Synthesis and physical properties of protein core mimetics.

A series of mimetic cores composed of a synthetic scaffold and amino acids have been constructed and their properties investigated in chloroform. A relative measure of H-bond strength was obtained by comparing temperature coefficients derived from variable-temperature (1)H NMR experiments. Although most templates had a strong H-bond, only a single template composed of D- and L-phenylalanines was able to form two strong H-bonds. Templates containing D- and L-leucines formed only a single H-bond. The results of these studies suggest that aromatic edge-to-face interactions provide greater stabilization energy than aliphatic-aromatic interactions in the tightly packed hydrophobic cores of proteins. Partial structures of the templates were derived by analyzing a series of two-dimensional (1)H NMR spectra and performing molecular mechanics calculations using AMBER and MMFF94 force fields.     

C2 isomers of C84F40 and C84F44 are cuboid and contain benzenoid and naphthalenoid aromatic patches

A 1:1 mixture of C84F40 and C84F44, both derived from the D2(IV) isomer, has been isolated from the fluorination of [84]fullerene with either MnF3 or CoF3 at 500 degrees C. The 1D and 2D COSY 19F NMR spectra showed that each derivative is cuboid, having benzenoid rings at four of the six octahedral sites; the two remaining sites have naphthalenoid rings for C84F40, and two slightly offset benzenoid rings for C84F44. The benzenoid rings each have six adjacent sp3-hybridised carbon atoms whilst the naphthalenoid moieties have eight, thus facilitating full delocalisation. In terms of the number and size of aromatic patches, C84F44 is the most aromatic fullerene derivative yet isolated.     

Direct NMR observation and pKa determination of the Asp102 side chain in a serine protease

The pK(a) value of aspartic acid in the catalytic triad of serine proteases has been a pivotal element in essentially every mechanism proposed for these enzymes over the past 40 years, but has, until now, eluded direct determination. Here, we have used the multinuclear 3D-NMR pulse programs HCACO and HCCH-TOCSY to directly identify and study the side-chain resonances of the aspartate and glutamate residues in uniformly (13)C-labeled α-lytic protease. Resonances from four of the six residues were detected and assigned, including that of Asp(102), which is notably the weakest of the four. pH titrations have shown all of the carboxylate (13)C signals to have unusually low pK(a) values: 2.0, 3.2, and 1.7 for Glu(129), Glu(174), and Glu(229), respectively, and an upper limit of 1.5 for Asp(102). The multiple H-bonds to Asp(102), long known from X-ray crystal studies, probably account for its unusually low pK(a) value through preferential stabilization of its anionic form. These H-bonds probably also contribute to the weakness of the NMR resonances of Asp(102) by restricting its mobility. The Asp(102)(13)C(γ) atom responds to the ionization of His(57) in the resting enzyme and to the inhibitor-derived oxyanion in a chloromethyl ketone complex, observations that strongly support the assignment. The low pK(a) value of Asp(102) would appear to be incompatible with mechanisms involving strong Asp(102)-His(57) H-bonds or high pK(a) values, but is compatible with mechanisms involving normal Asp(102)-His(57) H-bonds and moving His(57) imidazole rings, such as the reaction-driven ring flip.     

Helical aromatic oligoamides: reliable, readily predictable folding from the combination of rigidified structural motifs

Factors responsible for the folding of aromatic oligoamides with backbones rigidified by local three-center H-bonds were investigated. The stability of the three-center H-bonds was quantified by the half-lives of amide proton-deuterium exchange reactions, which show that the three-center H-bonds were largely intact at room temperature in the oligomer examined. This result is consistent with our current and previous 2D NMR studies. The overall helical conformation of nonamer 1 was found by variable-temperature NOESY studies to be dynamic. As temperature rose, the end-to-end NOEs rapidly disappeared, while the amide side chain NOEs were still readily detectable, corresponding to the "breath" and stretching of the helix by slightly twisting the local H-bonded rings. Based on the simple repetition of the same structural motif and local conformational preference, undecamer 2 was found to fold into well-defined helical conformation. The predictability of the folding of these backbone-rigidified aromatic oligoamides was demonstrated by a simple modeling method using structural parameters from oligomers with known crystal structures. The reliability and generality of the modeling methods were shown by the excellent agreement between the modeled structures corresponding to 1 and 2 and data from NOESY studies.     

Controlling multivalent interactions in triply-threaded two-component superbundles

We have investigated the (1)H NMR spectra, the absorption spectra, the fluorescence spectra and decays, and the electrochemical properties of i). a tritopic receptor in which three benzo[24]crown-8 macrorings are fused onto a triphenylene core, ii). a trifurcated trication wherein three dibenzylammonium ions are linked 1,3,5 to a central benzenoid core, and iii). their 1:1 adduct which constitutes a triply-threaded, two-component supramolecular bundle. X-Ray crystallography has established the precise geometry of this paucivalent recognition motif in the solid state. In addition to [N(+)-H...O] hydrogen bonding and [C-H...O] interactions between the NH(2) (+) centers on the three dibenzylammonium ion containing arms of the trication and the three crown ether rings in the tritopic receptor, there is a stabilizing [pi...pi] stacking interaction between the two aromatic cores. Mass spectrometry and (1)H NMR spectroscopy have confirmed the integrity of the 1:1 adduct beyond the solid state, provided the solvents are relatively apolar (e.g., chloroform and acetonitrile). The intense fluorescence emissions of the two recognition components are quenched upon association with the concomitant appearance of a lower energy, broad fluorescence band originating from the pi-pi stacking in the 1:1 adduct of the aromatic cores in the two matching components. Titration experiments, including Job plots, establish the 1:1 stoichiometry of the adduct, an observation which is also confirmed by electrochemical experiments. The electrochemical results show that, both in the tritopic receptor and in the superbundle itself, the first oxidation process is associated with the hexaalkoxytriphenylene core. The successive oxidation processes of the peripheral dioxybenzene units are affected by charge-transfer interactions in the tritopic receptor, whereas, in the superbundle, such units are not interacting. In acetonitrile solution, dethreading/rethreading of the 1:1 adduct can be controlled quantitatively by addition of base and acid. Dethreading and rethreading is also observed by (1)H NMR spectroscopy when dimethylsulfoxide is added to a solution of the 1:1 adduct in equal volumes of acetonitrile and chloroform. A trifurcated trication where methyl groups are located on the para positions of the three dibenzylammonium ions, which are linked 1,3,5 to the neutral benzenoid core, has been employed to demonstrate that dethreading of the 1:1 adduct involves doubly-threaded and singly-threaded species, that is, the paucivalent site is dismembered in a sequence of logical steps involving stable intermediates. This molecular recognition system is a rare example of a supramolecular entity based on a cooperative binding motif that can be switched on and off by chemical means.     

π-Electron currents in fixed π-sextet aromatic benzenoids

In view of different patterns of π-electron density currents in benzenoid aromatic compounds it is of interest to investigate the pattern of ring currents in various classes of compounds. Recently such a study using a graph theoretical approach to calculating CC bond currents was reported for fully benzenoid hydrocarbons, that is, benzenoid hydrocarbons which have either π-sextets rings or “empty” rings in the terminology of Clar. In this contribution we consider π-electron currents in benzenoid hydrocarbons which have π-electron sextets and C=C bonds fully fixed. Our approach assumes that currents arise from contributions of individual conjugated circuits within the set of Kekulé valence structures of these molecules.     

Dimeric liquid crystals with 5-(4-alkoxybenzoyloxy)tropone or 4-(4-alkoxybenzoyloxy)phenyl cores: evaluation of the tilt angles of the cores, spacers, and side chains

Two types of symmetric dimers with 5-(4-alkoxybenzoyloxy)tropone cores or with 4-(4-alkoxybenzoyloxy)phenyl cores were synthesized to evaluate the effect of the core structure and the length of the spacer on the mesomorphic properties. The former had smectic C phases whereas the latter had smectic C and F phases. Both types of dimer showed a remarkable odd-even effect on varying the spacer on the mesomorphic properties. Comparison of the thermal stability between them demonstrated that benzenoid twins are more stable than troponoid ones. The layer spacings of the smectic C phases were measured to determine the tilt angles of the core part, the spacer, and the side chains on changing the length of the spacer and the side chains. Troponoid dimers had a larger tilt angle of the core part of the smectic C phase than benzenoid twins, which lowered the thermal stability of the troponoid. Entropy changes of the smectic C phase to the isotropic liquid showed a contrast between troponoids and benzenoids. The former had smaller values and odd-even effects than the latter, which indicated that the former troponoids had a limited number of conformers in mesophases.     

Graph theoretical characterization and computer generation of certain carcinogenic benzenoid hydrocarbons and identification of bay regions

An algorithm is developed for generating and characterizing carcinogenic catacondensed benzenoid hydrocarbons. The bay regions in these structures are identified by a technique that we developed at Johns Hopkins. Using the three-digit code proposed by Balaban, and the concept of ring adjacency matrix expounded here, we generate catacondensed benzenoid hydrocarbons in the computer and identify the number of potentially carcinogenic bay regions in each of them. The results of computer generation agree with the combinatorial enumeration of Harary and Read. All structures containing up to five rings and some with six rings and the number of bay regions in these are presented. Computer results for the structures and bay regions of all seven-, eight-, and nine-membered unbranched catacondensed benzenoid hydrocarbons and the number of bays are available from the authors.     

NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone rings

Methanobactin (mb) is a small copper-binding peptide produced by methanotrophic bacteria and is intimately involved in both their copper metabolism and their role in the global carbon cycle. The structure for methanobactin comprises seven amino acids plus two chromophoric residues that appear unique to methanobactin. In a previously published structure, both chromophoric residues contain a thiocarbonyl attached to a hydroxyimidazolate ring. In addition, one is attached to a pyrrolidine ring, while the other is attached to an isopropyl ester. A published X-ray determined structure for methanobactin shows these two chromophoric groups forming an N2S2 binding site for a single Cu(I) ion with a distorted tetrahedral geometry. In this report we show that NMR, mass spectrometry, and chemical data reveal a chemical structure that is significantly different than the previously published one. Specifically, the 1H and 13C NMR assignments are inconsistent with an N-terminal isopropyl ester and point instead to a 3-methylbutanoyl group. Our data also indicate that oxazolone rings instead of hydroxyimidazolate rings form the core of the two chromophoric residues. Because these rings are directly involved in the binding of Cu(I) and other metals by methanobactin and are likely involved in the many chemical activities displayed by methanobactin, their correct identity is central to developing an accurate and detailed understanding of methanobactin's many chemical and biological roles. For example, the oxazolone rings make methanobactin structurally more similar to other bacterially produced bactins and siderophores and suggest pathways for its biosynthesis.     

Dimeric liquid crystals with 5‐(4‐alkoxybenzoyloxy)tropone or 4‐(4‐alkoxybenzoyloxy)phenyl cores: evaluation of the tilt angles of the cores,spacers, and side chains

Two types of symmetric dimers with 5‐(4‐alkoxybenzoyloxy)tropone cores or with 4‐(4‐alkoxybenzoyloxy)phenyl cores were synthesized to evaluate the effect of the core structure and the length of the spacer on the mesomorphic properties. The former had smectic C phases whereas the latter had smectic C and F phases. Both types of dimer showed a remarkable odd–even effect on varying the spacer on the mesomorphic properties. Comparison of the thermal stability between them demonstrated that benzenoid twins are more stable than troponoid ones. The layer spacings of the smectic C phases were measured to determine the tilt angles of the core part, the spacer, and the side chains on changing the length of the spacer and the side chains. Troponoid dimers had a larger tilt angle of the core part of the smectic C phase than benzenoid twins, which lowered the thermal stability of the troponoid. Entropy changes of the smectic C phase to the isotropic liquid showed a contrast between troponoids and benzenoids. The former had smaller values and odd–even effects than the latter, which indicated that the former troponoids had a limited number of conformers in mesophases.     

Benzenoid rings resonance energies and local aromaticity of benzenoid hydrocarbons

In this article, we consider partitioning of the analytical expression for resonance energy (RE) in smaller benzenoid hydrocarbons, to individual benzenoid rings of polycyclic molecules. The analytical expression for molecular RE, available since 1976, is given by the count of all linearly independent conjugated circuit in all Kekulé structures in a molecule. Analytical expression for local ring RE (RRE) is given by counting all linearly independent conjugated circuits involving single benzenoid ring in all Kekulé structures, which when added, gives the molecular RE. If for benzene ring the RRE is taken to be 1.000, rings in polycyclic benzenoid hydrocarbons have their ring RRE, which give the degree of their local aromaticity, smaller than 1.000. The difference to 1.000 is a measure of the similarity of a ring to benzene in this one-dimensional (1-D) representation of local aromaticities of benzenoid hydrocarbons. The plot of RRE against the distance of the same ring from benzene in the Local Aromaticity Map, in which benzenoid rings are characterized ring bond orders and average variations of adjacent CC bonds, shows linear correlation (with r = 0.91), reducing the local aromaticity in benzenoid hydrocarbons to 1-D molecular property. © 2018 Wiley Periodicals, Inc.     

Synthesis and characterization of new ferroelectric liquid crystals containing a (2S)-2-[6-(4-hydroxybiphenyl-4'-carbonyloxy)-2'- naphthyl] propionate mesogenic group and oligo(oxyethylene) spacers

Three series of ferroelectric liquid crystals containing a (2S)-2-(6-(4-hydroxybiphenyl-4'-carbonyloxy)-2'-naphthyl)propionate mesogenic group and oligo(oxyethylene) spacers were synthesized. These obtained liquid crystal compounds were characterized by NMR, differential scanning calorimetry (DSC), optical polarized microscopy (POM), and X-ray powder diffraction measurements. Some of these materials containing four phenyl rings of ester cores (i.e. -Ph-Ph-COO-naph-) and chiral heptyl tail exhibited a rich mesomorphic behaviour, a blue phase (BP), a cholesteric phase (Ch), a smectic A (S_A), a twist grain boundary A (TGB_A), and a chiral smectic C (S_C*) phase. Another series containing four phenyl rings of ester cores and chiral butyl and pentyl chain tails revealed only a S_A phase and a S_C* phase. Moreover, a crystal E phase was observed in the short spacer chain (n = 0 or 1) homologues of three series of compounds. Also, the mesomorphism properties were discussed as a function of spacer units, numbers of aromatic rings of core, and different terminal asymmetric moieties.     

Organization of acenes with a cruciform assembly motif

This study explores the assembly in the crystalline state of a class of pentacenes that are substituted along their long edges with aromatic rings forming rigid, cruciform molecules. The crystals were grown from the gas phase, and their structures were compared with DFT-optimized geometries. Both crystallographic and computed structures show that a planar acene core is the exception rather than the rule. In the assembly of these molecules, the phenyl groups block the herringbone motif and further guide the arrangement of the acene core into higher order structures. The packing for the phenyl-substituted derivatives is dictated by close contacts between the C-H's of the pendant aromatic rings and the carbons at the fusions in the acene backbone. Using thiophene substituents instead of phenyls creates cofacially stacked acenes. In thin films, the thiophene-substituted derivative forms devices with good electrical properties: relatively high mobility, high ON/OFF ratios, and low threshold voltage for device activation. An unusual result is obtained for the decaphenyl pentacene when devices are fabricated on its crystalline surface. Although its acene cores are well isolated from each other, this material still exhibits good electrical properties.     

含金纳米粒子链相关性探讨及其热稳定性的分子模拟

采用分子模拟法, 以金核外层吸附了不对称硫醚链的含金纳米粒子为研究对象, 以次序参数为依据, 对不同条件下的硫醚链及苯环间的相关性进行了探讨, 确定了较为合理的相关性判据.以此判据为依据, 并通过金核的径向分布函数的分析, 考察了纳米粒子的结构随温度变化的情况, 得出了含金纳米粒子的热稳定性较高的结论.     

Obituary: Professor Frank M. Leslie FRS (1935-2000)

The synthesis of five new cholesteryl-based monomers (M-1?M-5) and the corresponding smectic comb-like polymers containing cholesteryl groups (P-1?P-5) is presented. The chemical structures were characterised by FT-IR, 1H NMR and elemental analyses. The specific optical rotations were evaluated with a polarimeter. The phase behaviour was investigated by polarising optical microscopy, differential scanning calorimetry, thermogravimetric analysis, and X-ray diffraction. The specific optical rotation values of these monomers and polymers with the same number of phenyl rings and terminal groups were nearly equal; however, they decreased with increasing the aryl numbers in the mesogenic core. The monomers M-1?M-5 showed oily streak and focal conic optical textures, or finger print textures characteristic of the chiral nematic phase. The polymers P-1?P-5 showed the smectic A phase. The melting, clearing, and glass transition temperatures increased, and the mesophase temperature ranges widened with increasing the aryl number in the mesogenic core. However, although the molecular structures of M-4 and M-5 were similar to those of M-3, namely their mesogenic cores contained three phenyl rings, their phase behaviour differed considerably, and T _m and T _i of M-4 and M-5 were less than those of M-3. In addition, M-4 and M-5 showed a clear glass transition similar to the polymer. Furthermore, the ester linkage bond and aryl arrangement in the mesogenic core also affected the phase behaviour.     

The Intramolecular Interaction of Thiophene and Furan with Aromatic and Fluoroaromatic Systems in Some [3.3]Meta(heterocyclo)paracyclophanes: A Combined Computational and NMR Spectroscopic Study

Four thiophene‐ and furan‐containing [3.3]meta(heterocyclo)paracyclophanes were designed and synthesized to study the intramolecular interaction between standard heteroaromatic rings and tetra‐H‐ or tetra‐F‐substituted benzenes. A complete conformational analysis, carried out by DFT calculations and variable‐temperature NMR techniques, showed that, despite their structural similarity, these adducts have different conformational preferences and undergo different types of isomerizations depending on the nature of the heterocycle. The thiophene‐derived adducts adopted a parallel stacked arrangement of the aromatic systems in the ground‐state conformations. Their isomerization pathways involved a thiophene ring‐flip process passing through an edge‐to‐face arranged transition state in which the heterocycle is perpendicular to the benzene platform and its sulfur atom points toward the center of that ring. The threshold energy barrier to the ring‐flip process was higher by 10 kJ mol^?1 in the case of the adduct featuring the perfluorinated benzene. This difference was rationalized by assuming that the ground‐state conformations of the H‐ and F‐substituted compounds have different stability. On the contrary, the furan‐derived adducts were shown by calculations and NMR spectroscopy to adopt, in their ground‐state conformations, a perpendicular edge‐to‐face disposition of the rings with the oxygen atom pointing toward the benzene platform. The adoption of this arrangement was confirmed by X‐ray crystallography. In the case of these compounds, the isomerization process involved distortion of the CH₂SCH₂ bridges connecting the aromatic systems and the adoption of transition‐state geometries for which the rings were arranged in a parallel‐stacked orientation. Once again a very nice agreement was observed between the predicted and the experimentally determined geometries and pathways. In the case of the furan‐containing compounds, the threshold barriers were found to be much lower in energy that those observed for the thiophene derivatives. Remarkably, they were virtually independent of the presence of fluorine atoms on the platform benzene ring.     

Solution 1H, 15N NMR spectroscopic characterization of substrate-bound, cyanide-inhibited human heme oxygenase: water occupation of the distal cavity

A solution NMR spectroscopic study of the cyanide-inhibited, substrate-bound complex of uniformly (15)N-labeled human heme oxygenase, hHO, has led to characterization of the active site with respect to the nature and identity of strong hydrogen bonds and the occupation of ordered water molecules within both the hydrogen bonding network and an aromatic cluster on the distal side. [(1)H-(15)N]-HSQC spectra confirm the functionalities of several key donors in particularly robust H-bonds, and [(1)H-(15)N]HSQC-NOESY spectra lead to the identification of three additional robust H-bonds, as well as the detection of two more relatively strong H-bonds whose identities could not be established. The 3D NMR experiments provided only a modest, but important, extension of assignments because of the loss of key TOCSY cross-peaks due to the line broadening from a dynamic heterogeneity in the active site. Steady-state NOEs upon saturating the water signal locate nine ordered water molecules in the immediate vicinity of the H-bond donors, six of which are readily identified in the crystal structure. The additional three are positioned in available spaces to account for the observed NOEs. (15)N-filtered steady-state NOEs upon saturating the water resonances and (15)N-filtered NOESY spectra demonstrate significant negative NOEs between water molecules and the protons of five aromatic rings. Many of the NOEs can be rationalized by water molecules located in the crystal structure, but strong water NOEs, particularly to the rings of Phe47 and Trp96, demand the presence of at least an additional two immobilized water molecules near these rings. The H-bond network appears to function to order water molecules to provide stabilization for the hydroperoxy intermediate and to serve as a conduit to the active site for the nine protons required per HO turnover.     

Synthesis and characterisation of medium-sized ring systems by oxidative cleavage. Part 2: Insights from the study of ring expanded analogues

Variable temperature NMR analysis and computational methods have been used to develop a detailed understanding of the ¹H NMR spectra of a family of medium-sized ring containing compounds. The family consists of analogues containing 10-, 11- and 12-membered rings and in all cases the NMR spectra at room temperature showed a series of diastereotopic methylene signals despite the lack of a stereogenic centre in these systems. On repeating the NMR analysis at higher temperatures, all the signals coalesced for the 12-membered ring system consistent with full interconversion of ring conformers. This was not observed in the analogous 10- and 11-membered ring systems with the interchange of conformers remaining slow on the NMR timescale. However, 1D gs-NOESY/EXSY NMR experiments showed that in the smaller ring systems interconversion of diastereotopic protons did occur. Computational studies suggest that the dynamic process observed by NMR for the 10- and 11-membered rings systems is different from that observed in the 12-membered ring containing compound.