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Journal articles on the topic 'Conformation of molecules'

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Published: 7 June 2025

Last updated: 16 July 2025

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1

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

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Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify t

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2

Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic та ін. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR". Proceedings of the National Academy of Sciences 112, № 46 (2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

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Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like re

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3

Weng, Ze F., W. D. Sam Motherwell, Frank H. Allen, and Jacqueline M. Cole. "Conformational variability of molecules in different crystal environments: a database study." Acta Crystallographica Section B Structural Science 64, no. 3 (2008): 348–62. http://dx.doi.org/10.1107/s0108768108005442.

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A methodology is described for analysing the Cambridge Structural Database (CSD) in terms of molecular conformations. Molecular species that have more than a single occurrence across the complete CSD are identified, either as the sole crystal component or co-crystallized with other components. Cluster analysis, based on a root-mean-square fit of coordinates and chemical connectivity, is performed to identify conformational variance for each molecule. Results are analysed in terms of the number of discrete conformations observed versus the number of crystal environments and number of acyclic to

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Guo, Qing, Yufan He, and H. Peter Lu. "Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy." Proceedings of the National Academy of Sciences 112, no. 45 (2015): 13904–9. http://dx.doi.org/10.1073/pnas.1506405112.

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Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we succe

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Chinnakali, K., D. Sudha, M. Jayagopi, R. Raghunathan, and Hoong-Kun Fun. "4,4,7,7-Tetramethyl-2-tosyl-2,3,3a,4,6,7,8,9-octahydro-1H-pyrrolo[3,4-c]pyrano[6,5-b]cyclohexan-9-one." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (2007): o4436—o4437. http://dx.doi.org/10.1107/s1600536807052221.

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The title compound, C22H29NO4S, crystallizes with three independent molecules, A, B and C, in the asymmetric unit. Each of the three independent molecules adopts a folded conformation, with the phenylsulfonyl group lying over the pyranocyclohexanone ring system, and with the pyrrolidine and dihydropyran rings cis-fused. In all three molecules, the pyrrolidine ring has a twist conformation and the dihydropyran ring is in a half-chair conformation. The cyclohexenone rings adopt envelope conformations, with the flap atom puckered towards the phenylsulfonyl group in molecule A, and away from that

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6

Nagasawa, Yuya, Takeshi Koyama, and Susumu Okada. "Energetics and electronic structures of perylene confined in carbon nanotubes." Royal Society Open Science 5, no. 6 (2018): 180359. http://dx.doi.org/10.1098/rsos.180359.

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The energetics and geometries of perylene encapsulated in carbon nanotubes (CNTs) have been investigated employing density functional theory using the generalized gradient approximation combined with the van der Waals correction. Our calculations show that the encapsulated perylene molecules possess two metastable molecular conformations with respect to the CNT wall, which are almost degenerate with each other. A standing conformation, with respect to the CNT wall, is the ground state conformation for a semiconducting (19,0)CNT, while a lying conformation is the ground state for a metallic (11

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7

Grineva, Olga V. "Direct Determination of Ratios of All Conformations and Their Lifetimes for Small Flexible Molecules from Molecular Dynamics Simulations: 1,3-Propanediol in an Aqueous Environment." Molecules 30, no. 6 (2025): 1285. https://doi.org/10.3390/molecules30061285.

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For the first time in the course of molecular dynamics modeling of a liquid, the conformations of each of the small flexible molecules present in the system were fixed at short (1 ps) time intervals. This allowed the establishment of the ratios between various individual conformations and their families and determination of the average lifetimes of both individual conformations and families. As an example, data are presented for modeling boxes with different numbers of molecules (800, 2700, and 6400) for an aqueous solution with 1 mol. % 1,3-propanediol at 298.15 K and 1 atm. The results of th

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8

Chinnakali, K., D. Sudha, M. Jayagopi, R. Raghunathan, and Hoong-Kun Fun. "cis-4,4,10-Trimethyl-2-tosyl-1,2,3,3a,4,11b-hexahydro-11H-pyrrolo[3,4-c]pyrano[5,6-c]quinolin-11-one hemihydrate." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (2007): o4489—o4490. http://dx.doi.org/10.1107/s1600536807053287.

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The asymmetric unit of the title compound, C24H26N2O4S·0.5H2O, contains two independent molecules, A and B, with similar conformations, and a water molecule. The pyrrolidine ring adopts an envelope conformation in molecule A and a twist conformation in molecule B. In both molecules, the pyrrolidine and dihydropyran rings are cis-fused, and the dihydropyran ring has a half-chair conformation. Each of the independent molecules adopts a folded conformation, with the sulfonyl-bound benzene ring lying over the pyridinone ring. The two independent molecules, A and B, are linked together via C—H...O

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9

Savintseva, Liana A., Ilya S. Steshin, Alexander A. Avdoshin, et al. "Conformational Dynamics and Stability of Bilayers Formed by Mycolic Acids from the Mycobacterium tuberculosis Outer Membrane." Molecules 28, no. 3 (2023): 1347. http://dx.doi.org/10.3390/molecules28031347.

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Bilayers of mycolic acids (MAs) form the outer membrane of Mycobacterium tuberculosis that has high strength and extremely low permeability for external molecules (including antibiotics). For the first time, we were able to study them using the all-atom long-term molecular dynamic simulations (from 300 ns up to 1.2 μs) in order to investigate the conformational changes and most favorable structures of the mycobacterial membranes. The structure and properties of the membranes are crucially dependent on the initial packing of the α-mycolic acid (AMA) molecules, as well as on the presence of the

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10

Halder, Bijoy K., Angelica M. Palomino, and Jordan Hicks. "Influence of polyacrylamide conformation on fabric of “tunable” kaolin–polymer composite." Canadian Geotechnical Journal 55, no. 9 (2018): 1295–312. http://dx.doi.org/10.1139/cgj-2017-0200.

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“Tunable” clay–polymer composites have the potential to improve the engineering properties of clay materials. The importance of these materials derives from the ability of the responsive polymer to adopt various conformations (coiled, partially extended or extended), which in turn impacts the mesoscale properties of the material. However, the influence of polymer molecule conformation on particle arrangement and overall composite behavior is not well understood. The purpose of this study is to understand the fabric development due to the conformational behavior of the polymer, and thus the cla

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Yusufzai, Samina Khan, Hasnah Osman, Aisyah Saad Abdul Rahim, Suhana Arshad та Ibrahim Abdul Razak. "3β-Chloro-5α-cholestan-6-one". Acta Crystallographica Section E Structure Reports Online 68, № 4 (2012): o1211—o1212. http://dx.doi.org/10.1107/s1600536812012482.

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The asymmetric unit of the title compound, C27H45ClO, consists of two crystallographically independent molecules. In both molecules, the three cyclohexane rings in the steroid fused-ring systems adopt chair conformations, while the cyclopentane ring adopts a half-chair conformation in one molecule and an envelope conformation in the other. In the crystal, the molecules are linked into a two-dimensional network by weak C—H...O hydrogen bonds. The crystal studied is a nonmerohedral twin with a refined ratio of twin components of 0.264 (3):0.736 (3).

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12

Zaki, Mohamed, Ahmed Benharref, Jean-Claude Daran, and Moha Berraho. "(1R,4R,6S,7R)-5,5-Dibromo-1,4,8,8-tetramethyltricyclo[5.4.1.04,6]dodecan-12-one." Acta Crystallographica Section E Structure Reports Online 70, no. 5 (2014): o526. http://dx.doi.org/10.1107/s1600536814007351.

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The title compound, C16H24Br2O, was synthesized from the reaction of β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene), which was isolated from Atlas cedar (Cedrus atlantica). The asymmetric unit contains two independent molecules with similar conformations. Each molecule is built up from two fused seven-membered rings and an additional three-membered ring. In both molecules, one of the seven-membered rings has a chair conformation, whereas the other displays a screw-boat conformation.

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13

Kurz, Leonie, Peter Schmieder, Nicolás Veiga, and Dorothea Fiedler. "One Scaffold, Two Conformations: The Ring-Flip of the Messenger InsP8 Occurs under Cytosolic Conditions." Biomolecules 13, no. 4 (2023): 645. http://dx.doi.org/10.3390/biom13040645.

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Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” conformation with five axial substituents. Using 13C-labeled InsPs/PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger 1,5(PP)2-InsP4 (also termed InsP8) readily adopts both conformations at physiological

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14

Jia, Zongchao, Guy Tourigny, Louis T. J. Delbaere, Allan L. Stuart, and Sagar V. Gupta. "Structure and conformation of 5-methoxymethyl-2′-deoxycytidine." Canadian Journal of Chemistry 68, no. 6 (1990): 836–41. http://dx.doi.org/10.1139/v90-132.

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The three-dimensional structure of the antiviral agent 5-methoxymethyl-2′-deoxycytidine (MMdCyd) was deduced by X-ray crystallographic analysis. MMdCyd crystallized in space group P21 with a = 7.9255(6) Å; b = 16.1505(15) Å, c = 10.1861(5) Å, β = 103.801(5)°, and Z = 4 (2 molecules per asymmetric unit); R = 0.044 (Rw = 0.046) for 2560 observed reflections with net I > 3σ(I). The furanose ring adopts the C(3′)-exo envelope conformation (3E) in molecule A and the C(2′)-endo envelope conformation (2E) in molecule B. In the sugar ring of both crystallographically independent molecules A and B,

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15

van Roey, P., W. A. Pangborn, R. F. Schinazi, G. Painter, and D. C. Liotta. "Absolute Configuration of the Antiviral Agent (−)-cis-5-Fluoro-1-[2-Hydroxymethyl)-1,3-Oxathiolan-5-yl]Cytosine." Antiviral Chemistry and Chemotherapy 4, no. 6 (1993): 369–75. http://dx.doi.org/10.1177/095632029300400609.

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The structure and absolute configuration of (−)- cis-5-fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine (FTC), has been determined by X-ray crystallographic analysis. The results confirm that the L-isomer of the nucleoside analogue is the most active enantiomer and that the correct absolute configuration of (−)-FTC is 5-fluoro-(2′R,5′S)-(−)-1-[2-hydroxymethyl)oxathiolan-5-yl]-fluorocytosine. The two molecules in the asymmetric unit show conformations that combine conformational features of two other classes of potent antiviral nucleosides. Both oxathiolane rings have the 3′-sulphur ato

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16

Gonçalves, Karolina de Oliveira, Leandro Ribeiro, Cecilia Maria Alves de Oliveira, Jesiel Freitas Carvalho, and Felipe T. Martins. "New solvates of the drug naltrexone: protonation, conformation and interplay of synthons." Acta Crystallographica Section C Structural Chemistry 74, no. 3 (2018): 274–82. http://dx.doi.org/10.1107/s2053229618001791.

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Naltrexone [systematic name: (4R,4aS,7aR,12bS)-3-cyclopropylmethyl-4a,9-dihydroxy-2,4,5,6,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one] is an important morphine-related drug used for combating alcoholism and opioid dependence. Of the eight crystal forms of naltrexone known thus far, only one exists in the neutral form and it crystallizes as a monohydrate. We have isolated the naltrexone free base as two new solvate forms,i.e.the ethyl acetate 0.33-solvate, C20H23NO4·0.33C4H8O2, (I), and the diethyl ether hemisolvate, C20H23NO4·0.5C4H10O, (II). While just one solvent molecul

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17

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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18

Feigel, Martin, Gerhard Lugert, Javier Manero, and Matthias Bremer. "Konformation von Anthranilsäurepeptiden, 3 [1]: Konformationen kleiner Anthranilsäure-Prolinpeptide im Kristall, in Lösung und eine semiempirische (AM 1) Beschreibung der Prolin-Ramachandran-Hyperflächen / Conformation of Anthranilic Acid Peptides, 3 [1]: Conformation of Small Anthranilic-Acid-Proline-Peptides in Crystal, in Solution and a Semi-empirical (AM 1) Description of the Proline-Ramachandran Maps." Zeitschrift für Naturforschung B 45, no. 2 (1990): 258–66. http://dx.doi.org/10.1515/znb-1990-0220.

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Starting from tert-Butyloxycarbonyl(BOC)-Anthranilic-Acid(Abz) (1), BOC-Abz-Proline-Methyl-Ester (2) is synthesized. The crystal structure of both compounds are discussed. The conformational features of the crystal structures of 2 are compared with the conformation in solution. The whole conformational area (Φ and Ψ) of the amino acid part of 2 was investigated with the semi-empirical quantummechanical method AM 1, in order to check the general availability of the influence of ester functions to depsipeptide conformations. Cyclo-anthranoyl-prolinyl (3), which had already been described in the

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Exner, Otto, Václav Jehlička, and Bernard Tinant. "Conformations of molecules bearing two carbonyl groups on adjacent atoms." Collection of Czechoslovak Chemical Communications 53, no. 6 (1988): 1260–67. http://dx.doi.org/10.1135/cccc19881260.

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Conformation of α-acyloxyketones IIIa-IIIc was determined from their dipole moments in benzene solution. Around the C-O bond the ap conformation prevails over sc, around the C-C bond several conformations are present and those with a larger distance between the two carbonyl oxygens are preferred. The conformation in thus quite different than in crystal. Similarities of the crystal conformations of III to I or II are due mainly to crystal packing forces, while the interaction of the two carbonyl oxygen atoms is of little importance.

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20

Catipović, B., G. Talluri, J. Oh, et al. "Analysis of the structure of empty and peptide-loaded major histocompatibility complex molecules at the cell surface." Journal of Experimental Medicine 180, no. 5 (1994): 1753–61. http://dx.doi.org/10.1084/jem.180.5.1753.

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We compared the conformation of empty and peptide-loaded class I major histocompatibility complex (MHC) molecules at the cell surface. Molecular conformations were analyzed by fluorescence resonance energy transfer (FRET) between fluorescent-labeled Fab fragments bound to the alpha 2 domain of the MHC heavy chain and fluorescent-labeled Fab fragments bound to beta 2-microglobulin. No FRET was found between Fab fragments bound to empty H-2Kb, but FRET was detected when empty H-2Kb molecules were loaded with peptide. The magnitude of FRET depended on the sequence of the peptide used. The results

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21

Atioğlu, Zeliha, Mehmet Akkurt, Flavien A. A. Toze, Pavel V. Dorovatovskii, Narmina A. Guliyeva, and Humay M. Panahova. "Crystal structure and Hirshfeld surface analysis of dimethyl (3aS,6R,6aS,7S)-2-(2,2,2-trifluoroacetyl)-2,3-dihydro-1H,6H,7H-3a,6:7,9a-diepoxybenzo[de]isoquinoline-3a1,6a-dicarboxylate." Acta Crystallographica Section E Crystallographic Communications 74, no. 11 (2018): 1599–604. http://dx.doi.org/10.1107/s2056989018014305.

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The title molecule, C18H16F3NO7, comprises a fused cyclic system containing four five-membered (two dihydrofuran and two tetrahydrofuran) rings and one six-membered (piperidine) ring. The five-membered dihydrofuran and tetrahydrofuran rings adopt envelope conformations, and the six-membered piperidine ring adopts a distorted chair conformation. Intramolecular O...F interactions help to stabilize the conformational arrangement. In the crystal structure, molecules are linked by weak C—H...O and C—H...F hydrogen bonds, forming a three-dimensional network. The Hirshfeld surface analysis confirms t

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22

Shi, Xin-Wei, Qiang-Qiang Lu, Jun-Hui Zhou, and Xin-Ai Cui. "Crystal structure ofN-deacetyllappaconitine." Acta Crystallographica Section E Crystallographic Communications 71, no. 8 (2015): o576—o577. http://dx.doi.org/10.1107/s2056989015012335.

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The title compound, C30H42N2O7[systematic name: (1S,4S,5S,7S,8S,9S,10S,11S,13R,14S,16S,17R)-20-ethyl-4,8,9-trihydroxy-1,14,16-trimethoxyaconitan-4-yl 2-aminobenzoate], isolated from roots ofAconitum sinomontanumNakai, is a typical aconitane-type C19-diterpenoid alkaloid, which crystallizes with two independent molecules in the asymmetric unit. The conformations of the two independent molecules are closely similar. Each molecule comprises four six-membered rings (A,B,DandE) including one six-membered N-containing heterocyclic ring (E), and two five-membered rings (CandF). RingsA,BandEadopt chai

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23

Solopova, O. N., L. P. Pozdnyakova, N. E. Varlamov, et al. "Conformational Differences between Active Angiotensins and Their Inactive Precursors." Acta Naturae 4, no. 1 (2012): 74–77. http://dx.doi.org/10.32607/20758251-2012-4-1-74-77.

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The peptide conformation in the context of a protein polypeptide chain is influenced by proximal amino acid residues. However, the mechanisms of this interference remain poorly understood. We studied the conformation of angiotensins 1, 2 and 3, which are produced naturally in a sequential fashion from a precursor protein angiotensinogen and contain an identical peptide core structure. Using the example of angiotensins 1, 2 and 3, it was shown that similar amino acid sequences may have significant conformational differences in various molecules. In order to assess the conformational changes, we

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Bodek, Lukasz, Mads Engelund, Aleksandra Cebrat, and Bartosz Such. "Adsorption behavior of tin phthalocyanine onto the (110) face of rutile TiO2." Beilstein Journal of Nanotechnology 11 (May 26, 2020): 821–28. http://dx.doi.org/10.3762/bjnano.11.67.

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The adsorption behavior of tin phthalocyanine (SnPc) molecules on rutile TiO2(110) was studied by scanning tunneling microscopy (STM). Low-temperature STM measurements of single molecules reveal the coexistence of two conformations of molecules on the TiO2 surface. Density functional theory-based simulations (DFT) indicate that the difference originates from the position of the tin atom protruding from the molecule plane. The irreversible switching of Sn-up molecules into the Sn-down conformation was observed either after sample annealing at 200 °C or as a result of tip-induced manipulation. R

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Martynov, Alexander G., Marina A. Polovkova, Yulia G. Gorbunova, and Aslan Yu Tsivadze. "Redox-Triggered Switching of Conformational State in Triple-Decker Lanthanide Phthalocyaninates." Molecules 27, no. 19 (2022): 6498. http://dx.doi.org/10.3390/molecules27196498.

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Double- and triple-decker lanthanide phthalocyaninates exhibit unique physical-chemical properties, particularly single-molecule magnetism. Among other factors, the magnetic properties of these sandwiches depend on their conformational state, which is determined via the skew angle of the phthalocyanine ligands. Thus, in the present work we report the comprehensive conformational study of substituted terbium(III) and yttrium(III) trisphthalocyaninates in solution depending on the substituents at the periphery of molecules, redox-states and nature of solvents. Conjunction of UV-vis-NIR spectrosc

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Cao, Thong M., and Michael R. King. "Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force." Cellular and Molecular Bioengineering 14, no. 1 (2021): 65–74. http://dx.doi.org/10.1007/s12195-021-00666-z.

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Abstract Introduction E-selectin is a member of the selectin family of cell adhesion molecules expressed on the plasma membrane of inflamed endothelium and facilitates initial leukocyte tethering and subsequent cell rolling during the early stages of the inflammatory response via binding to glycoproteins expressing sialyl LewisX and sialyl LewisA (sLeX/A). Existing crystal structures of the extracellular lectin/EGF-like domain of E-selectin complexed with sLeX have revealed that E-selectin can exist in two conformation states, a low affinity (bent) conformation, and a high affinity (extended)

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Vishnupriya, R., M. Venkateshan, J. Suresh, R. V. Sumesh, R. Ranjith Kumar, and P. L. Nilantha Lakshman. "Crystal structure of 7′-(4-chlorophenyl)-2′′-(4-methoxyphenyl)-7′,7a',7′′,8′′-tetrahydro-1′H,3′H,5′′H-dispiro[indoline-3,5′-pyrrolo[1,2-c]thiazole-6′,6′′-quinoline]-2,5′′-dione and an unknown solvent." Acta Crystallographica Section E Crystallographic Communications 75, no. 2 (2019): 189–93. http://dx.doi.org/10.1107/s2056989019000112.

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The asymmetric unit of the title compound, C34H28ClN3O3S, contains two independent molecules (A and B). They differ essentially in the orientation of the 4-methoxyphenyl ring with respect to the pyridine ring of the quinoline moiety; this dihedral angle is 37.01 (18)° in molecule A but only 7.06 (17)° in molecule B. In both molecules, the cyclohexanone ring of the isoquinoline unit has a half-chair conformation. In the pyrrolothiazole ring system, the pyrrolo ring in molecule A has a twisted conformation on the N—C fused bond and an envelope conformation in molecule B with the N atom as the fl

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Syetov, Y. "Theoretical modeling of defects in the molecular crystal of 2-(2'-hydroxyphenyl)benzothiazole." Journal of Physics and Electronics 28, no. 1 (2020): 43–48. http://dx.doi.org/10.15421/332008.

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2-(2'-hydroxyphenyl)benzothiazole is a photoreactive compound that exhibits excited state intramolecular proton transfer in the structure with an OH...N hydrogen bond. Energy of various structures is calculated for isolated molecules, clusters and periodic structures of 2-(2'-hydroxyphenyl)benzothiazole by density-functional based tight-binding methods. It is shown that the most stable conformation of the isolated molecule is a planar structure with an OH...N hydrogen bond. Other conformations have significantly larger energy in comparison with the average room temperature heat energy that imp

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Yablon, Dalia, and George Flynn. "Investigation of The Self-Assembly of Chiral Molecules At Liquidsolid Interfaces Using Scanning Tunneling Microscopy Chemical Marker Groups: Driving Forces for 2-D Separation of Chiral Species." Microscopy and Microanalysis 7, S2 (2001): 848–49. http://dx.doi.org/10.1017/s1431927600030312.

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Self-assembly of molecules on surfaces is fundamentally a process whereby individual molecules, separated in the gas or liquid phase, fonn ordered arrays on a surface. The driving forces for these self-assembly processes are the attractive and repulsive interactions among the molecules themselves and between the molecular assemblies and the surface. Since physisorption causes minimal perturbation of chemical bonds, studies of physisorbed species provide an extremely convenient method for investigating issues of molecular structure, conformation, orientation and dynamics of molecules in their “

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Alshawi, Jasim, Muoayed Yousif, Karzan H. Zangana, Inigo J. Vitorica Yrezabal, Richard Winpenny, and Mohamad J. Al-Jeboori. "Crystal structure of diethyl 2,2′-[((1E,1′E)-{[(1R,4R)-cyclohexane-1,4-diyl]bis(azanylylidene)}bis(methanylylidene))bis(1H-pyrrole-2,1-diyl)]diacetate." Acta Crystallographica Section E Crystallographic Communications 71, no. 3 (2015): o165—o166. http://dx.doi.org/10.1107/s2056989015002674.

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The whole molecule of the title compound, C24H32N4O4, is generated by inversion symmetry. The cyclohexane ring adopts a chair conformation and the conformation about the C=N bonds isE. The pyrrole rings have ananticonfirmation with respect to the cyclohexane moiety and the ethyl acetate groups have extended conformations. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds forming chains, enclosingR22(10) ring motifs with inversion symmetry, propagating parallel to the (101) plane.

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31

Katoh, K., H. Koshimoto, A. Tani, and K. Mori. "Coding of odor molecules by mitral/tufted cells in rabbit olfactory bulb. II. Aromatic compounds." Journal of Neurophysiology 70, no. 5 (1993): 2161–75. http://dx.doi.org/10.1152/jn.1993.70.5.2161.

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1. Recordings of extracellular spike responses were made from single mitral/tufted cells in the ventromedial region of the main olfactory bulb of urethan-chloralose-anesthetized rabbits. Using periodic artificial inhalations, the olfactory epithelium was stimulated with series of aromatic and aliphatic compounds systematically varying in molecular conformation. 2. Analysis of response specificity of single mitral/tufted cells for alkylbenzenes indicated that the length of the hydrocarbon side chain attached to the benzene ring plays a role in determining the specificity of excitatory spike res

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Gil, Diana, Travis Kruger, and Javier de la Cruz. "CD3 molecules in a conformational equilibrium that is altered by TCR engagement (35.41)." Journal of Immunology 182, no. 1_Supplement (2009): 35.41. http://dx.doi.org/10.4049/jimmunol.182.supp.35.41.

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Abstract Previously we and others observed that the signaling module of the TCR, the CD3 complex, undergoes a conformational change at the level of its cytoplasmic tails when T cells are stimulated. At that time, we interpreted this data as proof that antigen recognition modifies the conformation of CD3 as part of the receptor triggering mechanism. In absence of specific structural information, the induced conformation has been referred to as "open CD3". Here we present new evidence that thymocytes display detectable amounts of "open CD3" even in the absence of antigenic stimulation. However,

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Mariyatra, Mahimaidoss Baby, and Helen Stoeckli-Evans. "Crystal structure ofN-(2,2,2-trichloro-1-hydroxyethyl)formamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (2015): 1501–4. http://dx.doi.org/10.1107/s2056989015020459.

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The title compound, C3H4Cl3NO2, crystallized with two independent molecules (AandB) in the asymmetric unit. The two molecules have the same conformation; the molecular overlap gives weighted and unit-weight r.m.s. fits of 0.047 and 0.043 Å, respectively. The conformation of theN-(hydroxethyl)formamide chains are very similar, as indicated by the C—N(H)—C=O and C—N(H)—C—O(H) torsion angles, which are, respectively, −1.8 (3) and −91.5 (2)° for moleculeA, and −2.1 (3) and −95.7 (2)° for moleculeB. In the crystal, individual molecules are linked by pairs of O—H...O hydrogen bonds, formingA–AandB–B

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34

Munro, Orde Quentin, and Lynette Mariah. "Conformational analysis: crystallographic, molecular mechanics and quantum chemical studies of C—H...O hydrogen bonding in the flexible bis(nosylate) derivative of catechol." Acta Crystallographica Section B Structural Science 60, no. 5 (2004): 598–608. http://dx.doi.org/10.1107/s0108768104019846.

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The single-crystal X-ray diffraction analysis of 2-{[(4-nitrophenoxy)sulfonyl]oxy}phenyl 4-nitrophenyl sulfate (4) reveals that an interesting intermolecular or extended structure (a one-dimensional hydrogen-bonded polymer) is formed because of pairs of intermolecular (aryl)C—H...O(nitro) hydrogen bonds between the C 2 symmetry monomer units. The axis of the hydrogen-bonded polymer runs co-linear with the [101] face diagonal of the monoclinic unit cell. Molecular mechanics calculations using a modified version of the MM+ force field and a random conformational search algorithm have been used t

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35

Wang, Yan. "Flow cytometry-based FRET to monitor β2 integrins activation". Journal of Immunology 212, № 1_Supplement (2024): 1295_5733. http://dx.doi.org/10.4049/jimmunol.212.supp.1295.5733.

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Abstract β2 integrins is very important for leukocyte arrest, rolling and transmigration. Neutrophils mainly express two β2 integrins, αLβ2 and αMβ2. Neutrophil arrest is triggered by rapid conformational change of β2 integrins from bent and low affinity to open and high affinity. Recent studies have reported a new conformation of β2 integrins bent high affinity (PMID: 27578049, PMID: 30605669). This conformation is very difficult to monitor. By dynamic molecular simulation, we found that bent high affinity conformation of integrin is close enough to membrane, less than 10nm. Förster resonance

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36

LIEBOVITCH, LARRY S., NIKITA D. ARNOLD, and LEV Y. SELECTOR. "NEURAL NETWORKS TO COMPUTE MOLECULAR DYNAMICS." Journal of Biological Systems 02, no. 02 (1994): 193–228. http://dx.doi.org/10.1142/s0218339094000155.

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Large molecules such as proteins have many of the properties of neural networks. Hence, neural networks may serve as a natural and thus efficient method to compute the time dependent changes of the structure in large molecules. We describe how to encode the spatial conformation and energy structure of a molecule in a neural network. The dynamics of the molecule can then be computed from the dynamics of the corresponding neural network. As a detailed example, we formulated a Hopfield network to compute the molecular dynamics of a small molecule, cyclohexane. We used this network to determine th

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37

Ramos Silva, Manuela, Vânia M. Moreira, Cláudia Cardoso, Ana Matos Beja та Jorge A. R. Salvador. "3-Oxoandrosta-4,6-dien-17β-yl 2-methyl-1H-imidazole-1-carboxylate and 3-oxo-5α-androst-17β-yl 2-methyl-1H-imidazole-1-carboxylate: C—H...π and π–π intermolecular interactions". Acta Crystallographica Section C Crystal Structure Communications 65, № 3 (2009): o88—o91. http://dx.doi.org/10.1107/s0108270109003278.

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The title compounds, C24H30N2O3, (I), and C24H34N2O3, (II), both contain an androstane backbone and a 2-methylimidazole-1-carboxylate moiety at the 17-position. Compound (I) contains two symmetry-independent molecules (denoted 1 and 2), while compound (II) contains just one molecule in the asymmetric unit. The C—C—O—C torsion angle that reflects the twisting of the 2-methylimidazole-1-carboxylate moiety from the mean steroid plane is 143.1 (2)° for molecule 1 of (I), 73.1 (3)° for molecule 2 of (I) and 86.63 (17)° for (II). The significance of this study lies in its observation of significant

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38

Shi, Hao. "(1R,4S,8R,12S,13S,14R,16S,19R)-14-Hydroxy-7,7-dimethyl-17-methylene-2,9,18-trioxo-3,10-dioxapentacyclo[14.2.1.01,13.04,12.08,12]nonadec-19-yl acetate." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (2007): o4439. http://dx.doi.org/10.1107/s1600536807052099.

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The title compound, C22H26O8, prepared from the natural diterpenoid Macrocalyxin J, is built up from five fused rings. Cyclohenane ring A adopts a chair conformation, ring B exists in a screw-boat conformation and ring C adopts a boat conformation; the two five membered rings adopt envelope conformations. Two unique molecules are present in the asymmetric unit; both independent molecules have the same absolute configuration, the absolute configuration being deduced from the chirality of Macrocalyxin A, which was isolated from the same plant (i.e. Rabdosia macrocalyx) as Macrocalyxin J. The cry

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39

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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40

Romero, Nancy, Sylvain Bernès, Luis F. Roa, Joel L. Terán, and Dino Gnecco. "Crystal structures of two chiral piperidine derivatives: 1-[(1R)-2-hydroxy-1-phenylethyl]piperidin-4-one and 8-[(1S)-1-phenylethyl]-1,4-dioxa-8-azaspiro[4.5]decane-7-thione." Acta Crystallographica Section E Crystallographic Communications 71, no. 10 (2015): 1207–11. http://dx.doi.org/10.1107/s2056989015017119.

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The crystal structures of the two title piperidine derivatives show different conformations for the six-membered heterocycle. TheN-substituted 4-piperidinone 1-[(1R)-2-hydroxy-1-phenylethyl]piperidin-4-one, C13H17NO2, (I), has a chair conformation, while the piperidine substituted in position 2 with a thiocarbonyl group, 8-[(1S)-1-phenylethyl]-1,4-dioxa-8-azaspiro[4.5]decane-7-thione, C15H19NO2S, (II), features a half-chair conformation. Comparison of the two structures, and data retrieved from the literature, suggests that the conformational flexibility is mainly related to the hybridization

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41

Zhao, Zhen-Dong, Yu-Xiang Chen, Yu-Min Wang, and Liang-Wu Bi. "1,4a,7-Trimethyl-7-vinyl-1,2,3,4,4a,4b,5,6,7,8,10,10a-dodecahydrophenanthrene-1-carboxylic acid." Acta Crystallographica Section E Structure Reports Online 65, no. 6 (2009): o1429. http://dx.doi.org/10.1107/s1600536809019308.

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The title compound, also known as isopimaric acid, C20H30O2, was isolated from slash pine rosin. There are two unique molecules in the unit cell. The two cyclohexane rings have classical chair conformations. The cyclohexene ring represents a semi-chair. The molecular conformation is stabilized by weak intramolecular C—H...O hydrogen-bonding interactions. The molecules are dimerized through their carboxyl groups by O—H...O hydrogen bonds, formingR22(8) rings.

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42

Mertsalov, Dmitriy F., Maryana A. Nadirova, Elena A. Sorokina, et al. "Crystal structure and Hirshfeld surface analysis of (RS)-3-hydroxy-2-{[(3aRS,6RS,7aRS)-2-(4-methylphenylsulfonyl)-2,3,3a,6,7,7a-hexahydro-3a,6-epoxy-1H-isoindol-6-yl]methyl}isoindolin-1-one." Acta Crystallographica Section E Crystallographic Communications 77, no. 3 (2021): 260–65. http://dx.doi.org/10.1107/s2056989021001626.

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The title compound, C24H24N2O5S, crystallizes with two independent molecules (A and B) in the asymmetric unit. In the central ring systems of both molecules, the tetrahydrofuran rings adopt envelope conformations, the pyrrolidine rings adopt a twisted-envelope conformation and the six-membered ring is in a boat conformation. In molecules A and B, the nine-membered groups attached to the central ring system are essentially planar (r.m.s. deviations of 0.002 and 0.003 Å, respectively). They form dihedral angles of 64.97 (9) and 56.06 (10)°, respectively, with the phenyl rings. In the crystal, st

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43

Timofeev, Vladimir I., Yury A. Gaponov, Dmitry E. Petrenko та ін. "How the Hinge Region Affects Interactions between the Catalytic and β-Propeller Domains in Oligopeptidase B". Crystals 13, № 12 (2023): 1642. http://dx.doi.org/10.3390/cryst13121642.

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In order to elucidate the effect of modification of the hinge region on structural polymorphism associated with conformational transitions, structural studies of hinge-modified oligopeptidase B from Serratia proteamaculans (SpOpBmod) in the crystalline state and solution were carried out. A new crystal structure of SpOpBmod in the intermediate conformation was obtained, and a molecular model of SpOpBmod in the open conformation was created using a combination of small-angle X-ray scattering with MD simulations. The improved electron density of the mobile H-loop carrying the catalytic H652 dist

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44

Budesinsky, Milos, Ivana Cisarova, Jaroslav Podlaha, et al. "Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo(Pip-Phe), cyclo(Pro-Phe) and their N-methyl derivatives." Acta Crystallographica Section B Structural Science 66, no. 6 (2010): 662–77. http://dx.doi.org/10.1107/s0108768110040243.

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The crystal structures of eight cyclodipeptides are determined, incorporating pipecolic acid or proline and phenylalanine or N-methyl phenylalanine. This set of structures allows the evaluation of the effects on molecular conformation and crystal packing of imino acid ring-size, relative configuration of the two amino acids, and N-methylation. In the non-methylated compounds, hydrogen-bonding interactions form one-dimensional motifs that dominate the packing arrangement. Three compounds have more than one symmetry-independent molecule in the asymmetric unit (Z′ > 1), indicative of a broad a

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45

Quiroga, Jairo, Jaime Gálvez, Justo Cobo, and Christopher Glidewell. "Methyl (3aRS,3cRS,6cSR,7RS,8RS,8aSR)-2,5-bis(4-chlorophenyl)-7,9-bis(1,3-diphenyl-1H-pyrazol-4-yl)-1,3,4,6-tetraoxododecahydro-1H-dipyrrolo[3,4-a:3′,4′-f]pyrrolizine-3b-carboxylate dimethylformamide disolvate: a three-dimensional hydrogen-bonded framework." Acta Crystallographica Section C Crystal Structure Communications 68, no. 11 (2012): o439—o442. http://dx.doi.org/10.1107/s0108270112039856.

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The racemic title dipyrrolopyrrolizine compound crystallizes from dimethylformamide as a disolvate, C55H39Cl2N7O6·2C3H7NO. None of the four fused heterocyclic rings is planar; one adopts an envelope conformation, two others adopt half-chair conformations and the fourth adopts a conformation intermediate between an envelope and a half-chair. The arrangement of the ring fusions is such as to preclude the possibility of internal mirror symmetry. The three independent molecular components are weakly linked by C—H...O hydrogen bonds, and the dipyrrolopyrrolizine molecules are linked by a combinatio

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46

Elerman, Yalçün, Mehmet Kabak, and Ayhan Elmali. "Crystal Structure and Conformation of N-(5-Chlorosalicylidene)- 2-hydroxy-5-chloroaniline." Zeitschrift für Naturforschung B 57, no. 6 (2002): 651–56. http://dx.doi.org/10.1515/znb-2002-0610.

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Abstract N-(5-Chlorosalicylidene)-2-hydroxy-5-chloroaniline was synthesized and its crystal structure determined. It crystallizes in the orthorhombic space group Pna21 with a = 14.668(4), b = 6.084(3), c = 27.980(4) Å , R = 0.051 for 4788 independent reflections). There are two independent nearly planar molecules in the asymmetric unit. The intramolecular hydrogen bonds occur between the pairs of atoms N1 and O1 [2.553(6) Å], N1 and O2 [2.585(5) Å], N2 and O3 [2.567(6) Å], N2 and O4 [2.620(5) Å], the hydrogen atoms essentially being bonded to the nitrogen atoms. The neighboring molecules are l

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47

Yue, Angxiao, Dixin Luo, and Hongteng Xu. "A Plug-and-Play Quaternion Message-Passing Module for Molecular Conformation Representation." Proceedings of the AAAI Conference on Artificial Intelligence 38, no. 15 (2024): 16633–41. http://dx.doi.org/10.1609/aaai.v38i15.29602.

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Graph neural networks have been widely used to represent 3D molecules, which capture molecular attributes and geometric information through various message-passing mechanisms. This study proposes a novel quaternion message-passing (QMP) module that can be plugged into many existing 3D molecular representation models and enhance their power for distinguishing molecular conformations. In particular, our QMP module represents the 3D rotations between one chemical bond and its neighbor bonds as a quaternion sequence. Then, it aggregates the rotations by the chained Hamilton product of the quaterni

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48

Pratap, J. V., R. Ravishankar, and M. Vijayan. "X-ray studies on crystalline complexes involving amino acids and peptides. XXXV. Invariance and variability in amino acid aggregation in the complexes of maleic acid with L-histidine and L-lysine." Acta Crystallographica Section B Structural Science 56, no. 4 (2000): 690–96. http://dx.doi.org/10.1107/s0108768100002202.

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The crystal structures of complexes of maleic acid with L-histidine and L-lysine have been determined. The two crystallographically independent amino acid molecules in the L-histidine complex have different closed conformations, while the lysine molecule in its complex has the most favourable conformation sterically with an all-trans sidechain trans to the α-carboxylate group. The maleic acid molecules exist as semi-maleate ions of similar conformation and contain a symmetric O...H...O hydrogen bond. Amino acid cations and semi-maleate anions aggregate into alternate layers in both the structu

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49

Temel, Ersin, Aydın Demircan, Gözde Beyazova, and Orhan Büyükgüngör. "(3aR*,6S*,7aR*)-7a-Chloro-6-methyl-2-(4-methylphenylsulfonyl)-2,3,3a,6,7,7a-hexahydro-3a,6-epoxy-1H-isoindole." Acta Crystallographica Section E Structure Reports Online 68, no. 4 (2012): o1102—o1103. http://dx.doi.org/10.1107/s1600536812009658.

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In the title compound, C16H18ClNO3S, the six-membered ring has a boat conformation. The two five-membered rings with the bridging O atom adopt envelope conformations, whereas the N-containing five-membered ring adopts a twisted conformation. In the crystal, C—H...O hydrogen bonds link the molecules into a three-dimensional network.

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50

Boldyrev, I. A. "Conformational Diversity of Lipids." JETP Letters 119, no. 7 (2024): 549–55. http://dx.doi.org/10.1134/s0021364023603573.

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The conformational diversity of hydrophobic lipid chains has been studied. The number of possible conformations of a lipid chain, as well as the number of these conformations that can be realized in a real system, has been determined. A set theory approach to the analysis of conformations of lipid molecules has been proposed, and a relation of the sets of conformations realized in a lipid structure to the energy of the system has been introduced. Using the set theory, it has been considered which conformations of hydrophobic lipid chains can be realized in the real system. The notion of the ke

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