pinecone/core-2020-05-10-deduplication huggingface dataset:
Conformational diversity in contryphans from conus venom: Cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop

Conformational diversity or\ud
“shapeshifting” in cyclic peptide natu-\ud
ral products can, in principle, confer a\ud
single molecular entity with the proper-\ud
ty of binding to multiple receptors.\ud
Conformational equilibria have been\ud
probed in the contryphans, which are\ud
peptides derived from\ud
Conus\ud
venom\ud
possessing a 23-membered cyclic disul-\ud
fide moiety. The natural sequences\ud
derived from\ud
Conus inscriptus\ud
,\ud
GCV\ud
D\ud
LYPWC* (In936) and\ud
Conus lor-\ud
oisii\ud
, GCP\ud
D\ud
WDPWC* (Lo959) differ in\ud
the number of proline residues within\ud
the macrocyclic ring. Structural charac-\ud
terisation of distinct conformational\ud
states arising from\ud
cis\ud
–\ud
trans\ud
equilibria\ud
about Xxx–Pro bonds is reported. Iso-\ud
merisation about the C2–P3 bond is\ud
observed in the case of Lo959 and\ud
about the Y5–P6 bond in In936. Evi-\ud
dence is presented for as many as four\ud
distinct species in the case of the syn-\ud
thetic analogue V3P In936. The Tyr-\ud
Pro-Trp segment in In936 is character-\ud
ised by distinct sidechain orientations\ud
as a consequence of aromatic/proline\ud
interactions as evidenced by specific\ud
sidechain–sidechain nuclear Overhaus-\ud
er effects and ring current shifted\ud
proton chemical shifts. Molecular dy-\ud
namics simulations suggest that Tyr5\ud
and Trp7 sidechain conformations are\ud
correlated and depend on the geometry\ud
of the Xxx–Pro bond. Thermodynamic\ud
parameters are derived for the\ud
cis\ud
$\ud
trans\ud
equilibrium for In936. Studies on\ud
synthetic analogues provide insights\ud
into the role of sequence effects in\ud
modulating isomerisation about Xxx–\ud
Pro bonds.Peer ReviewedPostprint (published version
Pt 3 Co Concave Nanocubes: Synthesis, Formation Understanding, and Enhanced Catalytic Activity toward Hydrogenation of Styrene

We report a facile synthesis route to prepare high‐quality Pt 3 Co nanocubes with a concave structure, and further demonstrate that these concave Pt 3 Co nanocubes are terminated with high‐index crystal facets. The success of this preparation is highly dependent on an appropriate nucleation process with a successively anisotropic overgrowth and a preservation of the resultant high‐index planes by control binding of oleyl‐amine/oleic acid with a fine‐tuned composition. Using a hydrogenation of styrene as a model reaction, these Pt 3 Co concave nanocubes as a new class of nanocatalysts with more open structure and active atomic sites located on their high‐index crystallographic planes exhibit an enhanced catalytic activity in comparison with low‐indexed surface terminated Pt 3 Co nanocubes in similar size.     Anisotropic overgrowth : Pt 3 Co concave nanocubes bounded by high‐index facets were prepared with a facile wet‐chemical method. The formation process for such concave nanostructures was systematically studied, and a plausible mechanism was proposed. These nanocrystals can be used as advanced nanocatalysts, showing high activity and reusability toward hydrogenation of styrene (see figure)
Solid-state interconversions:Unique 100 % reversible transformations between the ground and metastable states in single-crystals of a series of nickel(II) nitro complexes

The solid-state, low-temperature linkage isomerism in a series of five square planar group 10 phosphino nitro complexes have been investigated by a combination of photocrystallographic experiments, Raman spectroscopy and computer modelling. The factors influencing the reversible solid-state interconversion between the nitro and nitrito structural isomers have also been investigated, providing insight into the dynamics of this process. The cis-[Ni(dcpe)(NO)] (1) and cis-[Ni(dppe)(NO )] (2) complexes show reversible 100 % interconversion between the η-NO nitro isomer and the η-ONO nitrito form when single-crystals are irradiated with 400 nm light at 100 K. Variable temperature photocrystallographic studies for these complexes established that the metastable nitrito isomer reverted to the ground-state nitro isomer at temperatures above 180 K. By comparison, the related trans complex [Ni(PCy)(NO) ] (3) showed 82 % conversion under the same experimental conditions at 100 K. The level of conversion to the metastable nitrito isomers is further reduced when the nickel centre is replaced by palladium or platinum. Prolonged irradiation of the trans-[Pd(PCy)(NO) ] (4) and trans-[Pt(PCy)(NO )] (5) with 400 nm light gives reversible conversions of 44 and 27 %, respectively, consistent with the slower kinetics associated with the heavier members of group 10. The mechanism of the interconversion has been investigated by theoretical calculations based on the model complex [Ni(dmpe)Cl(NO)]. All or none: The factors that favour high levels of photoconversion between linkage isomers in a series of Group 10, square-planar nitro complexes were investigated. The highest levels of reversible conversions between the linkage isomers are observed for the kinetically labile Ni complexes in which the change in reaction cavity size upon interconversion is smallest (see scheme)
Supramolecular Hierarchy among Halogen-Bond Donors

Through a combination of structural chemistry, vibrational spectroscopy, and theory, we have systematically examined the relative structure-directing importance of a series of ditopic halogen-bond (XB) donors. The molecular electrostatic potential surfaces of six XB donors were evaluated, which allowed for a charge-based ranking. Each molecule was then co-crystallized with 21 XB acceptors and the results have made it possible to map out the supramolecular landscape describing the competition between I/Br-ethynyl donors, perfluorinated I/Br donors, and I/Br-phenyl based donors. The results offer practical guidelines for synthetic crystal engineering driven by robust and directional halogen bonds.\ud
Copyright 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Sequence-specific DNA recognition by cyclic pyrrole-imidazole cysteine-derived polyamide dimers.

Pyrrole-imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence-specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence-specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β-alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA
Concealed cyclotrimeric polymorph of lithium 2, 2, 6, 6- tetramethylpiperidide unconcealed : X-ray crystallographic and NMR spectroscopic studies

Lithium 2, 2, 6, 6-tetramethyl-piperidide (LiTMP), one of the most important polar organometallic reagents both in its own right and as a key component of ate compositions, has long been known for its classic cy-clotetrameric (LiTMP) solid-state structure. Made by a new approach through transmetalation of Zn(TMP) with tBuLi in n-hexane solution, a crystalline polymorph of LiTMP has been uncovered. X-ray crystallographic studies at 123(2) K revealed this polymorph crystallises in the hexagonal space group P6/m and exhibited a discrete cyclotrimeric (C) structure with a strictly planar (LiN) ring containing three symmetrically equivalent TMP chair-shaped ligands. The molecular structure of (LiTMP) was redeter-mined at 123(2) K, because its original crystallographic characterisation was done at ambient temperature. This improved redetermination confirmed a monoclinic C2/c space group with the planar (LiN) ring possessing pseudo (non-crystallographic) C symmetry. Investigation of both metalation and transmetalation routes to LiTMP under different conditions established that polymorph formation did not depend on the route employed but rather the temperature of crystallisation. Low-temperature (freezer at - 35°C) cooling of the reaction solution favoured (LiTMP); whereas high-temperature (bench) storage favoured (LiTMP). Routine H and C NMR spectroscopic studies in a variety of solvents showed that (LiTMP) and (LiTMP) exist in equilibrium, whereas H DOSY NMR studies gave diffusion coefficient results consistent with their relative sizes
Enantio- and Diastereoconvergent Cyclocondensation Reactions: Synthesis of Enantiopure cis-Decahydroquinolines.

Up to four stereocenters with a well-defined configuration are generated in a single synthetic step by the cyclocondensation of (R)-phenylglycinol or (1S,2R)-1-amino-2-indanol with stereoisomeric mixtures (racemates, meso forms, diastereoisomers) of cyclohexanone-based δ-keto-acid and δ-keto-diacid derivatives in enantio- and diastereoconvergent processes that involve dynamic kinetic resolution and/or desymmetrization of enantiotopic groups. A detailed analysis of the stereochemical outcome of this process is presented. This method provides easy access to enantiopure 8- and 6,8-substituted cis-decahydroquinolines, including alkaloids of the myrioxazine family
Enantioselective Synthesis and Application to the Allylic Imidate Rearrangement of Amine-Coordinated Palladacycle Catalysts of Cobalt Sandwich Complexes

The reaction of (η5-(N,N-dimethylaminomethyl)cyclopentadien-yl)(η4-tetraphenylcyclobutadiene)cobalt with sodium tetrachloropalladate and (R)-N-acetylphenylalanine gave planar chiral palladacycle di-μ-chloridebis[(η5-(Sp)-2-(N,N-dimethylaminomethyl)cyclopentadienyl,1-C,3′-N)(η4-tetraphenylcyclobutadiene)cobalt]dipalladium [(Sp)-Me2-CAP-Cl] in 92 % ee and 64 % yield. Enantiopurity (>98 % ee) was achieved by purification of the monomeric (R)-proline adducts and conversion back to the chloride dimer. Treatment with AgOAc gave (Sp)-Me2-CAP-OAc which was applied to asymmetric transcyclopalladation (up to 78 % ee). The (R)-N-acetylphenylalanine mediated palladation methodology was applicable also to the corresponding N,N-diethyl (82 % ee, 39 % yield) and pyrrolidinyl (>98 % ee, 43 % yield) cobalt sandwich complexes. A combination of 5 mol % of the latter [(Sp)-Pyrr-CAP-Cl] and AgNO3 (3.8 equiv) is a catalyst for the allylic imidate rearrangement of an (E)-N-aryltrifluoroacetimidate (up to 83 % ee), and this catalyst system is also applicable to the rearrangement of a range of (E)-trichloroacetimidates (up to 99 % ee). This asymmetric efficiency combined with the simplicity of catalyst synthesis provides accessible solutions to the generation of non-racemic allylic amine derivatives
Blending gelators to tune gel properties and probe anion-induced disassembly.

Blending different low molecular weight gelators (LMWGs) provides a convenient route to tune the properties of a gel and incorporate functionalities such as fluorescence. Blending a series of gelators having a common bis-urea motif, and functionalised with different amino acid-derived end-groups and differing length alkylene spacers is reported. Fluorescent gelators incorporating 1- and 2-pyrenyl moieties provide a probe of the mixed systems alongside structural and morphological data from powder diffraction and electron microscopy. Characterisation of the individual gelators reveals that although the expected α-urea tape motif is preserved, there is considerable variation in the gelation properties, molecular packing, fibre morphology and rheological behaviour. Mixing of the gelators revealed examples in which: 1) the gels formed separate, orthogonal networks maintaining their own packing and morphology, 2) the gels blended together into a single network, either adopting the packing and morphology of one gelator, or 3) a new structure not seen for either of the gelators individually was created. The strong binding of the urea functionalities to anions was exploited as a means of breaking down the gel structure, and the use of fluorescent gel blends provides new insights into anion-mediated gel dissolution
Using remote substituents to control solution structure and anion binding in lanthanide complexes.

A study of the anion-binding properties of three structurally related lanthanide complexes, which all contain chemically identical anion-binding motifs, has revealed dramatic differences in their anion affinity. These arise as a consequence of changes in the substitution pattern on the periphery of the molecule, at a substantial distance from the binding pocket. Herein, we explore these remote substituent effects and explain the observed behaviour through discussion of the way in which remote substituents can influence and control the global structure of a molecule through their demands upon conformational space. Peripheral modifications to a binuclear lanthanide motif derived from α,α′-bis(DO3 Ayl)-m-xylene are shown to result in dramatic changes to the binding constant for isophthalate. In this system, the parent compound displays considerable conformational flexibility, yet can be assumed to bind to isophthalate through a well-defined conformer. Addition of steric bulk remote from the binding site restricts conformational mobility, giving rise to an increase in binding constant on entropic grounds as long as the ideal binding conformation is not excluded from the available range of conformers
Effects of quantum nuclear delocalisation on NMR parameters from path integral molecular dynamics.

The influence of nuclear delocalisation on NMR chemical shifts in molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory calculations of shielding tensors. Nuclear quantum effects are shown to explain previously observed systematic deviations in correlations between calculated and experimental chemical shifts, with particularly large PIMD-induced changes (up to 23 ppm) observed for carbon atoms in methyl groups. The PIMD approach also enables isotope substitution effects on chemical shifts and J couplings to be predicted in excellent agreement with experiment for both isolated molecules and molecular crystals. An approach based on convoluting calculated shielding or coupling surfaces with probability distributions of selected bond distances and valence angles obtained from PIMD simulations is used to calculate isotope effects
On the importance of decarbonylation as a side-reaction in the ruthenium-catalysed dehydrogenation of alcohols : a combined experimental and density functional study

We report a density functional study (B97-D2 level) of the mechanism(s) operating in the alcohol decarbonylation that occurs as an important side-reaction during dehydrogenation catalysed by [RuH2(H2)(PPh3)3]. By using MeOH as the substrate, three distinct pathways have been fully characterised involving either neutral tris- or bis-phosphines or anionic bis-phosphine complexes after deprotonation. α-Agostic formaldehyde and formyl complexes are key intermediates, and the computed rate-limiting barriers are similar between the various decarbonylation and dehydrogenation paths. The key steps have also been studied for reactions involving EtOH and iPrOH as substrates, rationalising the known resistance of the latter towards decarbonylation. Kinetic isotope effects (KIEs) were predicted computationally for all pathways and studied experimentally for one specific decarbonylation path designed to start from [RuH(OCH3)(PPh3)3]. From the good agreement between computed and experimental KIEs (observed kH/kD=4), the rate-limiting step for methanol decarbonylation has been ascribed to the formation of the first agostic intermediate from a transient formaldehyde complex.PostprintPeer reviewe
Isolatable Organophosphorus(III)-Tellurium Heterocycles

A new structural arrangement Te-3(RPIII)(3) and the first crystal structures of organophosphorus(III)-tellurium heterocycles are presented. The heterocycles can be stabilized and structurally characterized by the appropriate choice of substituents in Te-m((PR)-R-III)(n) (m=1: n=2, R=OMes* (Mes*=supermesityl or 2,4,6-tri-tert-butylphenyl); n=3, R=adamantyl (Ad); n=4, R=ferrocene (Fc); m=n=3: R=trityl (Trt), Mesor by the installation of a (P2N2)-N-V anchor in RPIII[TePV(tBuN)(-NtBu)](2) (R=Ad, tBu).PostprintPeer reviewe
Steady-state and pseudo-steady-state photocrystallographic studies on linkage isomers of [Ni(Et4dien)(η2-O,ON)(η1-NO2)]:Identification of a new linkage isomer

At temperatures below 150K, the photoactivated metastable endo-nitrito linkage isomer [Ni(Et4dien)(η2-O,ON)(η1-ONO)] (Et4dien=N,N,N',N'-tetraethyldiethylenetriamine) can be generated with 100% conversion from the ground state nitro-(η1-NO2) isomer on irradiation with 500nm light, in the single crystal by steady-state photocrystallographic techniques. Kinetic studies show the system is no longer metastable above 150K, decaying back to the ground state nitro-(η1-NO2) arrangement over several hours at 150K. Variable-temperature kinetic measurements in the range of 150-160K show that the rate of endo-nitrito decay is highly dependent on temperature, and an activation energy of Eact=+48.6(4)kJmol-1 is calculated for the decay process. Pseudo-steady-state experiments, where the crystal is continually pumped by the light source for the duration of the X-ray experiment, show the production of a previously unobserved, exo-nitrito-(η1-ONO) linkage isomer only at temperatures close to the metastable limit (ca. 140-190K). This exo isomer is considered to be a transient excited-state species, as it is only observed in data collected by pseudo-steady-state methods
Distance Dependence of Bidirectional Concerted Proton–Electron Transfer in Phenol-Ru(2,2′-bipyridine)32+ Dyads

Proton-coupled electron transfer (PCET) was investigated in three covalent donor–bridge–acceptor molecules with different bridge lengths. Upon photoexcitation of their Ru(bpy)32+ (bpy=2,2′-bipyridine) photosensitizer in acetonitrile, intramolecular long-range electron transfer from a phenolic unit to Ru(bpy)32+ occurs in concert with release of the phenolic proton to pyrrolidine base. The kinetics of this bidirectional concerted proton–electron transfer (CPET) reaction were studied as a function of phenol–Ru(bpy)32+ distance by increasing the number of bridging p-xylene units. A distance decay constant (β) of 0.67±0.23 Å−1 was determined. The distance dependence of the rates for CPET is thus not significantly steeper than that for ordinary (i.e., not proton coupled) electron transfer across the same bridges, despite the concerted motion of oppositely charged particles into different directions. Long-range bidirectional CPET is an important reaction in many proteins and plays a key role in photosynthesis; our results are relevant in the context of photoinduced separation of protons and electrons as a means of light-to-chemical energy conversion. This is the first determination of β for a bidirectional CPET reaction
New RuII(arene) complexes with halogen-substituted bis- and tris(pyrazol-1-YL)borate ligands

[RuCl(arene)(-Cl)](2) dimers were treated in a 1:2 molar ratio with sodium or thallium salts of bis- and tris(pyrazolyl)borate ligands [Na(BpBr3)], [Tl(TpBr3)], and [Tl(Tp(iPr,4Br))]. Mononuclear neutral complexes [RuCl(arene)((2)-BpBr3)] (1: arene=p-cymene (cym); 2: arene=hexamethylbenzene (hmb); 3: arene=benzene (bz)), [RuCl(arene)((2)-TpBr3)] (4: arene=cym; 6: arene=bz), and [RuCl(arene)((2)-Tp(iPr,4Br))] (7: arene=cym, 8: arene=hmb, 9: arene=bz) have been always obtained with the exception of the ionic [Ru-2(hmb)(2)(-Cl)(3)][TpBr3] (5), which formed independently of the ratio of reactants and reaction conditions employed. The ionic [Ru(CH3OH)(cym)((2)-BpBr3)][X] (10: X=PF6, 12: X=O3SCF3) and the neutral [Ru(O2CCF3)(cym)((2)-BpBr3)] (11) have been obtained by a metathesis reaction with corresponding silver salts. All complexes 1-12 have been characterized by analytical and spectroscopic data (IR, ESI-MS, H-1 and (CNMR)-C-13 spectroscopy). The structures of the thallium and calcium derivatives of ligand TpBr3, [Tl(TpBr3)] and [Ca(dmso)(6)][TpBr3](2)2DMSO, of the complexes 1, 4, 5, 6, 11, and of the decomposition product [RuCl(cym)(Hpz(iPr,4Br))(2)][Cl] (7) have been confirmed by using single-crystal X-ray diffraction. Electrochemical studies showed that 1-9 and 11 undergo a single-electron (RuRuIII)-Ru-II oxidation at a potential, measured by cyclic voltammetry, which allows comparison of the electron-donor characters of the bis- and tris(pyrazol-1-yl)borate and arene ligands, and to estimate, for the first time, the values of the Lever E-L ligand parameter for BpBr3, TpBr3, and Tp(iPr,4Br). Theoretical calculations at the DFT level indicated that both oxidation and reduction of the Ru complexes under study are mostly metal-centered with some involvement of the chloride ligand in the former case, and also demonstrated that the experimental isolation of the (3)-binuclear complex 5 (instead of the mononuclear 5) is accounted for by the low thermodynamic stability of the latter species due to steric reasons
The synthesis of functionalised diaryltetraynes and their transport properties in single-molecule junctions.

The synthesis and characterisation is described of six diaryltetrayne derivatives [Ar-(C[TRIPLE BOND]C)4-Ar] with Ar=4-NO2-C6H4- (NO24), 4-NH(Me)C6H4- (NHMe4), 4-NMe2C6H4- (NMe24), 4-NH2-(2,6-dimethyl)C6H4- (DMeNH24), 5-indolyl (IN4) and 5-benzothienyl (BTh4). X-ray molecular structures are reported for NO24, NHMe4, DMeNH24, IN4 and BTh4. The stability of the tetraynes has been assessed under ambient laboratory conditions (20 °C, daylight and in air): NO24 and BTh4 are stable for at least six months without observable decomposition, whereas NHMe4, NMe24, DMeNH24 and IN4 decompose within a few hours or days. The derivative DMeNH24, with ortho-methyl groups partially shielding the tetrayne backbone, is considerably more stable than the parent compound with Ar=4-NH2C6H4 (NH24). The ability of the stable tetraynes to anchor in Au|molecule|Au junctions is reported. Scanning-tunnelling-microscopy break junction (STM-BJ) and mechanically controllable break junction (MCBJ) techniques are employed to investigate single-molecule conductance characteristics
A compact tetrathiafulvalene-benzothiadiazole dyad and its highly symmetrical charge-transfer salt: Ordered donor p-stacks closely bound to their acceptors

A compact and planar donor-acceptor molecule 1 comprising tetrathiafulvalene (TTF) and benzothiadiazole (BTD) units has been synthesised and experimentally characterised by structural, optical, and electrochemical methods. Solution-processed and thermally evaporated thin films of 1 have also been explored as active materials in organic field-effect transistors (OFETs). For these devices, hole field-effect mobilities of µFE=(1. 3±0.5)×10-3 and (2.7±0.4)×10-3 cm2 V s-1 were determined for the solution-processed and thermally evaporated thin films, respectively. An intense intramolecular charge-transfer (ICT) transition at around 495 nm dominates the optical absorption spectrum of the neutral dyad, which also shows a weak emission from its ICT state. The iodine-induced oxidation of 1 leads to a partially oxidised crystalline charge-transfer (CT) salt {(1)2I3}, and eventually also to a fully oxidised compound {1I3} 1/2I2. Single crystals of the former CT compound, exhibiting a highly symmetrical crystal structure, reveal a fairly good room temperature electrical conductivity of the order of 2 S cm-1. The one-dimensional spin system bears compactly bonded BTD acceptors (spatial localisation of the LUMO) along its ridge. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Peer ReviewedPostprint (published version