The structures of eight 2,4,6-trisubstituted-5-nitrosopyrimidines (one of which crystallizes in two polymorphs) have been determined, including seven O6-benzyl derivatives which are potential, or proven, in vitro inhibitors of the human DNA-repair protein O6-alkylguanine-DNA-transferase. In the derivatives having an amino substituent at the 4-position, an intramolecular N—H...O hydrogen bond with the nitroso O as an acceptor leads to an overall molecular shape similar to that of substituted purines. There is a marked propensity for these nitroso compounds to crystallize with Z′ = 2. The structure of an analogue with no nitroso group is also reported for comparative purposes. Compounds containing the N-alkyl substituents —NHCH2COOEt, —NHCH2CH2COOEt and —NHCH(CH2Ph)COOEt, derived from amino acid esters, exhibit a rich variety of conformational behaviour, and in all of the nitroso compounds the bond lengths provide strong evidence for a highly polarized electronic structure. Associated with this polarization is extensive charge-assisted hydrogen bonding between the molecules, leading to supramolecular aggregation in the form of finite (zero-dimensional) aggregates, chains, molecular ladders, sheets and frameworks.

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Three of the nine isomeric N-(nitrobenzylidene)iodoanilines, C13H9IN2O2, have been found, when crystallized from acetone, to yield polymorphs which differ from those obtained upon crystallization from ethanol. In the second polymorph of 2-iodo-N-(2-nitrobenzylidene)aniline, the molecules are disordered across inversion centres in space group C2/c, but there are no direction-specific interactions between the molecules. In the second polymorph of 2-iodo-N-(3-nitrobenzylidene)aniline, the molecules adopt a different conformation from those in the first polymorph, and they are linked into sheets by a combination of a three-centre iodo-nitro interaction and an aromatic pi-pi stacking interaction, both of which are absent from the supramolecular structure of the first polymorph. The second polymorph of 3-iodo-N-(2-nitrobenzylidene)aniline crystallizes with Z' = 2 in space group P2(1), and the molecules are linked into sheets by one C-H...O hydrogen bond and two C-H...pi(arene) hydrogen bonds.

The structures of 12 new N(6)-substituted 2-amino-4-chloro-5-formylpyrimidines, where the N(6) substituent is of the type NHR or NR(1)R(2), have been determined. The intramolecular dimensions provide strong evidence for the development of polarized, charge-separated molecular-electronic structures, with the positive charge delocalized over the two exocyclic amino N atoms and with negative charge on the formyl O atom. This polarization appears to be independent of the significant puckering, in seven of the compounds, of the pyrimidine rings from planarity towards boat, twist-boat or screw-boat conformations. In 11 of the compounds studied here, N-H...N hydrogen bonds link pairs of molecules into centrosymmetric R2(2)(8) dimer units, and their overall crystal structures are determined by the patterns of hydrogen bonds by which these units are further linked. Examples are reported in which no further hydrogen bonding occurs; in which the R2(2)(8) dimers are linked into chains of rings, or into sheets; and in which sheets are formed by the pi-stacking of hydrogen-bonded chains of rings. In the sole structure lacking the R2(2)(8) dimer motif, N-H...O and N-H...N hydrogen bonds cooperate to generate a three-dimensional framework structure.

The title compound (C(6)H(7)NO(3)S) exists as a zwitterion (4-ammoniobenzenesulfonate), +H(3)NC(6)H(4)SO(3)-, and these units are linked into a three-dimensional framework by two distinct two-centre N-H* * *O hydrogen bonds [H* * *O 1.84 and 1.87 A; N* * *O 2.767 (2) and 2.746 (2) A; N-H* * *O 166 and 172 degrees ] and a planar three-centre N-H* * *(O)(2) hydrogen bond [H* * *O 2.03 and 2.37 A; N* * *O 2.816 (2) and 2.877 (2) A; N-H* * *O 162 and 111 degrees; O* * *H* * *O 86 degrees ].

C10H13N5O4, Mr = 267.2, monoclinic, P2(1), a = 5.716 (3), b = 11.998 (8), c = 17.658 (10) A, beta = 94.26 (4) degrees, V = 1208 A3, Z = 4, D chi = 1.47 g cm-3, lambda (Mo K alpha) = 0.71069 A, mu = 7.5 cm-1, F(000) = 560, T = 293 K. R = 0.060 for 2138 unique observed [F greater than 4 sigma (F)] reflections. The N-glycosidic torsion angles chi have values -125.9 (5) and -172.0 (5) degrees, in the anti range. (Molecule-A values are given first throughout.) The sugar puckers are 2(3)T (C3'-exo/C2'-endo), with P = 171 (1) degrees and psi m = 14 (1) degrees, and 4(3)T (C4'-endo/C3'-exo), with P = 213 (1) degrees and psi m = 11 (1) degrees. The C4-C5 conformations, with gamma = 49.7 (5) and 173.7 (5) degrees, are + sc (gauche-gauche) and ap (gauche-trans). The conformational parameters used follow the guidelines of the IUPAC-IUB Joint Commission on Biochemical Nomenclature [Pure Appl. Chem. (1983), 55, 1273-1280]. The molecules in the asymmetric unit form a hydrogen-bonded, base-paired dimer. The bonding is as follows: N3A-0.973 A-H3A... 1.790 A...O2B, N3A...O2B 2.747 (8) A, angle at H3A 167 degrees and N3B-0.992 A-H3B...1.916 A...O2A, N3B...O2A 2.894 (8) A, angle at H3B 168 degrees. The propeller twist between the bases is 5 degrees [Wilson & Tollin (1987). Nucleosides Nucleotides, 6, 643-653].

In each of the isomeric compounds (Z)-5-(2-fluorobenzylidene)-2-thioxothiazolidin-4-one, C(10)H(6)FNOS(2), (I), and (Z)-5-(4-fluorobenzylidene)-2-thioxothiazolidin-4-one, C(10)H(6)FNOS(2), (II), there is a very wide C-C-C angle (ca 130 degrees ) at the methine C atom linking the two rings. In each isomer, paired N-H...O hydrogen bonds link the molecules into centrosymmetric R(2)(2)(8) dimers; the hydrogen-bonded dimers are linked into chains by an aromatic pi-pi stacking interaction in isomer (I) and by an antiparallel dipolar carbonyl-carbonyl interaction in isomer (II). (Z)-5-(3,4,5-Trimethoxybenzylidene)-2-thioxothiazolidin-4-one, C(13)H(13)NO(4)S(2), (III), which crystallizes with Z' = 2 in the space group P-1, shows the same very wide angle at the bridging methine C atom; the two independent molecules are linked into an isolated dimer having no crystallographic symmetry.

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