Relevant bibliographies by topics / Molecules

Academic literature on the topic 'Molecules'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2024

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Journal articles on the topic "Molecules"

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Vimala, G., J. Haribabu, S. Srividya, R. Karvembu, and A. SubbiahPandi. "Crystal structure ofN-[(4-ethoxyphenyl)carbamothioyl]cyclohexanecarboxamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 11 (October 7, 2015): o820—o821. http://dx.doi.org/10.1107/s205698901501806x.

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The asymmetric unit of the title compound, C16H22N2O2S, contains two crystallographically independent molecules (AandB). In moleculeA, the cyclohexane ring is disordered over two orientations [occupancy ratio 0.841 (10):0.159 (10)]. In each molecule, the central carbonyl thiourea unit is nearly planar (r.m.s. deviations for all non-H atoms of 0.034 Å in moleculeAand 0.094 Å in moleculeB). In both molecules, the cyclohexane ring adopts a chair conformation. The mean plane of the cyclohexane ring makes dihedral angles of 35.8 (4) (moleculeA) and 20.7 (3)° (moleculeB) with that of the benzene ring. Each molecule features an intramolecular N—H...O hydrogen bond, which closes anS(6) ring motif. In the crystal, molecules are linkedviapairs of weak N—H...S interactions, forming inversion dimers with anR22(8) ring motif for both molecules. The crystal structure also features weak C—H...π ring interactions.
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Zhao, Jian-Ping, Rui-Qin Liu, Zhi-Hao Jiang, and Sheng-Di Bai. "Crystal structure ofN′-(2,6-dimethylphenyl)benzenecarboximidamide tetrahydrofuran monosolvate." Acta Crystallographica Section E Crystallographic Communications 71, no. 1 (January 1, 2015): o28—o29. http://dx.doi.org/10.1107/s2056989014026255.

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The asymmetric unit of the title compound, C15H16N2·C4H8O, contains two amidine molecules (AandB) with slightly different conformations and two tetrahydrofuran (THF) solvent molecules. In the amidine molecules, the dimethylphenyl ring and the NH2group lie to the same side of the N=C bond and the dihedral angles between the aromatic rings are 54.25 (7) (moleculeA) and 58.88 (6) ° (moleculeB). In the crystal, N—H...N hydrogen bonds link the amidine molecules into [100]C(4) chains of alternatingAandBmolecules. Both amidine molecules form an N—H...O hydrogen bond to an adjacent THF solvent molecule.
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Szliszka, Ewelina, Zenon P. Czuba, Maciej Domino, Bogdan Mazur, Grzegorz Zydowicz, and Wojciech Krol. "Ethanolic Extract of Propolis (EEP) Enhances the Apoptosis- Inducing Potential of TRAIL in Cancer Cells." Molecules 14, no. 2 (February 13, 2009): 738–54. http://dx.doi.org/10.3390/molecules.

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Zukerman-Schpector, Julio, Ignez Caracelli, Hélio A. Stefani, Olga Gozhina, and Edward R. T. Tiekink. "Crystal structure of 5-(1,3-dithian-2-yl)-2H-1,3-benzodioxole." Acta Crystallographica Section E Crystallographic Communications 71, no. 3 (February 13, 2015): o167—o168. http://dx.doi.org/10.1107/s2056989015002455.

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In the title compound, C11H12O2S2, two independent but virtually superimposable molecules,AandB, comprise the asymmetric unit. In each molecule, the 1,3-dithiane ring has a chair conformation with the 1,4-disposed C atoms being above and below the plane through the remaining four atoms. The substituted benzene ring occupies an equatorial position in each case and forms dihedral angles of 85.62 (9) (moleculeA) and 85.69 (8)° (moleculeB) with the least-squares plane through the 1,3-dithiane ring. The difference between the molecules rests in the conformation of the five-membered 1,3-dioxole ring which is an envelope in moleculeA(the methylene C atom is the flap) and almost planar in moleculeB(r.m.s. deviation = 0.046 Å). In the crystal, molecules ofAself-associate into supramolecular zigzag chains (generated by glide symmetry along thecaxis)viamethylene C—H...π interactions. Molecules ofBform similar chains. The chains pack with no specific directional intermolecular interactions between them.
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Qachchachi, Fatima-Zahrae, Youssef Kandri Rodi, El Mokhtar Essassi, Michael Bodensteiner, and Lahcen El Ammari. "3-(2,3-Dioxoindolin-1-yl)propanenitrile." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (February 26, 2014): o361—o362. http://dx.doi.org/10.1107/s1600536814003985.

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The asymmetric unit of the title compound, C11H8N2O2, contains two independent molecules (AandB). Each molecule is build up from fused five- and six-membered rings with the former linked to a cyanoethyl group. The indoline ring and two carbonyl O atoms of each molecule are nearly coplanar, with the largest deviations from the mean planes being 0.0198 (9) (moleculeA) and 0.0902 (9) Å (moleculeB), each by a carbonyl O atom. The fused ring system is nearly perpendicular to the mean plane passing through the cyanoethyl chains, as indicated by the dihedral angles between them of 69.72 (9) (moleculeA) and 69.15 (9)° (moleculeB). In the crystal, molecules are linked by C—H...O and π–π [intercentroid distance between inversion-related indoline (A) rings = 3.6804 (7) Å] interactions into a double layer that stacks along thea-axis direction.
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Hofierka, Jaroslav, Brian Cunningham, Charlie M. Rawlins, Charles H. Patterson, and Dermot G. Green. "Many-body theory of positron binding to polyatomic molecules." Nature 606, no. 7915 (June 22, 2022): 688–93. http://dx.doi.org/10.1038/s41586-022-04703-3.

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AbstractPositron binding to molecules is key to extremely enhanced positron annihilation and positron-based molecular spectroscopy1. Although positron binding energies have been measured for about 90 polyatomic molecules1–6, an accurate ab initio theoretical description of positron–molecule binding has remained elusive. Of the molecules studied experimentally, ab initio calculations exist for only six; these calculations agree with experiments on polar molecules to at best 25 per cent accuracy and fail to predict binding in nonpolar molecules. The theoretical challenge stems from the need to accurately describe the strong many-body correlations including polarization of the electron cloud, screening of the electron–positron Coulomb interaction and the unique process of virtual-positronium formation (in which a molecular electron temporarily tunnels to the positron)1. Here we develop a many-body theory of positron–molecule interactions that achieves excellent agreement with experiment (to within 1 per cent in cases) and predicts binding in formamide and nucleobases. Our framework quantitatively captures the role of many-body correlations and shows their crucial effect on enhancing binding in polar molecules, enabling binding in nonpolar molecules, and increasing annihilation rates by 2 to 3 orders of magnitude. Our many-body approach can be extended to positron scattering and annihilation γ-ray spectra in molecules and condensed matter, to provide the fundamental insight and predictive capability required to improve materials science diagnostics7,8, develop antimatter-based technologies (including positron traps, beams and positron emission tomography)8–10, and understand positrons in the Galaxy11.
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Niemeyer, Jochen, and Noel Pairault. "Chiral Mechanically Interlocked Molecules – Applications of Rotaxanes, Catenanes and Molecular Knots in Stereoselective Chemosensing and Catalysis." Synlett 29, no. 06 (February 26, 2018): 689–98. http://dx.doi.org/10.1055/s-0036-1591934.

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Interlocked molecules, such as rotaxanes, catenanes, and molecular knots, offer conceptually new possibilities for the generation of chiral chemosensors and catalysts. Due to the presence of the mechanical or topological bond, interlocked molecules can be used to design functional systems with unprecedented features, such as switchability and deep binding cavities. In addition, classical elements of chirality can be supplemented with mechanical or topological chirality, which have so far only scarcely been employed as sources of chirality for stereoselective applications. This minireview discusses recent examples in this emerging area, showing that the application of chiral interlocked molecules in sensing and catalysis offers many fascinating opportunities for future research.1 Introduction2 Interlocked Molecules with Chiral Subcomponents2.1 Point Chirality2.2 Axial Chirality3 Mechanically Chiral Interlocked Molecules4 Topologically Chiral Interlocked Molecules5 Outlook
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Feng, Simin, Maria Cristina dos Santos, Bruno R. Carvalho, Ruitao Lv, Qing Li, Kazunori Fujisawa, Ana Laura Elías, et al. "Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering." Science Advances 2, no. 7 (July 2016): e1600322. http://dx.doi.org/10.1126/sciadv.1600322.

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As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (EF) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule’s vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10−11M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps.
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Enisoglu Atalay, Vildan, and Semse Asar. "Determination of the inhibition effect of hesperetin and its derivatives on Candida glabrata by molecular docking method." European Chemistry and Biotechnology Journal, no. 1 (January 2, 2024): 27–38. http://dx.doi.org/10.62063/ecb-15.

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In the study, it was aimed to develop new candidate inhibitor molecules by targeting the AWP1 protein structure of Candida glabrata organism. Hesperetin molecule was taken as a reference and different substituted groups were attached to the determined ends of the molecule to increase the inhibition potential on the protein structure. A total of 100 molecules were designed and after conformer distribution using the Molecular Mechanics/MMFF method for each designed molecule, the area, volume, weight, energy, EHOMO, ELUMO, polarizability, dipole moment, log P values of these molecules were calculated using the Semi Empirical/PM6 method. Molecular docking studies of the optimized molecules were carried out through the Autodock Vina program. After the docking studies, the interactions of the designed molecules with the active site amino acids of the protein structure were analyzed by BIOVIA Discovery Studio Client software in case of possible mutation. As a result of the analysis, five molecules with higher binding energies than other designed molecules and currently used antifungal drugs were recommended.
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Venkatraman, Vishwesh, Jeremiah Gaiser, Daphne Demekas, Amitava Roy, Rui Xiong, and Travis J. Wheeler. "Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)." Pharmaceuticals 17, no. 8 (July 26, 2024): 992. http://dx.doi.org/10.3390/ph17080992.

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Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.
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Dissertations / Theses on the topic "Molecules"

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Vichetti, Rafael Mário [UNESP]. "Síntese dos isótopos do monóxido de carbono no meio interestelar." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/91889.

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Made available in DSpace on 2014-06-11T19:25:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-12-21Bitstream added on 2014-06-13T19:53:20Z : No. of bitstreams: 1 vichietti_rm_me_rcla.pdf: 842604 bytes, checksum: 731ca276a75c1b92840e57bd7497b5e1 (MD5)
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De acordo com os resultados observacionais de condensações de nuvens moleculares escuras, grandes variações na razão 13CO/C18O são observadas quando se comparam os resultados obtidos nas condensações situadas dentro da mesma nuvem, bem como de nuvem para nuvem. O valor médio dessa razão na condensação principal de Ophiuchus é inferior a 5. Por outro lado, o valor encontrado nas condensações que estão situadas ao norte de Oph é maior que 10. Grandes diferenças também são encontradas quando se comparam os resultados observacionais de diferentes nuvens escuras, tais como Ophiuchus e Taurus, onde são observados também um decréscimo da razão C18O/C17O com o aumento da densidade. Os processos químicos e físicos que governam essas variações ainda não estão claros. Nesse sentido, o objetivo da presente proposta é analisar a influência do colapso gravitacional de condensações de nuvens moleculares escuras na síntese das moléculas CO, C17O, C18O, 13CO, 13C17O e 13C18O. Tal análise é feita com base em comparações entre modelos que consideram diferentes condições entre si, tais como, tamanho da cadeia química, velocidade de colapso, densidade inicial e processos de congelamento de espécies químicas na superfície de grãos de poeira. Os resultados obtidos mostram que o tamanho da cadeia química tem influência nas razões 13CO/C18O e C18O/C17O, mas não tanto quanto a densidade inicial e a velocidade do colapso. Além disso, o congelamento das espécies químicas nos grãos é mais significativo nos estágios mais avançados da evolução da condensação. Os modelos de condensações escuras que sofrem colapso gravitacional lento e em queda livre reproduzem satisfatoriamente as razões 13CO/C18O e C18O/C17O observadas, o que permite concluir que o colapso gravitacional pode ter um importante efeito nas referidas razões.
According to the observational results of dark molecular clouds condensations, large variations in the ratio 13CO/C18O are observed when comparing the results obtained in the condensations located within the same cloud and cloud to cloud. The average value of this ratio in the main condensation of Ophiuchus is below 5. On the other hand, the value found in the condensations that are located north of Oph is larger than 10. Large differences are also found when comparing the observational results of different dark clouds such as Ophiuchus and Taurus, in which are also found a decrease of the C18O/C17O ratio with increasing density. The chemical and physical processes that govern these variations are still unclear. In this sense, the objective of this proposal is to analyze the influence of the gravitational collapse of centrally condensed clumps of dense molecular gas in the synthesis of the CO, C17O, C18O, 13CO, 13C17O and 13C18O molecules. This analysis is based on comparisons among models that consider different condition, such as, chemical chain, initial density, speed of collapse and freezing processes of the chemical species on the surface of dust grains. The results show that the size of the chemical chain has influence on the 13CO/C18O and C18O/C17O ratios, but they are not as important as the initial density and the speed of the collapse. Furthermore, the freezing of chemical species on the grains occurs at later times of the collapse. The models of a gravitational free-fall collapsing core and of slowly contracting core with higher initial density are consistent with observations. These results indicate that the gravitational collapse of molecular cores can have an important effect in the 13CO/C18O and C18O/C17O ratios.
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Sargant, Robert John. "Molecular dynamics simulations of elongated molecules." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-elongated-molecules(35c31c02-aa1f-4c87-bab9-db81d813974b).html.

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The existence of a thermotropic biaxial nematic liquid crystal phase has been a topic of great interest for almost half a century. Of the various mesogenic shapes suggested as being able to form this phase, theory has suggested that the V-shaped or "bent-core" molecule is one of the most promising candidates. In this thesis we use a simple mesogenic model of a bent-core molecule, constructed from a number of repulsive Weeks-Chandler-Andersen potentials that are assembled into a rigid V shape. Using this model we explore the spontaneous phase behaviour that occurs in a wide array of different systems of mesogens, using molecular dynamics simulations and isotropic initial conditions. We study the relationship between molecular bend angle and phase behavior for molecules constructed from 11 potentials. We find that the phase behaviour splits into two regions, above and below a critical bend angle. Molecules wider than this angle exhibit isotropic, uniaxial nematic and smectic A phases. Narrower molecules show no uniaxially aligned phases, and instead have a clustered phase with short-range ordering and no global alignment director. Increasing system size improves the smectic layering in the wider molecules, but does not affect the global alignment of the narrower molecules. Our model is extended to include the effect of the arm length of the molecule by changing the number of potentials from which the mesogens are constructed. As the molecule is reduced in size, the critical bend angle is seen to move slowly towards more linear molecules, reducing the size of the parameter space in which uniaxial nematic alignment is possible. At 5 beads, all mesophases are seen to disappear and systems remain isotropic. We also study the behaviour of binary mixtures of bent-core molecules, both of differing arm lengths and of differing bend angles. For arm length mixtures, molecules are seen to remain mixed in the isotropic and nematic phases, and phase separate on transition to a smectic phase. In addition, uniaxial nematic phases are induced in systems that have no nematic phase of their own in isolation. For mixtures of different bend angles, systems remain fully mixed in the smectic phases for differences of up to 10 degrees, and beyond this the two components begin to separate at the nematic–smectic transition.
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Barrett, Michael John Sheiko Sergei. "Molecular visualization of individual molecules during flow." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2942.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2010.
Title from electronic title page (viewed Jun. 23, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Baker, Joseph Lee. "Steered Molecular Dynamics Simulations of Biological Molecules." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205416.

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Molecular dynamics (MD) simulation, which employs an empirical potential energy function to describe the interactions between the atoms in a system, is used to investigate atomistic motions of proteins. However, the timescale of many biological processes exceeds the reach of standard MD due to computational limitations. To circumvent these limitations, steered molecular dynamics (SMD), which applies external forces to the simulated system, can be used.Dynamical properties of the gonococcal type IV pilus (GC-T4P) from the bacteria Neisseria gonorrhoeae are first considered. T4 pili are long, filamentous proteins constructed from a subunit (pilin) found to emanate from the surface of pathogenic bacteria. They can withstand large forces (~100 pN), and are implicated in infection. SMD simulations are performed to study the response of the filament to an applied force. Our simulations reveal that stability of the pilus likely results from hydrophobic contacts between pilin domains buried within the filament core. Along the filament surface, gaps are formed between pilin globular head domains. These gaps reveal an amino acid sequence that was also observed to become exposed in the experimentally stretched filament. We propose two other regions initially hidden in the native filament that might become exposed upon stretching.The multidrug resistance transporter EmrD, found in the inner membrane of Escherichia coli is also the target of our studies. EmrD removes harmful drugs from the bacterial cell. We use MD to explore equilibrium dynamics of the protein, and MD/SMD to study drug interactions and transport along its central cavity. Motions supporting a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the central cavity were observed. Additionally, interactions of a few specific residues with CCCP have been identified.Finally, we describe network analysis as an approach for analyzing conformational sampling by MD simulations. We demonstrate for several model systems that networks can be used to visualize both the dominant conformational substates of a trajectory and the connectivity between them. Specifically, we compare the results of various clustering algorithms to the network layouts and show how information from both methods can be combined.
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Wildman, Jack. "Molecular dynamics simulations of conjugated semiconducting molecules." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3261.

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In this thesis, we present a study of conformational disorder in conjugated molecules focussed primarily on molecular dynamics (MD) simulation methods. Along with quantum chemical approaches, we develop and utilise MD simulation methods to study the conformational dynamics of polyfluorenes and polythiophenes and the role of conformational disorder on the optical absorption behaviour observed in these molecules. We first report a classical force-field parameterisation scheme for conjugated molecules which defines a density functional theory method of accuracy comparable to high-order ab-initio calculations. In doing so, we illustrate the role of increasing conjugated backbone and alkyl side-chain length on inter-monomer dihedral angle potentials and atomic partial charge distributions. The scheme we develop forms a minimal route to conjugated force-field parameterisation without substantial loss of accuracy. We then present a validation of our force-field parameterisation scheme based on self-consistent measures, such as dihedral angle distributions, and experimental measures, such as persistence lengths, obtained from MD simulations. We have subsequently utilised MD simulations to investigate the interplay of solvent and increasing side-chain lengths, the emergence of conjugation breaks, and the wormlike chain nature of conjugated oligomers. By utilising MD simulation geometries as input for quantum chemical calculations, we have investigated the role of conformational disorder on absorption spectral broadening and the formation of localised excitations. We conclude that conformational broadening is effectively independent of backbone length due to a reduction in the effect of individual dihedral angles with increasing length and also show that excitation localisation occurs as a result of large dihedral angles and molecular asymmetry.
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Schmid, Günter Maximilian. "Dynamical symmetry breaking in molecules and molecular aggregates." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/17393.

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Dean, Delphine Marguerite Denise 1978. "Molecular electromechanics : modeling electrostatic forces between GAG molecules." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/86649.

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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.
Includes bibliographical references (p. 81-83).
by Delphine Marguerite Denise Dean.
M.Eng.and S.B.
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Hatter, Nino [Verfasser]. "Fundamental Properties of Molecules on Surfaces : Molecular Switching and Interaction of Magnetic Molecules with Superconductors / Nino Hatter." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1123572216/34.

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Gatchell, Michael. "Molecular Hole Punching : Impulse Driven Reactions in Molecules and Molecular Clusters." Doctoral thesis, Stockholms universitet, Fysikum, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-129523.

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When molecules are excited by photons or energetic particles, they will cool through the emission of photons, electrons, or by fragmenting. Such processes are often thermal as they occur after the excitation energy has been redistributed across all degrees-of-freedom in the system. Collisions with atoms or ions may also lead to ultrafast fragmentation in Rutherford-like scattering processes, where one or several atoms can literally be knocked out of the molecule by the incoming projectile before the energy can be completely redistributed. The resulting fragmentation pathways can in such knockout processes be very different from those in thermal processes. This thesis covers extensive studies of collisions between ions/atoms and isolated Polycyclic Aromatic Hydrocarbon (PAH) molecules, isolated fullerene molecules, or clusters of these. The high stabilities and distinct fragmentation channels make these types of molecules excellent test cases for characterizing knockout-driven fragmentation and the reactions that these processes can lead to. I will present experimental measurements for a wide range of energies and compare them with my own molecular dynamics simulations and quantum chemical calculations. In this thesis, I present an in-depth study of the role of knockout in the energetic processing of molecules and clusters. The competition between knockout and thermally driven fragmentation is discussed in detail. Knockout-driven fragmentation is shown to result in exotic fragments that are far more reactive than the intact parent molecules or fragments from thermal processes. When such reactive species are formed within molecular clusters efficient molecular growth can take place on sub-picosecond timescales. The cluster environments are crucial here because they protect the newly formed molecules by absorbing excess energy. This is a possible pathway for the growth of large PAHs, fullerenes, and similar carbonaceous complexes found in, for instance, the interstellar medium.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Submitted.

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Taylor, Jason Matthew 1977. "Controlling molecules with lasers and lasers with molecules." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/38638.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, February 2007.
Includes bibliographical references (leaves 140-146).
I investigate quantum control of spin in molecules using shaped ultrafast lasers and the dynamics of those lasers when their cavities are modified to include programmable molecular masks. The ability to control quantum phenomena has had several large successes over the last decade. This field, known as Quantum Control, uses closed loop learning algorithms to shape ultrashort laser pulses in order to produce a desired state or state change. Interesting pulse shapes have been able to break chemical bonds, drive chemical reactions, selectively excite molecular states, and most recently, control photoisomerization in proteins [1, 2, 3]. In this thesis I began by seeking to apply this technique to manipulate spin. In our early work we pursued polarizing electron spins and nuclear spins for NMR Quantum Computation. We studied the electron spin triplet state properties of several molecules. Through this work we recognized that the laser and pulse shaper we were using could be modified to utilize the triplet properties of our molecules. We created a molecular triplet state spatial light modulator (SLM) to be used both outside and inside the laser cavity for ultrafast pulse shaping. The SLM consists of a liquid or thin film sample with a strong triplet state absorption.
(cont.) The molecule is selected to be transparent to the target light before pumping and strongly absorptive when pumped into the triplet state. The sample is exposed to laser light reflected off of a DMD chip to produce a 2D pattern to spatially populate the triplet ground state. This is, to our knowledge, the first triplet state ultrafast pulse shaper and the first all-optical inter-cavity spatial frequency modulator.
by Jason Matthew Taylor.
Ph.D.
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Books on the topic "Molecules"

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Nagakura, Saburo, ed. From Molecules to Molecular Systems. Tokyo: Springer Japan, 1998. http://dx.doi.org/10.1007/978-4-431-66868-8.

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Nagakura, Saburo. From Molecules to Molecular Systems. Tokyo: Springer Japan, 1998.

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Chiu, Chien-Yang. Putting Molecules into Molecular Electronics. [New York, N.Y.?]: [publisher not identified], 2011.

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VanCleave, Janice Pratt. Molecules. New York: Wiley, 1992.

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Atkins, P. W. Molecules. New York: Scientific American Library, 1987.

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Atkins, P. W. Molecules. New York: Scientific American Books, 1987.

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Atkins, P. W. Molecules. NewYork, NY: W.H. Freeman, 1987.

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Turro, Nicholas J. Modern molecular photochemistry of organic molecules. Sausalito, Calif: University Science Books, 2009.

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Turro, Nicholas J. Modern molecular photochemistry of organic molecules. Sausalito, Calif: University Science Books, 2009.

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A, Horton Michael, ed. Molecular biology of cell adhesion molecules. Chichester: Wiley, 1996.

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Book chapters on the topic "Molecules"

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Jones, R. O. "Molecules and Molecular Dynamics." In NATO ASI Series, 273–97. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4757-9975-0_12.

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Barham, Peter. "Sensuous Molecules — Molecular Gastronomy." In The Science of Cooking, 5–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56823-7_2.

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Tamvakis, Kyriakos. "Molecules." In Undergraduate Texts in Physics, 297–304. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-22777-7_16.

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Schwabl, Franz. "Molecules." In Quantum Mechanics, 263–80. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-662-02703-5_15.

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Horvath, Joan, and Rich Cameron. "Molecules." In 3D Printed Science Projects, 133–55. Berkeley, CA: Apress, 2016. http://dx.doi.org/10.1007/978-1-4842-1323-0_7.

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Khan, JaVed I., Thomas J. Kennedy, and Donnell R. Christian. "Molecules." In Basic Principles of Forensic Chemistry, 23–29. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-59745-437-7_3.

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Manini, Nicola. "Molecules." In Introduction to the Physics of Matter, 71–98. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-14382-8_3.

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McClain, William Martin. "Molecules." In Symmetry Theory in Molecular Physics with Mathematica, 99–112. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/b13137_9.

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Lindholm, E., and L. Åsbrink. "Molecules." In Lecture Notes in Chemistry, 76–86. Berlin, Heidelberg: Springer Berlin Heidelberg, 1985. http://dx.doi.org/10.1007/978-3-642-45595-7_6.

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Hodge, Paul. "Molecules." In The Andromeda Galaxy, 257–69. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-015-8056-4_16.

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Conference papers on the topic "Molecules"

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Rehner, Philipp, Johannes Schilling, and Andr� Bardow. "Computer-Aided Mixture Design Using Molecule Superstructures." In Foundations of Computer-Aided Process Design, 876–82. Hamilton, Canada: PSE Press, 2024. http://dx.doi.org/10.69997/sct.187490.

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Computer-aided molecular and process design (CAMPD) tries to find the best molecules together with their optimal process. If the optimization problem considers two or more components as degrees of freedom, the resulting mixture design is challenging for optimization. The quality of the solution strongly depends on the accuracy of the thermodynamic model used to predict the thermophysical properties required to determine the objective function and process constraints. Today, most molecular design methods employ thermodynamic models based on group counts, resulting in a loss of structural information of the molecule during the optimization. Here, we unlock CAMPD based on property prediction methods beyond first-order group-contribution methods by using molecule superstructures, a graph-based molecular representation of chemical families that preserves the full adjacency graph. Disjunctive programming is applied to optimize molecules from different chemical families simultaneously. The description of mixtures is enhanced with a recent parametrization of binary group/group interaction parameters. The design method is applied to determine the optimal working fluid mixture for an Organic Rankine cycle.
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Rob, Mohammad A., and Frank C. Franceschetti. "Atmospheric Multi-Component Pollution Analysis Using CO2 Laser." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/laca.1992.wc7.

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The laser spectroscopic techniques for detecting minor gaseous pollutants of the atmosphere have made rapid advances in the last few years. The most important optical process for detection of air pollutants is based on the extinction of radiation by molecular absorption. Each molecule absorbs light at a particular wavelength or a range of wavelengths, a characteristic of the molecule. Thus a measurement of absorption of light at the molecule's characteristic wavelength produces a mean of determining a particular molecule at the presence of other molecules. Problems can, and often arise from overlapping spectrums due to other molecules of the atmosphere. In this case, it is necessary to identify the molecules which cause these overlappings. In some cases, one might be interested in finding multiple pollutants of the atmosphere.
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Harris, T. D., J. J. Macklin, J. K. Trautman, and L. E. Brus. "Imaging and Time-Resolved Spectroscopy of Single Molecules." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/lacea.1996.lwd.5.

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Recent progress in the fluorescence detection of individual molecules [1-8] suggests that a single dye molecule can be a useful tool to probe chemical identity and activity. Measurement of fluorescence lifetime [5,6] and spectrum [6] can be augmented by knowledge of molecular orientation using polarized light [3], and triplet [2] and photoisomer excitation, as well as diffusion processes, via fluorescence-intensity correlation. Applications of fluorescent probes include the study of the dynamic conformation of membrane-bound proteins, transport of and signaling by messenger molecules, and the optical detection of the sequence of DNA. While molecules can be spatially located using near-field microscopy [5-8], near-field probes can perturb the molecule under study. We show here that molecular properties can be determined easily and in a non-perturbative manner using far-field illumination, and we obtain unperturbed spectral and lifetime data that cannot be extracted from an ensemble measurement.
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Castro, Alonso, and Brooks Shera. "Electrophoresis of Single Fluorescent Molecules." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.thd.3.

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The fast, efficient detection and separation of minute quantities of biologically important molecules plays a central role in a variety of fields, such as molecular biology, biotechnology, immunology, medical diagnostics, and forensic analysis. It has proven difficult to identify and separate biomolecules at such low concentrations by existing means. Thus, it is of importance to develop methods that are able to probe such low concentrations with adequate sensitivity, resolution and ease. Here, we describe a new method for detecting and identifying individual fluorescent molecules in solution. The technique involves the measurement of electrophoretic velocities of individual molecules in a mixture, and identification by comparison with the electrophoretic velocity known to be characteristic of a particular molecular species. The application of the method to the detection and size identification of DNA restriction fragments in solution at the single molecule level has been demonstrated. In a similar experiment, the electrophoretic velocities of single molecules of the protein phycoerythrin was determined. Although we have focused on the detection and identification of biologically important molecules, the technique has the potential to find applications in organic and inorganic chemical analysis.
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Sauer, M., K. H. Drexhage, K. T. Han, S. Nord, and C. Zander. "Following the Dynamics of Single Oligonucleotide Molecules in Water." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1998. http://dx.doi.org/10.1364/lacea.1998.lmc.14.

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The dynamic fluorescence characteristics of individual dye molecules in specific local environment are of particular interest for many biological applications.1,2 Furthermore, dye molecules that are influenced by the environment can act as molecular probes, i. e. they exhibit information about neighbouring groups and changes in the microenvironment. They also allow the direct observation of individual dynamic events such as conformational changes of a biological macromolecule if they are monitored on the single-molecule level. In addition, measurements on individual molecules are well suited for the study of complex systems in which it is not known whether all molecules exhibit the same characteristics or each molecule contributes with its individual characteristics to the observed behaviour.
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Hill, S. C., M. D. Barnes, W. B. Whitten, and J. M. Ramsey. "Modeling Fluorescence Collection from Single Molecules in Liquid Microspheres." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/lacea.1996.lwd.7.

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Optimization of molecular detection efficiencies is of central importance in analytical applications involving single molecule detection.1 In addition to limitations imposed on the fraction of molecules which can be detected by the average signal-to-noise ratio, experimental factors such as excitation inhomogeneity and molecular diffusion conspire to further limit "molecular detectability." Recent single molecule detection experiments in microdroplets suggest that such experimental limitations can be significantly reduced primarily because the molecule cannot diffuse away from the excitation volume. However, unlike fluorescence detection from bulk streams where the fluorescence intensity is isotropic in space, the large refractive index change at the surface of microdroplets implies that the fluorescence intensity collected by a lens will be strongly dependent on the position of the molecule within the droplet. In addition, the same refractive index discontinuity at the droplet surface produces a complicated excitation intensity distribution within the droplet as a result of interference between refracted and totally-internally-reflected rays. Thus, issues such as whether molecules near the surface of the sphere can "hide" from the detector as a result of total internal reflection of emission near the droplet surface, or poor excitation efficiency due to the molecule being located in a "shadow" region of the droplet will have a potential effect on molecular detection efficiencies. These questions are nontrivial to address in a quantitative way. Here we discuss development of numerical tools for modeling the fluorescence collected from a single molecule within a microdroplet as a function of position, orientation, and detection geometry based on the semiclassical electrodynamics formalism developed by Chew2 for light scattering in dielectric microspheres. In addition we also examine effects of excitation inhomogeneity within the sphere, molecular diffusion, and transition rate modification in order to obtain a realistic model of molecular detection efficiencies in microdroplets.
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Xie, Jian-Fei, and Bing-Yang Cao. "Molecular Dynamics Study on Fluid Flow in Nanochannels With Permeable Walls." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6421.

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This paper presents the fluid flow in nanochannels with permeable walls using the molecular dynamics (MD) simulations. A three-dimensional Couette flow has been carried out to investigate the effect of the permeable surface on the fluid density distributions and the slip velocity. The ordering layer of molecules is constructed near the smooth surface but it was destroyed by the permeable ones resulting in the density drop in porous wall. The fluid density in porous wall is large under strong fluid-structure interaction (FSI) and it is decreased under weak FSI. The negative slip is observed for fluid flow past solid walls under strong FSI, no-slip under medium FSI and positive slip under weak FSI whatever it is smooth or porous. Moreover, the largest slip velocity and slip length occur on the smooth surface of solid wall. As predicted by Maxwell theory, the molecule is bounced back when it impinges on the smooth surface. The molecules, however, can reside in porous wall by replacing the molecules that are trapped in the pores. Moreover, the molecule can escape from the pore and enter the channel becoming a free molecule. After travelling for a period time in the channel, the molecule can enter the pore again. During the molecular movement, the momentum exchange has been implemented not only between fluid molecules and wall but also between the fluid molecules themselves in the pore, and the multi-collision between fluid molecules takes place. The reduced slip velocity at the porous wall results in the larger friction coefficient compared to the smooth surface wall. The molecular boundary condition predicted by Maxwell theory on the smooth surface is no longer valid for flow past the permeable surface, and a novel boundary condition should be introduced.
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Sepiol, Jerzy, Frank Güttler, Marco Pirotta, Alois Renn, and Urs P. Wild. "High Resolution Spectroscopy on Single Molecules." In High Resolution Spectroscopy. Washington, D.C.: Optica Publishing Group, 1993. http://dx.doi.org/10.1364/hrs.1993.wa5.

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Single particle spectroscopy has become a source of valuable information on fundamental interactions between light and matter. Whereas trapping and cooling of ions and atoms has been sucessfully achieved, single molecules, because of their multilevel structure (high number of internal degrees of freedom) have not been observed in electromagnetic traps so far. However due to the presence of zero phonon lines in conjunction with inhomogeneous broadening the spectroscopic isolation and detection of single molecules ‘trapped in solids at very low temperatures' is made feasible [1,2]. Single molecule spectroscopy allows to study the distribution of molecular properties and not only the statistical average which is generally observed.
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Baumert, T., C. Röttgermann, R. Thalweiser, V. Weiß, and G. Gerber. "Femtosecond Time-Resolved Photochemistry of Molecules and Metal-Clusters." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.fd4.

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We report experimental studies of femtosecond time-resolved multiphoton ionization and - fragmentation of molecules and metal-clusters in molecular beam experiments. In particular we studied the real time dynamics of ionization and fragmentation of the diatomic Na2 molecule, of the triatomic Na3 cluster and of larger sodium metal-clusters Nan.
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Barnes, M. D., W. B. Whitten, J. M. Ramsey, and S. Arnold. "Photophysics of Surfactant Molecules in Microdroplets." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/lacea.1996.lwb.6.

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Over the last several years, the study of fluorescence properties in both time and frequency domain of atoms in micron-sized optical cavities has held considerable interest in the physics and quantum optics communities. In addition to fascinating purely scientific aspects of the phenomenon of cavity quantum electrodynamics (QED), the ability to modify molecular fluorescence properties in a microcavity offers potentially significant sensitivity advantages for ultrasensitive - or, single molecule - fluorescence detection. For example, two important quantities which limit sensitivity in single molecule fluorescence detection - the saturated absorption rate and the integrated fluorescence yield - can be significantly increased by enhancing the fluorescence decay rate. We have shown previously that fluorescence decay rates1 as well as the integrated fluorescence yield2 of rhodamine 6G can be significantly enhanced in glycerol microdroplets. However, exploitation of these effects in order to gain sensitivity in single molecule fluorescence detection is nontrivial for at least two important reasons. First, the magnitude of decay rate enhancement depends on the position of the molecule within the droplet; molecules near the center of the droplet are not coupled to high Q resonances while molecules near the surface may strongly interact with cavity resonances associated with droplet. Thus, diffusion limits the amount of time a given molecule may interact with the resonances thereby limiting the fluorescence decay rate. Second, the fluorescence decay rate depends on the orientation of the transition moment with respect to the cavity "axis"; e.g., the surface normal for spherical cavities.
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Reports on the topic "Molecules"

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Visco, Donald Patrick, Jr, Jean-Loup Michel Faulon, and Diana C. Roe. Enumerating molecules. Office of Scientific and Technical Information (OSTI), April 2004. http://dx.doi.org/10.2172/918764.

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Hintsa, E. Molecular beam photodissociation studies of polyatomic molecules and radicals. Office of Scientific and Technical Information (OSTI), March 1989. http://dx.doi.org/10.2172/6046463.

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Longacre, R. S. Hadron Molecules Revisted. Office of Scientific and Technical Information (OSTI), December 2013. http://dx.doi.org/10.2172/1122758.

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Genson, Kirsten Larson. Molecular Design of Branched and Binary Molecules at Ordered Interfaces. Office of Scientific and Technical Information (OSTI), January 2005. http://dx.doi.org/10.2172/861608.

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Chamovitz, Daniel A., and Zhenbiao Yang. Chemical Genetics of the COP9 Signalosome: Identification of Novel Regulators of Plant Development. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699844.bard.

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This was an exploratory one-year study to identify chemical regulators of the COP9 signalosome. Chemical Genetics uses small molecules to modify or disrupt the function of specific genes/proteins. This is in contrast to classical genetics, in which mutations disrupt the function of genes. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a biological, molecular or biochemical process. In addition to screens for chemicals which inhibit specific biological processes, chemical genetics can also be employed to find inhibitors of specific protein-protein interactions. Small molecules altering protein-protein interactions are valuable tools in probing protein-protein interactions. In this project, we aimed to identify chemicals that disrupt the COP9 signalosome. The CSN is an evolutionarily conserved eight-subunit protein complex whose most studied role is regulation of E3 ubiquitinligase activity. Mutants in subunits of the CSN undergo photomorphogenesis in darkness and accumulate high levels of pigments in both dark- and light-grown seedlings, and are defective in a wide range of important developmental and environmental-response pathways. Our working hypothesis was that specific molecules will interact with the CSN7 protein such that binding to its various interacting proteins will be inhibited. Such a molecule would inhibit either CSN assembly, or binding of CSN-interacting proteins, and thus specifically inhibit CSN function. We used an advanced chemical genetic screen for small-molecule-inhibitors of CSN7 protein-protein interactions. In our pilot study, following the screening of ~1200 unique compounds, we isolated four chemicals which reproducibly interfere with CSN7 binding to either CSN8 or CSN6.
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Calef, D. F. Molecular models for the intercalation of hydrogen molecules into modified graphites. Office of Scientific and Technical Information (OSTI), December 1995. http://dx.doi.org/10.2172/212469.

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Bartlett, Rodney J. Metastable Molecules in Ground and Excited States: Molecular Design with Theory. Fort Belvoir, VA: Defense Technical Information Center, June 2004. http://dx.doi.org/10.21236/ada426230.

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Strecker, Kevin E., and David W. Chandler. Micro-Kelvin cold molecules. Office of Scientific and Technical Information (OSTI), October 2009. http://dx.doi.org/10.2172/986607.

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Cote, Robin. Formation of Ultracold Molecules. Office of Scientific and Technical Information (OSTI), January 2016. http://dx.doi.org/10.2172/1236250.

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Eric Kessler, Eric Kessler. Exploring Molecules and Microbes. Experiment, March 2013. http://dx.doi.org/10.18258/0236.

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