skip to main content

Title: Ditopic halogen bonding with bipyrimidines and activated pyrimidines
The potential of pyrimidines to serve as ditopic halogen-bond acceptors is explored. The halogen-bonded cocrystals formed from solutions of either 5,5′-bipyrimidine (C 8 H 6 N 4 ) or 1,2-bis(pyrimidin-5-yl)ethyne (C 10 H 6 N 4 ) and 2 molar equivalents of 1,3-diiodotetrafluorobenzene (C 6 F 4 I 2 ) have a 1:1 composition. Each pyrimidine moiety acts as a single halogen-bond acceptor and the bipyrimidines act as ditopic halogen-bond acceptors. In contrast, the activated pyrimidines 2- and 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine (C 14 H 13 N 3 ) are ditopic halogen-bond acceptors, and 1:1 halogen-bonded cocrystals are formed from 1:1 mixtures of each of the activated pyrimidines and either 1,2- or 1,3-diiodotetrafluorobenzene. A 1:1 cocrystal was also formed between 2-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine and 1,4-diiodotetrafluorobenzene, while a 2:1 cocrystal was formed between 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine and 1,4-diiodotetrafluorobenzene.
; ; ;
Award ID(s):
1903581 1903593
Publication Date:
Journal Name:
Acta Crystallographica Section C Structural Chemistry
Page Range or eLocation-ID:
458 to 467
Sponsoring Org:
National Science Foundation
More Like this
  1. By varying the halogen-bond-donor molecule, 11 new halogen-bonding cocrystals involving thiourea or 1,3-dimethylthiourea were obtained, namely, 1,3-dimethylthiourea–1,2-diiodo-3,4,5,6-tetrafluorobenzene (1/1), C 6 F 4 I 2 ·C 3 H 8 N 2 S, 1 , thiourea–1,3-diiodo-2,4,5,6-tetrafluorobenzene (1/1), C 6 F 4 I 2 ·CH 4 N 2 S, 2 , 1,3-dimethylthiourea–1,3-diiodo-2,4,5,6-tetrafluorobenzene (1/1), C 6 F 4 I 2 ·C 3 H 8 N 2 S, 3 , 1,3-dimethylthiourea–1,3-diiodo-2,4,5,6-tetrafluorobenzene–methanol (1/1/1), C 6 F 4 I 2 ·C 3 H 8 N 2 S·CH 4 O, 4 , 1,3-dimethylthiourea–1,3-diiodo-2,4,5,6-tetrafluorobenzene–ethanol (1/1/1), C 6 F 4 I 2 ·C 3 H 8 N 2 S·C 2 H 6 O, 5 , 1,3-dimethylthiourea–1,4-diiodo-2,3,5,6-tetrafluorobenzene (1/1), C 6 F 4 I 2 ·C 3 H 8 N 2 S, 6 , 1,3-dimethylthiourea–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 3 H 8 N 2 S, 7 , 1,3-dimethylthiourea–1,1,2,2-tetraiodoethene (1/1), C 6 H 16 N 4 S 2 ·C 2 I 4 , 8 , [(dimethylamino)methylidene](1,2,2-triiodoethenyl)sulfonium iodide–1,1,2,2-tetraiodoethene–acetone (1/1/1), C 5 H 8 I 3 N 2 S + ·I − ·C 3 H 6 O·C 2 I 4 , 9 , 2-amino-4-methyl-1,3-thiazol-3-ium iodide–1,1,2,2-tetraiodoethene (2/3), 2C 4 H 7 N 2 S + ·2I − ·3C 2 I 4 ,more »10 , and 4,4-dimethyl-4 H -1,3,5-thiadiazine-3,5-diium diiodide–1,1,2,2-tetraiodoethene (2/3), 2C 5 H 12 N 4 S 2+ ·4I − ·3C 2 I 4 , 11 . When utilizing the common halogen-bond-donor molecules 1,2-, 1,3-, and 1,4-diiodotetrafluorobenzene, as well as 1,3,5-trifluoro-2,4,6-triiodobenzene, bifurcated I...S...I interactions were observed, resulting in the formation of isolated rings, chains, and sheets. Tetraiodoethylene (TIE) provided I...S...I cocrystals as well, but further yielded a sulfonium-containing product through the reaction of the S atom with TIE. This particular sulfonium motif is the first of its kind to be structurally characterized, and is stabilized in the solid state through a three-dimensional I...I halogen-bonding network. Thiourea reacted with acetone in the presence of TIE to provide two novel heterocyclic products, again stabilized in the solid state through I...I halogen bonding.« less
  2. Utilizing the N -heterocyclic chalcogenones hexahydro-1,3-bis(2,4,6-trimethylphenyl)-2 H -1,3-diazepine-2-thione ( SDiazMesS ) and hexahydro-1,3-bis(2,4,6-trimethylphenyl)-2 H -1,3-diazepine-2-selone ( SDiazMesSe ) as halogen-bond acceptors, a total of 24 new cocrystals were prepared. The solid-state structures of the parent molecules were also determined, along with those of their acetonitrile solvates. Through the reaction of the chalcogen atom with molecular diiodine, a variety of S—I—I and Se—I—I fragments were formed, spanning a wide range of I—I bond orders. With acetone as a reaction solvent, molecular diiodine causes the oxidative addition of acetone to the chalcogen atom, resulting in new C—S, C—Se and C—C covalent bonds under mild conditions. The common halogen-bond donors, iodopentafluorobenzene, 1,2-, 1,3- and 1,4-diiodotetrafluorobenzene, 1,3,5-trifluorotriiodobenzene and tetraiodoethylene resulted in halogen-bond-driven cocrystal formation. In most cases, the analogous SDiazMesS and SDiazMesSe cocrystals are isomorphic.
  3. This study expands and combines concepts from two of our earlier studies. One study reported the complementary halogen bonding and π-π charge transfer complexation observed between isomeric electron rich 4-N,N-dimethylaminophenylethynylpyridines and the electron poor halogen bond donor, 1-(3,5-dinitrophenylethynyl)-2,3,5,6-tetrafluoro-4-iodobenzene while the second study elaborated the ditopic halogen bonding of activated pyrimidines. Leveraging our understanding on the combination of these non-covalent interactions, we describe cocrystallization featuring ditopic halogen bonding and π-stacking. Specifically, red cocrystals are formed between the ditopic electron poor halogen bond donor 1-(3,5-dinitrophenylethynyl)-2,4,6-triflouro-3,5-diiodobenzene and each of electron rich pyrimidines 2- and 5-(4-N,N-dimethyl-aminophenylethynyl)pyrimidine. The X-ray single crystal structures of these cocrystals are described in terms of halogen bonding and electron donor-acceptor π-complexation. Computations confirm that the donor-acceptor π-stacking interactions are consistently stronger than the halogen bonding interactions and that there is cooperativity between π-stacking and halogen bonding in the crystals.
  4. The treatment of 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine with a threefold excess of 1,2,3,5-tetrafluoro-4,6-diiodobenzene in dichloromethane solution led to the formation of the unexpected 1:2 title co-crystal, C 14 H 13 N 3 ·2CF 4 I 2 . In the extended structure, two unique C—I...N halogen bonds from one of the 1,2,3,5-tetrafluoro-4,6-diiodobenzene molecules to the pyrimidine N atoms of the 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine molecule generate [110] chains and layers of these chains are π-stacked along the a- axis direction. The second 1,2,3,5-tetrafluoro-4,6-diiodobenzene molecule resides in channels formed parallel to the a -axis direction between stacks of 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine molecules and interacts with them via C—I...π(alkyne) contacts.
  5. The halogen-bond (X-bond) donors 1,3- and 1,4-diiodotetrafluorobenzene (1,3-di-I-tFb and 1,4-di-I-tFb, respectively) form cocrystals with trans-1,2-bis(2-pyridyl)ethylene (2,2′-bpe) assembled by N···I X-bonds. In each cocrystal, 2(1,3-di-I-tFb)·2(2,2′-bpe) and (1,4-di-I-tFb)·(2,2′-bpe), the donor molecules support the C=C bonds of 2,2′-bpe to undergo an intermolecular [2+2] photodimerization. UV irradiation of each cocrystal resulted in stereospecific and quantitative conversion of 2,2′-bpe to rctt-tetrakis(2-pyridyl)cyclobutane (2,2′-tpcb). In each case, the reactivity occurs via face-to-face π-stacked columns wherein nearest-neighbor pairs of 2,2′-bpe molecules lie sandwiched between X-bond donor molecules. Nearest-neighbor C=C bonds are stacked criss-crossed in both cocrystals. The reactivity was ascribed to the olefins undergoing pedal-like motion in the solid state. The stereochemistry of 2,2′-tpcb is confirmed in cocrystals 2(1,3-di-I-tFb)·(2,2′-tpcb) and (1,4-di-I-tFb)·(2,2′-tpcb).