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Molecular Ensembles (molecular + ensembles)

Distribution by Scientific Domains

Chemistry	85%

Selected Abstracts

String Fit: a new structurally oriented X-ray and neutron reflectivity evaluation technique

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2001
Erich Politsch
A novel method for the analysis of neutron and X-ray reflectivity measurements is presented. In contrast to existing methods, the new data fitting approach is structurally oriented and therefore only requires information about the chemical structure of studied molecules and no other ad hoc assumptions. Apart from the inversion of reflectivity into scattering length density profile, the inversion of scattering length density profile into molecular arrangement is addressed systematically for non-trivial molecular conformations for the first time. This includes the calculation of structural characteristics, such as radius of gyration or chain order parameters, based on measured reflectograms. Another important option is the possibility to evaluate simultaneously neutron and X-ray reflectograms of a given sample. For better convergence, especially for complex simultaneous evaluations, an effective extension of the normally used least-squares deviation function is introduced. Different simulated molecular ensembles are used to illustrate the features of the new approach; typically, excellent agreement between the simulated starting and final deduced data sets is achieved. [source]

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2008
Ivelin Georgiev
Abstract One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

Random Computer Generation of 3D Molecular Structures: Theoretical and Statistical Analysis

MACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2006
Alain Porquet
Abstract Summary: A computer program has been developed to generate three-dimensional molecular structures randomly from a given collection of elementary chemical functional groups: the so-called fragment database. The gradual assembly of the various fragments present in the database is performed according to a "self-generation algorithm" (SGA). The latter is based on the covalent binding, step by step, between the unoccupied electronic valencies associated with the fragments of the database, and those of the growing molecular structure. When the number of electronic valencies of the molecular structure is zero, the growth process for this particular molecule is completed. It is shown that SGA is able to reproduce the asymmetric mass distributions of some natural colloids, like humic substances. In this article, particular attention is given to the analysis of the relationship existing between the fragment composition of the database and that of the collection of molecules generated. Mathematical expressions are derived and discussed, to understand the relationship between the proportions of the different types of fragments and the final composition of the generated molecular ensembles. For that purpose, a "pathway" formalism is proposed to describe exhaustively the whole set of generated molecules by specifying the distribution function of all of the fragments therein integrated. A statistical analysis that satisfactorily reproduces the predictions of the pathway model is extensively discussed. Example of a three-dimensional structure obtained with the "self-generation algorithm" (SGA). [source]

3,3,,5,5,-Tetramethyl-4,4,-bipyrazole,pentafluorophenol (2/3)

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2008
Konstantin V. Domasevitch
In the title compound, 2C10H14N4·3C6HF5O, one of the pentafluorophenol molecules resides on a mirror plane bisecting the O...F axis. The components aggregate by N,H...N, N,H...O and O,H...N hydrogen bonds involving equal disordering of the H atoms into molecular ensembles based on a 2:1 pyrazole,phenol cyclic pattern [O...N = 2.7768,(16),Å and N...N = 2.859,(2),Å], crosslinked into one-dimensional columns via hydrogen bonding between the outer pyrazole groups and additional pentafluorophenol molecules. The latter yields a 1:1 pyrazole,phenol catemer with alternating strong O,H...N [2.5975,(16),Å] and weaker N,H...O [2.8719,(17),Å] hydrogen bonds. This is the first reported molecular adduct of a pentafluorinated phenol and a nitrogen base, and suggests the utility of highly acidic phenols and pyrazoles for developing hydrogen-bonded cocrystals. [source]

Proton- and Redox-Controlled Switching of Photo- and Electrochemiluminescence in Thiophenyl-Substituted Boron,Dipyrromethene Dyes

CHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2006
Holger Röhr Dipl.-Phys.
Abstract A luminescent molecular switch in which the active thiol/disulfide switching element is attached to a meso -phenyl-substituted boron,dipyrromethene (BDP) chromophore as the signalling unit is presented. The combination of these two functional units offers great versatility for multimodal switching of luminescence: 1) deprotonation/protonation of the thiol/thiolate moiety allows the highly fluorescent meso - p -thiophenol-BDP and its nonfluorescent thiolate analogue to be chemically and reversibly interconverted, 2) electrochemical oxidation of the monomeric dyes yields the fluorescent disulfide-bridged bichromophoric dimer, also in a fully reversible process, and 3) besides conventional photoexcitation, the well separated redox potentials of the BDP also allow the excited BDP state to be generated electrochemically (i.e., processes 1) and 2) can be employed to control both photo- and electrochemiluminescence (ECL) of the BDP). The paper introduces and characterizes the various states of the switch and discusses the underlying mechanisms. Investigation of the ortho analogue of the dimer provided insight into potential chromophore,chromophore interactions in such bichromophoric architectures in both the ground and the excited state. Comparison of the optical and redox properties of the two disulfide dimers further revealed structural requirements both for redox switches and for ECL-active molecular ensembles. By employing thiol/disulfide switching chemistry and BDP luminescence features, it was possible to create a prototype molecular ensemble that shows both fully reversible proton- and redox-gated electrochemiluminescence. In dieser Arbeit wird ein lumineszierender molekularer Schalter vorgestellt, bei dem das aktive Thiol/Disulfid-Schaltelement an einen meso-phenylsubstituierten Bordipyrromethen (BDP) Farbstoff als Signal gebende Komponente gekoppelt ist. Die Kombination dieser beiden funktionellen Einheiten offeriert eine hohe Vielseitigkeit für das multimodale Schalten der Lumineszenz: 1) die Deprotonierung/Protonierung der Thiol/Thiolat-Gruppe erlaubt es, das stark fluoreszierende meso-p-Thiophenol-BDP und das analoge, nicht fluoreszierende Thiolat chemisch reversibel ineinander zu überführen, 2) die elektrochemische Oxidation der monomeren Farbstoffe ergibt das fluoreszierende, disulfidverbrückte, bichromophore Dimer,dieser Prozess ist ebenfalls vollständig reversibel, und 3) neben der konventionellen Anregung mit Licht erlauben die deutlich getrennten Redoxpotenziale des BDPs ebenfalls eine elektrochemische Generierung des angeregten BDP-Zustandes, d.h., Prozesse 1) und 2) können dazu eingesetzt werden, sowohl die Photo- als auch die Elektrochemilumineszenz (ECL) des BDP zu steuern. Diese Arbeit stellt die Charakteristika der verschiedenen Zustände des Schalters vor und diskutiert die zu Grunde liegenden Mechanismen. Die Untersuchung des ortho-Analogen des Dimers vermittelte zudem Einsicht in mögliche Chromophor,Chromophor-Wechselwirkungen im Grund- wie im angeregten Zustand von solchen bichromophoren Architekturen. Der Vergleich der optischen und Redoxeigenschaften der beiden Disulfid-Dimere gab des Weiteren Aufschluss über strukturelle Voraussetzungen von Redoxschaltern sowie ECL-aktiven molekularen Ensembles. Unter Einsatz schaltbarer Thiol/Disulfid-Chemie und mit den Lumineszenzeigenschaften der BDPs war es möglich, ein erstes molekulares Ensemble zu entwickeln, das vollständig reversible protonen- als auch redoxgesteuerte Elektrochemilumineszenz zeigt. [source]

Ensemble Measurement of Diffusion: Novel Beauty and Evidence

CHEMPHYSCHEM, Issue 15 2009
Christian Chmelik Dr.
Abstract Recording the evolution of concentration profiles in nanoporous materials opens a new field of diffusion research with particle ensembles. The technique is based on the complementary application of interference microscopy and IR micro-imaging. Combining the virtues of diffusion measurements with solids and fluids, it provides information of unprecedented wealth and visual power on transport phenomena in molecular ensembles. These phenomena include the diverging uptake and release patterns for concentration-dependent diffusivities, the mechanisms of mass transfer at the fluid,solid interface and opposing tendencies in local and global concentration evolution. [source]

Oriented Ensembles in Ultrafast Electron Diffraction

CHEMPHYSCHEM, Issue 7 2006
J. Spencer Baskin
Abstract Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles. [source]