KNI-272, a highly selective and potent peptidic HIV protease inhibitor

Kynostatin {KNI-272; systematic name: 3-[3-benzyl-2-hydroxy-9-(isoquinolin-5-yl­oxy)-6-methyl­sulfanyl­methyl-5,8-dioxo-4,7-di­aza­nonanoyl]-N-tert-butyl-1,3-thia­zolane-4-carbox­amide}, a highly selective and potent HIV protease inhibitor containing allo­phenyl­norstatin [(2S,3S)-3-amino-2-hydroxy-4-phenyl­butyric acid], has been crystallized as the hydrate, C₃₃H₄₁N₅O₆S₂·0.803H₂O, from aqueous hexyl­ene glycol. The observed disorder of the phenyl group in the structure is related to the mode of hydration. The backbone conformation of the mol­ecule is twisted and the overall conformation of the free inhibitor is similar to that observed in its complex with HIV protease.     

Methyl 1‐(4‐chloro­benzyl)‐2‐(4‐methyl­piperazin‐1‐yl)‐1H‐benz­imidazole‐5‐carboxyl­ate hemihydrate

The title compound, C₂₁H₂₃ClN₄O₂·0.5H₂O, contains two independent mol­ecules in the asymmetric unit. In each mol­ecule the piperazine ring adopts a chair conformation; the deviations of the piperazine N atoms from the best plane through the remaining four C atoms are ?0.678 (3) and 0.662 (3) Å in mol­ecule A, and 0.687 (3) and ?0.700 (3) Å in mol­ecule B. The mol­ecules are linked by two hydrogen bonds of the O—H?N type involving the O atom of the water mol­ecule of crystallization.     

Aqua(2,2′‐di­amino‐4,4′‐bi‐1,3‐thia­zole‐κ2N,N′)(imino­diacetato‐κ3O,N,O′)­chromium(III) chloride mono­hydrate

Crystals of the title compound, [Cr(C₄H₅NO₄)(C₆H₆N₄S₂)(H₂O)]Cl·H₂O, consist of Cr^III complex cations, Cl⁻ counter‐ions and lattice water mol­ecules. The complex cation assumes an octahedral coordination geometry, formed by a tridentate imino­di­acetate dianion (IDA), a di­amino­bi­thia­zole (DABT) mol­ecule and a water mol­ecule. The planar DABT group chelates the Cr^III ion with normal Cr—N distances [2.0574 (17) and 2.0598 (17) Å], but the DABT mol­ecule is inclined to the coordination plane by a dihedral angle of 17.23 (7)°. In the monodentate carboxylate groups of the IDA ion, the coordinated C—O bonds [1.288 (3) and 1.284 (3) Å] are much longer than the uncoordinated C—O bonds [1.222 (3) and 1.225 (3) Å].     

(±)‐6‐Benzyl‐3,3‐di­methyl­morpholine‐2,5‐dione and its 5‐mono­thio and 2,5‐di­thio derivatives

The morpholine ring of the title dione, C₁₃H₁₅NO₃, shows a boat conformation that is distorted towards a twist‐boat, with the boat ends being the two Csp³ atoms of the ring. The benzyl substituent is in the favoured `exo' position. In the mono­thione derivative, (±)‐6‐benzyl‐3,3‐di­methyl‐5‐thioxo­morpholin‐2‐one, C<sub>13</sub>H<sub>15</sub>NO<sub>2</sub>S, this ring has a much flatter conformation that is midway between a boat and an envelope, with the di­methyl end being almost planar. The orientation of the benzyl group is `endo'. The di­thione derivative, (±)‐6‐benzyl‐3,3‐di­methyl­morpholine‐2,5‐di­thione, C₁₃H₁₅N­OS₂, has two symmetry‐independent mol­ecules, which show different puckering of the morpholine ring. One mol­ecule has a flattened envelope conformation distorted towards a screw‐boat, while the conformation in the other mol­ecule is similar to that in the mono­thione derivative. Intermolecular hydrogen bonds link the mol­ecules in the three compounds, respectively, into centrosymmetric dimers, infinite chains, and dimers made up of one of each of the symmetry‐independent mol­ecules.     

Rotenone α‐oxime

The structure determination of the title compound, rotenone α‐oxime [systematic name: 1,2,12,12a‐tetra­hydro‐8,9‐di­meth­oxy‐2‐(1‐methyl­ethenyl)‐[1]­benzo­py­rano­[3,4‐b]­furo­[2,3‐h][1]benzo­pyran‐6(6H)‐one oxime], C₂₃H₂₃NO₆, confirms that the mol­ecule has an approximately V‐shaped structure. One of the rings has a typical cyclo­hexene‐like monoplanar conformation and the central ring adopts a 1,2‐diplanar conformation.     

3,5‐Di­amino‐6‐(2‐fluoro­phenyl)‐1,2,4‐triazine–di­methyl­form­amide (1/1)

The title compound, C₉H₈FN₅·C₃H₇NO, contains two independent complexes in the asymmetric unit, each consisting of one 3,5‐di­amino‐6‐(2‐fluoro­phenyl)‐1,2,4‐triazine mol­ecule and one di­methyl­form­amide solvent mol­ecule. One triazine mol­ecule is disordered over two conformations within the crystal, the occupancies being 62 (1) and 38 (1)%. The phenyl ring of this mol­ecule resolves into two conformations rotated by almost 180° about the bridging bond between the two rings, while the triazine rings approximately superimpose on each other. The triazine mol­ecules of the asymmetric unit differ in the dihedral angles between their respective phenyl and triazine ring planes, these being 57.6 (2)° for the fully occupied, and 76.9 (6) and 106.8 (8)° for the partially occupied mol­ecules. An extensive network of hydrogen bonds maintains the crystal structure.     

Cinnamolid‐3β‐ol hemihydrate and 3β‐hydroxycinnamolide acetate,two drimanolide‐class sesquiterpene lactones from Warburgia ugandensis

3β‐Hydr­oxy‐7‐drimen‐12,11‐olide hemihydrate, C₁₅H₂₂O₃·0.5H₂O, (I), has two sesquiterpene mol­ecules and one water mol­ecule in the asymmetric unit. The OH groups of both mol­ecules and both H atoms of the water mol­ecule are involved in near‐linear inter­molecular hydrogen bonds, having O⋯O distances in the range 2.632 (3)–2.791 (2) Å. 3β‐Acet­oxy‐7‐drimen‐12,11‐olide, C₁₇H₂₄O₄, (II), has its ring system in very nearly the same conformation as the two mol­ecules of (I).     

(5,11,17,23‐Tetra‐tert‐butyl‐26,28‐di­hydroxy­calix­[4]­arene‐25,27‐dioxy)­di­acetic acid N,N‐di­methyl­form­amide trisolvate

The title compound, C₄₈H₆₀O₈·3C₃H₇NO, is a derivative of calix­[4]­arene in the cone conformation, modified with distal carboxylic acid functional groups at the lower rim. A clathrate di­methyl­form­amide (DMF) mol­ecule is located within the calix­[4]­arene cone, and two DMF solvate mol­ecules participate in hydrogen bonding with the carboxylic acid groups. Intramolecular hydrogen bonds are also formed between the OH groups and the adjacent ether groups in the partially substituted calix­[4]­arene.     

Unusual conformations of 1,3‐dialk­oxy­thia­calix[4]arenes in the solid state

The structures of three syn‐1,3‐dialkoxy­thia­calix[4]arenes with unusual conformations in the solid state are reported. The pinched cone conformation of syn‐2²,4²‐dihydroxy‐1²,3²‐bis­(prop‐2‐enyl­oxy)thia­calix[4]arene, C₃₀H₂₄O₄S₄, (3a), is stabilized by two intra­molecular hydrogen bonds, remarkably formed from both OH groups to the same ether O atom. In syn‐2²,4²‐dihydroxy‐1⁵,2⁵,3⁵,4⁵‐tetra­nitro‐1²,3²‐bis­(prop‐2‐enyl­oxy)thia­calix[4]arene acetone disolvate, C₃₀H₂₀N₄O₁₂S₄·2C₃H₆O, (3b1), the mol­ecule is found in the 1,3‐alternate conformation. The crystallographic C2 symmetry is due to a twofold rotation axis running through the centre of the calixarene ring. The hydroxy groups cannot form intra­molecular hydrogen bonds as in (3a) and both are bonded to an acetone solvent mol­ecule. The mol­ecule of the pseudo‐polymorph of (3b1) in which the same compound crystallized without any solvent, viz. (3b2), is located on a crystallographic mirror plane. Only one of the two hydroxy groups forms a hydrogen bond, and this is with a nitro group of a neighbouring mol­ecule as acceptor. Mol­ecular mechanics calculations for syn‐1,3‐diethers suggest a preference of the 1,3‐alternate over the usual cone conformation for thia­calix[4]arene versus calix[4]arene and for para‐nitro versus para‐H derivatives.     

Dibenzyl 2,2′‐(ethane‐1,2‐diyl­idene)dihydrazinecarbodithioate bis(di­methyl­formamide) solvate

The title compound, C₁₈H₁₈N₄S₄·2C₃H₇NO, crystallizes with the dibenzyl dihydrazinecarbodithioate mol­ecule residing on a crystallographic inversion centre. The mol­ecule adopts a trans conformation with respect to the central C—C single bond. The dihedral angle between the phenyl group and the thio­thio­semicarbazone unit is 74.1 (1)°.     

Ranitidine hydro­chloride,a polymorphic crystal form

In the title compound, di­methyl­({5‐[2‐(1‐methyl­amino‐2‐nitro­eth­enyl­amino)­ethyl­thio­methyl]‐2‐furyl}­methyl)­ammon­ium chloride, C₁₃H₂₃N₄O₃S⁺·­Cl^?, protonation occurs at the di­methyl­amino N atom. The ranitidine mol­ecule adopts an eclipsed conformation. Bond lengths indicate extensive electron delocalization in the N,N′‐di­methyl‐2‐nitro‐1,1‐ethenedi­amine system of the mol­ecule. The nitro and methyl­amino groups are trans across the side chain C=C double bond, while the ethyl­amino and nitro groups are cis. The Cl^? ions link mol­ecules through hydrogen bonds.     

tert‐Butyl (3S,6R,9R)‐(5‐oxo‐3‐{[1(R)‐phenyl­ethyl]­carbamoyl}‐1,2,3,5,6,7,8,8a‐octa­hydro­indolizin‐6‐yl)­carbamate monohydrate at 95 K

The asymmetric unit of the title compound, C₂₂H₃₁N₃O₄·H₂O, incorporates one water mol­ecule, which is hydrogen bonded to the 3‐oxo O atom of the indolizidinone system. The two rings of the peptidomimetic mol­ecule are trans‐fused, with the six‐membered ring having a slightly distorted half‐chair conformation and the five‐membered ring having a perfect envelope conformation. The structure is stabilized by intermolecular O—H?O interactions between the water and adjacent peptide mol­ecules, and by N—H?O interactions between the peptide mol­ecules, which link the mol­ecules into infinite chains.     

Oxythiamine hexafluorophosphate monohydrate,a thiamine antagonist with the same conformation as ­thiamine

In the title compound, 3‐[(3,4‐di­hydro‐2‐methyl‐4‐oxopyrimidin‐5‐yl)­methyl]‐5‐(2‐hydroxy­ethyl)‐4‐methyl­thia­zolium hexa­fluoro­phosphate monohydrate, C₁₂H₁₆N₃O₂S⁺·PF₆^?·H₂O, oxy­thi­amine is a monovalent cation with a neutral oxo­pyrimidine ring. The mol­ecule assumes the F conformation, which is a common form for thi­amine but which is substantially different from the unusual V conformation found in the chloride and hydro­chloride salts of oxy­thi­amine. The anion‐bridging interaction, C—H?anion?pyrimidine, is emphasized as being important for stabilization of the F conformation.     

The 1:1 adduct of 2,5-dihydroxy-1,4-benzoquinone with 4,4′-bipyridine

2,5-Di­hydroxy-1,4-benzo­quinone (DHBQ) and 4,4′-bi­pyridine (BPY) crystallize in a 1:1 ratio as a neutral molecular adduct, C₆H₄O₄·C₁₀H₈N₂, in space group C2/c, with half of each mol­ecule in the asymmetric unit. The mol­ecules are linked by a strong O—H⃛N hydrogen bond [O⃛N 2.6323 (15) Å] and a weak C—H⃛O hydrogen bond [C⃛O 3.2082 (17) Å] to form infinite stacks of parallel one-dimensional hydrogen-bonded ribbons. The two rings of the bi­pyridine are twisted at 28.3° with respect to each other, and the benzo­quinone ring is inclined at an angle of 18.3° with respect to the plane of the neighbouring pyridine ring. The 4,4′-bi­pyridine mol­ecule lies on a twofold axis and the benzo­quinone mol­ecule lies across an inversion centre.     

Conformation and structure of bis­(glycyl‐l‐aspartic acid) oxalate 0.4‐hydrate

The title bis­(glycyl‐l ‐aspartic acid) oxalate complex {systematic name: bis­[2‐(2‐ammonio­acetamido)butane­dioic acid] oxalate 0.4‐hydrate}, 2C₆H₁₁N₂O₅⁺·C₂O₄²⁻·4H₂O, crystallizes in a triclinic space group with the planar peptide unit in a trans conformation. The asymmetric unit consists of two glycyl‐l ‐aspartic acid mol­ecules with positively charged amino groups and neutral carboxyl groups, and an oxalate dianion. The twist around the C—Cα bond indicates that both the peptide mol­ecules adopt extended conformations, while the twist around the N—Cα bond shows that one has a folded and the other a semi‐extended state. The present complex can be described as an inclusion compound with the dipeptide mol­ecule as the host and the oxalate anion as the guest. The usual head‐to‐tail sequence of aggregation is not observed in this complex, as is also the case with the glycyl‐l ‐aspartic acid dihydrate mol­ecule. The study of aggregation and inter­action patterns in binary systems is the first step towards understanding more complex phenomena. This further leads to results that are of general interest in bimolecular aggregation.     

Model porphyrin precursors: 1,2,4,5‐tetrakis(cyanomethyl)­benzene,methyl 3,4,5‐triacetoxy­benzoate and 2‐(N‐phthalimidomethyl)benzoic acid

In the crystalline state, the centrosymmetric mol­ecule 1,2,4,5‐tetrakis­(cyano­methyl)­benzene, C₁₄H₁₀N₄, has one cyano­methyl group in the benzene plane and one cyano­methyl group rotated 67.2 (2)° out of the benzene plane. Molecules of methyl 3,4,5‐tri­acetoxy­benzoate, C₁₄H₁₄O₈, form chains with each mol­ecule twisted 89.6 (1)° from the preceding mol­ecule. In this orientation, a close C—H?O contact is formed, with an H?O distance of 2.34 Å. The structure of 2‐(N‐phthalimido­methyl)­benzoic acid, C₁₆H₁₁NO₄, reveals hydrogen‐bonded dimers linked by the carboxyl groups of adjacent mol­ecules. The O4?O3 distance is 2.636 (2) Å and the O4—H?O3 angle is 171 (2)°.     

Water molecules in the crystal structure of tricyclic acyclovir

The biologically important mol­ecule tricyclic acyclo­vir, presented here as 3‐[(2‐hydroxy­ethoxy)­methyl]‐6‐methyl‐3H‐imidazolo­[1,2‐a]­purin‐9(5H)‐one dihydrate, C₁₁H₁₃N₅O₃·2H₂O, shows conformational flexibility, which is observed in the solid state as two symmetrically independent mol­ecules with different side‐chain conformations. Additionally, one of these mol­ecules exhibits side‐chain disorder, such that there are three different conformations in the crystal. Water mol­ecules found in the crystal form (H₂O)₈ clusters which are located between mol­ecules of tricyclic acyclovir. The complex hydrogen‐bond network formed between water and tricyclic acyclovir in the solid state may be related to the solvation of the mol­ecules in solution.     

Chloro(2,9-dimethyl-1,10-phenanthroline-N,N′)(isoquinoline-1-carboxylato-O,N)copper(II)

The asymmetric unit of the title compound, [CuCl(C₁₀H₆NO₂)(C₁₄H₁₂N₂)], contains two monomeric copper mol­ecules, A and B. Each Cu atom is coordinated to one 2,9-di­methyl-1,10-phenanthroline (neocuproine) ligand via both N atoms, to one iso­quinoline-1-carboxyl­ate anion (IQC⁻) via the N and one O atom, and to one Cl⁻ anion. The environment of the Cu atom is approximately square pyramidal, with the apical position occupied by an N atom of neocuproine. In mol­ecule A, the Cu atom is 0.301 (1) Å above the basal plane; this distance is 0.316 (1) Å in mol­ecule B. The crystal packing is characterized by several hydrogen bonds.     

Moxifloxacinium chloride–water–methanol (2/1/1), a novel anti­bacterial agent

Moxifloxacin, a novel fluoro­quinolone with a broad spectrum of anti­bacterial activity, is available as the solvated monohydro­chloride salt 7‐[(S,S)‐2‐aza‐8‐azoniabicyclo­[4.3.0]non‐8‐yl]‐1‐cyclo­propyl‐6‐fluoro‐8‐meth­oxy‐4‐oxo‐1,4‐dihydroquinoline‐3‐carboxylic acid chloride–water–methanol (2/1/1), C₂₁H₂₅FN₃O₄⁺·Cl⁻·0.5H₂O·0.5CH₃OH. The asymmetric unit contains two cations, two chloride ions, a mol­ecule of water and one methanol mol­ecule. The two cations adopt conformations that differ by an almost 180° rotation with respect to the piperidinopyrrolidine side chain. The cyclo­propyl ring and the meth­oxy group are not coplanar with the quinoline ring system. The carboxylic acid function, the protonated terminal piperidyl N atom, the water mol­ecule, the chloride ion and the methanol mol­ecule participate in O—H⋯O, O—H⋯Cl, N—H⋯O and N—H⋯Cl hydrogen bonding, linking the mol­ecules into extended two‐dimensional networks.     

Gallic acid monohydrate

In the crystal structure of the title compound, 3,4,5‐tri­hydroxy­benzoic acid monohydrate, C₇H₆O₅·H₂O, the gallic acid mol­ecule has an intramolecular hydrogen bond involving a pair of hydroxyl groups, and it is also linked to a water mol­ecule by a three‐centre (bifurcated) OW—H?O hydrogen bond. The packing of the mol­ecules is stabilized by intermolecular O—H?O and C—H?O hydrogen bonds.