A chiral N-methylbenzamide: Spontaneous generation of optical activity

Conformer generation with OMEGA: learning from the data set and the analysis of failures

We recently published a high quality validation set for testing conformer generators, consisting of structures from both the PDB and the CSD (Hawkins, P. C. D. et al. J. Chem. Inf. Model. 2010, 50, 572.), and tested the performance of our conformer generator, OMEGA, on these sets. In the present publication, we focus on understanding the suitability of those data sets for validation and identifying and learning from OMEGA's failures. We compare, for the first time we are aware of, the coverage of the applicable property spaces between the validation data sets we used and the parent compound sets to determine if our data sets adequately sample these property spaces. We also introduce the concept of torsion fingerprinting and compare this method of dissimilation to the more traditional graph-centric diversification methods we used in our previous publication. To improve our ability to programmatically identify cases where the crystallographic conformation is not well reproduced computationally, we introduce a new metric to compare conformations, RMSTanimoto. This new metric is used alongside those from our previous publication to efficiently identify reproduction failures. We find RMSTanimoto to be particularly effective in identifying failures for the smallest molecules in our data sets. Analysis of the nature of these failures, particularly those for the CSD, sheds further light on the issue of strain in crystallographic structures. Some of the residual failure cases not resolved by simple changes in OMEGA's defaults present significant challenges to conformer generation engines like OMEGA and are a source of new avenues to further improve their performance, while others illustrate the pitfalls of validating against crystallographic ligand conformations, particularly those from the PDB.

Spontaneous Resolution of Aromatic Sulfonamides: Effective Screening Method and Discrimination of Absolute Structure

An effective screening method combining parallel synthesis and solid-state CD measurements was established to identify achiral aromatic sulfonamides that show spontaneous resolution with rapidity. We found that 4 of the 12 achiral sulfonamides crystallized as chiral crystals through this method. The chirality of each sulfonamide was discriminated by solid-state CD spectra and Flack parameter in an X-ray analysis. Correspondence between the observed Cotton effect and the absolute configuration could be confirmed by time-dependent DFT calculations. [structure: see text]

Conformational communication between the Ar–CO and Ar–N axes in 2,2′-disubstituted benzanilides and their derivatives

Benzanilides containing two or more potentially stereogenic amide axes exist in solution as mixtures of conformers which are detectable by NMR. For simple tertiary benzanilides carrying an ortho substituent on each ring, conformational control can be high (up to about 10:1) providing the substituents are large, indicating that the two axes are in conformational communication with one another. For more complex diamides, conformational communication breaks down, and mixtures of conformers are evident by NMR.

Ring-opening polymerization of coordination complexes: silver(i) complexes with bis(amidopyridine) ligands derived from thiophene

The thiophene-based bis(N-methylamido-pyridine) ligand SC4H2-2,5-{C(=O)N(Me)-4-C5H4N}2 reacts with silver(I) salts AgX to give 1 : 1 complexes, which are characterized in the solid state as the macrocyclic complexes [Ag(2){SC4H2-2,5-(CONMe-4-C5H4N)2}2][X]2, which have the cis conformation of the C(=O)N(Me) group, when X = CF3CO2, NO3, or CF3SO3 but as the polymeric complex [Ag(n){SC4H2-2,5-(CONMe-4-C5H4N)2}n][X]n, with the unusual trans conformation of the C(=O)N(Me) group, when X = PF6. The bis(amido-pyridine) ligand SC4H2-2,5-{C(=O)NHCH2-3-C5H4N}2 reacts with silver(I) trifluoroacetate to give the polymeric complex [Ag(n){SC4H2-2,5-(CONHCH2-3-C5H4N)2}n][X]n, X = CF3CO2. The macrocyclic complexes contain transannular argentophilic secondary bonds. The polymers self assemble into sheet structures through interchain C=O...Ag and S...Ag bonds in [Ag(n){SC4H2-2,5-(CONMe-4-C5H4N)2}n][PF6]n and through Ag...Ag, C=O...Ag and Ag...O(trifluoroacetate)...HN secondary bonds in [Ag(n){SC4H2-2,5-(CONHCH2-3-C5H4N)2}n][CF3CO2]n.

Disilver(I) macrocycles: variation of cavity size with anion binding

Reaction of the N-methylated bis(amidopyridine) ligand, LL = C6H4(1,3-CONMe-4-C5H4N)2, with the silver salts AgNO3, AgO2CCF3, AgO3SCF3, AgBF4, and AgPF6 gave the corresponding cationic disilver(I) macrocycles [Ag2(micro-LL)2]X2, 2a-e. The transannular silver...silver distance in the macrocycles varies greatly from 2.99 to 7.03 A, and these differences arise through a combination of different modes ofanion binding and from the presence or absence of silver...silver secondary bonding. In all complexes, the ligand adopts a conformation in which the methyl group and oxygen atom of the MeNCO units are mutually cis, but the overall macrocycle can exist in either boat (X = PF6 only) or chair conformation. Short transannular silver...silver distances are found in complexes 2b,c, in which the anions CF3CO2- and CF3SO3- bind above and below the macrocycle, but longer silver...silver distances are found for 2a,d,e, in which the anions are present, at least in part, inside the disilver macrocycle. Easy anion exchange occurs in solution, and studies using ESI-MS indicate that the anion binding to form [Ag2X(micro-LL)2]+ follows the sequence X = CF3CO2- > NO3- > CF3SO3-.

Absolute Helical Arrangement of Sulfonamide in the Crystal

[reaction: see text] 1,2-Bis(N-benzenesulfonyl-N-methylamino)benzene (2), which has no fixed asymmetric element, was crystallized from ethyl acetate as chiral crystals belonging to space group P4(1)2(1)2 (No. 92) or P4(3)2(1)2 (No. 96). The array of molecules built by the CH-pi interaction along the c-axis forms an enantiomeric helical superstructure in each individual crystal. The absolute configurations of the chiral crystals of 2 were determined by X-ray crystal structure analysis using the Flack parameter method. The solid-state CD spectra of the chiral crystals in KBr were mirror images. The equilibrium between the two enantiomers in solution is fast during crystallization at ambient temperature, and the energy barrier (DeltaG()) is estimated to be 11.7 +/- 0.3 kcal/mol (233 K).

Dynamic helical chirality of an intramolecularly hydrogen-bonded bisoxazoline

The synthesis and conformational properties of 2,6-bis-[2-((4S)-4-methyl-4,5-dihydro-1,3-oxazol-2-yl)phenyl]carbam oylpyridines, 2, have been described. Bisoxazoline 2a was prepared in five steps from 2-nitrobenzoyl chloride in an overall yield of 71%. In contrast to related structures such as 1, bisoxazoline 2a exhibits a highly biased P-type helical conformation in solution and in the solid state. In the crystal lattice, 2a further assembles into a left-handed helical superstructure aligned along the crystallographic c axis. The barrier to helical interconversion, as measured by line-shape analysis of the temperature-dependent (1)H NMR spectra of thiobenzyl derivative 2b, was determined to be quite low ((Delta)G(++) = 12.3 kcal/mol), indicating the presence of a highly dynamic helical chirality.

[Discovery of cis-preference of aromatic N-methylamides and its application to molecular constructions]

Aromatic secondary amides such as benzanilide (1) exist in a trans-amide form both in the crystal and in the solution, whereas N-methylbenzanilide (2) exists in cis form in the crystal, and predominantly in a cis form in the solution. Similar cis conformational preferences were observed in aromatic N,N'-dimethylated ureas and guanidines, in which two aromatic rings are located face to face. The cis preferences of N-methylated amides, ureas and guanidines could be utilized to construct interesting aromatic architecture. N,N',N"-Trimethyl-N,N',N"-triphenyl-1,3,5-benzenetricarboxamide (20) and a cyclic triamide (24) have crystal structures in which three N-phenyl groups direct to the same orientation (syn conformation). 1,2-Bis(N-benzoyl-N-methylamino)benzene (22), which have no fixed asymmetric center, afforded chiral crystals by simple recrystallization. Furthermore, aromatic multi-layered structures could be built and applied to obtain aromatic molecules which have potent DNA-binding ability.