Interpreting Substituent Effects on the Crystal Packing of Long-Chain Diacyl Peroxides. The Crystal Structures of D1 (11 Bromoundecanoyl) Peroxide and Di (Undecanoyl) Peroxide

Author(s):  
J. Michael Mcbride ◽  
Steven B. Bertman ◽  
Donna Z. Cioffi ◽  
Brigitte E. Segmuller ◽  
Bruce A. Weber
CrystEngComm ◽  
2014 ◽  
Vol 16 (19) ◽  
pp. 3867-3882 ◽  
Author(s):  
Andrew G. P. Maloney ◽  
Peter A. Wood ◽  
Simon Parsons

In the short chain amines H-bonding dominates crystal packing, but dispersion wins-out for the long chain compounds. The cross-over point occurs between butyl and pentylamine, where interactions are finely balanced.


2018 ◽  
Vol 74 (11) ◽  
pp. 1427-1433 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Waldemar Tejchman ◽  
Jadwiga Handzlik

The arylidene–imidazolone derivatives are a group of compounds of great interest in medicinal chemistry due to their various pharmacological actions. In order to study the possible conformations of an arylidene–imidazolone derivative, two new crystal structures were determined by X-ray diffraction, namely (Z)-5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-5(4H)-one, C15H17ClN4O, (6), and its salt 4-[5-(4-chlorobenzylidene)-5-oxo-4,5-dihydro-3H-imidazol-2-yl]-1-methylpiperazin-1-ium 3-{5-[4-(diethylamino)benzylidene]-4-oxo-2-thioxothiazolidin-3-yl}propionate, C15H18ClN4O+·C17H19N2O3S2 −, (7). Both compounds crystallize in the space group P\overline{1}. The basic form (6) crystallizes with two molecules in the asymmetric unit. In the acid form of (6), the N atom of the piperazine ring is protonated by proton transfer from the carboxyl group of the rhodanine acid derivative. The greatest difference in the conformations of (6) and its protonated form, (6c), is observed in the location of the arylidene–imidazolone substituent at the N atom. In the case of (6c), the position of this substituent is close to axial, while for (6), the corresponding position is intermediate between equatorial and axial. The crystal packing is dominated by a network of N—H...O hydrogen bonds. Furthermore, the crystal structures are stabilized by numerous intermolecular contacts of types C—H...N and C—H...Cl in (6), and C—H...O and C—H...S in (7). The geometry with respect to the location of the substituents at the N atoms of the piperazine ring was compared with other crystal structures possessing an N-methylpiperazine moiety.


Biochemistry ◽  
2012 ◽  
Vol 51 (20) ◽  
pp. 4138-4146 ◽  
Author(s):  
Brandon R. Goblirsch ◽  
Janice A. Frias ◽  
Lawrence P. Wackett ◽  
Carrie M. Wilmot

2013 ◽  
Vol 69 (12) ◽  
pp. 1549-1552 ◽  
Author(s):  
Vladimir V. Chernyshev ◽  
Sergey Y. Efimov ◽  
Ksenia A. Paseshnichenko ◽  
Andrey A. Shiryaev

The title salt, C8H12NO+·C7H10NO5−, crystallizes in two polymorphic modifications,viz.monoclinic (M) and orthorhombic (O). The crystal structures of both polymorphic modifications have been established from laboratory powder diffraction data. The crystal packing motifs in the two polymorphs are different, but the conformations of the anions are generally similar. InM, the anions are linked by pairs of hydrogen bonds of the N—H...O and O—H...O types into chains along theb-axis direction, and neighbouring molecules within the chain are related by the 21screw axis. The cations link these chainsviaO—H...O and N—H...O hydrogen bonds into layers parallel to (001). InO, the anions are linked by O—H...O hydrogen bonds into helices along [001], and neighbouring molecules within the helix are related by the 21screw axis. The neighbouring helical turns are linked by N—H...O hydrogen bonds. The cations link the helicesviaO—H...O and N—H...O hydrogen bonds, thus forming a three-dimensional network.


2010 ◽  
Vol 66 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Angelo Gavezzotti

A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule–molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ∼ 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom–atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.


2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.


2001 ◽  
Vol 34 (6) ◽  
pp. 710-714 ◽  
Author(s):  
James A. Kaduk ◽  
Jason A. Hanko

The crystal structures of isostructural 2,6-naphthalenedicarboxylate tetrahydrate salts of nickel(II) and cobalt(II) have been determined using Monte Carlo simulated annealing techniques and laboratory X-ray powder diffraction data. These compounds crystallize in the triclinic space groupP\bar{1}, withZ= 2;a= 10.0851 (4),b= 10.9429 (5),c= 6.2639 (3) Å, α = 98.989 (2), β = 87.428 (3), γ = 108.015 (2)°,V= 649.32 (5) Å3for [Ni(C12H6O4)(H2O)4], anda= 10.1855 (6),b= 10.8921 (6),c= 6.2908 (5) Å, α = 98.519 (4), β = 87.563 (4), γ = 108.304 (3)°,V= 655.28 (8) Å3for [Co(C12H6O4)(H2O)4]. The water-molecule H atoms were located by quantum chemical geometry optimization usingCASTEP. The structure consists of alternating hydrocarbon and metal/oxygen layers parallel to theacplane. Each naphthalenedicarboxylate anion bridges two metal cations; each carboxyl group is monodentate. The resulting structure contains infinite chains parallel to [111]. The octahedral coordination sphere of the metal cations containstranscarboxylates and four equatorial water molecules. The carboxyl groups are rotated by 15–20° out of the naphthalene plane. The metal/oxygen layers are characterized by an extensive hydrogen-bonding network. The orientations of the carboxyl groups are determined by the formation of short (O...O = 2.53 Å) hydrogen bonds between the carbonyl O atoms and theciswater molecules. Molecular mechanics energy minimizations suggest that coordination and hydrogen-bonding interactions are most important in determining the crystal packing.


2003 ◽  
Vol 59 (11) ◽  
pp. m484-m486 ◽  
Author(s):  
Philip A. W. Dean ◽  
Donald C. Craig ◽  
Marcia L. Scudder ◽  
Ian G. Dance

The reported crystal structures of Ph4P+·I− and Ph4As+·I− have been re-examined. An apparent instance of substitutional dimorphism could not be reproduced and, contrary to an earlier report, tetraphenylarsonium iodide, [As(C6H5)4]I or Ph4As+·I−, was found to be isostructural with the phosphorus compound. The cation and anion are both located on \overline 4 symmetry sites. The crystal packing involves linear chains of cations in fourfold phenyl embraces.


1999 ◽  
Vol 55 (4) ◽  
pp. 873-876 ◽  
Author(s):  
Toshiyuki Chatake ◽  
Tomoko Sunami ◽  
Akira Ono ◽  
Yoshihito Ueno ◽  
Akira Matsuda ◽  
...  

The DNA dodecamer of (CGCGmo6AATCCGCG) containing 2′-deoxy-N 6-methoxyadenosine has been crystallized for X-ray analysis in order to investigate the effects of the modified adenosine on base pairing. It has been found that the crystal changes from one form to another during data collection in a manner similar to a phase transition. The two crystal structures show that this phenomenon, ascribed to differences in humidity, is correlated with a change in the contact angle between the two duplexes.


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