Academic literature on the topic 'Conformation of molecules'

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Journal articles on the topic "Conformation of molecules"

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Gaalswyk, Kari, and Christopher N. Rowley. "An explicit-solvent conformation search method using open software." PeerJ 4 (May 31, 2016): e2088. http://dx.doi.org/10.7717/peerj.2088.

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Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules α-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.
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Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic та ін. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR". Proceedings of the National Academy of Sciences 112, № 46 (2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

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Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like receptor conformations. Individual receptor molecules in the apo form repeatedly sample both conformations, with a bias toward the inactive conformation. Experiments in the presence of drug ligands show that binding of the full agonist formoterol shifts the conformational distribution in favor of the active-like conformation, whereas binding of the inverse agonist ICI-118,551 favors the inactive conformation. Analysis of single-molecule dwell-time distributions for each state reveals that formoterol increases the frequency of activation transitions, while also reducing the frequency of deactivation events. In contrast, the inverse agonist increases the frequency of deactivation transitions. Our observations account for the high level of basal activity of this receptor and provide insights that help to rationalize, on the molecular level, the widely documented variability of the pharmacological efficacies among GPCR-targeting drugs.
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Weng, Ze F., W. D. Sam Motherwell, Frank H. Allen, and Jacqueline M. Cole. "Conformational variability of molecules in different crystal environments: a database study." Acta Crystallographica Section B Structural Science 64, no. 3 (2008): 348–62. http://dx.doi.org/10.1107/s0108768108005442.

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A methodology is described for analysing the Cambridge Structural Database (CSD) in terms of molecular conformations. Molecular species that have more than a single occurrence across the complete CSD are identified, either as the sole crystal component or co-crystallized with other components. Cluster analysis, based on a root-mean-square fit of coordinates and chemical connectivity, is performed to identify conformational variance for each molecule. Results are analysed in terms of the number of discrete conformations observed versus the number of crystal environments and number of acyclic torsion angles in the molecule. Special subsets of environments are also analysed, namely polymorphs, co-crystals and solvates. In general, conformational diversity increases with an increasing number of different crystal environments and with an increasing number of flexible torsion angles. Overall, molecules with one or more acyclic flexible torsion angle are observed to exist in more than one conformation in ca 40% of cases. There is evidence that solvated molecules exhibit more conformational flexibility on average, compared with polymorphs and co-crystals.
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Guo, Qing, Yufan He, and H. Peter Lu. "Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy." Proceedings of the National Academy of Sciences 112, no. 45 (2015): 13904–9. http://dx.doi.org/10.1073/pnas.1506405112.

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Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2–amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme–substrate interactions, enzyme–substrate active complex formation, and protein folding–binding interactions.
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Chinnakali, K., D. Sudha, M. Jayagopi, R. Raghunathan, and Hoong-Kun Fun. "4,4,7,7-Tetramethyl-2-tosyl-2,3,3a,4,6,7,8,9-octahydro-1H-pyrrolo[3,4-c]pyrano[6,5-b]cyclohexan-9-one." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (2007): o4436—o4437. http://dx.doi.org/10.1107/s1600536807052221.

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The title compound, C22H29NO4S, crystallizes with three independent molecules, A, B and C, in the asymmetric unit. Each of the three independent molecules adopts a folded conformation, with the phenylsulfonyl group lying over the pyranocyclohexanone ring system, and with the pyrrolidine and dihydropyran rings cis-fused. In all three molecules, the pyrrolidine ring has a twist conformation and the dihydropyran ring is in a half-chair conformation. The cyclohexenone rings adopt envelope conformations, with the flap atom puckered towards the phenylsulfonyl group in molecule A, and away from that group in molecules B and C, resulting in a different overall conformation for molecule A compared to B and C. In all molecules, the tosyl group is equatorially attached to the pyrrolidine ring. In the crystal structure, the molecules are linked into a three-dimensional framework by C—H...O hydrogen bonds.
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Nagasawa, Yuya, Takeshi Koyama, and Susumu Okada. "Energetics and electronic structures of perylene confined in carbon nanotubes." Royal Society Open Science 5, no. 6 (2018): 180359. http://dx.doi.org/10.1098/rsos.180359.

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The energetics and geometries of perylene encapsulated in carbon nanotubes (CNTs) have been investigated employing density functional theory using the generalized gradient approximation combined with the van der Waals correction. Our calculations show that the encapsulated perylene molecules possess two metastable molecular conformations with respect to the CNT wall, which are almost degenerate with each other. A standing conformation, with respect to the CNT wall, is the ground state conformation for a semiconducting (19,0)CNT, while a lying conformation is the ground state for a metallic (11,11)CNT. Cooperation and competition between perylene–perylene and perylene–CNT interactions cause these possible perylene conformations inside CNTs. However, the electronic structure of the CNT encapsulating the perylene molecules is found to be insensitive to the molecular conformation.
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Grineva, Olga V. "Direct Determination of Ratios of All Conformations and Their Lifetimes for Small Flexible Molecules from Molecular Dynamics Simulations: 1,3-Propanediol in an Aqueous Environment." Molecules 30, no. 6 (2025): 1285. https://doi.org/10.3390/molecules30061285.

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For the first time in the course of molecular dynamics modeling of a liquid, the conformations of each of the small flexible molecules present in the system were fixed at short (1 ps) time intervals. This allowed the establishment of the ratios between various individual conformations and their families and determination of the average lifetimes of both individual conformations and families. As an example, data are presented for modeling boxes with different numbers of molecules (800, 2700, and 6400) for an aqueous solution with 1 mol. % 1,3-propanediol at 298.15 K and 1 atm. The results of the conformational analysis turned out to be very close for systems with different numbers of molecules and with different choices of initial conformations. For the systems under investigation, the tTTg conformation, which does not have intramolecular hydrogen bond, predominated (37–39%), and the total fractions of all conformations in the TT family were 74–76%. Only 0.4–0.5% of 1,3-propanediol molecules had conformations with the possible formation of intramolecular hydrogen bond, although the most stable conformers of free 1,3-propanediol molecules exhibit such a bond. The average lifetimes of each individual conformation did not exceed 7 ps in simulated systems, while the maximum lifetimes reached 60 ps. The average lifetimes of the main chain vary from ~110 ps in TT family to ~12 ps in GG′ family, in which the conformations tend to have intramolecular hydrogen bonds. It was found that calculations for an individual 1,3-propanediol molecule at the MP2/aug-cc-pVDZ or MP2/aug-cc-pVTZ theoretical levels lead to 22 conformers both in vacuum and by using the PCM model for implicit aqueous solvation (at the MP2/aug-cc-pVDZ level) and that such solvation reduces the energy difference between the conformers.
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Chinnakali, K., D. Sudha, M. Jayagopi, R. Raghunathan, and Hoong-Kun Fun. "cis-4,4,10-Trimethyl-2-tosyl-1,2,3,3a,4,11b-hexahydro-11H-pyrrolo[3,4-c]pyrano[5,6-c]quinolin-11-one hemihydrate." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (2007): o4489—o4490. http://dx.doi.org/10.1107/s1600536807053287.

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The asymmetric unit of the title compound, C24H26N2O4S·0.5H2O, contains two independent molecules, A and B, with similar conformations, and a water molecule. The pyrrolidine ring adopts an envelope conformation in molecule A and a twist conformation in molecule B. In both molecules, the pyrrolidine and dihydropyran rings are cis-fused, and the dihydropyran ring has a half-chair conformation. Each of the independent molecules adopts a folded conformation, with the sulfonyl-bound benzene ring lying over the pyridinone ring. The two independent molecules, A and B, are linked together via C—H...O hydrogen bonds and C—H...π interactions. The A–B pairs are linked into a chain along the a axis by O—H...O and C—H...O hydrogen bonds, as well as C—H...π interactions. The inversion- and screw-related molecules in adjacent chains are cross-linked via C—H...O and C—H...N interactions, forming a three-dimensional framework.
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Savintseva, Liana A., Ilya S. Steshin, Alexander A. Avdoshin, et al. "Conformational Dynamics and Stability of Bilayers Formed by Mycolic Acids from the Mycobacterium tuberculosis Outer Membrane." Molecules 28, no. 3 (2023): 1347. http://dx.doi.org/10.3390/molecules28031347.

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Bilayers of mycolic acids (MAs) form the outer membrane of Mycobacterium tuberculosis that has high strength and extremely low permeability for external molecules (including antibiotics). For the first time, we were able to study them using the all-atom long-term molecular dynamic simulations (from 300 ns up to 1.2 μs) in order to investigate the conformational changes and most favorable structures of the mycobacterial membranes. The structure and properties of the membranes are crucially dependent on the initial packing of the α-mycolic acid (AMA) molecules, as well as on the presence of the secondary membrane components, keto- and methoxy mycolic acids (KMAs and MMAs). In the case of AMA-based membranes, the most labile conformation is W while other types of conformations (sU as well as sZ, eU, and eZ) are much more stable. In the multicomponent membranes, the presence of the KMA and MMA components (in the W conformation) additionally stabilizes both the W and eU conformations of AMA. The membrane in which AMA prevails in the eU conformation is much thicker and, at the same time, much denser. Such a packing of the MA molecules promotes the formation of a significantly stronger outer mycobacterial membrane that should be much more resistant to the threatening external factors.
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Halder, Bijoy K., Angelica M. Palomino, and Jordan Hicks. "Influence of polyacrylamide conformation on fabric of “tunable” kaolin–polymer composite." Canadian Geotechnical Journal 55, no. 9 (2018): 1295–312. http://dx.doi.org/10.1139/cgj-2017-0200.

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“Tunable” clay–polymer composites have the potential to improve the engineering properties of clay materials. The importance of these materials derives from the ability of the responsive polymer to adopt various conformations (coiled, partially extended or extended), which in turn impacts the mesoscale properties of the material. However, the influence of polymer molecule conformation on particle arrangement and overall composite behavior is not well understood. The purpose of this study is to understand the fabric development due to the conformational behavior of the polymer, and thus the clay–polymer composite, over a wide range of solids content and stress levels. The polymer molecule conformation was controlled using selected fluid pH and ionic concentrations. Results show that the polymer conformation significantly influences clay fabric formation. When the polymer molecules are likely to have extended conformation, the dominant fabric mode is face-to-face and particle mobilization increases. Both face-to-face and edge-to-edge fabric formation dominate the behavior of the composite when coiled conformation is likely, resulting in a decrease in interparticle movement. Thus, the polymer conformation can be used to manipulate both the interparticle spacing between particles and (or) aggregates and arrangement of particles.
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Dissertations / Theses on the topic "Conformation of molecules"

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Tedesco, Daniele <1984&gt. "Chiroptical properties of bioactive molecules: sensitivity to conformation and solvation." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6337/1/Tedesco_Daniele_tesi.pdf.

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Chiroptical spectroscopies play a fundamental role in pharmaceutical analysis for the stereochemical characterisation of bioactive molecules, due to the close relationship between chirality and optical activity and the increasing evidence of stereoselectivity in the pharmacological and toxicological profiles of chiral drugs. The correlation between chiroptical properties and absolute stereochemistry, however, requires the development of accurate and reliable theoretical models. The present thesis will report the application of theoretical chiroptical spectroscopies in the field of drug analysis, with particular emphasis on the huge influence of conformational flexibility and solvation on chiroptical properties and on the main computational strategies available to describe their effects by means of electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The combination of experimental chiroptical spectroscopies with state-of-the-art computational methods proved to be very efficient at predicting the absolute configuration of a wide range of bioactive molecules (fluorinated 2-arylpropionic acids, β-lactam derivatives, difenoconazole, fenoterol, mycoleptones, austdiol). The results obtained for the investigated systems showed that great care must be taken in describing the molecular system in the most accurate fashion, since chiroptical properties are very sensitive to small electronic and conformational perturbations. In the future, the improvement of theoretical models and methods, such as ab initio molecular dynamics, will benefit pharmaceutical analysis in the investigation of non-trivial effects on the chiroptical properties of solvated systems and in the characterisation of the stereochemistry of complex chiral drugs.
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Tedesco, Daniele <1984&gt. "Chiroptical properties of bioactive molecules: sensitivity to conformation and solvation." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6337/.

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Chiroptical spectroscopies play a fundamental role in pharmaceutical analysis for the stereochemical characterisation of bioactive molecules, due to the close relationship between chirality and optical activity and the increasing evidence of stereoselectivity in the pharmacological and toxicological profiles of chiral drugs. The correlation between chiroptical properties and absolute stereochemistry, however, requires the development of accurate and reliable theoretical models. The present thesis will report the application of theoretical chiroptical spectroscopies in the field of drug analysis, with particular emphasis on the huge influence of conformational flexibility and solvation on chiroptical properties and on the main computational strategies available to describe their effects by means of electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The combination of experimental chiroptical spectroscopies with state-of-the-art computational methods proved to be very efficient at predicting the absolute configuration of a wide range of bioactive molecules (fluorinated 2-arylpropionic acids, β-lactam derivatives, difenoconazole, fenoterol, mycoleptones, austdiol). The results obtained for the investigated systems showed that great care must be taken in describing the molecular system in the most accurate fashion, since chiroptical properties are very sensitive to small electronic and conformational perturbations. In the future, the improvement of theoretical models and methods, such as ab initio molecular dynamics, will benefit pharmaceutical analysis in the investigation of non-trivial effects on the chiroptical properties of solvated systems and in the characterisation of the stereochemistry of complex chiral drugs.
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Weber, Alexander. "Supramolecular organisation, conformation and electronic properties of porphyrin molecules on metal substrates." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/201.

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The investigation and control of molecular properties is currently a dynamic research field. Here I present molecular level studies of porphyrin molecules adsorbed on metal surfaces via Low Temperature Scanning Tunneling Microscopy/Spectroscopy (STM/STS), supported by complementary X-ray absorption experiments. Intermolecular and molecule-surface interactions of tetrapyrdil porphyrin (TPyP) on Ag(111) and Cu(111) were investigated. TPyP self-assembles on Ag(111) over a wide sample temperature range into large, highly-ordered 2D chiral domains. By contrast, adsorption of TPyP on the more reactive Cu(111) leads to temperature dependent assemblies, governed decisively by the strong substrate influence. The increased metal-surface interactions on Cu(111) are accompanied by a conformational distortion of the porphyrin macrocycle. The TPyP’s pyridil groups were coordinated with single iron molecules, forming metal-organic complexes. Furthermore, the porphyrin’s macrocycle was metalated by exposing a layer of well-ordered TPyP to an iron atom beam, demonstrating a novel approach towards the fabrication of metallo-tetraaryl porphyrins performed in two dimensions under ultrahigh vacuum conditions. This method was similarly used to form lanthanideporphyrinates by coordinating tetraphenyl porphyrin (TPP) macrocycles with cerium. The influence of the metal center on the porphyrins’ electronic structure was investigated via STS for TPP, TPyP,Fe−TPyP, Fe−TPP, Ce−TPP, and Co−TPP, whereby the inhomogenous electron density distribution associated with individual frontier orbitals were imaged via dI/dV mapping. The symmetry and form of the molecular orbitals could be directly correlated to the saddle-shaped conformational adaptation for the case of Co −TPP.
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Sandin, Sara. "Cryo-electron tomography of individual protein molecules /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.

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Back, Kevin. "The crystallisation of conformationally flexible molecules." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/the-crystallisation-of-conformationally-flexible-molecules(e00131ab-f91f-4bc9-902b-421e4d70fd74).html.

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Crystallising large, flexible molecules, which are becoming more common in pharmaceutical development, often presents significant challenges for chemists and particle scientists. These difficulties are sometimes attributed to the flexibility of the molecule, and the existence of multiple conformers in solution. Structurally related impurities, frequently present when crystallising these materials, can also impact on growth and habit, and both these aspects are considered in this thesis. This work considers two pharmaceutical compounds, a relatively small but nonetheless flexible molecule, ethenzamide, and a precursor of Amprenavir, a much larger molecule. Both compounds typically grow as thin needles in a wide variety of solvents, and effort was required to grow suitable crystals for structure determination. Ethenzamide has an unusual structure, the amide group being out-of-plane relative to the ring, while in all known co-crystals of the compound, including three new co-crystal structures determined in this work, it has a planar structure with an intramolecular hydrogen bond not seen in the single component crystal. Theoretical structure generation calculations suggest a second polymorph with a planar conformation may exist, though a screen has not found any further solid phases. ab initio work suggests the planar conformation is the stable arrangement in vacuo. Several structures for the Amprenavir intermediate have been determined, as an ethanol solvate, a methanol solvate and a hydrate. A phase diagram has been measured in the industrial solvent mix, and the nucleation and growth properties of this molecule, both pure and in the presence of several structurally related impurities, have been measured. The Cambridge Structural Database has been searched for similar structures, and conformational searches have been carried out for both molecules, using vacuum phase ab initio energy calculations. Infrared spectroscopy has been used to investigate solution phase structure. These theoretical and practical studies will try to relate conformational properties to crystallisation behaviour.
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Clark, Jenny. "Intermolecular interactions in π-conjugated molecules : optical probes of chain conformation". Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597713.

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A study of interactions between molecules of the same material was performed on a model polymer system. Regio-regular poly(3-hexylthiophene) (P3HT) self-organises into two-dimensional π-stacked lamellar structures. Although the chains pack at a distance of only 3.8Å, the resonant coulomb interaction between nearest-neighbour molecules is small, owing to large average conjugation lengths within the lamellae. When the resonant coulomb (or excitonic) interaction is smaller than the vibrational relaxation energy, the excitation is localised on a single molecule and the coupling is termed <i>weak. </i>Here we demonstrate that the polymer absorption and emission spectra can be comprehensively explained using a weakly interacting H-aggregate model. Using an analytic form of the model we can estimate the excitonic interaction energy from the ratio of the 0-0 and 0-1 absorbance peaks. It was found to vary between 5-30meV. We use this powerfully simple tool to determine how film micromorphology depends on processing. We find that films spun from low boiling point solvents show a decrease in crystalline quality, an increase in excitonic coupling and more amorphous regions, than films spun from high boiling point solvents. We correlate these findings with field-effect transistor characteristics to produce a model of film micro-morphology. We also demonstrate preliminary results that show that due to the aggregate nature of the primary neutral excitation, photo-induced charge generation in P3HT is due to exciton-exciton annihilation. Finally, we study the intermolecular interactions at an interface between two different molecules (a hole transporting polymer, TFB (Poly(9,9-dioctylfluorene –<i>co</i>-N-(4-butylphenyl)diphenylamine)) and an electron-transporting disoctic, HATNA-SC12 (Hexa-azatrinaphthylene)). Depending on the energetics of the interface between two materials, the inter-molecular state can be stabilised by either coulomb interactions (as in the case of single material interfaces) or charge-transfer interactions. In this case, we find that the charge-transfer interactions dominate and an excited-state complex, or exciplex, is formed. The exciplex is generated efficiently in light-emitting diodes, producing a pure red emission. In polymer/polymer blends efficient bulk exciton emission can occur due to endothermic transfer from the exciplex to the bulk exciton. In this system, however the exciplex is stable at the interface, acting as an energy bottleneck with inefficient transfer to bulk exciton states. Furthermore, the yield of charge separation is low.
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Zhang, Fang. "The regulation of conformation and binding kinetics of integrin alphaLbeta2." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/24678.

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Thesis (M. S.)--Biomedical Engineering, Georgia Institute of Technology, 2008.<br>Committee Chair: Zhu, Cheng; Committee Member: Babensee , Julia; Committee Member: Garcia, Andres; Committee Member: McIntire, Larry; Committee Member: Selvaraj, Periasamy; Committee Member: Springer, Timothy
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Лопаткін, Юрій Михайлович, Юрий Михайлович Лопаткин, Yurii Mykhailovych Lopatkin, et al. "Biphenyl Molecules as Elements of Nanoelectronics in the Electric Field." Thesis, Sumy State University, 2012. http://essuir.sumdu.edu.ua/handle/123456789/35480.

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This paper presents the results of investigations of the influence of the longitudinal and transverse electric field on the potential surface, the dipole moment and electronic spectra of the substituted biphenyl molecules that are offered for the role of the elements of nanoelectronics. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35480
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Nanjunda, Rupesh K. "Sequence-Specific and Conformation-Specific Targeting of Duplex and Quadruplex DNA Grooves with Small Molecules." Digital Archive @ GSU, 2010. http://digitalarchive.gsu.edu/chemistry_diss/47.

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Small molecule mediated chemical intervention of biological processes using nucleic acid targets has proven extremely successful and is continually providing exciting new avenues for the development of anti-cancer agents and molecular probes. Among the alternative DNA confrormations, G-quadruplexes has certainly garnered much recognition due to increase in evidences supporting their involvement in diverse biological process. The grooves of the quadruplexes offer an alternate recognition site for ligand interactions with potentially higher selectivity than the traditional terminal stacking sites. DB832, a bifuryl-phenyl diamidine, was recently reported to selectively recognize human telomeric G-quadruplex, as a stacked species, with significant selectivity over duplex sequences. A series of biophysical studies were conducted to test the groove-binding mode of DB832, along with the selectivity for diverse quadruplex forming sequences. To gain better understanding of quadruplex groove-recognition by DB832, a series of structurally similar heterocyclic diamidines were also evaluated. The unique binding mode of DB832 may allow it to serve as a paradigm for the design of new class of highly selective quadruplex groove-binding molecules. Beyond the alternative secondary structures, it is also becoming increasingly apparent that the structure and dynamics of the canonical Watson–Crick DNA double helix play pivotal roles in diverse biological functions. DB1878, a phenyl-furan-indole diamidine, was shown to recognize a mixed GC/AT motif as a stacked antiparallel dimer, and a detailed structural analysis is reported here. Interestingly, the DNA recognition is completely different from the reported molecules in literature, and represents an entirely new motif for DNA minor groove recognition.
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NGADI, LEON. "Synthese de mono et bis-acridinones-9 et thio-9 acridinones substituees en position 1 : analyse conformationnelle et etude de proprietes antimicrobiennes de molecules temoins." Aix-Marseille 2, 1989. http://www.theses.fr/1989AIX22970.

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Books on the topic "Conformation of molecules"

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Hartmut, Frank, Holmstedt Bo, Testa Bernard, and Tübingen Symposium on Chirality and Biological Activity (1st : 1988), eds. Chirality and biological activity: Proceedings of an international symposium held at Tubingen, Federal Republic of Germany, April 5-8, 1988. A.R. Liss, 1990.

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Kwon, Youngah. Understanding and Controlling Conjugated Polymer Conformation and Photophysics: From Single Molecules to Aggregates. [publisher not identified], 2020.

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1946-, Sedzik Jan, Riccio Paolo 1942-, Karolinska institutet, and MARIE Network, eds. Molecules: Nucleation, aggregation, and crystallization : beyond medical and other implications. World Scientific, 2009.

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1923-, Ramaseshan S., Balaram P, and Ramachandran G. N. 1922-, eds. Molecular conformation and biological interactions. Indian Academy of Sciences, 1991.

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Brogaard, Rasmus Y. Molecular Conformation and Organic Photochemistry. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29381-8.

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Crippen, G. M. Distance geometry and molecular conformation. Research Studies Press, 1988.

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Hamaguchi, Kōzō. The protein molecule: Conformation, stability, and folding. Japan Scientific Societies Press, 1992.

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NATO, Advanced Research Workshop on Structures and Conformations of Non-Rigid Molecules (1992 Reisensburg Germany). Structures and conformations of non-rigid molecules. Kluwer Academic Publishers, 1993.

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Laane, Jaan, Marwan Dakkouri, Ben Veken, and Heinz Oberhammer, eds. Structures and Conformations of Non-Rigid Molecules. Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-2074-6.

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J, Langone John, ed. Molecular design and modeling: Concepts and applications. Academic Press, 1991.

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Book chapters on the topic "Conformation of molecules"

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Grajcar, L., N. Leygue, M. H. Baron, S. Becouarn, S. Czernecki, and J. M. Valery. "Marker of Local Conformation of Oligonucleotides." In Spectroscopy of Biological Molecules: Modern Trends. Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5622-6_104.

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March, Norman H. "Conformation and Electronic Structure of Polyatomic Molecules." In Chemical Bonds Outside Metal Surfaces. Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2117-0_3.

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Semprini, E., G. Perez, Ferdinanda Stefani, Patrizia Cafarelli, A. De Stefanis, and A. A. G. Tomlinson. "Molecular Dynamics Simulation of Organic Molecules Distorted Conformation in Zeolites." In Advances in Science and Technology. Trans Tech Publications Ltd., 2006. http://dx.doi.org/10.4028/3-908158-07-9.140.

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Pohle, W., R. N. A. H. Lewis, R. N. Mcelhaney, P. Nuhn, B. Dobner, and C. Selle. "Fourier-Transform Infrared Spectroscopic Monitoring of the Conformation of Glycerophospholipids." In Spectroscopy of Biological Molecules. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0371-8_171.

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Taneva, Stefka G., Sonia Bañuelos, and Arturo Muga. "Protein-membrane interaction: Lipid environment modulates protein conformation." In Spectroscopy of Biological Molecules: New Directions. Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4479-7_152.

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Misselwitz, R., G. Hausdorf, K. Welfle, W. E. Höhne, and H. Welfle. "Conformation and Stability of Recombinant HIV-1 Capsid Protein P24 (rp24)." In Spectroscopy of Biological Molecules. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0371-8_46.

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Wüthrich, K. "Glucagon Conformation in Different Environments: Implications for Molecular Recognition." In Design and Synthesis of Organic Molecules Based on Molecular Recognition. Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-70926-5_6.

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Williamson, Mike P. "Pressure-Dependent Conformation and Fluctuation in Folded Protein Molecules." In Subcellular Biochemistry. Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9918-8_6.

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Beiersdörfer, Susanne, Jens Schmitt, Markus Sauer, et al. "Finding the conformation of organic molecules with genetic algorithms." In Parallel Problem Solving from Nature — PPSN IV. Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/3-540-61723-x_1060.

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Charra, F., J. Messier, C. Sentein, A. Proń, and M. Zagórska. "Influence of Conformation on Two-Photon Spectra of Polyalkylthiophene." In Organic Molecules for Nonlinear Optics and Photonics. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3370-8_19.

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Conference papers on the topic "Conformation of molecules"

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Gu, S., Z. Zhu, and Y. Li. "THz wave regulates molecular conformational transition." In 2024 IEEE International Conference on Plasma Science (ICOPS). IEEE, 2024. http://dx.doi.org/10.1109/icops58192.2024.10627156.

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Sikes, C. Steven, Andrzej Wierzbicki, and J. D. Sallis. "Molecular Mechanisms of Control of Formation of Calcium Oxalate." In CORROSION 1995. NACE International, 1995. https://doi.org/10.5006/c1995-95473.

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Abstract The design of inhibitors of crystallization is aided by an understanding of the binding of the inhibitors at the molecular level and the influence of the binding on crystal morphology. Binding of citrate and phosphocitrate to calcium oxalate monohydrate (COM) crystals has been studied using scanning electron microscopy and molecular modeling. The COM crystal lattice presents two distinct surfaces that are not only calcium-rich but also have oxalate groups that are perpendicular to the liquid interface. This offers the best possibility for interaction with incoming anionic groups of an inhibitor molecule, allowing the most effective coordination with calcium ions of the lattice surface. For example, conformation and binding energies of citrate and phosphocitrate at (-1 0 1) and (0 1 0) surfaces of COM have been evaluated. The superior performance of phosphocitrate as an inhibitor of COM formation can be attributed to the more favorable coordination of its functional groups with calcium ions of the (-1 0 1) and (0 1 0) surfaces. These concepts may be relevant to the design of new antiscalants.
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Golodnizky, Daniel, Carlos E. S. Bernardes, Maya Davidovich-Pinhas, Ronit Bitton, and Yulia Shmidov. "Isotropic liquid state of triacylglycerols: The starting point of fats and oils crystallization." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/ggfh1118.

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Over the years, several models of triacylglycerol (TAG) molecular conformations and bulk arrangements in isotropic liquid state have been proposed and are still up for debate. This organization is the starting state, from which the molecules self-assemble and form the initial stable nucleus, which then grows to form the solid crystal. The current research aims to explore the isotropic liquid state, while focusing on its impact on nucleation and crystal formation. This aim was addressed by implementing experimental methods, such as X-ray diffraction and small-angle X-ray scattering coupled with a computational method, such as molecular dynamics simulation. These techniques were used to study tristearin and triolein as models for saturated and unsaturated TAGs, respectively. Four different conformations were suggested for the two TAGs, and the results showed conformation abundancy in the order: trident (Tr) &gt; chair (Ch) &gt; propeller (Pr) &gt; tuning-fork (Tf). The existence of clusters was demonstrated, each of which exhibited a heterogeneous distribution of conformations. The preferability to find a specific pair of conformations next to each other was analyzed and, surprisingly, it was found that Tf will preferably pair only with Tr although Tf is the preferable conformation in most crystal polymorphs. High general conversion rates from any conformation to another, and high specific conversion rates from and to the Tf conformation were calculated. It is proposed that the high conversion rates observed enable the crystallization process, despite the low proportion of Tf molecules. Overall, the results confirm the formation of specific structures in the liquid state, which combine all previously suggested models and further expand the knowledge using experimental and computational tools.
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Pratt, David W. "Methyl rotors in large molecules: probes of intramolecular vibrational relaxation and electronic structure." In OSA Annual Meeting. Optica Publishing Group, 1990. http://dx.doi.org/10.1364/oam.1990.fg2.

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A methyl (CH3) group that is attached to a large molecule by a covalent bond adopts a preferred conformation with respect to nearby bonds and exhibits large-amplitude torsional motion. Both the preferred conformations and torsional motions are influenced by the local electronic environment. Additionally, the low-frequency torsional modes may couple to other molecular vibrational modes, providing a mechanism for intramolecular vibrational energy redistribution (IVR).
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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. 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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Philips, Laura A., Christopher L. Brummel, and Steven W. Mork. "High resolution infrared spectroscopy as a tool to measure chemical reaction dynamics." In OSA Annual Meeting. Optica Publishing Group, 1991. http://dx.doi.org/10.1364/oam.1991.thq4.

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Both intra- and intermolecular interactions play an important role in determining the potential surface for a chemical reaction. Such interactions determine both physical structure and chemical reactivity. High resolution infrared spectroscopy has been used to probe both molecular structure and vibrationally induced chemistry. 2-fluorethanol is an example of a molecule in which the strong attractive interactions between F and the OH moity not only determine the lowest energy conformation of the molecule, but also the most efficient vibrational excitation for inducing conformational isomerization. An analogue of 2-fluoroethanol, 1,2-difluoroethane, although similar in structure, has quite different intramolecular interactions. These differences are apparent in both the isomerization dynamics and the spectroscopy. Spectra were measured using a color center laser with optothermal detection (resolution = 10-4 cm-1). The spectra of these molecules allow us to link vibrational mode-coupling to chemical reactivity.
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Kazerounian, Kazem, Khalid Latif, Kimberly Rodriguez, and Carlos Alvarado. "ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57243.

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Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.
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Leshenyuk, N. S., M. V. Prigun, E. E. Apanasevitsh, and G. S. Kruglik. "Conformation change of enzyme molecules in laser radiation field." In The International Conference on Coherent and Nonlinear Optics, edited by Sergey A. Tikhomirov, Thomas Udem, Valery Yudin, Maxim Pshenichnikov, and Oleg M. Sarkisov. SPIE, 2007. http://dx.doi.org/10.1117/12.752458.

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Worden, Matt, Hongbo Wang, Anant Paravastu, and William S. Oates. "NMR Characteristics of Photomechanics and Thermomechanics of Azobenzene Polymer Networks." In ASME 2012 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/smasis2012-8076.

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Azobenzene polymer networks have drawn interests in the area of adaptive materials and structures due to their novel photo-responsive material coupling. These materials undergo a complex light driven molecular conformation change of the azobenzene chromophore when the material is exposed to ultraviolet (UV) or blue-green light. This photoisomerization process is characterized by a molecular conformation change from a rod shaped molecule to a strongly kinked molecule, also known as trans-cis photoisomerization under UV light exposure. Exposure to blue-green light can lead to a trans-cis-trans photoisomerization or a relaxation from the kinked cis state back to the trans rod state. The latter process is of strong interests for adaptive structure applications because the relaxation back to the trans state can be controlled by the orientation of polarized light. When these azobenzene molecules undergo this process in a polymer network, bending and twisting deformation can be controlled by the polarization orientation of the blue-green light. To better understand the distribution of the molecular conformation changes that influences macroscopic polymer deformation, we have conducted solid state Nuclear Magnetic Resonance (ss-NMR) tests on fluorine doped azobenzene polymer networks. Here, we illustrate measurable chemical shifts due to blue light exposure near the 450 nm wavelength using a static ss-NMR probe. The results are compared to ss-NMR at different temperatures using Magic Angle Spinning (MAS) NMR to understand any potential influences of heat relative to photoisomerization.
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Salac, David, and Wei Lu. "Designed Formation of Nanocomposites via Dipole Interaction." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-14991.

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The formation of designed nanocomposites by multiple layers of adsorbate molecules is studied. We consider the presence of two types of molecules in each layer, which are characterized by different dipole moments. The nanostructures are characterized by the non-uniform distribution of the two molecules. A phase field model is developed to simulate the molecular diffusion and patterning under the combined actions of dipole moments, intermolecular forces, entropy, and external electric field. The study reveals self-alignment, structure conformation and the possibility to reduce the domain sizes via a layer by layer approach. It is also shown that the structure in a layer may define the roadway for molecules to travel on top it. This combined with electrodes embedded in the substrate gives much flexibility to guide the molecular organization and fabrication of designed nanocomposites.
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Reports on the topic "Conformation of molecules"

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Kokpol, Sirirat, Supot Hannongbua, and Prayong Doungdee. A study of the influence of Na[superscript +] on the conformation of glycine zwitterion in aqueous solution. Chulalongkorn University, 1987. https://doi.org/10.58837/chula.res.1987.15.

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The interaction of glycine zwitterion and water is calculated using ab initio method with minimized GLO basis set. The first hydration shell of glycine zwitterion is predicted to compose of five water molecules. The influence of the first hydration to the internal rotation of glycine zwitterion is studied and the energy optimized pathway is compared with that of isolated molecule. The investigation of glycine zwitterion-Na[superscript +] complex in water provides that the two coordinated water of aquo complex of Na[superscript +] are dehydrated and replaced by glycine zwitterion. Thus the formula of the complex is described as [ Na(gly) (H[subscript 2]O[subscript 4] ] [superscript +]. The Na[superscript +]-OH[subscript 2] distances in the complex are 2.20 A. The effect of . Na[superscript +] and its coordinated water on the first hydration shell of glycine zwitterion are discussed on the basis of both charge distribution and stabilization energies.
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Bowers, Michael T. Conformations of Macro Molecules. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada419807.

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Mohs, John C. Applications of Molecular Modeling to Transition State Energies and Conformations. Defense Technical Information Center, 1992. http://dx.doi.org/10.21236/ada257130.

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Meza, J. C., and M. L. Martinez. A numerical study of hybrid optimization methods for the molecular conformation problems. Office of Scientific and Technical Information (OSTI), 1993. http://dx.doi.org/10.2172/10175387.

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Lu, Hong P. Controlling Protein Conformations to Explore Unprecedented Material Properties by Single-Molecule Surgery. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada584676.

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Seeman, Jeffrey I., Henry V. Secor, P. J. Breen, V. H. Grassian, and E. R. Bernstein. A Study of Non-Rigid Aromatic Molecules by Supersonic Molecular Jet Spectroscopy: Observation and Spectroscopic Analysis of the Stable Conformations of Various Alkylbenzenes. Defense Technical Information Center, 1988. http://dx.doi.org/10.21236/ada199409.

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Rempe, Susan, Josh Vermaas, and Emad Tajkhorshid. Coupling Chemical Energy with Protein Conformational Changes to Translocate Small Molecules Across Membranes. Office of Scientific and Technical Information (OSTI), 2016. http://dx.doi.org/10.2172/1563079.

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Collins, Brian. Polarized resonant X-ray scattering to measure molecular orientation and conformation in organic nanostructures. Office of Scientific and Technical Information (OSTI), 2023. https://doi.org/10.2172/2267577.

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Laurence, Ted Alfred. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions. Office of Scientific and Technical Information (OSTI), 2002. http://dx.doi.org/10.2172/813378.

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Schutt, Timothy C., and Manoj K. Shukla. Computational Investigation on Interactions Between Some Munitions Compounds and Humic Substances. Engineer Research and Development Center (U.S.), 2021. http://dx.doi.org/10.21079/11681/39703.

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Humic acid substances (HAs) in natural soil and sediment environments effect the retention and degradation of insensitive munitions compounds and legacy high explosives (MCs): DNAN, DNi- NH4+, nMNA, NQ, NTO (neutral and anionic forms), TNT, and RDX.A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons. Ionization potentials suggest HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs are very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed the HAs tend to radicalize first thus buffering MCs against reductive as well as oxidative attacks.
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