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Journal articles on the topic 'Molecule'

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Published: 4 June 2021
Last updated: 7 September 2023

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1

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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2

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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3

Gregory, Philip D., Jacob A. Blackmore, Frye Matthew D, Luke M. Fernley, Sarah L. Bromley, Jeremy M. Hutson, and Simon L. Cornish. "Molecule–molecule and atom–molecule collisions with ultracold RbCs molecules." New Journal of Physics 23, no. 12 (December 1, 2021): 125004. http://dx.doi.org/10.1088/1367-2630/ac3c63.

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Abstract Understanding ultracold collisions involving molecules is of fundamental importance for current experiments, where inelastic collisions typically limit the lifetime of molecular ensembles in optical traps. Here we present a broad study of optically trapped ultracold RbCs molecules in collisions with one another, in reactive collisions with Rb atoms, and in nonreactive collisions with Cs atoms. For experiments with RbCs alone, we show that by modulating the intensity of the optical trap, such that the molecules spend 75% of each modulation cycle in the dark, we partially suppress collisional loss of the molecules. This is evidence for optical excitation of molecule pairs mediated via sticky collisions. We find that the suppression is less effective for molecules not prepared in the spin-stretched hyperfine ground state. This may be due either to longer lifetimes for complexes in the dark or to laser-free decay pathways. For atom–molecule mixtures, RbCs + Rb and RbCs + Cs, we demonstrate that the rate of collisional loss of molecules scales linearly with the density of atoms. This indicates that, in both cases, the loss of molecules is rate-limited by two-body atom–molecule processes. For both mixtures, we measure loss rates that are below the thermally averaged universal limit.
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4

Tao, Feng. "Nanoscale surface chemistry in self- and directed-assembly of organic molecules on solid surfaces and synthesis of nanostructured organic architectures." Pure and Applied Chemistry 80, no. 1 (January 1, 2008): 45–57. http://dx.doi.org/10.1351/pac200880010045.

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This article briefly reviews the interplay of weak noncovalent interactions involved in the formation of self-assembled monolayers of organic molecules and the strong chemical binding in directed-assembly of organic molecules on solid surfaces. For a self-assembled monolayer, each molecule involves at least three categories of weak interactions, including molecule-substrate interactions, molecule-molecule interactions in a lamella, and molecule-molecule interactions between two adjacent lamellae. Basically, molecule-substrate interactions play a major role in determining molecular configuration. Molecule-molecule interactions, particularly the interactions of molecular ending functional groups between two adjacent lamellae, such as hydrogen bonds, play a dominant role in determining the molecular packing pattern in a monolayer. These weak interactions may induce or influence molecular chirality. This understanding at the atomic scale allows us to design 2D nanostructured organic materials via precisely manipulating these weak noncovalent interactions. Compared to the self-assembled monolayer formed via weak noncovalent interactions, the structure of directed-assembled monolayer/multilayers formed through strong chemical bonds is significantly dependent on the geometric arrangement and reactivity of active sites on the solid surface. In contrast to the significant role of weak intermolecular interactions in determining molecular packing in a self-assembled monolayer, strong chemical binding between molecules and reactive sites of a substrate plays a major role in determining the molecular packing pattern in a directed-assembly monolayer. Controllable chemical attachment between organic functional groups and reactive sites of the solid surface is crucial for the formation of a highly oriented organic monolayer and the following multilayer.
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5

Fan, Yang, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, and Tao Qin. "Back translation for molecule generation." Bioinformatics 38, no. 5 (December 7, 2021): 1244–51. http://dx.doi.org/10.1093/bioinformatics/btab817.

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Abstract Motivation Molecule generation, which is to generate new molecules, is an important problem in bioinformatics. Typical tasks include generating molecules with given properties, molecular property improvement (i.e. improving specific properties of an input molecule), retrosynthesis (i.e. predicting the molecules that can be used to synthesize a target molecule), etc. Recently, deep-learning-based methods received more attention for molecule generation. The labeled data of bioinformatics is usually costly to obtain, but there are millions of unlabeled molecules. Inspired by the success of sequence generation in natural language processing with unlabeled data, we would like to explore an effective way of using unlabeled molecules for molecule generation. Results We propose a new method, back translation for molecule generation, which is a simple yet effective semisupervised method. Let X be the source domain, which is the collection of properties, the molecules to be optimized, etc. Let Y be the target domain which is the collection of molecules. In particular, given a main task which is about to learn a mapping from the source domain X to the target domain Y, we first train a reversed model g for the Y to X mapping. After that, we use g to back translate the unlabeled data in Y to X and obtain more synthetic data. Finally, we combine the synthetic data with the labeled data and train a model for the main task. We conduct experiments on molecular property improvement and retrosynthesis, and we achieve state-of-the-art results on four molecule generation tasks and one retrosynthesis benchmark, USPTO-50k. Availability and implementation Our code and data are available at https://github.com/fyabc/BT4MolGen. Supplementary information Supplementary data are available at Bioinformatics online.
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6

Petrov, Victor, and Marta Avilova. "Theoretical Investigations of the Interaction of Gaseous Pollutants Molecules with the Polyacrylonitrile Surface." Chemosensors 6, no. 3 (September 13, 2018): 39. http://dx.doi.org/10.3390/chemosensors6030039.

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This work presents theoretical studies of the interaction of molecules of several gaseous pollutants with polyacrylonitrile (PAN) surface in the presence of a water and/or oxygen molecule. For this purpose, a PAN cluster model has been proposed by the methods of quantum chemical calculations and molecular modeling. The energy-favorable positions, in which the gas molecules are located relative to the surface of the PAN cluster, are determined and the thermodynamic and the following geometric parameters of the systems are calculated: “PAN cluster − oxygen molecule”, “PAN cluster − oxygen molecule − gas molecule”, “PAN cluster − water molecule − molecule of oxygen”, and “PAN cluster − a molecule of water − an oxygen molecule − a gas molecule”. It is concluded that PAN in atmospheric air in the presence of oxygen molecules is sensitive to carbon oxide (IV), sulfur (IV) oxide, chlorine, hydrogen sulfide and carbon oxide (II). In an anoxic environment, PAN films will show selective sensitivity to chlorine. The presence of water molecules in the investigated air should not affect the gas sensitivity of PAN films.
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7

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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8

Magrashi, Maryam Ali, and Elham Shafik Aazam. "The co-crystal 4,6-diacetylresorcinol–1-aminopyrene (2/1)." Acta Crystallographica Section E Crystallographic Communications 78, no. 6 (May 31, 2022): 679–81. http://dx.doi.org/10.1107/s2056989022005588.

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The structure of the title molecular complex, C16H11N·2C10H10O4, at 150 K has been determined. The molecules form stacks consisting of aggregates with disordered 1-aminopyrene molecule surrounded by two 4,6-diacetylresorcinol molecules. Neighbouring stacks are linked by hydrogen bonds between the amine H atoms of the 1-aminopyrene molecule with the adjacent carbonyl oxygen atom of the 4,6-diacetylresorcinol molecule.
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9

Chia, Tze Shyang, and Ching Kheng Quah. "Temperature-induced phase transition of isonicotinamide-malonic acid (2/1) and supramolecular construct analysis of isonicotinamide structures." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 8 (July 26, 2018): 539–54. http://dx.doi.org/10.1515/zkri-2017-2109.

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Abstract The isonicotinamide-malonic acid (2/1) co-crystal salt (2IN·C3) exhibits a first-order displacive structural phase transition from low-temperature triclinic P1̅ crystal structure to high-temperature monoclinic C2/c crystal structure and vice versa at the transition temperatures of 298 (1) and 295 (1) K, respectively, as determined by variable-temperature SCXRD analysis and DSC measurements. The asymmetric unit of 2IN·C3 comprises three malonic acid molecules and six isonicotinamide molecules at the low-temperature phase, and this is reduced to a half-molecule of malonic acid and an isonicotinamide molecule in the high-temperature phase. The carboxyl and pyridinium H atoms are disordered at both phases. The observed phase transition near room temperature is triggered by the molecular displacement of the isonicotinamide molecule and the syn-anti conformational transformation of the malonic acid molecule with deviation angles of 10.4 and 11.7°, respectively, which induced an energy change of 19.1 kJ mol−1 in the molecular cluster comprising a central isonicotinamide molecule and eight neighboring molecules. However, the total interaction energy of the molecular cluster of a central malonic acid molecule and eight neighboring molecules does not change significantly upon the phase transition. The molecules of isonicotinamide structures except IN·IN+·triazole‒ form zero-dimensional finite arrays or one-dimensional chains as the primary supramolecular construct by carboxyl···pyridyl (−35.9 to −56.7 kJ mol−1) and carboxamide···carboxamide (−53.6 to −68.7 kJ mol−1) or carboxyl···carboxamide (−52.6 to −67.1 kJ mol−1) synthons.
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10

Avilova, Marta M., Ekaterina A. Mar'yeva, Olga V. Popova, and Tat'yana G. Ivanova. "MOLECULAR MODELING OF ADSORPTION OF POLLUTANT GASES ON CADMIUM-CONTAINING POLYACRYLONITRILE." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENII KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 63, no. 4 (April 16, 2020): 49–54. http://dx.doi.org/10.6060/ivkkt.20206304.6008.

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The paper presents theoretical studies of the adsorption of pollutant gases on the surface of cadmium-containing polyacrylonitrile (Cd-polyacrylonitrile) in the absence and presence of water molecules and oxygen molecules in the environment. The list of gases to which the Cd-polyacrylonitrile surface may have the highest sensitivity is determined. Nitrogen dioxide, methane, ammonia, sulfur oxide (II), hydrogen sulfide, ozone, carbon monoxide, carbon oxide (II), chlorine were chosen as pollutant gases. The following software packages are used for modeling: HyperChem, Gaussian 09, Сhemoffice 2010. Polyacrylonitrile macromolecule models were obtained from HyperChem, Gaussian 09, from which a pentamer macromolecule was chosen to produce a Cd-polyacrylonitrile cluster. Then, implementing the molecular mechanics method in Сhemoffice 2010, namely in the Chem3D subroutine, the Cd-polyacrylonitrile cluster model is constructed. Further, using the molecular modeling method, the following thermodynamic parameters were determined: «Cd-polyacrylonitrile cluster – gas molecule», «Cd-polyacrylonitrile cluster – oxygen molecule», «Cd-polyacrylonitrile cluster – water molecule», «Cd-polyacrylonitrile cluster – oxygen molecule gas molecule», «Cd-polyacrylonitrile cluster – water molecule – gas molecule». As a result of molecular modeling, it was established that Cd-polyacrylonitrile in the atmospheric air exhibits selective sensitivity to gaseous chlorine and carbon monoxide; in an oxygen-free environment – also to hydrogen sulfide. The results of molecular modeling confirm the previously obtained experimental data on the evaluation of the gas sensitivity of Cd-polyacrylonitrile and indicate the presence of van der Waals forces between the Cd-polyacrylonitrile and the adsorbed gas molecule. The presence or absence of water molecules in atmospheric air should not affect the change in the sensitivity of Cd-polyacrylonitrile to pollutant gases.
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11

ORRIT, M., and J. BERNARD. "SINGLE MOLECULE SPECTROSCOPY." Modern Physics Letters B 05, no. 11 (May 10, 1991): 747–51. http://dx.doi.org/10.1142/s0217984991000927.

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We report unambiguous optical detection of single molecules of pentacene in p-terphenyl crystal. The relative shift of the molecular resonance frequencies with temperature changes demonstrates the phenomenon of activated spectral diffusion. These results show the feasibility of the optical study of a single molecule and its local environment.
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12

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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13

Geagea, Elie, Judicael Jeannoutot, Frank Palmino, and Frédéric Chérioux. "On-Surface Reactivity of Disubstituted-Bianthryl Molecules on Cu(111) and Au(111) Surfaces." ECS Journal of Solid State Science and Technology 11, no. 3 (March 1, 2022): 035006. http://dx.doi.org/10.1149/2162-8777/ac5d67.

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On-surface π-conjugated 1D polymers, like graphene nanoribbons, have emerged as a class of promising materials. On-surface chemical properties of 9,9′-bianthryl molecules are widely developed as they can be used as starting building blocks to provide graphene nanoribbons. Here, we propose to investigate the chemical behavior of 10,10′-disubstituted-9,9′-bianthryl molecules on Cu(111) and Au(111) surfaces by using scanning tunneling microscopy under ultra-high vacuum. We demonstrated that the balance between molecule-molecule interaction, molecule-substrate interaction, and molecular rearrangement, drastically alter the chemical properties of the adsorbed molecule by thermal annealing.
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14

Levitt, Malcolm H. "Spectroscopy of light-molecule endofullerenes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1998 (September 13, 2013): 20120429. http://dx.doi.org/10.1098/rsta.2012.0429.

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Molecular endofullerenes are supramolecular systems consisting of fullerene cages encapsulating small molecules. Although most early examples consist of encapsulated metal clusters, recently developed synthetic routes have provided endofullerenes with non-metallic guest molecules in high purity and macroscopic quantities. The encapsulated light molecule behaves as a confined quantum rotor, displaying rotational quantization as well as translational quantization, and a rich coupling between the translational and rotational degrees of freedom. Furthermore, many encapsulated molecules display spin isomerism. Spectroscopies such as inelastic neutron scattering, nuclear magnetic resonance and infrared spectroscopy may be used to obtain information on the quantized energy level structure and spin isomerism of the guest molecules. It is also possible to study the influence of the guest molecules on the cages, and to explore the communication between the guest molecules and the molecular environment outside the cage.
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15

Rangel, E., L. F. Magana, L. E. Sansores, and G. J. Vázquez. "Generation of hydrogen peroxide on a pyridine-like nitrogen-nickel doped graphene surface." MRS Proceedings 1451 (2012): 69–74. http://dx.doi.org/10.1557/opl.2012.1335.

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ABSTRACTDensity functional theory and molecular dynamics were used to study the generation of hydrogen peroxide around a nickel atom anchored on a pyridine-like nitrogen-doped graphene (PNG) layer. First, we found that two hydrogen molecules are adsorbed around the nickel atom, with adsorption energy 0.95 eV/molecule. Then we studied the interaction of oxygen molecules with this system at atmospheric pressure and 300 K. It is found that two hydrogen peroxide molecules are formed. However, at 700 K, one hydrogen peroxide molecule, and one water molecule are desorbed. One oxygen atom stays bound to the nickel atom.
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16

Fayos, Jose. "Space Group Approximation of a Molecular Crystal by Classifying Molecules for Their Electric Potentials and Roughness on Their Inertial Ellipsoid Surface." Advances in Chemistry 2014 (October 16, 2014): 1–9. http://dx.doi.org/10.1155/2014/737480.

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In order to predict the most probable space group where a molecule crystallizes, it is assumed that molecular shape and electric potential distribution on the molecular surface are the main factors or predictors. However, to compare and classify molecules by these two factors seems to be very difficult for in general such different objects. Thus, in order to compare molecules, they are reduced to their inertial ellipsoid in which surface 26 equally spaced points were chosen where a roughness factor and an electric potential due to all atomic charges of the whole molecule are calculated. By this procedure, different molecules encoded by these two predictor vectors can be compared and classified, showing that molecules that crystallize in the same space group have more similar predictor vectors. This result opens the possibility to predict the more probable spatial group associated with a molecule.
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17

Henault, Emilie S., Maria H. Rasmussen, and Jan H. Jensen. "Chemical space exploration: how genetic algorithms find the needle in the haystack." PeerJ Physical Chemistry 2 (July 31, 2020): e11. http://dx.doi.org/10.7717/peerj-pchem.11.

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We explain why search algorithms can find molecules with particular properties in an enormous chemical space (ca 1060 molecules) by considering only a tiny subset (typically 103−6 molecules). Using a very simple example, we show that the number of potential paths that the search algorithms can follow to the target is equally vast. Thus, the probability of randomly finding a molecule that is on one of these paths is quite high and from here a search algorithm can follow the path to the target molecule. A path is defined as a series of molecules that have some non-zero quantifiable similarity (score) with the target molecule and that are increasingly similar to the target molecule. The minimum path length from any point in chemical space to the target corresponds is on the order of 100 steps, where a step is the change of and atom- or bond-type. Thus, a perfect search algorithm should be able to locate a particular molecule in chemical space by screening on the order of 100s of molecules, provided the score changes incrementally. We show that the actual number for a genetic search algorithm is between 100 and several millions, and depending on the target property and its dependence on molecular changes, the molecular representation, and the number of solutions to the search problem.
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18

Weiss, Alarich. "Approaches to the Study of van der Waals Interactions in Solids." Zeitschrift für Naturforschung A 48, no. 3 (March 1, 1993): 471–77. http://dx.doi.org/10.1515/zna-1993-0306.

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Abstract Van der Waals forces are of short range. In molecular crystals the interacting atoms or groups of atoms of a molecule are fixed in their position with respect to the atoms of the neighboring molecules. From measurements of the intermolecular interactions via properties which can be assigned to the individual atoms (groups), such as hyperfine interactions or vibrational frequencies, as a function of the intermolecular distances, the van der Waals (vdW) potentials may be evaluated. We propose the use of discrete changes of intermolecular distances for studying vdW-interactions, the method of “Several Solid States”, a) by combining a molecule A with different moleculs Bi, in stoichiometric proportions and in a crystallographically ordered way to molecular solid complexes; b) by investigating the changes of atomic (group) properties in systems with two ore more solid phases appearing in the phase diagram as a function of temperature (pressure). This way of using several solid states is offered only by chance; c) by using the fact that in many molecular solids there is more than one molecule in the asymmetric unit of the elementary cell in the crystal structure, and therefore several vdW-potentials for chemically identical intermolecular neighbors; d) by the synthesis of compounds containing the atoms (groups), the vdW-interactions of which one wants to study, with one or more centers of chirality. With one center of asymmetry in the molecule one finds the molecule considered in two different situations of vdW-contacts at least, and, in first approximation, one can assume identical intramolecular interactions (besides the optical activity). Two chirality centers within the molecule lead to three (at least) different crystal fields: a) (±); b) (− −) respectively (+ +); c) (− −, + +). Examples of hyperfine interaction studies, based on this "Several Solid States" concept are discussed.
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19

ZHENG, HAO, YONG XU, GUO-CAI DONG, JÖRG KRÖGER, and RICHARD BERNDT. "STRUCTURE OF A PHTHALOCYANINE DYE ON ZnO." Surface Review and Letters 26, no. 06 (July 2019): 1850204. http://dx.doi.org/10.1142/s0218625x18502049.

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Room temperature scanning tunneling microscopy was used to investigate the adsorption of a dye molecule, iron-phthalocyanine (FePc), on ZnO(0001). Submolecular resolution reveals the orientation of molecules with respect to crystallographic directions of the surface. Upon adsorption, the molecular symmetry is reduced. First-principles calculations trace these observations to a strong molecule-substrate bond, which induces deformations of the molecule.
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20

Peng, Jinbo, Sophia Sokolov, Daniel Hernangómez-Pérez, Ferdinand Evers, Leo Gross, John M. Lupton, and Jascha Repp. "Atomically resolved single-molecule triplet quenching." Science 373, no. 6553 (July 22, 2021): 452–56. http://dx.doi.org/10.1126/science.abh1155.

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The nonequilibrium triplet state of molecules plays an important role in photocatalysis, organic photovoltaics, and photodynamic therapy. We report the direct measurement of the triplet lifetime of an individual pentacene molecule on an insulating surface with atomic resolution by introducing an electronic pump-probe method in atomic force microscopy. Strong quenching of the triplet lifetime is observed if oxygen molecules are coadsorbed in close proximity. By means of single-molecule manipulation techniques, different arrangements with oxygen molecules were created and characterized with atomic precision, allowing for the direct correlation of molecular arrangements with the lifetime of the quenched triplet. Such electrical addressing of long-lived triplets of single molecules, combined with atomic-scale manipulation, offers previously unexplored routes to control and study local spin-spin interactions.
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21

Park, Ki-Min, Hankook Oh, and Youngjin Kang. "2,2′-Bi(9,9-diethylfluorene)." Acta Crystallographica Section E Structure Reports Online 70, no. 2 (January 22, 2014): o185. http://dx.doi.org/10.1107/s1600536814001378.

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The title compound, C34H34, systematic name 9,9,9′,9′-tetraethyl-2,2′-bi(9H-fluorene), crystallized with two crystallographically independent molecules (AandB) in the asymmetric unit. These differ mainly in the orientation of the lateral ethyl chains: in moleculeA, they are both on the same side of the molecule whereas in moleculeB, one diethylfluorene moiety has undergone a 180° rotation such that the two pairs of ethyl residues appear on opposite sides of the molecule. The fluorene ring systems subtend dihedral angles of 31.37 (4) and 43.18 (3)° in moleculesAandB, respectively. Hence the two fluorene moieties are tilted slightly toward one another. This may be due to the presence of intermolecular C—H...π interactions between neighboring molecules. The lateral ethyl chains (excluding H atoms) are also almost planar, with each pair almost perpendicular to the plane of the fluorene system to which they are attached with dihedral angles between the ethyl and fluorene planes in the range 86.04 (8)–89.5 (1)°.
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22

Sivanathan, M., and B. Karthikeyan. "Computational Studies of Self Assembled 3,5 Bis(Tri Fluoro Methyl) Benzyl Amine Phenyl Alanine Nano Tubes." Materials Science Forum 1070 (October 13, 2022): 105–13. http://dx.doi.org/10.4028/p-ftw4x6.

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In this work 3,5 Bis(Tri fluro methyl)Benzyl amine phenyl alanine a monmer molecule is DFT theoretically optimized to get the structural insight of the molecule. Band gap energy, Mullikan atomic charges, DOS spectral analysis, HOMO - LUMO, Electrostatic surface potential , molecular electrostatic potential and theoretical Raman spectral analysis is computed and compared with the experimental data .Since this molecule shows self assembly similar to peptide molecules it is quite interesting to analyze its structure based on theory and experimental the results suggests the H –boding interactions between the molecules is the key mechanism. The band energy from DOS plots suggests the molecular interactions through π-π .The possibility of the self assembly is explained further from Raman spectral studies that tells the mode specific interaction among the molecules..
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23

Cui, Xing-Qian, Qian Liu, Zhi-Qiang Fan, and Zhen-Hua Zhang. "Effects of oxygen adsorption on spin transport properties of single anthracene molecular devices." Acta Physica Sinica 69, no. 24 (2020): 248501. http://dx.doi.org/10.7498/aps.69.20201028.

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With the miniaturization of molecular devices, high-performance nano devices can be fabricated by controlling the spin states of electrons. Because of their advantages such as low energy consumption, easy integration and long decoherence time, more and more attention has been paid to them. So far, the spin filtration efficiency of molecular device with graphene electrode is not very stable, which will decrease with the increase of voltage, and thus affecting its applications. Therefore, how to enhance the spin filtration efficiency of molecular device with graphene electrode becomes a scientific research problem. Using the first principle calculations based on density functional theory combined with non-equilibrium Green’s function, the physical mechanism of regulating the spin polarization transport properties of single anthracene molecule device with graphene nanoribon as electrode is investigated by molecular oxygen adsorption. In order to explore the effect of the change of the connection mode between single anthracene molecule and zigzag graphene nanoribbon electrode on the spin transport properties of the device, we establish two models. The first model is the model M1, which is the single anthracene molecule longitudinal connection, and the second model is the model M2, which is the single anthracene molecule lateral connection. The adsorption model of single oxygen molecule is denoted by M1O and M2O respectively. The results show that when none of oxygen molecules is adsorbed, the spin filtering effect of single anthracene molecule connecting graphene nanoribbons laterally (M2) is better than that of single anthracene molecule connecting graphene nanoribbons longitudinally (M1). After oxygen molecules are adsorbed on single anthracene molecule, the enhanced localized degree of transport eigenstate will make the spin current of the two kinds of devices decrease by nearly two orders of magnitude. However, molecular oxygen adsorption significantly improves the spin filtering efficiency of the device and enhances the application performance of the device. The maximal spin filtering efficiency of single anthracene molecule connecting graphene nanoribbons longitudinal (M1O) can be increased from 72% to 80%. More importantly, the device with single anthracene molecule connecting graphene nanoribbons laterally (M2) maintains nearly 100% spin filtering efficiency in a bias range from –0.5 V to +0.5 V. These results provide more theoretical guidance for practically fabricating spin molecular devices and regulating their spin transport properties.
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Chen, Bingrun, and Ke Xu. "Single Molecule-Based Electronic Devices: A Review." Nano 14, no. 11 (November 2019): 1930007. http://dx.doi.org/10.1142/s179329201930007x.

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In the face of the fact that the development of traditional silicon-based electronic devices is increasingly limited, single molecule electronic device, which has been attracting more and more attention, is considered as one of the most hopeful candidates to realize the miniaturization of conventional electronic devices. In this paper, an overview of single molecule electronic devices is provided, including molecular electronic devices and electrode types. First, several molecular electronic devices are presented, including molecular diodes, molecular memories, molecular wires, molecular field effect transistors (FET) and molecular switches. Then the influence of different electrode types of the transport characteristics is introduced, showing that graphene is a promising electrode material for single molecule electronic devices. Moreover, other excellent characteristics of molecular devices are briefly introduced, such as potential thermoelectric effects, new thermally induced spin transport phenomena and negative differential resistance (NDR) behavior. Finally, the future challenges to the development of electronic devices based on single molecules are described.
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Sun, Zhong-Fa, Marc C. van Hemert, Jérôme Loreau, Ad van der Avoird, Arthur G. Suits, and David H. Parker. "Molecular square dancing in CO-CO collisions." Science 369, no. 6501 (July 16, 2020): 307–9. http://dx.doi.org/10.1126/science.aan2729.

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Knowledge of rotational energy transfer (RET) involving carbon monoxide (CO) molecules is crucial for the interpretation of astrophysical data. As of now, our nearly perfect understanding of atom-molecule scattering shows that RET usually occurs by only a simple “bump” between partners. To advance molecular dynamics to the next step in complexity, we studied molecule-molecule scattering in great detail for collision between two CO molecules. Using advanced imaging methods and quasi-classical and fully quantum theory, we found that a synchronous movement can occur during CO-CO collisions, whereby a bump is followed by a move similar to a “do-si-do” in square dancing. This resulted in little angular deflection but high RET to both partners, a very unusual combination. The associated conditions suggest that this process can occur in other molecule-molecule systems.
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26

Efimov, Ilya, Pavel Slepukhin, and Vasiliy Bakulev. "Crystal structure of ethyl 3-(4-chlorophenyl)-5-[(E)-2-(dimethylamino)ethenyl]-1,2-oxazole-4-carboxylate." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (December 1, 2015): o1028. http://dx.doi.org/10.1107/s2056989015023257.

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In the title compound, C16H17ClN2O3, two molecules,AandB, with different conformations, comprise the asymmetric unit. In moleculeA, the C=O group of the ester points away from the benzene ring [C—C—C=O = −170.8 (3)°], whereas in moleculeB, it points back towards the benzene ring [C—C—C=O = 17.9 (4)°]. The dihedral angles betweeen the oxazole and benzene rings also differ somewhat [46.26 (13) for moleculeAand 41.59 (13) for moleculeB]. Each molecule features an intramolecular C—H...O interaction, which closes anS(6) ring. In the crystal, theBmolecules are linked into [001]C(12) chains by weak C—H...Cl interactions.
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Subasi, Erk, and Cagatay Basdogan. "A New Haptic Interaction and Visualization Approach for Rigid Molecular Docking in Virtual Environments." Presence: Teleoperators and Virtual Environments 17, no. 1 (February 1, 2008): 73–90. http://dx.doi.org/10.1162/pres.17.1.73.

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Many biological activities take place through the physicochemical interaction of two molecules. This interaction occurs when one of the molecules finds a suitable location on the surface of the other for binding. This process is known as molecular docking, and it has applications to drug design. If we can determine which drug molecule binds to a particular protein, and how the protein interacts with the bonded molecule, we can possibly enhance or inhibit its activities. This information, in turn, can be used to develop new drugs that are more effective against diseases. In this paper, we propose a new approach based on a human-computer interaction paradigm for the solution of the rigid body molecular docking problem. In our approach, a rigid ligand molecule (i.e., drug) manipulated by the user is inserted into the cavities of a rigid protein molecule to search for the binding cavity, while the molecular interaction forces are conveyed to the user via a haptic device for guidance. We developed a new visualization concept, Active Haptic Workspace (AHW), for the efficient exploration of the large protein surface in high resolution using a haptic device having a small workspace. After the discovery of the true binding site and the rough alignment of the ligand molecule inside the cavity by the user, its final configuration is calculated off-line through time stepping molecular dynamics (MD) simulations. At each time step, the optimum rigid body transformations of the ligand molecule are calculated using a new approach, which minimizes the distance error between the previous rigid body coordinates of its atoms and their new coordinates calculated by the MD simulations. The simulations are continued until the ligand molecule arrives at the lowest energy configuration. Our experimental studies conducted with six human subjects testing six different molecular complexes demonstrate that given a ligand molecule and five potential binding sites on a protein surface, the subjects can successfully identify the true binding site using visual and haptic cues. Moreover, they can roughly align the ligand molecule inside the binding cavity such that the final configuration of the ligand molecule can be determined via the proposed MD simulations.
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LLOYD, John B. "Intestinal permeability to polyethyleneglycol and sugars: a re-evaluation." Clinical Science 95, no. 1 (July 1, 1998): 107–10. http://dx.doi.org/10.1042/cs0950107.

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1.Previous studies have indicated that the permeability of polyethyleneglycol across the human intestine is anomalously high in comparison with the permeability of sugars with similar molecular mass. In consequence it has been proposed that two or more distinct mechanisms must exist for the translocation of these classes of molecule or, alternatively, that the molecular parameter determining rate of penetration is each molecule's minimum molecular dimension. 2.The notional hydrogen-bonding capacity of a molecule correlates well with oil–water partition coefficient and also, in a variety of experimental systems, with rate of passive diffusion across biological membranes. A molecule's hydrogen-bonding capacity is calculated by inspecting the structural formula and summing the individual theory-derived hydrogen-bonding capacities of the molecule's functional groups. 3.A classic set of intestinal permeability data that includes several ethyleneglycol oligomers and several sugars is re-analysed. A good correlation between permeability and hydrogen-bonding capacity is demonstrated. Specifically, there is no discontinuity between the polyethyleneglycols and the sugars. The data are compatible with a simple model in which all the molecules studied cross the intestine by passive diffusion across cellular membranes.
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Fu, Tianfan, Cao Xiao, Xinhao Li, Lucas M. Glass, and Jimeng Sun. "MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization." Proceedings of the AAAI Conference on Artificial Intelligence 35, no. 1 (May 18, 2021): 125–33. http://dx.doi.org/10.1609/aaai.v35i1.16085.

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Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative models and reinforcement learning approaches made initial success, but still face difficulties in simultaneously optimizing multiple drug properties. To address such challenges, we propose the MultI-constraint MOlecule SAmpling (MIMOSA) approach, a sampling framework to use input molecule as an initial guess and sample molecules from the target distribution. MIMOSA first pretrains two property agnostic graph neural networks (GNNs) for molecule topology and substructure-type prediction, where a substructure can be either atom or single ring. For each iteration, MIMOSA uses the GNNs’ prediction and employs three basic substructure operations (add, replace, delete) to generate new molecules and associated weights. The weights can encode multiple constraints including similarity and drug property constraints, upon which we select promising molecules for next iteration. MIMOSA enables flexible encoding of multiple property- and similarity-constraints and can efficiently generate new molecules that satisfy various property constraints and achieved up to 49.1% relative improvement over the best baseline in terms of success rate.
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Ezhilarasi, K. S., A. Akila, S. Ponnuswamy, B. K. Revathi, and G. Usha. "Crystal structure of 2,2,4-trimethyl-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepine hemihydrate." Acta Crystallographica Section E Crystallographic Communications 71, no. 8 (July 15, 2015): o570—o571. http://dx.doi.org/10.1107/s2056989015013201.

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The title compound, C12H18N2·0.5H2O, crystallizes with two independent organic molecules (AandB) in the asymmetric unit, together with a water molecule of crystallization. The diazepine rings in each molecule have a chair conformation. The dihedral angle between benzene ring and the mean plane of the diazepine ring is 21.15 (12)° in moleculeAand 17.42 (11)° in moleculeB. In the crystal, molecules are linked by N—H...O and O—H...N hydrogen bonds, forming zigzag chains propagating along [001].
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Nordon, Galia, Aviram Magen, Ido Guy, and Kira Radinsky. "Learning to Rank Articles for Molecular Queries." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 11 (June 28, 2022): 12594–600. http://dx.doi.org/10.1609/aaai.v36i11.21532.

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The cost of developing new drugs is estimated at billions of dollars per year. Identification of new molecules for drugs involves scanning existing bio-medical literature for relevant information. As the potential drug molecule is novel, retrieval of relevant information using a simple direct search is less likely to be productive. Identifying relevant papers is therefore a more complex and challenging task, which requires searching for information on molecules with similar characteristics to the novel drug. In this paper, we present the novel task of ranking documents based on novel molecule queries. Given a chemical molecular structure, we wish to rank medical papers that will contribute to a researcher's understanding of the novel molecule drug potential. We present a set of ranking algorithms and molecular embeddings to address the task. An extensive evaluation of the algorithms is performed over the molecular embeddings, studying their performance on a benchmark retrieval corpus, which we share with the community. Additionally, we introduce a heterogeneous edge-labeled graph embedding approach to address the molecule ranking task. Our evaluation shows that the proposed embedding model can significantly improve molecule ranking methods. The system is currently deployed in a targeted drug delivery and personalized medicine research laboratory.
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MATSUI, A. H., M. TAKESHIMA, K. MIZUNO, and T. AOKI-MATSUMOTO. "PHOTOPHYSICAL OVERVIEW OF EXCITATION ENERGY TRANSFER IN ORGANIC MOLECULAR ASSEMBLIES — A ROUTE TO STUDY BIO-MOLECULAR ARRAYS —." International Journal of Modern Physics B 15, no. 28n30 (December 10, 2001): 3857–60. http://dx.doi.org/10.1142/s0217979201008846.

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Excitonic processes in organic molecular crystals are discussed in terms of two parameters, the crystal size and the constituent molecule size. From the luminescence and absorption spectra of a series of aromatic molecular crystals we find a systematic change in exciton energy transport as functions of the size of crystal and its constituent molecule size. Characteristic features of bulk crystals and microcrystallites are as follows. (1) In bulk crystals exciton energy transport depends on the constituent molecule size. When molecules are small, the exciton energy transport occurs by free excitons, but when molecules are large free exciton transport disappears because excitons get self-trapped. (2) In microcrystallites, exciton energy transport depends on the crystallite size. When the size is larger than a critical one, excitons travel as quantum mechanical waves but when the size is smaller than the critical one the exciton waves get confined within the crystallite. The results are independent of the chemical species of constituent molecules and thus applicable to novel molecular arrays such as biological molecular arrays.
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Shamima Shultana, Kazi M Maraz, Arwah Ahmed, Tanzila Sultana, and Ruhul A Khan. "Drug design, discovery and development and their safety or efficacy on human body." GSC Biological and Pharmaceutical Sciences 17, no. 2 (November 30, 2021): 113–22. http://dx.doi.org/10.30574/gscbps.2021.17.2.0330.

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Drug Design, often mentioned as rational drug design or just rational design. It is defined as the study of the shape of molecules in order to determine how they will bind receptors on cells or combine with other molecules. It is based on molecular shape or architecture is an alternative to blindly testing hundreds of molecules to see if one or more of them will bind cellular or molecular targets. The drug is an organic molecule, when it is bind to target site it can either inhibit or activate the function of a bio-molecule which results in therapeutic benefit.
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El-Khoury, Patrick Z., Grant E. Johnson, Irina V. Novikova, Yu Gong, Alan G. Joly, James E. Evans, Mikhail Zamkov, Julia Laskin, and Wayne P. Hess. "Enhanced Raman scattering from aromatic dithiols electrosprayed into plasmonic nanojunctions." Faraday Discussions 184 (2015): 339–57. http://dx.doi.org/10.1039/c5fd00036j.

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We describe surface enhanced Raman spectroscopy (SERS) experiments in which molecular coverage is systematically varied from 3.8 × 105 to 3.8 × 102 to 0.38 molecules per μm2 using electrospray deposition of ethanolic 4,4′-dimercaptostilbene (DMS) solutions. The plasmonic SERS substrate used herein consists of a well-characterized 2-dimensional (2D) array of silver nanospheres (see El-Khoury et al., J. Chem. Phys., 2014, 141, 214308), previously shown to feature uniform topography and plasmonic response, as well as intense SERS activity. When compared to their ensemble averaged analogues, the spatially and temporally averaged spectra of a single molecule exhibit several unique features including: (i) distinct relative intensities of the observable Raman-active vibrational states, (ii) more pronounced SERS backgrounds, and (iii) broader Raman lines indicative of faster vibrational dephasing. The first observation may be understood on the basis of an intuitive physical picture in which the removal of averaging over multiple molecules exposes the tensorial nature of Raman scattering. When an oriented single molecule gives rise to the recorded SERS spectra, the relative orientation of the molecule with respect to vector components of the local electric field determines the relative intensities of the observable vibrational states. Using a single molecule SERS framework, described herein, we derive a unique molecular orientation in which a single DMS molecule is isolated at a nanojunction formed between two silver nanospheres in the 2D array. The DMS molecule is found lying nearly flat with respect to the metal. The derived orientation of a single molecule at a plasmonic nanojunction is consistent with observations (ii) and (iii). In particular, a careful inspection of the temporal spectral variations along the recorded single molecule SERS time sequences reveals that the time-averaged SERS backgrounds arise from individual molecular events, marked by broadened SERS signatures. We assign the broadened spectra along the SERS time sequence – which sum up to a SERS background in the averaged spectra – to instances in which the π-framework of the DMS molecule is parallel to the metal at a classical plasmonic nanojunction. This also accounts for Raman line broadening as a result of fast vibrational dephasing, and driven by molecular reorientation at a plasmonic nanojunction. Furthermore, we report on the molecular orientation dependence of single molecule SERS enhancement factors. We find that in the case of a single DMS molecule isolated at a plasmonic nanojunction, molecular orientation may affect the derived single molecule SERS enhancement factor by up to 5 orders of magnitude. Taking both chemical effects as well as molecular orientation into account, we were able to estimate a single molecule enhancement factor of ∼1010 in our measurements.
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McNab, Iain. "H2+: the molecule of molecules." Physics World 8, no. 8 (August 1995): 17. http://dx.doi.org/10.1088/2058-7058/8/8/17.

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Witze, Alexandra. "Molecules: Molecule knots itself up." Science News 181, no. 2 (January 18, 2012): 12. http://dx.doi.org/10.1002/scin.5591810212.

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Napolitano, Hamilton, Lóide Sallum, Paulo Carvalho-Jr, Valter Henrique Silva, Gilberto Aquino, and Ademir Camargo. "The Effect of the Methanol Molecule in the Stabilization of C18H18O4Chalcone." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C662. http://dx.doi.org/10.1107/s2053273314093371.

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The (E)-3-(4-hydroxy-3,5-dimethoxyphenyl)-1-p-tolylprop-2-en-1-one crystallizes in the triclinic centrossymetric P1 ¯ space group as a solvate structure (Figure 1). The asymmetric unit is described by a 2[(C18H18O4).(CH3OH)] molecular complex, in which each independent C18H18O4 molecules is bonded to a specific methanol molecule (R1 = 0.1237, wR2 = 0.1869 to all data). The presence of methanol in this crystal lattice results in a unit cell with Z' > 1 which two molecules of methanol and chalcone (alpha molecule and beta molecule) forming a stable molecular complex. With the aim of understanding the process of crystal lattice stabilization, a combination of technique has been used including X-ray diffraction (XRPD), computational molecular modeling and a molecular dynamic. The results show: alpha molecule and beta molecule are sterically barred to form direct hydrogen bond each other. On the another hand, the presence of methanol molecule stabilizes the crystal structure by bifurcated O-H...O interaction acting as a bridge between them. The theoretical thermodynamic parameter and the rigid potential energy surface scan comprise the role of methanol in the energetic stabilization of the crystal. The absence the methanol compound in the asymmetric unit destabilizes the crystalline structure, turning the formation process of the asymmetric unit not spontaneous. The energy difference between alpha and beta molecules is around 0.80 kcal/mol, indicating that both are stable and are equally possible in the crystal lattice. The analyze of the energetic profile of the C14 – O2...H1 – O3 and O2 – H1...O3 – C17 torsion angles in the packing crystal show that the alpha and beta molecules are confined in the stable potential region, in agreement with the two conformer in the asymmetric unit. The MEP show that the methanol have no steric effect that avoid small motion around the torsions angles. The authors would like to acknowledge the Brazilian agencies for financial support: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de Amparo Pesquisa do Estado de Goias (FAPEG).
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Rahman, Mahmudur, Kazi Rafiqul Islam, Md Rashedul Islam, Md Jahirul Islam, Md Rejvi Kaysir, Masuma Akter, Md Arifur Rahman, and S. M. Mahfuz Alam. "A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices." Micromachines 13, no. 6 (June 18, 2022): 968. http://dx.doi.org/10.3390/mi13060968.

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Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Hoshide, Mitsutoshi, Hyuma Masu, and Yuji Sasanuma. "Crystal structure of butane-1,4-diyl bis(furan-2-carboxylate)." Acta Crystallographica Section E Crystallographic Communications 75, no. 6 (May 24, 2019): 872–74. http://dx.doi.org/10.1107/s2056989019007175.

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The asymmetric unit of the title compound, C14H14O6, a monomeric compound of poly(butylene 2,5-furandicarboxylate), consists of one half-molecule, the whole all-trans molecule being generated by an inversion centre. In the crystal, the molecules are interconnected via C—H...O interactions, forming a molecular sheet parallel to (10\overline{2}). The molecular sheets are further linked by C—H...π interactions.
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SHARMA, RAJVEER, K. S. DAYA, and PREM SARAN TIRUMALAI. "LIGHT ASSISTED IN-VIVO MICROWAVE SENSING FOR ELECTRICAL CHARACTERIZATION OF PROKARYOTES." Biophysical Reviews and Letters 07, no. 03n04 (December 2012): 219–27. http://dx.doi.org/10.1142/s1793048012500105.

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This paper reports an in vivo characterization technique to characterize dielectric properties of living tissues and bio-molecules at microwave frequency using cavity perturbation technique, where a slot ring resonant sensor has been used, that works at 8 GHz and has been designed to enumerate the effective dielectric constant of Spirulina platensis and chlorophyll molecule. Observed value of the dielectric constant of Spirulina platensis was 8 ± 0.04 in the absence of light and 14.575 ± 0.145 in the presence of light. Molecular polarizability of chl a molecule was 5.07 ± 0.05 × 104 Å3. Experimentally calculated local electric field actually experienced by chl a molecule was 14.197 ± 0.003 V/m for applied field of 9.79 V/m across the slot ring, dipole moment of chl a molecule was 2.175 ± 0.005 × 105 Debye and total polarisation produced due to these molecules was 1.545 ± 0.005 C/m 2. Observed relaxation time of chl a molecule was 8.09 ± 0.18 × 10-9 s . The proposed sensing method can be an alternate to spectral characterisation technique, generally used to characterize light sensitive bio-molecules and can also be extended to characterize light sensitive bio-molecules in plant cells.
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Liu, Ya-Ling, Pei Zou, Hao Wu, Min-Hao Xie, and Shi-Neng Luo. "3,4,6-Tri-O-acetyl-1,2-O-[1-(exo-ethoxy)ethylidene]-β-D-mannopyranose 0.11-hydrate." Acta Crystallographica Section C Crystal Structure Communications 68, no. 9 (August 1, 2012): o338—o340. http://dx.doi.org/10.1107/s0108270112032076.

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The title compound, C16H24O10·0.11H2O, is a key intermediate in the synthesis of 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG), which is the most widely used molecular-imaging probe for positron emission tomography (PET). The crystal structure has two independent molecules (AandB) in the asymmetric unit, with closely comparable geometries. The pyranose ring adopts a4C1conformation [Cremer–Pople puckering parameters:Q= 0.553 (2) Å, θ = 16.2 (2)° and ϕ = 290.4 (8)° for moleculeA, andQ= 0.529 (2) Å, θ =15.3 (3)° and ϕ = 268.2 (9)° for moleculeB], and the dioxolane ring adopts an envelope conformation. The chiral centre in the dioxolane ring, introduced during the synthesis of the compound, has anRconfiguration, with the ethoxy groupexoto the mannopyranose ring. The asymmetric unit also contains one water molecule with a refined site-occupancy factor of 0.222 (8), which bridges between moleculesAandB viaO—H...O hydrogen bonds.
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Fernandez, Julio M. "S3B1 Protein mechanics studied with single molecule AFM techniques.(Single Molecure Dynamics and Reactions)." Seibutsu Butsuri 42, supplement2 (2002): S13. http://dx.doi.org/10.2142/biophys.42.s13_4.

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43

Yoshida, Norimasa, Kyoichi Kassai, Hironobu Murase, Yukiko Tanaka, Satoshi Kokura, Hiroshi Ichikawa, Yuji Naito, Takeshi Okanoue, and Toshikazu Yoshikawa. "Effects ofHelicobacter pyloriWater Extract on Expression of Endothelial Adhesion Molecules." Canadian Journal of Gastroenterology 18, no. 6 (2004): 387–91. http://dx.doi.org/10.1155/2004/158638.

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The present study investigated whetherHelicobacter pyloriwater extract induces the upregulation of intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin on human umbilical vein endothelial cells, using an ELISA. The nature of the substances mediating this upregulation was also analyzed.H pyloriwater extract derived from type strain (NCTC 11637) significantly upregulated intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin to the same extent as interleukin-1. Treatments with extracts from clinical strains showed no significant increases in expression of these adhesion molecules. In a fractionation study, approximately 7 kDa fraction showed peak activity. This activity was tolerant to heating and trypsin digestion. These results indicate thatH pyloriwater extract contains water-soluble, low-molecular, nonprotein substances which induce upregulation of adhesion molecules on human umbilical vein endothelial cells, suggesting that products ofH pylorimay elicit gastric mucosal inflammation by promoting expression of endothelial adhesion molecules.
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44

Masan, Samuel E. P. P., Fitri N. Febriana, Andi H. Zaidan, Ira Puspitasari, and Febdian Rusydi. "Evaluation of the Electronic Structure Resulting from ab-initio Calculations on Simple Molecules Using the Molecular Orbital Theory." Jurnal Penelitian Pendidikan IPA 7, no. 1 (January 28, 2021): 107. http://dx.doi.org/10.29303/jppipa.v7i1.545.

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Hartree Fock (HF) and Density Functional Theory (DFT) have been commonly used to model chemical problems. This study uses the Molecular Orbital Theory (MOT) to evaluate the electronic structure of five diatomic molecules generated by HF and DFT calculations. The evaluation provides an explanation of how the orbitals of a molecule come to be and how this affects the calculation of the physical quantities of the molecule. The evaluation is obtained after comparing the orbital wave functions calculated by MOT, HF, and DFT. This study found that the nature of the Highest Occupied Molecular Orbital (HOMO) of a molecule is determined by the valence orbital properties of the constituent atoms. This HOMO property greatly influences the precision of calculating the molecular electric dipole moment. This shows the importance of understanding the orbital properties of a molecule formed from the HF and DFT calculations
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Cieplik, Jerzy, Janusz Pluta, Iwona Bryndal, and Tadeusz Lis. "N-(4-Methoxyphenyl)-6-methyl-2-phenyl-5-{[4-(trifluoromethyl)anilino]methyl}pyrimidin-4-amine." Acta Crystallographica Section E Structure Reports Online 69, no. 12 (November 27, 2013): o1831—o1832. http://dx.doi.org/10.1107/s160053681303170x.

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The title compound, C26H23F3N4O, crystallizes with two symmetry-independent molecules in the asymmetric unit, denotedAandB, which differ mainly in the rotation of the methoxyphenyl ring. The –CF3group of moleculeBis disordered by rotation, with the F atoms split over two sets of sites; the occupancy factor for the major component is 0.853 (4). The dihedral angles between the pyrimidine ring and the attached phenyl, methoxyphenyl and trifluoromethylphenyl rings are 8.1 (2), 37.5 (2) and 70.7 (2)°, respectively, in moleculeA, and 9.3 (2), 5.3 (2) and 79.7 (2)° in moleculeB. An intramolecular N—H...N hydrogen bond occurs in each molecule. In the crystal, two crystallographically independent molecules associate into a dimerviaa pair of N—H...N hydrogen bonds, with a resultingR22(12) ring motif and π–π stacking interactions [centroid–centroid distance = 3.517 (4) Å] between the pyrimidine rings. For theAmolecules, there are intermolecular C—H...O hydrogen bonds between an aryl C atom of methoxyphenyl ring and a methoxy O atom of an adjacent molecule. A similar interaction is lacking in theBmolecules.
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46

Ghosh, Siddharth, Narain Karedla, and Ingo Gregor. "Single-molecule confinement with uniform electrodynamic nanofluidics." Lab on a Chip 20, no. 17 (2020): 3249–57. http://dx.doi.org/10.1039/d0lc00398k.

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A single-molecule nanofluidic detection method resolving fundamental limit of molecular shot noise along with 1D manipulation of sub-3 nm sized single molecules – a potential application for early detection of COVID-19, cancer and protein misfolding.
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47

Deniz, Ashok A., Samrat Mukhopadhyay, and Edward A. Lemke. "Single-molecule biophysics: at the interface of biology, physics and chemistry." Journal of The Royal Society Interface 5, no. 18 (May 22, 2007): 15–45. http://dx.doi.org/10.1098/rsif.2007.1021.

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Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to probe molecular structure, dynamics and function, unhindered by the averaging inherent in ensemble experiments. This review presents an overview of the burgeoning field of single-molecule biophysics, discussing key highlights and selected examples from its genesis to our projections for its future. Following brief introductions to a few popular single-molecule fluorescence and manipulation methods, we discuss novel insights gained from single-molecule studies in key biological areas ranging from biological folding to experiments performed in vivo .
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48

Hersam, M. C., and R. G. Reifenberger. "Charge Transport through Molecular Junctions." MRS Bulletin 29, no. 6 (June 2004): 385–90. http://dx.doi.org/10.1557/mrs2004.120.

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AbstractIn conventional solid-state electronic devices, junctions and interfaces play a significant if not dominant role in controlling charge transport. Although the emerging field of molecular electronics often focuses on the properties of the molecule in the design and understanding of device behavior, the effects of interfaces and junctions are often of comparable importance. This article explores recent work in the study of metal–molecule–metal and semiconductor–molecule–metal junctions. Specific issues include the mixing of discrete molecular levels with the metal continuum, charge transfer between molecules and semiconductors, electron-stimulated desorption, and resonant tunneling. By acknowledging the consequences of junction/interface effects, realistic prospects and limitations can be identified for molecular electronic devices.
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49

Filho, Eloi Alves da Silva, Fabricio Uliana, Stêner Romanel Ambrozio, Cleverton Oliveira, Renan Martin, and Arlan da Silva Gonçalves. "COMPUTATIONAL STUDY OF ORGANIC COMPOUNDS – AN APPLICATION FOR LEARNING IN CHEMISTRY." Revista Ifes Ciência 5, no. 1 (November 22, 2019): 257–66. http://dx.doi.org/10.36524/ric.v5i1.293.

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Organic chemistry is a theme not so easy to understand by undergraduating students. The motivation of this work was carried out computational study of three different molecules by molecular modeling using classic and semi-empirical methods besides open-source softwares. The optimized structures were visualized through 3D representations which made the study more understanding. Physical chemistry properties were extracted from all molecules. For the molecule one there was good correlation between the calculation methods. For the molecule two and more complex structures like molecule three and four there was possible influence of steric effect showing that each method is applicable for each study system.
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Obayes, Hasan R., Ghadah H. Alwan, Ahmed A. Al-Amiery, Abdul Amir H. Kadhum, and Abu Bakar Mohamad. "Thermodynamic and Theoretical Study of the Preparation of New Buckyballs from Corannulene, Coronene, and Circulene." Journal of Nanomaterials 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/451920.

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We applied density functional theory (DFT) to study three polycyclic aromatic compounds (PAHs), corannulene, coronene, and circulene, for the preparation of twelve new buckyballs with molecular dimensions of less than a nanometer. The results showed that the corannulene molecule is bowl-shaped, the coronene molecule is planar, and the circulene molecule has a unique saddle-shaped structure. Cyclic polymerization of the three molecules can be used to prepare new buckyballs, and this process produces hydrogen molecules. The most symmetric buckyball is also the most stable based on the values of the HOMO energy levels and has the most efficient gap energy, making it potentially useful for solar cell applications.
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