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Journal articles on the topic 'Intramolecular contacts'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Smith, Ben E., Jeremy M. Carr, and Gregory S. Tschumper. "Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts." Molecules 24, no. 14 (2019): 2523. http://dx.doi.org/10.3390/molecules24142523.

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A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the c i s isomers are lowered by roughly 3 to 4 kcal mol−1 when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. Th

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2

Bindya, S., C. S. Chidan Kumar, S. Naveen, B. P. Siddaraju, Ching Kheng Quah, and Md Abu Raihan. "Crystal structure and Hirshfeld surface analysis of a bromochalcone: (E)-1-(3-bromophenyl)-3-(2,6-dichlorophenyl)prop-2-en-1-one." Acta Crystallographica Section E Crystallographic Communications 75, no. 2 (2019): 264–67. http://dx.doi.org/10.1107/s205698901900104x.

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In the title chalcone derivative, C15H9BrCl2O, the aryl rings are inclined to each by 14.49 (17)°, and the configuration about the C=C bond is E. There is a short intramolecular C—H...Cl contact present resulting in the formation of an S(6) ring motif. In the crystal, the shortest intermolecular contacts are Cl...O contacts [3.173 (3) Å] that link the molecules to form a 21 helix propagating along the b-axis direction. The helices stack up the short crystallographic a axis, and are linked by offset π–π interactions [intercentroid distance = 3.983 (1) Å], forming layers lying parallel to the ab

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3

Burling, F. T., and B. M. Goldstein. "A database study of nonbonded intramolecular sulfur–nucleophile contacts." Acta Crystallographica Section B Structural Science 49, no. 4 (1993): 738–44. http://dx.doi.org/10.1107/s0108768193000709.

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4

Flores-Alamo, Marcos, Ruth Meléndrez-Luévano, José A. Ortiz Márquez, Estibaliz Sansinenea Royano, and Blanca M. Cabrera-Vivas. "Crystal structure of (E)-1-(2-nitrobenzylidene)-2,2-diphenylhydrazine." Acta Crystallographica Section E Structure Reports Online 70, no. 9 (2014): o909—o910. http://dx.doi.org/10.1107/s1600536814016109.

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The title compound, C19H15N3O2, shows anEconformation of the imine bond. The dihedral angle between the planes of the phenyl rings in the diphenylhydrazine groups is 88.52 (4)°. The 2-nitrobenzene ring shows a torsion angle of 10.17 (8)° with the C=N—N plane. A short intramolecular C—H...O contact occurs. In the crystal, only van der Waals contacts occur between the molecules.

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5

Qiu, Lin, Li Wang, and Yong-Mei Zhao. "2-Hydroxy-2′,4,4′-trimethoxybenzophenone." Acta Crystallographica Section E Structure Reports Online 62, no. 5 (2006): o1980—o1981. http://dx.doi.org/10.1107/s1600536806013821.

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6

Mahmoud, Abdallah G., M. Fátima C. Guedes da Silva, Kamran T. Mahmudov, and Armando J. L. Pombeiro. "Arylhydrazone ligands as Cu-protectors and -catalysis promoters in the azide–alkyne cycloaddition reaction." Dalton Transactions 48, no. 5 (2019): 1774–85. http://dx.doi.org/10.1039/c8dt04771e.

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7

Murthy, T. N. Sanjeeva, Zeliha Atioğlu, Mehmet Akkurt, et al. "Crystal structure and Hirshfeld surface analysis of (E)-3-(2-chlorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one." Acta Crystallographica Section E Crystallographic Communications 75, no. 2 (2019): 124–28. http://dx.doi.org/10.1107/s2056989018018066.

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The molecular structure of the title compound, C13H7Cl3OS, consists of a 2,5- dichlorothiophene ring and a 2-chlorophenyl ring linked via a prop-2-en-1-one spacer. The dihedral angle between the 2,5-dichlorothiophene and 2-chlorophenyl rings is 9.69 (12)°. The molecule has an E configuration about the C=C bond and the carbonyl group is syn with respect to the C=C bond. The molecular conformation is stabilized by two intramolecular C—H...Cl contacts and one intramolecular C—H...O contact, forming S(5)S(5)S(6) ring motifs. In the crystal, the molecules are linked along the a-axis direction throu

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8

de Vries, Sjoerd J., and Alexandre M. J. J. Bonvin. "Intramolecular surface contacts contain information about protein–protein interface regions." Bioinformatics 22, no. 17 (2006): 2094–98. http://dx.doi.org/10.1093/bioinformatics/btl275.

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9

Mounce, Bryan C., Neşe Kurt, Paul A. Ellison, and Silvia Cavagnero. "Nonrandom distribution of intramolecular contacts in native single-domain proteins." Proteins: Structure, Function, and Bioinformatics 75, no. 2 (2009): 404–12. http://dx.doi.org/10.1002/prot.22258.

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10

Dias, H. V. Rasika, and Jose Thankamani. "Thallium(I) complexes of fluorinated bis- and tris(pyrazolyl)borate ligands: [H2B{3,5-(CF3)2pz}2]Tl and [HB{3,5-(CF3)2pz}3]Tl." Acta Crystallographica Section C Crystal Structure Communications 69, no. 9 (2013): 959–62. http://dx.doi.org/10.1107/s0108270113016612.

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X-ray crystal structural data at 100 (2) K for the thallium(I) complex of a fluorinated bis(pyrazolyl)borate, {bis[3,5-bis(trifluoromethyl)-1H-pyrazol-1-yl-κN2]borato}thallium(I), [Tl(C10H4BF12N4)], abbreviated as [H2B{3,5-(CF3)2pz}2]Tl, and the related tris(pyrazolyl)borate, {tris[3,5-bis(trifluoromethyl)-1H-pyrazol-1-yl-κN2]borato}thallium(I), [Tl(C15H4BF18N6)], abbreviated as [HB{3,5-(CF3)2pz}3]Tl, are reported. [H2B{3,5-(CF3)2pz}2]Tl features a two-coordinate TlIatom with a bent geometry and a boat-shaped bis(pyrazolyl)borate ligand. It also has several additional inter- and intramolecular

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11

Asgarova, Ayten R. "Crystal structure and Hirshfeld surface analysis of 5-(3,5-di-tert-butyl-4-hydroxyphenyl)-3-phenyl-4,5-dihydro-1H-pyrazole-1-carboxamide." Acta Crystallographica Section E Crystallographic Communications 75, no. 10 (2019): 1467–71. http://dx.doi.org/10.1107/s205698901901243x.

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In the title compound, C24H31N3O2, the mean plane of the central pyrazole ring [r.m.s. deviation = 0.095 Å] makes dihedral angles of 11.93 (9) and 84.53 (8)°, respectively, with the phenyl and benzene rings. There is a short intramolecular N—H...N contact, which generates an S(5) ring motif. In the crystal, pairs of N—H...O hydrogen bonds link inversion-related molecules into dimers, generating an R 2 2(8) ring motif. The Hirshfeld surface analysis indicates that the most significant contribution involves H...H contacts of 68.6%

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12

Bilton, Clair, Frank H. Allen, Gregory P. Shields, and Judith A. K. Howard. "Intramolecular hydrogen bonds: common motifs, probabilities of formation and implications for supramolecular organization." Acta Crystallographica Section B Structural Science 56, no. 5 (2000): 849–56. http://dx.doi.org/10.1107/s0108768100003694.

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A systematic survey of the Cambridge Structural Database (CSD) has identified all intramolecular hydrogen-bonded ring motifs comprising less than 20 atoms with N and O donors and acceptors. The probabilities of formation Pm of the 50 most common motifs, which chiefly comprise five- and six-membered rings, have been derived by considering the number of intramolecular motifs which could possibly form. The most probable motifs (Pm > 85%) are planar conjugated six-membered rings with a propensity for resonance-assisted hydrogen bonding and these form the shortest contacts, whilst saturated six-

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13

Jabłoński, Mirosław. "Blue-shifting intramolecular CH⋯O(S) contacts in sterically strained systems." Journal of Molecular Structure: THEOCHEM 820, no. 1-3 (2007): 118–27. http://dx.doi.org/10.1016/j.theochem.2007.06.015.

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14

Constantin, Catalina, and Bogdan C. Simionescu. "Influence of inter- and intramolecular contacts on the second virial coefficient." European Polymer Journal 30, no. 9 (1994): 1071–74. http://dx.doi.org/10.1016/0014-3057(94)90202-x.

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15

Ho, Luong Phong, and Matthias Tamm. "Stabilization of a bismuth–bismuth double bond by anionic N-heterocyclic carbenes." Dalton Transactions 50, no. 4 (2021): 1202–5. http://dx.doi.org/10.1039/d1dt00140j.

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Anionic N-heterocyclic carbenes have been employed for the isolation of the first dicarbene–dibismuth complex; the resulting dibismuthene features a trans-bent geometry with a Bi–Bi double bond and short intramolecular Bi–C<sub>ipso</sub> contacts.

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16

Socol, Marius, Renjie Wang, Daniel Jost, et al. "Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes." Nucleic Acids Research 47, no. 12 (2019): 6195–207. http://dx.doi.org/10.1093/nar/gkz374.

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Abstract DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion

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17

Blake, Alexander J., Bernard A. J. Clark, Hedi Gierens, et al. "Intramolecular and intermolecular geometry of thiophenes with oxygen-containing substituents." Acta Crystallographica Section B Structural Science 55, no. 6 (1999): 963–74. http://dx.doi.org/10.1107/s0108768199003547.

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The intramolecular and intermolecular geometries of six thiophenes carrying oxygen-containing substituents have been determined. Crystals of 2-methoxythiophene and 3-methoxythiophene were grown in situ on a diffractometer from liquid samples. The 2-methoxy group introduces significant distortions to the thiophene nucleus and each molecule participates in four S...O contacts leading to an infinite bilayer. The extended structure of 3-methoxythiophene comprises zigzag chains of molecules linked by S...O contacts. Molecules of 2-acetyl-3-methoxythiophene are arranged in pairs about inversion cent

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18

Wannapaiboon, Suttipong, Yuranan Hanlumyuang, Kantapat Chansaenpak, et al. "Crystal structure and Hirshfeld surface analysis of the product of the ring-opening reaction of a dihydrobenzoxazine: 6,6′-[(cyclohexylazanediyl)bis(methylene)]bis(2,4-dimethylphenol)." Acta Crystallographica Section E Crystallographic Communications 76, no. 8 (2020): 1239–44. http://dx.doi.org/10.1107/s2056989020009184.

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In the title unsymmetrical tertiary amine, C24H33NO2, which arose from the ring-opening reaction of a dihydrobenzoxazine, two 2,4-dimethylphenol moieties are linked by a 6,6′-(cyclohexylazanediyl)-bis(methylene) bridge: the dihedral angle between the dimethylphenol rings is 72.45 (7)°. The cyclohexyl ring adopts a chair conformation with the exocyclic C—N bond in an equatorial orientation. One of the phenol OH groups forms an intramolecular O—H...N hydrogen bond, generating an S(6) ring, and a short intramolecular C—H...O contact is also present. In the crystal, O—H...O hydrogen bonds link the

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19

Morawitz, Thorsten, Hans-Wolfram Lerner та Michael Bolte. "cyclo-Tris(μ2-3-phenyl-1H-pyrazole)tricopper(I)". Acta Crystallographica Section E Structure Reports Online 62, № 7 (2006): m1474—m1476. http://dx.doi.org/10.1107/s1600536806020708.

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The crystal structure of the title compound, [Cu3(C9H7N2)3], consists of discrete CuI–phenylpyrazolyl trimers, with Cu atoms bridged by exo-bidentate phenylpyrazolyl ligands having short intramolecular Cu...Cu contacts [3.2076 (14)–3.2402 (14) Å]. The Cu3N6 nine-membered rings are essentially planar.

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20

Akhter, Sidra, Muhammad Iqbal Choudhary, Hina Siddiqui, and Sammer Yousuf. "Crystal structure and Hirshfeld surface analysis of N-(2-chlorophenylcarbamothioyl)-4-fluorobenzamide and N-(4-bromophenylcarbamothioyl)-4-fluorobenzamide." Acta Crystallographica Section E Crystallographic Communications 75, no. 7 (2019): 1026–29. http://dx.doi.org/10.1107/s2056989019008569.

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The title compounds, C14H10ClFN2OS (1) and C14H10BrFN2OS (2), were synthesized by two-step reactions. The dihedral angles between the aromatic rings are 31.99 (3) and 9.17 (5)° for 1 and 2, respectively. Compound 1 features an intramolecular bifurcated N—H...(O,Cl) link due to the presence of the ortho-Cl atom on the benzene ring, whereas 2 features an intramolecular N—H...O hydrogen bond. In the crystal of 1, inversion dimers linked by pairs of N—H...S hydrogen bonds generate R 2 2(8) loops. The extended structure of 2 features the same motif but an additional weak C—H...S interaction links t

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21

Saravanan, Raju, Harkesh B. Singh, and Ray J. Butcher. "Bis(2-nitrophenyl) selenide, bis(2-aminophenyl) selenide and bis(2-aminophenyl) telluride: structural and theoretical analysis." Acta Crystallographica Section C Structural Chemistry 77, no. 6 (2021): 271–80. http://dx.doi.org/10.1107/s2053229621005015.

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Three organoselenium and organotellurium compounds containing ortho substitutents, namely, bis(2-nitrophenyl) selenide, C12H8N2O4Se, 2, bis(2-aminophenyl) selenide, C12H12N2Se, 3, and bis(2-aminophenyl) telluride, C12H12N2Te, 7, have been investigated by both structural and theoretical methods. In the structures of all three compounds, there are intramolecular contacts between both Se and Te with the ortho substituents. In the case of 2, this is achieved by rotation of the nitro group from the arene plane. For 3, both amino groups exhibit pyramidal geometry and are involved in intramolecular N

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22

Dalal, Aarti, Ramesh C. Kamboj, Dinesh Kumar, Mahendra Kumar Sharma, and Nagendran Selvarajan. "Crystal structure of (Z)-3-[5-chloro-2-(prop-2-ynyloxy)phenyl]-3-hydroxy-1-[4-(trifluoromethyl)phenyl]prop-2-en-1-one." Acta Crystallographica Section E Crystallographic Communications 71, no. 8 (2015): o556—o557. http://dx.doi.org/10.1107/s2056989015012748.

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The title compound, C19H12ClF3O3, obtained by the photochemical transformation of 2-[5-chloro-2-(prop-2-ynyloxy)benzoyl]-3-[4-(trifluoromethyl)phenyl]oxirane adopts aZconformation with respect to the enolic C=C double bond. The dihedral angle between the benzene rings is 12.25 (16)° and an intramolecular O—H...O hydrogen bond closes anS(6) ring. An intramolecular C—H...O interaction also leads to anS(6) ring. In the crystal, very weak C—H...O interactions and short Cl...Cl contacts [3.3221 (16) Å] are seen, as well as weak aromatic π–π stacking interactions [centroid–centroid separation = 3.87

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23

Chandrasekhar, Vadapalli, Tristram Chivers, James F. Fait, and Santhanathan S. Kumaravel. "Synthesis and structure of azo dyes with short, intramolecular selenium-nitrogen contacts." Journal of the American Chemical Society 112, no. 13 (1990): 5373–74. http://dx.doi.org/10.1021/ja00169a068.

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24

Khavasi, Hamid Reza, and Narjes Rahimi. "Coordination Polymers with Intramolecular Fluorine-Involved Contacts in Two-Dimensional Sheet Windows." Crystal Growth & Design 17, no. 2 (2017): 834–45. http://dx.doi.org/10.1021/acs.cgd.6b01673.

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25

Mohamed, Shaaban K., Mehmet Akkurt, Farouq E. Hawaiz, Mzgin M. Ayoob, and Eric Hosten. "Crystal structure of (6E,20E)-3,24-difluoro-13,14,28,29-tetrahydro-5H,22H-tetrabenzo[e,j,p,u][1,4,12,15]tetraoxacyclodocosine-5,22-dione." Acta Crystallographica Section E Crystallographic Communications 73, no. 1 (2017): 13–16. http://dx.doi.org/10.1107/s2056989016018934.

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The conformation of the title compound, C34H26F2O6, is cone-shaped, partially determined by intramolecular C—H...O short contacts. The benzene rings at the top of the cone are inclined to one another by 73.10 (7)°, while the benzene rings at the bottom of the cone are inclined to one another by 35.49 (8)°. In the crystal, molecules are linked by C—H...O and C—H...F hydrogen bonds, forming a three-dimensional supramolecular structure. There are also C—H...π contacts present within the framework structure.

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26

Stützer, Albert, Peter Bissinger, and Hubert Schmidbaur. "Gold Chains and Gold Pairs in the Layer Structure of 1,1,1-Tris[chloro-gold(I)-dimethylphosphanylmethyl]ethane." Zeitschrift für Naturforschung B 47, no. 9 (1992): 1261–65. http://dx.doi.org/10.1515/znb-1992-0908.

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The title compound, 1,1,1-tris[chloro-gold(I)-dimethylphosphanylmethyl]ethane (1) has been prepared from the tripodal tertiary phosphine ligand and three equivalents of chloro(dimethylsulfide)gold(I) in good yield. The complex has been characterized by means of its 1H, 13C, and 31P NMR, and 197Au Mößbauer spectra, by elemental analysis, and by a single crystal X-ray structure analysis. The crystals have a layer structure. In each of the crystallographically equivalent individual molecules two of the gold(I) centers are associated via a short intramolecular Au · · · Au contact [3.077(2) Å]. The

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27

Saranya, Matheswaran, Annamalai Subashini, Chidambaram Arunagiri, and Packianathan Thomas Muthiah. "Crystal structure of 2-{[(2-chlorophenyl)imino]methyl}phenol." Acta Crystallographica Section E Crystallographic Communications 71, no. 1 (2015): o48. http://dx.doi.org/10.1107/s2056989014026978.

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In the title compound, C13H10ClNO, the dihedral angle between the planes of the aromatic rings is 51.42 (9)° and an intramolecular O—H...N hydrogen bond closes anS(6) ring. The Cl atom and the N atom aresyn. No directional interactions beyond van der Waals contacts are observed in the crystal.

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28

Moreno-Fuquen, Rodolfo, Nory J. Mariño, and Alan R. Kennedy. "Crystal structure ofN-(2-hydroxy-5-methylphenyl)benzamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (2015): o943. http://dx.doi.org/10.1107/s2056989015020575.

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In the title compound, C14H13NO2, the mean plane of the non-H atoms of the central amide fragment C—N—C(=O)—C (r.m.s. deviation = 0.029 Å) forms dihedral angles of 5.63 (6) and 10.20 (5)° with the phenyl and hydroxyphenyl rings, respectively. A short intramolecular N—H...O contact is present. In the crystal, the molecules are linked by O—H...O hydrogen bonds to generateC(7) chains along [100]. The chains are reinforced by weak C—H...O contacts, which together with the O—H...O bonds lead toR22(7) loops. Very weak N—H...O interactions link the molecules into inversion dimers.

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29

Liu, Xian-Rong, and Yan-Ling Zhou. "Crystal structure of 1-methyl-3-[2,2,2-trifluoro-1-(1-methyl-1H-indol-3-yl)-1-phenylethyl]-1H-indole." Acta Crystallographica Section E Structure Reports Online 70, no. 11 (2014): o1156. http://dx.doi.org/10.1107/s1600536814021916.

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The title compound, C26H21F3N2, was prepared by the palladium-catalysed reaction of (2,2,2-trifluoroethyl)benzene with 1-methyl-1H-indole. The dihedral angle between the planes of the indole-ring systems is 52.13 (6)° and theN-methyl groups point away from each other. Three short intramolecular C—H...F contacts are observed.

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30

Jios, Jorge L., Rudolf Wartchow, Gustavo A. Echeverría, and Helmut Duddeck. "Aryl Naphthoates: A Conformational Analysis Supported by Single-Crystal X-Ray Diffraction." Australian Journal of Chemistry 69, no. 3 (2016): 291. http://dx.doi.org/10.1071/ch15071.

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The conformational study by X-ray diffraction of 12 aroyl esters of ortho-acetyl phenols is reported. The data are supported by theoretical calculations and described in terms of co-planarity, intramolecular steric interference, and intermolecular contacts. The observed hindrance was correlated with the C=O stretching vibration values in infrared spectroscopy.

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31

Gao, Xiao-Li, Si-Si Feng, Cai-Xia Yuan, and Miao-Li Zhu. "2-[(E)-(4-Bromophenyl)iminomethyl]-4-chlorophenol." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (2014): o235—o236. http://dx.doi.org/10.1107/s1600536814000981.

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In the title compound, C13H9BrClNO, the dihedral angle between the substituted benzene rings is 44.25 (11)°. There are strong intramolecular O—H...N hydrogen bonds, which generateS(6) rings, and also intermolecular Cl...Cl [3.431 (3) Å] and Br... Br [3.846 (1) Å] contacts. The crystal packing a C—H...O and C—H...π interactions.

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32

Khamees, Hussien Ahmed, Kumara Chaluvaiah, Nasseem Ahmed El-khatatneh, et al. "Crystal structure, DFT calculation, Hirshfeld surface analysis and energy framework study of 6-bromo-2-(4-bromophenyl)imidazo[1,2-a]pyridine." Acta Crystallographica Section E Crystallographic Communications 75, no. 11 (2019): 1620–26. http://dx.doi.org/10.1107/s2056989019013410.

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The title imidazo[1,2-a] pyridine derivative, C13H8Br2N2, was synthesized via a single-step reaction method. The title molecule is planar, showing a dihedral angle of 0.62 (17)° between the phenyl and the imidazo[1,2-a] pyridine rings. An intramolecular C—H...N hydrogen bond with an S(5) ring motif is present. In the crystal, a short H...H contact links adjacent molecules into inversion-related dimers. The dimers are linked in turn by weak C—H...π and slipped π–π stacking interactions, forming layers parallel to (110). The layers are connected into a three-dimensional network by short Br...H c

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33

Naghiyev, Farid N., Maria M. Grishina, Victor N. Khrustalev, et al. "Crystal structure and Hirshfeld surface analysis of ethyl 6′-amino-2′-(chloromethyl)-5′-cyano-2-oxo-1,2-dihydrospiro[indoline-3,4′-pyran]-3′-carboxylate." Acta Crystallographica Section E Crystallographic Communications 77, no. 7 (2021): 739–43. http://dx.doi.org/10.1107/s2056989021006459.

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The molecular conformation of the title compound, C17H14ClN3O4, is stabilized by an intramolecular C—H...O contact, forming an S(6) ring motif. In the crystal, the molecules are connected by N—H...O hydrogen-bond pairs along the b-axis direction as dimers with R 2 2(8) and R 2 2(14) ring motifs and as ribbons formed by intermolecular C—H...N hydrogen bonds. There are weak van der Waals interactions between the ribbons. The most important contributions to the surface contacts are from H...H (34.9%), O...H/H...O (19.2%), C...H/H...C (11.9%), Cl...H/H...Cl (10.7%) and N...H/H...N (10.4%) interact

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34

El-Emam, Ali A., Ebtehal S. Al-Abdullah, Hanaa M. Al-Tuwaijri, C. S. Chidan Kumar, and Hoong-Kun Fun. "N-(Adamantan-1-yl)-1,2,3,4-tetrahydroisoquinoline-2-carbothioamide." Acta Crystallographica Section E Structure Reports Online 69, no. 12 (2013): o1815. http://dx.doi.org/10.1107/s1600536813031516.

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In the title compound, C20H26N2S, the N-containing six-membered ring adopts a boat conformation and the dihedral angle between the thiocarbamide group and the benzene ring is 49.67 (9)°. An intramolecular C—H...S hydrogen bond generates anS(6) ring motif. The N—H group is sterically hindered and there are no significant intermolecular interactions beyond van der Waals contacts.

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35

Ezkurdia, Iakes, Osvaldo Graña, José M. G. Izarzugaza, and Michael L. Tress. "Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8." Proteins: Structure, Function, and Bioinformatics 77, S9 (2009): 196–209. http://dx.doi.org/10.1002/prot.22554.

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36

Lupyan, Dmitry, Yuriy A. Abramov, and Woody Sherman. "Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation." Journal of Computer-Aided Molecular Design 26, no. 11 (2012): 1195–205. http://dx.doi.org/10.1007/s10822-012-9610-x.

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37

Mossine, Valeri V., Charles L. Barnes та Thomas P. Mawhinney. "Multicentered hydrogen bonding in 1-[(1-deoxy-β-D-fructopyranos-1-yl)azaniumyl]cyclopentanecarboxylate (`D-fructose-cycloleucine')". Acta Crystallographica Section E Crystallographic Communications 75, № 8 (2019): 1096–101. http://dx.doi.org/10.1107/s2056989019009253.

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The title compound, C12H21NO7, (I), is conformationally unstable; the predominant form present in its solution is the β-pyranose form (74.3%), followed by the β- and α-furanoses (12.1 and 10.2%, respectively), α-pyranose (3.4%), and traces of the acyclic carbohydrate tautomer. In the crystalline state, the carbohydrate part of (I) adopts the 2 C 5 β-pyranose conformation, and the amino acid portion exists as a zwitterion, with the side chain cyclopentane ring assuming the E 9 envelope conformation. All heteroatoms are involved in hydrogen bonding that forms a system of antiparallel infinite ch

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38

Vologzhanina, Anna V., Alexander A. Korlyukov, and Mikhail Yu Antipin. "Special features of intermolecular bonding A...D (A = Si, Ge and D = nucleophile) in crystal structures." Acta Crystallographica Section B Structural Science 64, no. 4 (2008): 448–55. http://dx.doi.org/10.1107/s0108768108016170.

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An investigation of the crystal structures of 3346 silicon- and 718 germanium-containing compounds was carried out with a geometrical–topological analysis. The descriptors of inter- and intramolecular contacts A...D are given. Information on the descriptors of T—A...D (where T = leaving group) interactions in terms of a stereoatomic model of crystal structures was described as being helpful in modelling SN2 reactions. It was established that the formation of multiple intermolecular contacts in crystal structures is unfavorable. The dependence of the descriptors of intermolecular contacts T—A..

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39

Karalai, Chatchanok, Nisakorn Saewon, Kan Chantrapromma, Suchada Chantrapromma, Hoong-Kun Fun, and Ibrahim Abdul Razak. "1-[4-(3,5-Dimethoxy-2-methylphenoxy)-2,6-dihydroxy-3-methylphenyl]ethanone." Acta Crystallographica Section E Structure Reports Online 57, no. 1 (2000): o18—o19. http://dx.doi.org/10.1107/s1600536800018213.

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The benzene rings of the title compound, C18H20O6, are nearly perpendicular to each other [dihedral angle 75.2 (1)°]. The two methoxy groups and the acetyl group are almost coplanar to their attached benzene rings. One hydroxyl group is involved in an intramolecular O—H...O hydrogen bond with the adjacent acetyl O atom. The crystal structure is stabilized by intermolecular O—H...O contacts.

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40

Ben Ali, Abdelkader, Youness El Bakri, Chin-Hung Lai, et al. "Crystal structure, computational study and Hirshfeld surface analysis of ethyl (2S,3R)-3-(3-amino-1H-1,2,4-triazol-1-yl)-2-hydroxy-3-phenylpropanoate." Acta Crystallographica Section E Crystallographic Communications 75, no. 12 (2019): 1919–24. http://dx.doi.org/10.1107/s2056989019015743.

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In the title molecule, C13H16N4O3, the mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intramolecular C—H...O and C—H...π(ring) interactions. In the crystal, layers parallel to (101) are generated by O—H...N, N—H...O and N—H...N hydrogen bonds. The layers are connected by inversion-related pairs of C—H...O hydrogen bonds. The experimental molecular structure is close to the gas-phase geometry-optimized structure calculated by DFT methods. Hirshfeld surface analysis indicates that the most important interaction involving hydrogen in the ti

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41

Simkovic, Felix, Sergey Ovchinnikov, David Baker, and Daniel J. Rigden. "Applications of contact predictions to structural biology." IUCrJ 4, no. 3 (2017): 291–300. http://dx.doi.org/10.1107/s2052252517005115.

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Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallography, cryo-EM or NMR. Integrative structural bioi

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42

Paulus, Georgiana, Huey Chong Kwong, Karen A. Crouse, and Edward R. T. Tiekink. "2-[(1E)-[(Z)-2-({[(1Z)-[(E)-2-[(2-Hydroxyphenyl)methylidene]hydrazin-1-ylidene]({[(4-methylphenyl)methyl]sulfanyl})methyl]disulfanyl}({[(4-methylphenyl)methyl]sulfanyl})methylidene)hydrazin-1-ylidene]methyl]phenol: crystal structure, Hirshfeld surface analysis and computational study." Acta Crystallographica Section E Crystallographic Communications 76, no. 8 (2020): 1245–50. http://dx.doi.org/10.1107/s2056989020008762.

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The complete molecule of the title hydrazine carbodithioate derivative, C32H30N4O2S4, is generated by a crystallographic twofold axis that bisects the disulfide bond. The molecule is twisted about this bond with the C—S—S—C torsion angle of 90.70 (8)° indicating an orthogonal relationship between the symmetry-related halves of the molecule. The conformation about the imine bond [1.282 (2) Å] is E and there is limited delocalization of π-electron density over the CN2C residue as there is a twist about the N—N bond [C—N—N—C torsion angle = −166.57 (15)°]. An intramolecular hydroxyl-O—H...N(imine

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43

Kast, Denis, L. Kecke, and J. Ankerhold. "Charge transfer through single molecule contacts: How reliable are rate descriptions?" Beilstein Journal of Nanotechnology 2 (August 3, 2011): 416–26. http://dx.doi.org/10.3762/bjnano.2.47.

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Background: The trend for the fabrication of electrical circuits with nanoscale dimensions has led to impressive progress in the field of molecular electronics in the last decade. However, a theoretical description of molecular contacts as the building blocks of future devices is challenging, as it has to combine the properties of Fermi liquids in the leads with charge and phonon degrees of freedom on the molecule. Outside of ab initio schemes for specific set-ups, generic models reveal the characteristics of transport processes. Particularly appealing are descriptions based on transfer rates

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Mikulcik, P., P. Bissinger, J. Riede, and H. Schmidbaur. "Bindung von Metall-Ionen an Dipeptide: Struktur von Thallium(I)-(3-benzyl-6-carboxylatomethyl-2,5-diketopiperazin) / Binding of Metal Ions by Dipeptides: Structure of Thallium(I) 3-Benzyl-6-carboxylatomethyl-2,5-diketopiperazine." Zeitschrift für Naturforschung B 47, no. 7 (1992): 952–56. http://dx.doi.org/10.1515/znb-1992-0710.

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Ester cleavage of aspartame (L-α-aspartyl-L-phenylalanine methylester) (1), by equimolar quantities of thallium ethoxide is accompanied by intramolecular cyclisation to give thallium 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine (2). The solid state structure of the crystalline product was determined by single-crystal X-ray diffraction analysis. The cations were found to form four short and four elongated contacts to seven oxygen atoms and one nitrogen atom of a total of six neighbouring 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine anions. There are inter-anionic hydrogen bonds only

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45

Liang, Ying, Li-Qiao Shi, and Zi-Wen Yang. "Crystal structure ofN-{4-[(6-chloropyridin-3-yl)methoxy]phenyl}-2,6-difluorobenzamide." Acta Crystallographica Section E Crystallographic Communications 72, no. 1 (2016): 60–62. http://dx.doi.org/10.1107/s2056989015023701.

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In the title compound, C19H13ClF2N2O2, the conformation of the N—H bond in the amide segment isantito the C=O bond. The molecule is not planar, with dihedral angles between the central benzene ring and the outer benzene and pyridyl rings of 73.35 (7) and 81.26 (6)°, respectively. A weak intramolecular C—H...O hydrogen bond occurs. In the crystal, N—H...N, C—H...O and C—H...F hydrogen bonds lead to the formation of dimers. The N—H...N inversion dimers are linked by π–π contacts between adjacent pyridine rings [centroid–centroid = 3.8541 (12) Å] and C—H...π interactions. These contacts combine t

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46

Zukerman-Schpector, Julio, Karinne E. Prado, Luccas L. Name, Rodrigo Cella, Mukesh M. Jotani, and Edward R. T. Tiekink. "2-[(4-Chlorophenyl)selanyl]-3,4-dihydro-2H-benzo[h]chromene-5,6-dione: crystal structure and Hirshfeld analysis." Acta Crystallographica Section E Crystallographic Communications 73, no. 6 (2017): 918–24. http://dx.doi.org/10.1107/s2056989017007605.

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The title organoselenium compound, C19H13ClO3Se {systematic name: 2-[(4-chlorophenyl)selanyl]-2H,3H,4H,5H,6H-naphtho[1,2-b]pyran-5,6-dione}, has the substituted 2-pyranyl ring in a half-chair conformation with the methylene-C atom bound to the methine-C atom being the flap atom. The dihedral angle between the two aromatic regions of the molecule is 9.96 (9)° and indicates a step-like conformation. An intramolecular Se...O interaction of 2.8122 (13) Å is noted. In the crystal, π–π contacts between naphthyl rings [inter-centroid distance = 3.7213 (12) Å] and between naphthyl and chlorobenzene ri

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47

Pandiyan, B. Vijaya, P. Deepa, and P. Kolandaivel. "Does the occurrence of resonance (by the delocalization of radical/cationic/anionic charges) induce the existence of intramolecular halogen–halogen contacts?" RSC Advances 6, no. 71 (2016): 66870–78. http://dx.doi.org/10.1039/c6ra14270b.

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Exotic intramolecular homo/hetero dihalogen bonding (C–X⋯X–C: X = Br, Cl and F) in radical, cationic and anionic five-membered ring systems was analyzed using wave functional theory (MP2/aug-cc-pVTZ) analysis.

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48

Durka, Krzysztof, Sergiusz Luliński, and Janusz Serwatowski. "2-Methoxy-3-(trimethylsilyl)phenylboronic acid." Acta Crystallographica Section E Structure Reports Online 69, no. 12 (2013): o1818. http://dx.doi.org/10.1107/s1600536813031656.

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The molecular structure of the title compound, C10H17BO3Si, features an intramolecular O—H...O hydrogen bond; the boronic group group has anexo–endoconformation. In the crystal, the molecules interact with each other by O—H...O hydrogen bonds, producing centrosymmetric dimers that are linked by weak π–π stacking interactions featuring specific short B...C contacts [e.g. 3.372 (2) Å], forming an infinite columnar structure aligned along thea-axis direction.

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49

Dileep, C. S., V. Lakshmi Ranganatha, N. K. Lokanath, S. A. Khanum, and M. A. Sridhar. "(4-Fluorophenyl)(2-hydroxy-5-methylphenyl)methanone." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (2014): o286. http://dx.doi.org/10.1107/s1600536814001883.

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In the title compound, C14H11FO2, the dihedral angles beteen the central C3O ketone residue and the fluoro- and hydroxy-substituted benzene rings are 50.44 (9) and 12.63 (10)°, respectively. The planes of the benzene rings subtend a dihedral angle of 58.88 (9)° and an intramolecular O—H...O hydrogen bond closes anS(6) ring. No directional interactions beyond van der Waals packing contacts were identified in the crystal structure.

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50

Belaj, F. "Structures of the Phosphazenes [ClC(NPCl3)2]+PCl6 − and [CH3C(NPCl3)2]+SbCl6 − at 90 K." Acta Crystallographica Section B Structural Science 53, no. 6 (1997): 953–60. http://dx.doi.org/10.1107/s0108768197008343.

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The asymmetric units of both ionic compounds [N-(chloroformimidoyl)phosphorimidic trichloridato]trichlorophosphorus hexachlorophosphate, [ClC(NPCl3)2]+PCl^{-}_{6} (1), and [N-(acetimidoyl)phosphorimidic trichloridato]trichlorophosphorus hexachloroantimonate, [CH3C(NPCl3)2]+SbCl^{-}_{6} (2), contain two formula units with the atoms located on general positions. All the cations show cis–trans conformations with respect to their X—C—N—P torsion angles [X = Cl for (1), C for (2)], but quite different conformations with respect to their C—N—P—Cl torsion angles. Therefore, the two NPCl3 groups of a

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