851(2) A. Although the experimental data neither confirm nor refute the existence of the Jahn-Teller effect in ReF6, OsF6, and IrF6, they ensure that if present the distortion from Oh symmetry must be small.

Journal Article↗