A 2 × 6 isomer grid of six N-(difluorophenyl)benzamides (F2-xx) and six N-(phenyl)difluorobenzamides (xx-F2) (xx = 23/24/25/26/34/35) integrating crystal structure analyses (at 294 K), gas phase calculations and conformational analyses is reported. All 12 isomers (C13H9N1O1F2) aggregate via N–H⋯OC intermolecular interactions and usually in combination with intermolecular C–H⋯O/F/π interactions and often F⋯F contacts. The F2-25 crystal structure has a remarkably supershort intermolecular C–H⋯F interaction for a neutral organic, while the 25-F2 (amide-bridged reversed) has an analogous short C–H⋯F in a twinned, disordered structure. The results demonstrate a promising 2,5-difluorobenzene effect being responsible for shorter C–H⋯F contacts than would normally be expected. An understanding of the relationships between F/H atom permutations in substituted difluorobenzenes is realised with the influence of fluorine substitution patterns on molecular aggregation rationalised in a series of twelve isomers.

Fluorine and chlorine derived macrocycles (FIO)3/4 and (ClIO)3/4 are synthesised from the reaction of isophthaloyl dichloride with 2-amino-5-fluoropyridine and 2-amino-5-chloropyridine, respectively. Solvents of crystallisation are present in the six F/Cl crystal structures and occupy 12–43% of crystal lattice. Halogenated solvents (CH2Cl2; CHCl3) typically link macrocycles through halogen and hydrogen bonding interactions forming 1-D chains through halogen bonding, whereas dimethylsulfoxide (DMSO) incorporation promotes solvent channel formation. For (ClIO)3, the total (%) solvent comprising DMSO and water molecules is 43% of the structure volume with 3.5(DMSO)·3(H2O) per (ClIO)3 macrocycle resulting in extensive channel formation. The solvent channel aggregation assists 2-D network formation in combination with short C–Cl⋯OC halogen bonding interactions and C–Cl⋯Cl–C contacts (Cl⋯O, Cl⋯Cl; both Nc = 0.90). Of further note is that (ClIO)4·CH2Cl2 is isomorphous with two methylated analogues (MIO)4·CH2Cl2 and (MIO)4·CHCl3.

•Comprehensive chemical and structural study of an organometallic 3 × 3 isomer grid.•Trends correlating physicochemical data with crystal and molecular structure.•Examination of structural variability with substituent position.•Variable aggregation highlights the unpredictable nature of molecular assembly.The nine ethyl 4-/3-/2-{[(4-/3-/2-ferrocenylphenyl)carbonyl]amino}benzoates, {4-/3-/2-FcC6H4-CONH-(4-/3-/2-C6H4)CO2Et, where Fc = (η5-C5H5)Fe(η5-C5H4)} have been synthesised by coupling either the para-, meta- or ortho(ferrocenyl)benzoic acids (FcC6H4COOH), or their acid chlorides (FcC6H4COCl) with ethyl p-/m-/o-aminobenzoates, H2NC6H4CO2Et using (i) 1,3-dicyclohexylcarbodiimide (DCC), 1-hydroxybenzotriazole (HOBt) or (ii) acid chloride coupling reactions. The isomers were characterised by spectroscopic techniques; single crystal X-ray diffraction structures of all nine isomers are reported and reveal the inherent linearity of the para–para substituted isomer (pp) compared to the twisted geometry of the ortho–ortho system (oo). Intra-/intermolecular interactions and distinct patterns of molecular aggregation are evaluated and correlated with physicochemical measurements showing distinct trends. A rich and somewhat congested amide…amide hydrogen bonding is noted in (mp) and (mm), contrasting with a lack of amide…amide interactions in (pp) and (pm) and unexpected amide…ester hydrogen bonding in dimers of (om). The series highlights the unpredictable nature of molecular assembly.The unpredictable nature of self-assembly is revealed in a variety of hydrogen bonding motifs (depending on substituent position), as highlighted by the congested amide…amide interactions in (mm) (graphic), and contrasting with their absence in (pp) and the cyclic amide…ester interactions in hydrogen bonded dimers of (om).

The synthesis of asymmetric diester derivatives of pyridyl-tetrazole ligands was successfully undertaken. Five crystal structures are reported including three asymmetric diesters (one of which is a mixed methyl ethyl ester derivative), a dicarboxylic acid and a monosodium (dicarboxylic acid)(monoacid-carboxylate) dihydrate intermediate. The dicarboxylic acid assembles by an unusual and unexpected route with the primary assembly based on carboxylic…pyridine (COOH⋯N) synthons that form an unusual cyclic hydrogen bonded ring with the R22(17) motif. Assembly in hydrogen bonding motifs using ‘odd’ numbers of atoms is the exception rather than the rule.The synthesis of asymmetric diester derivatives of pyridyl-tetrazole ligands was successfully undertaken. Five crystal structures are reported including a dicarboxylic acid where the primary assembly, based on carboxylic…pyridine (COOH⋯N) synthons, forms an unusual cyclic hydrogen bonded ring with the R22(17) motif.

Reaction of isophthaloyl dichloride (I) with 2-amino-5-bromopyridine (BrO) and 2-amino-5-bromopyrimidine (26BrO) produces the trimeric (trezimide) and tetrameric (tennimide) imide-based macrocycles (BrIO)3 and (BrIO)4, and (26BrIO)3 and (26BrIO)4, respectively, in one-step and in modest yields. Macrocyclisation (forming 18-/24-membered rings) is facilitated by the imide hinge [OC–N(R)–CO] (R = ortho-N-substituted-pyridine/pyrimidine), though competing reactions also lead to considerable oligomer/polymer formation. The macrocycles (having 3 or 4 Br atoms) lack classical strong hydrogen bonding donors (i.e. N–H, O–H), but contain numerous acceptors (i.e. Naromatic, CO, arene) participating in halogen and weaker hydrogen bonding. Five crystal structures are analysed with the macrocycles typically aggregating through short C–Br⋯OCcarbonyl and/or C–Br⋯Naromatic halogen bonds (Nc ≤ 0.90) and often associated with longer C–Br⋯H/π(arene) contacts. Of note, (BrIO)3 exhibits three types of Br⋯OC/π(arene) halogen bonds with Br⋯H and C–H⋯O contacts. The C–Br⋯N/O halogen bonds, in promoting overall aggregation, typically link macrocycles into 1-D halogen bonded chains.

A 3 × 3 isomer grid of nine methoxyphenyl-N-pyridinylcarbamates (C13H12N2O3) as CxxOMe (x = para-/meta-/ortho-) represents the first phenyl-N-pyridinylcarbamate crystal structures to be reported. Structural relationships have been correlated in all nine crystal structures as derived from ab initio calculations and the solid-state using conformational analysis. N–H···N hydrogen bonds dominate as the primary interaction in all nine isomers. Two isomers (CmmOMe, CmoOMe) form unusual cyclic N–H···N trimer synthons as R33(15) with two distinct conformations isolated in the CmoOMe structure, whereas the three CoxOMe isomers form N–H···N hydrogen bonded dimers based on the R22(8) motif. For all isomers, C–H···O interactions assist in aggregation, and in most cases the methoxy group augments the hydrogen bonding. The solid state and modeled conformations are mismatched in three isomers where the methoxy groups and meta-methoxyphenyl rings (mOMe) (in the solid state) adopt metastable or unstable conformations compared to their optimized computational models. This is rationalized in terms of preferred solid state conformations and observed interactions as compared to the computational models.

The reaction of isophthaloyl dichloride with 2-aminopyridine or 2-aminopyrimidine provides a facile entry into a new class of imide-based “3 + 3” macrocyclic trimer (trezimide), together with the known tetramer scaffold (tennimide). The trezimides can adopt two distinct asymmetric conformations in the solid state, isolated as (P) in (IO)3 (from 2-aminopyridine) and (R) in (26IO)3 (from 2-aminopyrimidine). The tennimide crystal structure (26IO)4 (from 2-aminopyrimidine) exhibits three discrete conformational states, highlighting subtle geometric changes with the tennimide channel (pore) open (o) and/or closed (c), as noted by three macrocycle conformations with their channel pores observed as cc/oc/oo. Macrocycle formation (though in competition with oligomer/polymer formation) relies on the o-pyr(im)idine N functionality and preorganized imide hinge (the “CO···CO” twist) together with the inherent flexibility of the isophthaloyl groups.

A 3 × 3 isomer grid of nine N-(tolyl)pyridinecarboxamides (NxxM, x = para-/meta-/ortho-) integrating crystal structure analyses, ab initio calculations (gas phase and PCM-SMD solvated in CH2Cl2, H2O) and conformational studies is described. Three 5-Cl-NoxM derivatives (side-products from the NoxM syntheses) and NmpFM (a 50:50 mixture of NmpF and NmpM) are reported. The six NpxM/NmxM isomers aggregate via N–H⋯N or N–H⋯OC hydrogen bonds, whereas the six NoxM/5-Cl-NoxM structures exhibit intramolecular N–H⋯N interactions influencing co-planarity. The NmmM isomer is isomorphous and isostructural with its bridge-flippedMmm isomer providing a rare case of isostructuralism between such isomers. Our objectives are to (a) understand correlations between the p-/m-/o-N/CH3 substituent permutations with solid state molecular conformations and supramolecular aggregation, (b) explain the influence of molecular conformation on inter/intramolecular interactions, (c) correlate physico-chemical properties and (d) compare and rationalise differences between crystal and calculated structures.

A 3 × 3 isomer grid of N-(fluorophenyl)pyridinecarboxamides is reported and integrating crystal structure analyses, ab initio optimisation calculations (gas phase and solvated forms in CH2Cl2, H2O) and conformational analyses. The nine NxxF isomers (x = 4-, 3- or 2-substitution on N and F) are investigated and compared to determine and correlate factors underpinning (a) the roles of the F/N atom substituents on molecular conformation and overall supramolecular aggregation, (b) competition between intermolecular amide⋯amide (in NppF) or intra-/intermolecular amide⋯pyridine hydrogen bond formation and (c) structural and physico-chemical properties. Crystal structure analyses of the NxxF isomers reveal different primary aggregation processes as either N–H⋯N or N–H⋯OC and with NmpF forming an unusual cyclic N–H⋯N hydrogen bonded tetrameric assembly [as a R44(24) ring]. Compounds NpmF and NpoF are isomorphous and the latter is also disordered. Conformational analysis of the NxxF molecular structures from DFT calculations differs from the crystal structure results for several isomers and highlighting the co-operative effects of intra-/intermolecular interactions in the solid state.

A 3 × 3 isomer grid of nine methyl-N-(pyridyl)benzamides (C13H12N2O) as Mxx (x = para-/meta-/ortho-) has been synthesized and characterised to evaluate and correlate structural relationships from both ab initio calculations (gas-phase, PCM-SMD model solvated forms) and the solid-state. The effect of methyl group (Mx) and pyridine N atom (x) substitution patterns on molecular conformations from calculations and in terms of molecular organisation is evaluated. The primary hydrogen bonding is amideN–H⋯Npyridine in eight isomers but is amideN–H⋯OCamide in Mpm. The N–H⋯N interactions form C(6) chains in the Mxp series, C(5) chains in Mmm, Mom and cyclic centrosymmetric R22(8) rings in the Mxo series. Of note is the short intradimer C–H⋯π(arene) interaction in Moo, one of the shortest reported in a neutral organic system C⋯Cg = 3.3875(18) Å, H⋯Cg = 2.46 Å [2.33 Å] and C–H⋯Cg = 167° [166°] [with normalised C–H distances]. Conformational features and differences between the computational calculations and crystal structures are discussed.

A series of Ni(η5-C5H5)(PPh3)–CC–Ar complexes, 1 are reported, where Ar = (a) C6H5, (b) 4-PhC6H4, (c) 1-C10H7 (1-naphthyl), (d) 2-C10H7 (2-naphthyl), (e) 9-C14H9 (9-phenanthryl), (f) 9-C14H9 (9-anthryl), (g) 1-C16H9 (1-pyrenyl), (h) 1-C20H11 (1-perylenyl), (i) 2-C4H3S (2-thienyl), (j) C10H9Fe (ferrocenyl), (k) SiMe3, and (l) H. 1a–1i react with Co2(CO)8 to give the {Ni(η-C5H5)(PPh3)–CC–Ar}{Co2(CO)6} derivatives 2. All 1 and 2 have been characterised by elemental analysis and spectroscopy (IR, UV–Vis, 1H NMR and 13C NMR), X-ray diffraction for 1e (Ar = 9-phenanthryl), 1j (Ar = ferrocenyl) and 1l (Ar=H), electrochemistry for all 1, and spectroelectrochemistry for 1j.The structures, spectroscopy and electrochemistry of Ni(η5-C5H5)(PPh3)–CC–Ar complexes suggest that there is only limited interaction between the Ni and the aryl groups via the acetylide linkage.

A series of N-para-ferrocenyl benzoyl amino acid ethyl esters 1–8 have been prepared by coupling para-ferrocenyl benzoic acid with the amino acid esters using the conventional 1,3-dicyclohexylcarbodiimide (DCC), 1-hydroxybenzotriazole (HOBt) protocol. The amino acids employed in the synthesis were glycine, l-alanine, l-leucine, l-phenylalanine, β-alanine, 4-aminobutyric acid, (±)-2-aminobutyric acid and 2-aminoisobutyric acid. The compounds were fully characterized by a range of spectroscopic techniques such as NMR and mass spectrometry. In addition the X-ray crystal structures of the glycyl 1 and (±)-2-aminobutyrate 7 derivatives have been determined. Analysis of relevant fragments in crystal structures on the Cambridge Structural Database indicates a relative paucity of common fragments such as the α-aminobutyrate group in comparison to the glycyl moiety.N-para-Ferrocenyl benzoyl amino acid ethyl esters 1–8 were prepared by coupling para-ferrocenyl benzoic acid with the appropriate amino acid ethyl ester using the 1,3-dicyclohexylcarbodiimide (DCC), 1-hydroxybenzotriazole (HOBt) protocol. The compounds were structurally characterized by a combination of NMR and mass spectrometry. The X-ray crystal structures of the glycyl 1 and (±)-2-aminobutyrate 7 derivatives have been determined.

The N-ferrocenoyl amino acid ester derivatives FcCOR {Fc=(η5-C5H5)Fe(η5-C5H4)} where R=Gly(OMe) 1, Gly(OEt) 2, Gly(OBn) 3, l-Ala(OMe) 4, l-Ala(OEt) 5, l-Leu(OMe) 6, l-Leu(OEt) 7, l-Leu(OBn) 8, l-Phe(OMe) 9 and l-Phe(OEt) 10, were prepared by coupling ferrocene carboxylic acid with the appropriate amino acid ester starting materials using the 1,3-dicyclohexylcarbodiimide (DCC), 1-hydroxybenzotriazole (HOBt) protocol and these have been characterised by spectroscopic techniques. The electrochemical anion sensing behaviour of compounds 1–10 with several anions using a platinum microdisk working electrode is described, together with 1H NMR anion complexation studies. The X-ray single crystal structure of N-ferrocenoyl-l-alanine methyl ester 4 has been determined and contains two molecules which differ slightly in conformation in the asymmetric unit of space group P21 (No. 4); principal dimensions are amide N(H)CO 1.224(6) and 1.231(6) Å, ester CO 1.220(10) and 1.190(7) Å, with N–H⋯OC(amide) as the primary intermolecular hydrogen bond, N⋯O 2.992(6) and 2.971(6) Å and with graph set C(4).N-Ferrocenoyl amino acid ester derivatives were prepared by coupling ferrocene carboxylic acid with the appropriate amino acid esters using the 1,3-dicyclohexylcarbodiimide (DCC), 1-hydroxybenzotriazole (HOBt) protocol. The electrochemical anion sensing behaviour of the derivatives with several anions is described, together with 1H NMR anion complexation studies. The X-ray single crystal structure of N-ferrocenoyl-l-alanine methyl ester has been determined.

Oxalic acid catalyses the hydrolysis of the Ni(II) acetylide [Ni(η5-C5H5)(PPh3)CCCH(OEt)2] 1, to the alkynylaldehyde [Ni(η5-C5H5)(PPh3)CCCHO] 2, in high yield. Condensation reactions of 2 with phenylhydrazine and dinitrophenylhydrazine in the presence of acetic acid, and with malononitrile and 3-phenyl-5-isoxazolone (C9H7NO2) in the presence of triethylamine yield [Ni(η5-C5H5)(PPh3)CCX] derivatives where X = CHNNHC6H53, CHNNHC6H3(NO2)2-2,4 4, CHC(CN)25, and CHC9H5NO26. The reactivity of [Ni(η5-C5H5)(PPh3)CCX] complexes towards [Co2(CO)8] is a function of X. Thus 1 and 2, where X = CH(OEt)2 or CHO, react readily to give the bridging alkyne derivatives [{μ-η1:η1-Ni(η5-C5H5)(PPh3)CCCH(OEt)2}{Co2(CO)6}] 7, and [{μ-η1:η1-Ni(η5-C5H5)(PPh3)CCCHO}{Co2(CO)6}] 8, but 5, where X is the strongly electron-withdrawing CHC(CN)2 group, does not react even after 24 h at room temperature. Furthermore, coordination of the alkyne to a Co2(CO)6 fragment appears to inhibit the normal reactions of the group X in 7 and 8. Thus the acetal grouping in 7 does not undergo oxalic acid-catalysed hydrolysis to an aldehyde in 8, and the aldehyde function in 8 does not undergo a Knoevenagel condensation with CH2(CN)2. The IR spectra of 1, and 3–6 show a single ν(CC) band the frequency of which decreases along the series X = CH(OEt)2 > CHNNHC6H5 > CHNNHC6H3(NO2)2-2,4 > CHC(CN)2 ≈ CHC9H5NO2; that of 2 is anomalous in that it can show two ν(CC) bands. The UV-visible spectra of 1–6 show a strong charge transfer absorption band which increases in wavelength 1 < 3 < 2 < 4 < 5 < 6. These spectroscopic data and the 13C chemical shifts suggest that the (η5-C5H5)(Ph3P)Ni moiety is a donor and, when X is an acceptor, charge separated cumulenic mesomers such as Ni+CCX− contribute to the description of the bonding in 1–6. This is not reflected in the molecular dimensions of 1, 2 and 5 as determined by X-ray diffraction. However, the crystal structure of [{μ-η1:η1-Ni(η5-C5H5)(PPh3)CCCHO}{Co2(CO)6}], 8, shows that the C2Co2 cluster core is severely distorted because of the strong donor (Ni) and acceptor (CHO) substituents on the acetylenic carbon atoms.