Subduction of coset representations. An application to enumeration of chemical structures with achiral and chiral ligands

Molecules derived from a parent skeleton are enumerated where both achiral ligands as well as chiral ligands are allowed. Chirality fittingness of an orbit is proposed in order to permit chiral ligands. The enumeration is conducted with and without consideration of obligatory minimum valency (OMV). The effect of the OMV is formulated by assigning different weights to the respective orbits of the parent skeleton. The importance of coset representations and their subduction by subgroups is discussed. The subduced representations are classified into three classes through their chirality fittingness, which determines the mode of substitution with chiral and achiral ligands. Several novel concepts such as a unit subduced cycle index and a subduced cycle index are given in general forms.     

Interchain-solvent-induced chirality change of 1D helical chains: from achiral to chiral crystallization

Three helical supramolecular stereoisomers of meso-2, Delta-2, and Delta-3 with the formula of cis-[Ni(f-rac-L)][Ni(CN)4] were successfully constructed based on the [Ni(f-rac-L)2+ and [Ni(CN)4]2- building blocks (L = 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane). In all three supramolecular stereoisomers, cis-[Ni(f-rac-L)]2+ cations are alternately bridged by [Ni(CN)4]2- anions through two cis (in meso-2 and Delta-2) or trans (in Delta-3) cyano groups to form one-dimensional (1D) helical chains of cis-[Ni(f-rac-L)][Ni(CN)4]. In meso-2, the right/left-handed chirality of the originally formed chain is transferred oppositely to adjacent chains through the interchain hydrogen-bonding interactions of hexameric water clusters, leading to the formation of meso-2 with a central symmetrical space group, P21/n, in which the 1D helical chains are packed in an alternating right- and left-handed chirality. In Delta-2 and Delta-3, the right/left-handed chirality of the original chain is transferred uniformly to adjacent chains through the zipper-like interchain hydrophobic interactions, resulting in the formation of Delta-2 and Delta-3 with chiral space groups of P212121 and P3121, respectively, in which all of the 1D helical chains are arranged in the same right/left-handed chirality.     

Template-assisted self-assembly of achiral plasmonic nanoparticles into chiral structures

The acquisition of strong chiroptical activity has revolutionized the field of plasmonics, granting access to novel light–matter interactions and revitalizing research on both the synthesis and application of nanostructures. Among the different mechanisms for the origin of chiroptical properties in colloidal plasmonic systems, the self-assembly of achiral nanoparticles into optically active materials offers a versatile route to control the structure–optical activity relationships of nanostructures, while simplifying the engineering of their chiral geometries. Such unconventional materials include helical structures with a precisely defined morphology, as well as large scale, deformable substrates that can leverage the potential of periodic patterns. Some promising templates with helical structural motifs like liquid crystal phases or confined block co-polymers still need efficient strategies to direct preferential handedness, whereas other templates such as silica nanohelices can be grown in an enantiomeric form. Both types of chiral structures are reviewed herein as platforms for chiral sensing: patterned substrates can readily incorporate analytes, while helical assemblies can form around structures of interest, like amyloid protein aggregates. Looking ahead, current knowledge and precedents point toward the incorporation of semiconductor emitters into plasmonic systems with chiral effects, which can lead to plasmonic–excitonic effects and the generation of circularly polarized photoluminescence.

Diverse templating materials and assembly strategies can be used to induce collective optical activity on achiral plasmonic building blocks. We present the advances, applications, challenges, and prospects of plasmonic–excitonic hybrids.     

Recent advances of achiral and chiral diene ligands in transition-metal catalyses

A series of achiral and chiral diene and the related ligands in transition-metal complexes is evaluated by percent buried volume (%V_bur) based on their molecular structures by X-ray analysis. Steric bulk of cyclic diene ligands in [Ru(acac)₂L] and [RhClL]₂ are sorted in the order of %V_bur. Recent developments on transition-metal catalyses using these ligands such as (i) conjugate arylations, alkenylation, and alkynylation, (ii) imine-arylations and alkenylations, (iii) kinetic resolutions, (iv) allylation, (v) cyclizations, (vi) defluorinations, (vii) CH bond activations, and (viii) cross-dimerizations are reviewed.     

A chiral layered Co(II) coordination polymer with helical chains from achiral materials

A layered coordination polymer Co(PDC)(H2O)2.H2O containing two helical chains was synthesized, and the resultant crystals were not racemic as evidenced by the observation of strong signals in vibrational circular dichroism (VCD) spectra.     

A homochiral 3D covalent framework assembled from vertical chiral layers with achiral bridging ligands

A novel metal-organic coordination polymer, [Cd(HPT)₂(4,4′-bpy)]_n (PT=phthalate), has been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. Colorless crystals crystallized in the tetragonal system, space group I4₁22, a=8.294(5), b=8.294(5), c=33.7535(17) Å, V=2321.8(18) Å³, Z=4 and R=0.0207. The structure of the compound exhibiting a homochiral 3D covalent framework based on achiral bridging ligands has been constructed by an alternating assembly of vertical chiral layers consisting of homochiral helices.     

SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands

Summary SPLICE is a program that processes partial query solutions retrieved from 3D, structural databases to generate novel, aggregate ligands. It is designed to interface with the database searching program FOUNDATION, which retrieves fragments containing any combination of a user-specified minimum number of matching query elements. SPLICE eliminates aspects of structures that are physically incapable of binding within the active site. Then, a systematic rule-based procedure is performed upon the remaining fragments to ensure receptor complementarity. All modifications are automated and remain transparent to the user. Ligands are then assembled by linking components into composite structures through overlapping bonds. As a control experiment, FOUNDATION and SPLICE were used to reconstruct a know HIV-1 protease inhibitor after it had been fragmented, reoriented, and added to a sham database of fifty different small molecules. To illustrate the capabilities of this program, a 3D search query containing the pharmacophoric elements of an aspartic proteinase-inhibitor crystal complex was searched using FOUNDATION against a subset of the Cambridge Structural Database. One hundred thirty-one compounds were retrieved, each containing any combination of at least four query elements. Compounds were automatically screened and edited for receptor complementarity. Numerous combinations of fragments were discovered that could be linked to form novel structures, containing a greater number of pharmacophoric elements than any single retrieved fragment.     

From achiral ligands to chiral coordination polymers: spontaneous resolution, weak ferromagnetism, and topological ferrimagnetism

Using the achiral diazine ligands bearing two bidentate pyridylimino groups as sources of conformational chirality, five azido-bridged coordination polymers are prepared and characterized crystallographically and magnetically. The chirality of the molecular units is induced by the coordination of the diazine ligands in a twisted chiral conformation. The use of L(1) (1,4-bis(2-pyridyl)-1-amino-2,3-diaza-1,3-butadiene) and L(2) (1,4-bis(2-pyridyl)-1,4-diamino-2,3-diaza-1,3-butadiene) induces spontaneous resolution, yielding conglomerates of chiral compounds [Mn(3)(L(1))(2)(N(3))(6)](n) (1) and [Mn(2)(L(2))(2)(N(3))(3)](n)(ClO(4))(n).nH(2)O (2), respectively, where triangular (1) or double helical (2) chiral units are connected into homochiral one-dimensional (1D) chains via single end-to-end (EE) azido bridges. The chains are stacked via hydrogen bonds in a homochiral fashion to yield chiral crystals. When L(3) (2,5-bis(2-pyridyl)-3,4-diaza-2,4-hexadiene) is employed, a partial spontaneous resolution occurs, where binuclear chiral units are interlinked into fish-scale-like homochiral two-dimensional (2D) layers via single EE azido bridges. The layers are stacked in a heterochiral or homochiral fashion to yield simultaneously a racemic compound, [Mn(2)(L(3))(N(3))(4)](n) (3a), and a conglomerate, [Mn(2)(L(3))(N(3))(4)](n).nMeOH (3b). On the other hand, the ligand without amino and methyl substituents (L(4), 1,4-bis(2-pyridyl)-2,3-diaza-1,3-butadiene) does not induce spontaneous resolution. The resulting compound, [Mn(2)(L(4))(N(3))(4)](n) (4), consists of centrosymmetric 2D layers with alternating single diazine, single EE azido, and double end-on (EO) azido bridges, where the chirality is destroyed by the centrosymmetric double EO bridges. These compounds exhibit very different magnetic behaviors. In particular, 1 behaves as a metamagnet built of homometallic ferrimagnetic chains with a unique "fused-triangles" topology, 2 behaves as a 1D antiferromagnet with alternating antiferromagnetic interactions, 3a and 3b behave as spin-canted weak ferromagnets with different critical temperatures, and 4 also behaves as a spin-canted weak ferromagnet but exhibits two-step magnetic transitions.     

Ruthenium hydride complexes of chiral and achiral diphosphazane ligands and asymmetric transfer hydrogenation reactions

The half-sandwhich ruthenium chloro complexes bearing chelated diphosphazane ligands, [(η⁵-Cp)RuCl{κ²-P,P-(RO)₂PN(Me)P(OR)₂}] [R = C₆H₃Me₂-2,6] (1) and [(η⁵-Cp^∗)RuCl{κ²-P,P-X₂PN(R)PYY′}] [R = Me, X = Y = Y′ = OC₆H₅ (2); R = CHMe₂, X₂ = C₂₀H₁₂O₂, Y = Y′ = OC₆H₅ (3) or OC₆H₄^tBu-4 (4)] have been prepared by the reaction of CpRu(PPh₃)₂Cl with (RO)₂PN(Me)P(OR)₂ [R = C₆H₃Me₂-2,6 (L¹)] or by the reaction of [Cp^∗RuCl₂]_n with X₂PN(R)PYY′ in the presence of zinc dust. Among the four diastereomers (two enantiomeric pairs) possible for the “chiral at metal” complexes 3 and 4, only two diastereomers (one enantiomeric pair) are formed in these reactions. The complexes 1, 2, 4 and [(η⁵-Cp)RuCl{κ²-P,P-Ph₂PN((S)-^∗CHMePh)PPhY}] [Y = Ph (5) or N₂C₃HMe₂-3,5 (S_CS_PR_Ru)-(6)] react with NaOMe to give the corresponding hydride complexes [(η⁵-Cp)RuH{κ²-P,P-(RO)₂PN(Me)P(OR)₂}] (7), [(η⁵-Cp^∗)RuH{κ²-P,P′-X₂PN(R)PY₂}] [R = Me, X = Y = OC₆H₅ (8); R = CHMe₂, X₂ = C₂₀H₁₂O₂, Y = OC₆H₄^tBu-4 (9)] and [(η⁵-Cp)RuH{κ²-P,P-Ph₂PN((S)-^∗CHMePh)PPhY}][Y = Ph (10) or N₂C₃HMe₂-3,5 (S_CS_PR_Ru)-(11a) and (S_CS_PS_Ru)-(11b)]. Only one enantiomeric pair of the hydride 9 is obtained from the chloro precursor 4 that bears sterically bulky substituents at the phosphorus centers. On the other hand, the optically pure trichiral complex 6 that bears sterically less bulky substituents at the phosphorus gives a mixture of two diastereomers (11a and 11b). Protonation of complex 7 using different acids (HX) gives a mixture of [(η⁵-Cp)Ru(η²-H₂){κ²-P,P-(RO)₂PN(Me)P(OR)₂}]X (12a) and [(η⁵-Cp)Ru(H)₂{κ²-P,P-(RO)₂PN(Me)P(OR)₂}]X (12b) of which 12a is the major product independent of the acid used; the dihydrogen nature of 12a is established by T₁ measurements and also by synthesizing the deuteride analogue 7-D followed by protonation to obtain the D-H isotopomer. Preliminary investigations on asymmetric transfer hydrogenation of 2-acetonaphthone in the presence of a series of chiral diphosphazane ligands show that diphosphazanes in which the phosphorus centers are strong π-acceptor in character and bear sterically bulky substituents impart moderate levels of enantioselectivity. Attempts to identify the hydride intermediate involved in the asymmetric transfer hydrogenation by a model reaction suggests that a complex of the type, [Ru(H)(Cl){κ²-P,P-X₂PN(R)PY₂}(solvent)₂] could be the active species in this transformation.     

Synthesis of complementary double-stranded helical oligomers through chiral and achiral amidinium-carboxylate salt bridges and chiral amplification in their double-helix formation

A series of complementary molecular strands from 2-mer to 5-mer that are composed of m-terphenyl units bearing chiral/achiral amidine or achiral carboxyl groups linked via Pt(II) acetylide complexes were synthesized by sequential stepwise reactions, and their chiroptical properties on the double-helix formation were investigated by circular dichroism (CD) and (1)H NMR spectroscopies. In CHCl(3), the "all-chiral" amidine strands consisting of (R)- or (S)-amidine units formed preferred-handed double helices with the complementary achiral carboxylic acid strands through the amidinium-carboxylate salt bridges, resulting in characteristic induced CDs in the Pt(II) acetylide complex regions, indicating that the chiral substituents on the amidine units biased a helical sense preference. The Cotton effect patterns and intensities were highly dependent on the molecular lengths. The complementary double-helix formation was also explored using the chiral/achiral amidine strands with different sequences in which a chiral amidine unit was introduced at the center (center-chiral) or a terminus (edge-chiral) of the amidine strands. The effect of the sequences of the chiral and achiral amidine units on the amplification of chirality (the "sergeants and soldiers" effect) in the double-helix formation was investigated by comparing the CD intensities with those of the corresponding all-chiral amidine double helices with the same molecular lengths. Variable-temperature CD experiments of the all-chiral and chiral/achiral amidine duplexes demonstrated that the Pt(II)-linked complementary duplexes are dynamic and their chiroptical properties including the chirality transfer from the chiral amidine unit to the achiral amidine ones are significantly affected by the molecular lengths, sequences, and temperatures. On the basis of the above results together with molecular dynamics simulation results, key structural features of the Pt(II)-linked oligomer duplexes and the effect of the chiral/achiral amidine sequences on the amplification of chirality are discussed.     

A novel strategy to assemble the beta-diketo acid pharmacophore of HIV integrase inhibitors on purine nucleobase scaffolds

Claisen condensation, the key step in constructing the pharmacophore of aryl beta-diketo acids (DKA) as integrase inhibitors, fails in certain cases of highly electron-deficient heterocycles such as purines. A general synthetic strategy to assemble the DKA motif on the purine scaffold has been accomplished. The synthetic sequence entails a palladium-catalyzed cross-coupling, a C-acylation involving a tandem addition/elimination reaction, and a novel ferric ion-catalyzed selective hydrolysis of an enolic ether in the presence of a carboxylic acid ester.     

Spontaneous chiral resolution of a coordination polymer with distorted helical structure consisting of achiral building blocks

Reaction of achiral 2,5-diphenyl-3,4-di(3-pyridyl)cyclopenta-2,4-dien-1-one (2) with ZnCl2 and HgBr2, respectively, afforded the helically chiral coordination polymers [(2)ZnCl2]infinity and [(2)HgBr2]infinity, which show spontaneous chiral resolution, forming colonies of homochiral crystals.     

Characteristic monomials with chirality fittingness for combinatorial enumeration of isomers with chiral and achiral ligands

A new method of combinatorial enumeration based on characteristic monomials with chirality fittingness (CM-CFs) has been proposed in order to enumerate isomers with chiral ligands as well as with achiral ones. The CM-CFs have been defined as monomials that consist of three kinds of dummy variables in light of the subduction of the Q-conjugacy representations for chiral and achiral cyclic groups. A procedure of calculating CM-CFs for cyclic groups and finite groups has been discribed so as to tabulate them as CM-CF tables. Then the CM-CF method has been applied to the enumeration of isomers with achiral ligands as well as chiral ones.     

Palladium and platinum complexes of chiral and achiral calix[4]arene bisphosphite ligands

Chiral and achiral p-tert-butyl-calix[4]arene bisphosphites (L¹–L³) have been synthesized by the reaction of p-tert-butyl-calix[4]arene and the phosphorodichloridites, ROPCl₂ [R = (1S,2R,5R)-(+)-iso-menthyl (L¹), (1R,2S,5R)-(−)-menthyl (L²) or C₆H₄Bu^t-4 (L³)]. These bisphosphites function as chelating ligands in palladium(II) and platinum(II) complexes which are formed in good yields by the reaction of PdCl₂(PhCN)₂, MCl₂(COD) (M = Pd or Pt) or PdMeCl(COD) with the respective calix[4]arene bisphosphite. Single crystal X-ray diffraction studies performed on the complexes [PdCl₂(L¹)], [PdCl₂(L²)], [PdCl₂(L³)] and [PtCl₂(L³)] reveal a near square planar geometry around the metal with the two chloride ligands in a cis disposition. The crystal packing in the complexes [PdCl₂(L¹)] and [PdCl₂(L²)], which crystallize in the chiral (P6₁22) space group, shows different hydrophobic channels with intermolecular C–H?Cl hydrogen bonding. The complexes [PdCl₂(L³)] and [PtCl₂(L³)] are isostructural and the molecules in the crystal lattice are linked by intermolecular C–H?Cl and C–H?O hydrogen bonds.     

A novel strategy to assemble colloidal gold nanoparticles at the water-air interface by the vapor of formic acid

We report a novel strategy on the controlled assembly of gold nanoparticles (NPs) at the air-water interface by designing a concentration gradient of electrolytes utilizing volatile weak acidic electrolytes. Films of close-packed Au NPs can be facilely obtained by exposing citrate-protected gold colloids to the vapor of formic acid for several hours in an airtight desiccator at room temperature. Both the higher interfacial concentration of formic acid and the buffer effect of citrate solution play the key roles in the assembly. They engender a gradient distribution of hydrogen ions such that to trigger the interfacial assembly of gold NPs while preventing the bulk colloid from aggregation and coagulation. Comparative investigations have also been performed either using other volatile electrolytes like weaker acetic acid and stronger hydrochloric acid or adding an electrolyte directly into the colloids. The as-prepared films of gold NPs can serve as good substrates for surface-enhanced Raman scattering (SERS). This strategy has also been applied to the assembly of some other NPs like colloidal Pt at the air-water interface.     

Increased enantioselectivity in the addition of diethylzinc to benzaldehyde by the use of chiral ligands containing the alpha-phenylethylamino group in combination with achiral ligands

Chiral ligands (S,S)-1, (S,S)-2, (S,S)-3, (S)-4, (S)-5, (S,S)-6, (S,S)-7, and (S,S)-8 turned out to be effective promoters in the enantioselective addition of diethylzinc to benzaldehyde. Interestingly, diamine (S,S)-3 and amino alcohols (S)-5 and (S,S)-7 induce the preferential formation of carbinol (R)-10 (unlike stereoinduction) whereas amido analogues (S,S)-2, (S)-4, and (S,S)-6 favor (S)-10 (like stereoinduction). Molecular modeling at the semiempirical PM3 level provided a reasonable interpretation based on conformational effects in the corresponding transition structures. Combinations of chiral ligands 1-8 with an achiral, flexible ligand (9) gave rise to an activated catalytic system that resulted in faster and higher yielding reactions. Furthermore, substantial increases in the observed enantiomeric excesses of product 10 confirmed the relevant role of achiral bis(sulfonamide) 9 as activator and "chiral environment amplifier".     

Mixtures of chiral and achiral monodentate ligands in asymmetric Rh-catalyzed olefin hydrogenation: reversal of enantioselectivity

The recently described method of combinatorial asymmetric transition metal catalysis based on the use of mixtures of chiral monodentate P-ligands has been extended to include mixtures of chiral and achiral monodentate P-ligands, reversal of enantioselectivity in Rh-catalyzed olefin hydrogenation being possible in appropriate cases.     

A novel strategy to determine protein structures using exclusively residual dipolar coupling

Recent advances in NMR techniques to measure anisotropic spin interactions such as residual dipolar coupling (RDC) have provided better insights into protein structure as well as dynamics. Exploitation of RDC, however, still remains challenging because its successful application requires a reasonable starting model. Using the singular value decomposition method, we have recently developed an RDC restraint potential to optimally extract orientational information from RDC without the prerequisite of any structural information. In the present study, its efficacy is further illustrated by folding a beta-hairpin and alpha-helix of protein G from extended conformations with RDC restraints alone by employing the replica exchange torsion angle molecular dynamics (REX-TAMD) technique. Subsequently, the entire structure of protein G has been determined accurately using the developed fragment superposition method (FRAGSUM). In FRAGSUM, each overlapping fragments (10 amino acids long) is first folded individually by REX-TAMD, and then the common amino acids are superimposed to determine the entire structure. Because FRAGSUM does not require any additional information besides RDC, it offers a new strategy for de novo structure determination using exclusively RDC.     

A chiral luminescent Au16 ring self-assembled from achiral components

A luminescent supramolecular chiral Au16 ring with 4.822 nm perimeter that self-assembled from a tetrameric array of achiral Au2 units is described. Intra- and intermolecular Au...Au interactions play an important role in directing its chiral self-assembly.