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Molecular Fragments (molecular + fragment)

Distribution by Scientific Domains

Chemistry	70%
Life Sciences	17%

Selected Abstracts

Bond Orders between Molecular Fragments

CHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2006
Adam J. Bridgeman Dr.
Abstract An extension of the Mayer bond order for the interaction between molecular fragments is presented. This approach allows the classical chemical concepts of bond order and valence to be utilised for fragments and the interactions between the fragments and symmetry-adapted linear combinations to be analysed. For high-symmetry systems, the approach allows the contribution from each irreducible representation to be assessed and provides a semiquantitative measure of the role of each bonding mode to interfragment interactions. The utility of this tool has been examined by a study of the bonding in symmetrical sandwich complexes. The validity of the frontier-orbital approach and the contributions from each frontier-orbital interaction can also be assessed within this model. As demonstrated by a study of a number of mixed-sandwich complexes, the model proves to be especially useful for low-symmetry systems in which separation of the ,, , and , roles in bonding of the ligand is difficult to assess. The fragment bond order describes the interaction between preoptimized fragment orbitals and is independent of the charges that are placed on these fragments. Although the method allows the chemist to define fragments in any way they choose, most insight is gained by using the same frontier orbitals employed so successfully in perturbational molecular-orbital approaches. The results are free from the influence of the electron-counting method used to describe fragments, such as the rings and metals in sandwich complexes. [source]

From Molecular Shape to Potent Bioactive Agents I: Bioisosteric Replacement of Molecular Fragments

CHEMMEDCHEM, Issue 1 2009
Ewgenij Proschak
Ligand-based virtual screening: By means of shape- and pharmacophore-based virtual screening, a potent PPAR,-selective activator was identified from a large compound collection with minimal experimental effort. This compound represents a scaffold-hop from known PPAR agonists and provides proof-of-concept for a novel ligand-based virtual screening approach. [source]

Monitoring structural transformations in crystals.

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2007

Structural changes proceeding in a crystal during the Yang photocyclization of the salt 6,6-diethyl-5-oxo-5,6,7,8-tetrahydronaphthalene-2-carboxylate with (1S)-1-(4-methylphenyl)ethylamine were monitored by means of X-ray structure analysis. The course of the photoreaction was evaluated on the basis of the geometrical parameters for the pure reactant crystal. Variations in the cell constants, the product content, the geometry of the reaction centre, the orientation of molecular fragments and the geometry of hydrogen bonds were described and analyzed. It was found that the cell volume increased until 56% product content and decreased thereafter. The distance between the directly reacting C atoms was constant, ,,3.0,Å, until ,,75% reaction progress. Analysis of the distance between atoms that would participate in the formation of the second (unobserved) enantiomorph excluded the formation of such an isomer. Molecular fragments varied their orientation during the photoreaction, and the largest change was observed for the carboxylate group despite its participation in strong hydrogen bonds. The geometry of the hydrogen bonds changed during the photoreaction. The largest change was 0.17,Å for the D...A distance and 13° for the D,H...A angle. A comparison of the intra- and intermolecular parameters for the studied salt with data for other compounds undergoing the Yang photocyclization in crystals revealed a diversity of structural changes brought about by this type of photochemical reaction. [source]

Efficient blue-green-emitting poly[(5-diphenylamino-1,3-phenylenevinylene)- alt -(2,5-dihexyloxy-1,4-phenylenevinylene)] derivatives: Synthesis and optical properties

JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 7 2006
Liang Liao
Abstract New poly(phenylene vinylene) derivatives with a 5-diphenylamino-1,3-phenylene linkage (including polymers 2, 3, and 5) have been synthesized to improve the charge-injection properties. These polymers are highly photoluminescent with fluorescent quantum yields as high as 76% in tetrahydrofuran solutions. With effective ,-conjugation interruption at adjacent m -phenylene units, chromophores of different conjugation lengths can be incorporated into the polymer chain in a controllable manner. In polymer 2, the structural regularity leads to an isolated, well-defined emitting chromophore. Isomeric polymer 3 of a random chain sequence, however, allows the effective emitting chromophores to be joined in sequence by sharing a common m -phenylene linkage (as shown in a molecular fragment). Double-layer light-emitting-diode devices using 2, 3, and 5 as emitting layers have turn-on voltages of about 3.5 V and produce blue-green emissions with peaks at 493, 492, and 482 nm and external quantum efficiencies up to 1.42, 0.98, and 1.53%, respectively. In comparison with a light-emitting diode using 2, a device using 3 shows improved charge injection and displays increased brightness by a factor of ,3 to 1400 cd/m2 at an 8-V bias. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2307,2315, 2006 [source]

High-efficiency stimulated Raman scattering from alcohols: theory and experiments

JOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2005
Lorenzo Echevarría
Abstract The coherent Raman emission from primary alcohols [CH3(CH2)nOH, n = 0,10], 2-propyl alcohol and tert -butyl alcohol was studied using a frequency-doubled Nd:YAG pump laser (532 nm). We show that increases in the chain length (CH2 groups) and the number of CH3 groups in the alcohols (CH3 > CH2) enhance the Raman emission efficiency. Theoretical density functional theory (DFT) calculations and frequency scaling allow one to associate the vibrational wavenumbers with the molecular fragment responsible for the vibration. We obtained good agreement between the observed phenomena and the predictions of the theory. Copyright © 2005 John Wiley & Sons, Ltd. [source]

A new biodegradation prediction model specific to petroleum hydrocarbons

ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 8 2005
Philip Howard
Abstract A new predictive model for determining quantitative primary biodegradation half-lives of individual petroleum hydrocarbons has been developed. This model uses a fragment-based approach similar to that of several other biodegradation models, such as those within the Biodegradation Probability Program (BIOWIN) estimation program. In the present study, a half-life in days is estimated using multiple linear regression against counts of 31 distinct molecular fragments. The model was developed using a data set consisting of 175 compounds with environmentally relevant experimental data that was divided into training and validation sets. The original fragments from the Ministry of International Trade and Industry BIOWIN model were used initially as structural descriptors and additional fragments were then added to better describe the ring systems found in petroleum hydrocarbons and to adjust for nonlinearity within the experimental data. The training and validation sets had r2 values of 0.91 and 0.81, respectively. [source]

Predicting ready biodegradability in the Japanese ministry of international trade and industry test

ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 10 2000
Jay Tunkel
Abstract Two new predictive models for assessing a chemical's biodegradability in the Japanese Ministry of International Trade and Industry (MITI) ready biodegradation test have been developed. The new methods use an approach similar to that in the existing BIOWIN© program, in which the probability of rapid biodegradation is estimated by means of multiple linear or nonlinear regression against counts of 36 chemical substructures (molecular fragments) plus molecular weight (mol wt). The data set used to develop the new models consisted of results (pass/no pass) from the MITI test for 884 discrete organic chemicals. This data set was first divided into randomly selected training and validation sets, and new coefficients were derived for the training set using the BIOWIN fragment library and mol wt as independent variables. Based on these results, the fragment library was then modified by deleting some fragments and adding or refining others, and the new set of independent variables (42 substructures and mol wt) was fit to the MITI data. The resulting linear and nonlinear regression models accurately classified 81% of the chemicals in an independent validation set. Like the established BIOWIN models, the MITI models are intended for use in chemical screening and in setting priorities for further review. [source]

Phased rotation, conformation and translation function: theory and computer program

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2006
Frantisek Pavelcik
A new crystallographic function, phased rotation conformation and translation (PRCTF), has been developed. The function is designed for automatic interpretation of electron density utilizing molecular fragments with some conformational freedom. A computer program, NUT, has been written for the calculation of the PRCTF. [source]

Polymer hydration and microphase decomposition in poly(N -vinylcaprolactam),water complex

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2003
Vassili Lebedev
Poly(N -vinylcaprolactam) (PVCL) is a synthetic analogue of biomolecules (enzymes, proteins). It demonstrates a specific hydration and undergoes a coil,globule transition. The PVCL,D2O system (PVCL mass M = 106) has been investigated by small-angle neutron scattering (SANS) at T = 296,316,K to identify the structural features of the collapse at concentration C = 0.5,wt% near the threshold of the coil overlap. (The collapse leads to the segregation of the phase enriched with polymer at T > 305,K). The SANS experiments at q = 0.1,5,nm,1 (scales from monomer unit to globule gyration radius RG, 16,nm) have revealed a stretched coil,globule transformation in the range 305,309,K. Using high-resolution SANS (q = 0.002,0.02 nm,1) the globule association to form fractal structures (sponge-like) of surface dimension DF, 2.4,2.6 was examined. The coexistence of globules and disordered chains (regions ,5,10,nm) was found. The growth of the content of globular phase was induced by the conformational transition in disordered molecular fragments from coiled (dimension D, 1.8) to stretched chains (D, 1.2). [source]

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2005
Jianhan Chen
Abstract We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254,265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone ,/, and side chain ,1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1565,1578, 2005 [source]

Non-mathematical problem solving in organic chemistry

JOURNAL OF RESEARCH IN SCIENCE TEACHING, Issue 6 2010
David P. Cartrette
Abstract Differences in problem-solving ability among organic chemistry graduate students and faculty were studied within the domain of problems that involved the determination of the structure of a molecule from the molecular formula of the compound and a combination of IR and 1H NMR spectra. The participants' performance on these tasks was compared across variables that included amount of research experience, year of graduate study, and level of problem-solving confidence. Thirteen of the 15 participants could be classified as either "more successful" or "less successful." The participants in this study who were "more successful" adopted consistent approaches to solving the problems; were more likely to draw molecular fragments obtained during intermediate stages in the problem-solving process; were better at mining the spectral data; and were more likely to check their final answer against the spectra upon which the answer was based. Experience from research, teaching, and course work were found to be important factors influencing the level of participants' success. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 47:643,660, 2010 [source]

Natural intramolecular isotope measurements in physiology: elements of the case for an effort toward high-precision position-specific isotope analysis,

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 15 2001
J. T. Brenna
Chemical information available in organisms can be categorized into three major domains, macromolecular, small molecules, and isotope ratios. Information about physiological state is commonly obtained by qualitative and quantitative analysis in the macromolecular and small molecule domains. Genomics and proteomics are emerging approaches to analysis of macromolecules, and both areas yield definitive information on present physiological state. There is relatively little record of past physiological states of the individual available in these domains. Natural isotopic variability, particularly on an intramolecular level, is likely to retain more physiological history. Because of ubiquitous isotopic fractionation, every stereochemically unique position in every molecule has an isotope ratio that reflects the processes of synthesis and degradation. This fact highlights a vast amount of organismal chemical information that is essentially unstudied. Isotope measurements can be classified according to the chemical complexity of the analyte into bulk, compound-specific, and position-specific or intramolecular levels. Recent advances in analysis of isotope ratios are transforming natural science, and particularly answering questions about ecosystems using bulk methods; however, they have had relatively little impact on physiology. This may be because the vast complexities of physiological questions demand very selective information available in position-specific isotope analysis (PSIA). The relatively few high-precision PSIA studies, based on isotope ratio mass spectrometry (IRMS), have revealed intramolecular isotope ratio differences in pivotal physiological compounds including amino acids, glucose, glycerol, acetate, fatty acids, and purines. The majority of these analyses have been accomplished by laborious offline methods; however, recent advances in instrumentation presage rapid PSIA that will be necessary to attack real physiological problems. Gas-phase pyrolysis has been shown to be an effective method to determine 13C/12C at high precision for molecular fragments, and technologies to extend C-based PSIA to N and other organic elements are emerging. Two related efforts are warranted, (a) development of rapid, convenient, and sensitive methods for high-precision PSIA, a necessary precursor to (b) a concerted investigation into the relationship of metabolic state to intramolecular isotope ratio. Inherent in this latter goal is the need to identify long-lived molecules in long-lived cells that retain a record of early isotopic conditions, as has been shown for post-mortem human neuronal DNA. Using known metabolic precursor-product relationships between intramolecular positions, future studies of physiological isotope fractionation should reveal the relationship of diet and environment to observed isotope ratio. This science of isotope physiology, or simply isotopics, should add an important tool for elucidation of early factors that effect later health, probably the most difficult class of biomedical issues. Copyright © 2001 John Wiley & Sons, Ltd. [source]

Structure determination of seven phases and solvates of Pigment Yellow 183 and Pigment Yellow 191 from X-ray powder and single-crystal data

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009
Svetlana N. Ivashevskaya
The crystal structures of two industrially produced laked yellow pigments, Pigment Yellow 183 [P.Y. 183, Ca(C16H10Cl2N4O7S2), , phase] and Pigment Yellow 191 [P.Y. 191, Ca(C17H13ClN4O7S2), , and , phases], were determined from laboratory X-ray powder diffraction data. The coordinates of the molecular fragments of the crystal structures were found by means of real-space methods (simulated annealing) with the program DASH. The coordinates of the calcium ions and the water molecules were determined by combining real-space methods (DASH and MRIA) and repeated Rietveld refinements (TOPAS) of the partially finished crystal structures. TOPAS was also used for the final Rietveld refinements. The crystal structure of ,-P.Y. 183 was determined from single-crystal data. The , phases of the two pigments are isostructural, whereas the , phases are not. All four phases exhibit a double-layer structure, built from nonpolar layers containing the C/N backbone and polar layers containing the calcium ions, sulfonate groups and water molecules. Furthermore, the crystal structures of an N,N -dimethylformamide solvate of P.Y. 183, and of P.Y. 191 solvates with N,N -dimethylformamide and N,N -dimethylacetamide were determined by single-crystal X-ray analysis. [source]

Monitoring structural transformations in crystals.

Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor?

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2001
A crystallographic database investigation
The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N,T,C,N (push,pull nitriles) and N,(Csp3)n,C,N molecular fragments show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push,pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C,N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pKHB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N,(Csp3)n,C,N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations. [source]

Comparative QSAR Studies on Toxicity of Phenol Derivatives Using Quantum Topological Molecular Similarity Indices

CHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2010
Bahram Hemmateenejad
Quantitative structure activity relationship (QSAR) analyses using a novel type of electronic descriptors called quantum topological molecular similarity (QTMS) indices were operated to describe and compare the mechanisms of toxicity of phenols toward five different strains (i.e., Tetrahymena pyriformis, L1210 Leukemia, Pseudomonas putida, Raja japonica and Cucumis sativus). The appropriate QSAR models for the toxicity data were obtained separately employing partial least squares (PLS) regression combined with genetic algorithms (GA), as a variable selection method. The resulting QSAR models were used to identify molecular fragments of phenol derivatives whose electronic properties contribute significantly to the observed toxicities. Using this information, it was feasible to discriminate between the mechanisms of action of phenol toxicity to the studied strains. It was found that toxicities of phenols to all strains, except with L1210 Leukemia, are significantly affected by electronic features of the phenolic hydroxyl group (C-O-H). Meanwhile, the resulting models can describe the inductive and resonance effects of substituents on various toxicities. [source]