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Journal articles on the topic 'Molecule'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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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 (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 rin

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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 (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) (molecule

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3

Wang, Shuhua. "Drug–drug interaction analysis based on information bottleneck graph neural network: A review." Medicine 104, no. 25 (2025): e42904. https://doi.org/10.1097/md.0000000000042904.

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The objective of learning drug–drug interactions is to understand the interaction behavior between compound molecules, which has garnered significant interest in the field of compound molecular science due to the potential harm adverse drug interactions may cause to organisms. Existing machine learning methods mostly rely on manually designed representations of compound molecules, overlooking the essence of compound molecules being composed of multiple molecular substructures and constrained by the knowledge of domain experts in the field of compound molecules. In this work, we propose a novel

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4

Gregory, Philip D., Jacob A. Blackmore, Frye Matthew D, et al. "Molecule–molecule and atom–molecule collisions with ultracold RbCs molecules." New Journal of Physics 23, no. 12 (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 colli

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5

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 (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 configuratio

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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 (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 molecu

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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 (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 molecul

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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 (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

Fan, Yang, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, and Tao Qin. "Back translation for molecule generation." Bioinformatics 38, no. 5 (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

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10

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 (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 is

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11

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 (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 201

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12

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 (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 rearrangem

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13

Burkin, Gleb M., Elizaveta A. Kvyatkovskaya, Victor N. Khrustalev, et al. "Crystal structure and Hirshfeld surface analysis of 8-benzyl-1-[(4-methylphenyl)sulfonyl]-2,7,8,9-tetrahydro-1H-3,6:10,13-diepoxy-1,8-benzodiazacyclopentadecine ethanol hemisolvate." Acta Crystallographica Section E Crystallographic Communications 80, no. 4 (2024): 418–22. http://dx.doi.org/10.1107/s2056989024002275.

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The asymmetric unit of the title compound, 2C31H28N2O4S·C2H6O, contains a parent molecule and a half molecule of ethanol solvent. The main compound stabilizes its molecular conformation by forming a ring with an R 1 2(7) motif with the ethanol solvent molecule. In the crystal, molecules are connected by C—H...O and O—H...O hydrogen bonds, forming a three-dimensional network. In addition, C—H...π interactions also strengthen the molecular packing.

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14

Sadikhova, Nurlana D., Zeliha Atioğlu, Narmina A. Guliyeva, et al. "Crystal structure and Hirshfeld surface analysis of 3-benzyl-2-[bis(1H-pyrrol-2-yl)methyl]thiophene." Acta Crystallographica Section E Crystallographic Communications 80, no. 1 (2023): 72–77. http://dx.doi.org/10.1107/s2056989023010800.

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In the title compound, C20H18N2S, the asymmetric unit comprises two similar molecules (A and B). In molecule A, the central thiophene ring makes dihedral angles of 89.96 (12) and 57.39 (13)° with the 1H-pyrrole rings, which are bent at 83.22 (14)° relative to each other, and makes an angle of 85.98 (11)° with the phenyl ring. In molecule B, the corresponding dihedral angles are 89.49 (13), 54.64 (12)°, 83.62 (14)° and 85.67 (11)°, respectively. In the crystal, molecular pairs are bonded to each other by N—H...N interactions. N—H...π and C—H...π interactions further connect the molecules, formi

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15

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 (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

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16

ORRIT, M., and J. BERNARD. "SINGLE MOLECULE SPECTROSCOPY." Modern Physics Letters B 05, no. 11 (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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17

Enisoglu Atalay, Vildan, and Semse Asar. "Determination of the inhibition effect of hesperetin and its derivatives on Candida glabrata by molecular docking method." European Chemistry and Biotechnology Journal, no. 1 (January 2, 2024): 27–38. http://dx.doi.org/10.62063/ecb-15.

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In the study, it was aimed to develop new candidate inhibitor molecules by targeting the AWP1 protein structure of Candida glabrata organism. Hesperetin molecule was taken as a reference and different substituted groups were attached to the determined ends of the molecule to increase the inhibition potential on the protein structure. A total of 100 molecules were designed and after conformer distribution using the Molecular Mechanics/MMFF method for each designed molecule, the area, volume, weight, energy, EHOMO, ELUMO, polarizability, dipole moment, log P values of these molecules were calcul

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18

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

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19

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 thi

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20

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 (s

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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 (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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22

Weiss, Alarich. "Approaches to the Study of van der Waals Interactions in Solids." Zeitschrift für Naturforschung A 48, no. 3 (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 meth

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23

Uemura, Sotaro. "Comprehensive quantitative analysis of single-molecule proteins using ribosome fusion nanopore technology." Impact 2023, no. 3 (2023): 6–8. http://dx.doi.org/10.21820/23987073.2023.3.6.

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The detection and analysis of proteins is important for science and medicine and methods for sequencing and synthesising proteins have been developed to assist with this. The analysis of single molecules provides more detailed and targeted information and the development of single-molecule techniques has helped to advance molecular research. Professor Sotaro Uemura, The University of Tokyo, Japan, has over 20 years experience in this field of research, with a focus on singling out and measuring single-molecule proteins using optical tweezers, fluorescence imaging and other techniques. Labellin

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24

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

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25

Park, Ki-Min, Hankook Oh, and Youngjin Kang. "2,2′-Bi(9,9-diethylfluorene)." Acta Crystallographica Section E Structure Reports Online 70, no. 2 (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

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26

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 scientif

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27

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 (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, where

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28

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 (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 propo

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29

Levitt, Malcolm H. "Spectroscopy of light-molecule endofullerenes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1998 (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 spi

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30

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 (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

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31

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 (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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32

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 (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

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33

El-Khoury, Patrick Z., Grant E. Johnson, Irina V. Novikova, et al. "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 × 10<sup>5</sup> to 3.8 × 10<sup>2</sup> to 0.38 molecules per μm<sup>2</sup> 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 e

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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 (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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Shamima, Shultana, M. Maraz Kazi, Ahmed Arwah, Sultana Tanzila, and A. Khan Ruhul. "Drug design, discovery and development and their safety or efficacy on human body." GSC Biological and Pharmaceutical Sciences 17, no. 2 (2021): 113–22. https://doi.org/10.5281/zenodo.5763084.

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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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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 (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 exci

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Peng, Jinbo, Sophia Sokolov, Daniel Hernangómez-Pérez, et al. "Atomically resolved single-molecule triplet quenching." Science 373, no. 6553 (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 atom

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Venkatraman, Vishwesh, Jeremiah Gaiser, Daphne Demekas, Amitava Roy, Rui Xiong, and Travis J. Wheeler. "Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)." Pharmaceuticals 17, no. 8 (2024): 992. http://dx.doi.org/10.3390/ph17080992.

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Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show t

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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 (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 understan

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Rahman, Mahmudur, Kazi Rafiqul Islam, Md Rashedul Islam, et al. "A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices." Micromachines 13, no. 6 (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 adv

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Wang, Huibin, Zehui Wang, Minghua Shi, Zixian Cheng, and Ying Qian. "Enhancing Unconditional Molecule Generation via Online Knowledge Distillation of Scaffolds." Molecules 30, no. 6 (2025): 1262. https://doi.org/10.3390/molecules30061262.

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Generating new drug-like molecules is an essential aspect of drug discovery, and deep learning models significantly accelerate this process. Language models have demonstrated great potential in generating novel and realistic SMILES representations of molecules. Molecular scaffolds, which serve as the key structural foundation, can facilitate language models in discovering chemically feasible and biologically relevant molecules. However, directly using scaffolds as prior inputs can introduce bias, thereby limiting the exploration of novel molecules. To combine the above advantages and address t

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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 (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 (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. Experi

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Yoshida, Norimasa, Kyoichi Kassai, Hironobu Murase, et al. "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 increas

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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 (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

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Shiraogawa, Takafumi, Giulia Dall'Osto, Roberto Cammi, Masairo Ehara, and Stefano Corni. "Inverse design of molecule–metal nanoparticle systems interacting with light for desired photophysical properties." Phys Chem Chem Phys 24 (September 22, 2024): 22768–77. https://doi.org/10.1039/D2CP02870K.

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Molecules close to a metal nanoparticle (NP) have significantly different photophysical properties from those of the isolated one. In order to harness the potential of the molecule–NP system, appropriate design guidelines are required. Here, we propose an inverse design method of the optimal molecule–NP systems and incident electric field for desired photophysical properties. It is based on a gradient-based optimization search within the time-dependent quantum chemical description for the molecule and the continuum model for the metal NP. We designed the optimal molecule, relative

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Liu, Haoran, Youzhi Luo, Tianxiao Li, James Caverlee, and Martin Renqiang Min. "Learning Disentangled Equivariant Representation for Explicitly Controllable 3D Molecule Generation." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 18 (2025): 18816–24. https://doi.org/10.1609/aaai.v39i18.34071.

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We consider the conditional generation of 3D drug-like molecules with explicit control over molecular properties such as drug-like properties (e.g., Quantitative Estimate of Druglikeness or Synthetic Accessibility score) and effectively binding to specific protein sites. To tackle this problem, we propose an E(3)-equivariant Wasserstein autoencoder and factorize the latent space of our generative model into two disentangled aspects: molecular properties and the remaining structural context of 3D molecules. Our model ensures explicit control over these molecular attributes while maintaining equ

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Chen, Bingrun, and Ke Xu. "Single Molecule-Based Electronic Devices: A Review." Nano 14, no. 11 (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

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Liu, Ya-Ling, Pei Zou, Hao Wu, Min-Hao Xie та 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, № 9 (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

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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 (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 si

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