Structures of spiropyrans exhibiting photochromic properties in the solid state

Russian Chemical Bulletin - Solid-state photochromic indoline spiropyrans bearing a formyl group at the 6′ and 8′ positions of the 2H-chromene moiety of the molecules were...     

A foldamer-based chiroptical molecular switch that displays complete inversion of the helical sense upon anion binding

Chiral indolocarbazole dimers fold into a helical conformation by virtue of intramolecular hydrogen bonds, as demonstrated by (1)H NMR and CD spectra and optical rotations. In particular, the optical properties of the dimers were found to be extremely sensitive to the nature of the solvent, depending on whether they are folded or not. The helical sense of the dimers can be reversibly switched by binding sulfate ion, which gives rise to complete inversion of the CD spectra. The binding mode and absolute stereochemistry of the sulfate complexes was unequivocally determined by single-crystal X-ray structures, which are all consistent with the CD and (1)H NMR spectra in solution.     

The inversion phenomenon of the helical twist sense in antiferroelectric liquid crystal phase from electronic and vibrational circular dichroism

The investigation of the helical pitch and the helical twist sense for several liquid crystal compounds in antiferroelectric phase have been performed. Electronic circular dichroic (ECD) and vibrational circular dichroic (VCD) spectroscopies have proved the existence of unwound helical structure in antiferroelctric phase. Obtained results may confirm the assumption connected via the inversion phenomena in liquid crystalline chiral phase with the change of the concentration of different conformers promoting opposite handedness. Two examples of such conformers, obtained by conformational analysis, have been proposed.     

Switching of chiral induction in helical aromatic oligoamides using solid state-solution state equilibrium

The introduction of an R asymmetric center in an aromatic oligoamide that adopts stable helical conformations leads to a significant shift of the equilibrium between the right-handed and left-handed helices in solution: the R-P and R-M helices are diastereoisomers. However, these two species were found to cocrystallize in 1:1 proportions. Thus the chiral induction observed in solution is switched off in the solid state. This phenomenon represents an original and unexpected means to control handedness in helical oligomers.     

Self-assembly of helical supramolecular channels from chiral aminopyrimidine hydrogen bonding motifs in the solid state

The H-bond mediated self-assembly of the chiral C₂-symmetric bis-(2-amino-4-chloro-pyrimidines) 3 and 4 allows for the molecular recognition directed generation of helical superstructures. In the former case, unoccupied channel structures defined by the cylindrical interior of the derived supramolecular helix result, as revealed by X-ray crystallographic analysis using a synchrotron source. Upon crystallization, racemic 3 spontaneously resolves to form homochiral crystals exhibiting a helical packing motif identical to that determined for optically pure 3. The data provide insight into the interplay of the different structural and interactional features of the molecular components to the generation of the channel structure and suggest design strategies toward porous organic molecular solids of variable size.     

Spectroscopic analysis of pindolol irradiated in the solid state

Pindolol ((2RS)-(1-(1H-indol-4-iloxy)-3- [(1-metyloetylo)amino]-2-propanol) in substantia was exposed to ionising radiation emitted by high energy electrons from an accelerator, in the standard sterilisation dose of 25 kGy and in higher doses from the range 50–400 kGy. The effects of irradiation were checked by spectrometric methods (UV, MS, FT-IR, EPR) and hyphenated methods (HPLC-MS) and the results were referred to those obtained for non-irradiated sample. EPR results indicated the presence of free radicals in irradiated samples, in the amount of 1.36 × 10¹⁶ spin g^?1 for 25 kGy and 3.70×10¹⁶ spin g^?1 for 400 kGy. The loss of pindolol content determined by HPLC was 1.34% after irradiation with 400 kGy, while the radiolytic yield of the total radiolysis for this dose of irradiation was 2.69×10⁷ mol J^?1. By means of HPLC-MS it was possible to separate and identify one product of radiolytic decomposition, which probably is 2-((R)-3-(1H-indol-4-yloxy)-2-hydroxypropylamino)propan-1-ol formed upon oxidation. In the range of sterilisation doses (25–50 kGy), pindolol was found to show high radiochemical stability and would probably be safely sterilised by the standard dose of 25 kGy.      

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins

Contact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent-accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp-I and Sccomp-S), with relatively fast execution times, correctly predict chi1 angles for 92-93% of buried residues and 82-84% for all residues, with an RMSD of approximately 1.7 A for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive; i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of Cbeta atoms on the accuracy of side-chain prediction are examined. The Sccomp-S and Sccomp-I programs can be accessed through the Web (http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms.     

Sign inversion of the helical pitch in carbohydrate-based liquid crystals

A four-step synthesis starting from tri-O-acetyl-D-glucal leads to chiral trioxadecalin compounds containing a cyano group. The mesogenic properties of a homologous series of liquid crystals are reported; for two derivatives a helix inversion of the cholesteric phase is observed.     

Thermally reversible fluorescent polymorphs of alkoxy-cyano-substituted diphenylbutadienes: role of crystal packing in solid state fluorescence

Correlation of fluorescence and crystal packing in thermally interconvertible polymorphic states of octyloxy-cyano-substituted diphenylbutadiene possessing visually distinguishable fluorescence reveals that solid state fluorescence of this class of derivatives depends on their monomer-J-aggregate ratio, controlled by variations in their molecular packing.     

The temperature and concentration dependence of helical pitch in the mixtures of antiferroelectric compounds with the opposite helical twist sense

The temperature dependence of helical pitch for members of an homologous series of orthoconic antiferroelectric compounds (3FmHPhF) and their bicomponent mixtures (m = 3 and 5 as well as m = 3 and 7) has been measured by the method of selective light reflection. The compounds have the same chiral centre but they have different temperature dependence of the helical pitch as well as the helical twisting sense in SmC*_A phase: right for member m = 3, left for m = 7, and both right and left for m = 5. For this last homologue, the change of twisting sense is connected with the appearance of the unwound structure. Concentration dependence on helical pitch was investigated in the mixtures. It was demonstrated that it is possible to obtain mixtures with desirable high pitch and also with totally unwound structure.     

On the van der Waals interactions and the stability of polypeptide chains in helical conformations

In this work, we aim to investigate the contribution of van der Waals (vdW) interactions to the stability of polypeptides in helical conformations studying infinitely long chains of alanine and glycine with density functional theory. To account for vdW interactions, we have used the interatomic pairwise dispersion approach proposed by Tkatchenko–Scheffler (TS), the TS approach with self‐consistent screening (SCS) that self‐consistently includes long‐range electrostatic effects (TS + SCS), the D2 and D3 methods of Grimme et al., and the Langreth–Lundqvist procedure that treats nonlocally the correlation part of the approximation to the exchange‐correlation (xc) functional (called DF). First, we have tested the performance of these strategies studying a set of representative hydrogen bonded dimers. Next, we have studied polyalanine and polyglicine in π‐helix, α‐helix, ‐helix, 2₇, and polyproline‐II conformations and in a fully extended structure. We have found that the DF methodology in combination with a modified version for the Becke approximation to the exchange (optB86b), the D2, D3, TS, and TS + SCS strategies in combination with the Perdew–Burke–Ernzerhof approximation to the xc functional, describe fairly well dimer association energies. Furthermore, the DF method and the D2, D3, TS, and TS + SCS strategies predict very similar helical stabilities even though the approximation used in DF for describing the long‐range dispersion interactions is different that the one used in D2/D3 and TS/TS + SCS. We found that the stability doubles for π and α helices if vdW interactions are taken into account. © 2015 Wiley Periodicals, Inc.     

Glycopeptides related to beta-endorphin adopt helical amphipathic conformations in the presence of lipid bilayers

A series of glycosylated endorphin analogues designed to penetrate the blood-brain barrier (BBB) have been studied by circular dichroism and by 2D-NMR in the presence of water; TFE/water; SDS micelles; and in the presence of both neutral and anionic bicelles. In water, the glycopeptides showed only nascent helix behavior and random coil conformations. Chemical shift indices and nuclear Overhauser effects (NOE) confirmed helices in the presence of membrane mimics. NOE volumes provided distance constraints for molecular dynamics calculations used to provide detailed backbone conformations. In all cases, the glycopeptides were largely helical in the presence of membrane bilayer models (micelles or bicelles). Plasmon waveguide resonance (PWR) studies showed hen egg phosphatidyl choline (PC) bilayers produce amphipathic helices laying parallel to the membrane surface, with dissociation constants (K(D)) in the low nanomolar to micromolar concentration range. Two low-energy states are suggested for the glycosylated endorphin analogues, a flexible aqueous state and a restricted membrane bound state. Strong interactions between the glycopeptide amphipaths and membranes are crucial for penetration of the BBB via an endocytotic mechanism (transcytosis).     

Kinetic and thermodynamic analysis of degradation of doripenem in the solid state

The kinetic and thermodynamic parameters of degradation of doripenem were studied using a high‐performance liquid chromatography method. In dry air, the degradation of doripenem was a first‐order reaction depending on the substrate concentration. At increased relative air humidity, doripenem was degraded according to the autocatalysis kinetic model. The dependence ln k = f1/T) was described by the equations ln k = 5.10 ± 13.06 ? (7576 ± 4939)(1/T) in dry air and ln k = 46.70 ± 22.44 ? (19,959 ± 8031)(1/T) at 76.4% relative humidity (RH). The thermodynamic parameters E_a, ΔH^≠a, and ΔS^≠a of the degradation of doripenem were calculated. The dependence ln k = f (RH%) was described by the equation ln k = (0.155 ± 0.077) × 10^?1 (RH%) ? (3.45 ± 21.8) × 10^?10. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 722–728, 2012     

Conformational analysis of alkylated biuret and triuret: evidence for helicity and helical inversion in oligoisocyanates

The conformations of several oligoisocyanates have been investigated by NMR in order to study the onset and dynamics of helicity in polyisocyanates. Pentaethylbiuret and hexaethyltriuret were found to adopt turns and helices in solution. For hexaethyltriuret, symmetric and asymmetric helices are present. Not only is an interconversion of these forms observed (DeltaG(SA)(double dagger) = 9.3 +/- 0.4 kcal/mol) but also a reversal of helicity (DeltaG(PM)(double dagger) = 9.0 +/- 0.4 kcal/mol). The coalescence pattern for the latter process provides direct evidence for a concerted, conrotatory helical inversion.     

Precise values of the 13C component vicinal coupling constants for calculating side-chain conformations in amino acids

From consideration of ¹H–¹H vicinal coupling constants and ¹³C? ¹H long-range coupling constants in a series of amino acid derivatives, the precise values of ¹³C component vicinal coupling constants have been calculated for the three minimum energy staggered rotamers for the C(α)H? C(β)H₂ side-chains of amino acids.     

Relationship among ligand conformations in solution, in the solid state, and at the Hsp90 binding site: geldanamycin and radicicol

The unknown effects of a receptor's environment on a ligand's conformation presents a difficult challenge in predicting feasible bioactive conformations, particularly if the receptor is ill-defined. The primary hypothesis of this work is that a structure's conformational ensemble in solution presents viable candidates for protein binding. The experimental solution profile can be achieved with the NAMFIS (NMR analysis of molecular flexibility in solution) method, which deconvolutes the average NMR spectrum of small flexible molecules into individual contributing conformations with varying populations. Geldanamycin and radicicol are structurally different macrocycles determined by X-ray crystallography to bind to a common site on the cellular chaperone heat shock protein 90 (Hsp90). Without benefit of a receptor structure, NAMFIS has identified the bioactive conformers of geldanamycin and radicicol in CDCl3 solution with populations of 4% and 21%, respectively. Conversely, docking the set of NAMFIS conformers into the unliganded proteins with GLIDE followed by MM-GBSA scoring reproduces the experimental crystallographic binding poses.     

Ionic conduction in the solid state

Solid state ionic conductors are important from an industrial viewpoint. A variety of such conductors have been found. In order to understand the reasons for high ionic conductivity in these solids, there have been a number of experimental, theoretical and computational studies in the literature. We provide here a survey of these investigations with focus on what is known and elaborate on issues that still remain unresolved. Conductivity depends on a number of factors such as presence of interstitial sites, ion size, temperature, crystal structure etc. We discuss the recent results from atomistic computer simulations on the dependence of conductivity in NASICONs as a function of composition, temperature, phase change and cation among others. A new potential for modelling of NASICON structure that has been proposed is also discussed. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

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.     

ESR analysis of the initial reaction products in the solid state photopolymerization of diacetylenes

In order to investigate the mechanism of the solid state photopolymerization of single crystals of the bis(p-toluene sulphonate) ester of 2,4-hexadiyne-1,6 diol (TSHD) the low temperature UV-photoproducts are analyzed by ESR-spectroscopy. In this paper we report the fine structure, hyperfine structure and temperature dependence of a series of thermally activated triplet diradicals. The structure of these diradical dimer and trimer initiators of the UV-photopolymerization process is deduced from the analysis of the ESR data.