Frustrated Lewis pair addition to conjugated diynes: formation of zwitterionic 1,2,3-butatriene derivatives

The frustrated Lewis pair B(C(6)F(5))(3)/P(o-tolyl)(3) (4a) reacts with 4,6-decadiyne to give the trans-1,2-addition product 5. In contrast, the B(C(6)F(5))(3)/P(t)Bu(3) FLP (4b) reacts with this substrate to give the trans-1,4-adduct trans-6. The cumulene trans-6 undergoes trans-/cis-isomerization upon photolysis to give a ca. 1:1 trans-6/cis-6 mixture. The FLP 4b reacts with 2,6-hexadiyne at r.t. to yield a ca. 4:1 mixture of their trans-1,2- and trans-1,4-addition products (7,8). DFT calculations showed that the zwitterionic 1,4-addition products are favored under thermodynamic control. Thermolysis of the kinetic trans-1,2-addition product (7) (80 °C, bromobenzene) does not lead to the thermodynamically favored 1,4-isomer (8), but instead elimination of isobutylene occurs to the formal trans-1,2-adduct (9) of the B(C(6)F(5))(3)/PH(t)Bu(2) pair. Compounds 5, 6, 7, 8, 9 were analyzed by X-ray diffraction.     

Development of polyphosphate parameters for use with the AMBER force field

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems.     

The solvation structure,transport properties and reduction behavior of carbonate-based electrolytes of lithium-ion batteries

Despite the extensive employment of binary/ternary mixed-carbonate electrolytes (MCEs) for Li-ion batteries, the role of each ingredient with regards to the solvation structure, transport properties, and reduction behavior is not fully understood. Herein, we report the atomistic modeling and transport property measurements of the Gen2 (1.2 M LiPF₆ in ethylene carbonate (EC) and ethyl methyl carbonate (EMC)) and EC-base (1.2 M LiPF₆ in EC) electrolytes, as well as their mixtures with 10 mol% fluoroethylene carbonate (FEC). Due to the mixing of cyclic and linear carbonates, the Gen2 electrolyte is found to have a 60% lower ion dissociation rate and a 44% faster Li⁺ self-diffusion rate than the EC-base electrolyte, while the total ionic conductivities are similar. Moreover, we propose for the first time the anion–solvent exchange mechanism in MCEs with identified energetic and electrostatic origins. For electrolytes with additive, up to 25% FEC coordinates with Li⁺, which exhibits a preferential reduction that helps passivate the anode and facilitates an improved solid electrolyte interphase. The work provides a coherent computational framework for evaluating mixed electrolyte systems.

The different roles of the anion, cyclic and linear carbonates, and additive in mixed-carbonate electrolytes are revealed. The anion–solvent exchange mechanism and factors influencing the solid electrolyte interphase (SEI) formation are deciphered.     

Structural characterization of metallopeptides designed as scaffolds for the stabilization of nickel(II)-Fe(4)S(4) bridged assemblies by X-ray absorption spectroscopy

In earlier work, de novo designed peptides with a helix-loop-helix motif and 63 residues have been synthesized as potential scaffolds for stabilization of the [Ni(II)-X-Fe(4)S(4)] bridged assembly that is the spectroscopically deduced structure of the A-Cluster in clostridial carbon monoxide dehydrogenase. The 63mers contain a consensus tricysteinyl ferredoxin domain in the loop for binding an Fe(4)S(4) cluster and Cys and His residues proximate to the loop for binding Ni(II), with one Cys residue designed as the bridge X. The metallopeptides HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M, containing three His and one Cys residue for Ni(II) coordination and two His and two Cys residues for binding M = Ni(II) and Co(II), have been examined by Fe-, Ni-, and Co-K edge spectroscopy and EXAFS. All peptides bind an [Fe(4)S(4)](2+) cubane-type cluster. Interpretation of the Ni and Co data is complicated by the presence of a minority population of six-coordinate species with low Z ligands, designated for simplicity as [M(OH(2))(6)](2+). Best fits of the data were obtained with ca. 20% [M(OH(2))(6)](2+) and ca. 80% M(II) with mixed N/S coordination. The collective XAS results for HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M demonstrate the presence of an Fe(4)S(4) cluster and support the existence of the distorted square-planar coordination units [Ni(II)(S.Cys)(N.His)(3)] and [Ni(II)(S.Cys)(2)(N.His)(2)] in the HC(4)H(2) and HC(5)H metallopeptides, respectively. In the HC(5)H metallopeptide, tetrahedral [Co(II)(S.Cys)(2)(N.His)(2)] is present. We conclude that the designed scaffolded binding sites, including Ni-(mu(2)-S.Cys)-Fe bridges, have been achieved. This is the first XAS study of a de novo designed metallopeptide intended to stabilize a bridged biological assembly, and one of a few XAS analyses of metal derivatives of designed peptides. The scaffolding concept should be extendable to other bridged metal assemblies.     

Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case

We have developed a receptor-based pharmacophore method which utilizes a collection of protein structures to account for inherent protein flexibility in structure-based drug design. Several procedures were systematically evaluated to derive the most general protocol for using multiple protein structures. Most notably, incorporating more protein flexibility improved the performance of the method. The pharmacophore models successfully discriminate known inhibitors from drug-like non-inhibitors. Furthermore, the models correctly identify the bound conformations of some ligands. We used unliganded HIV-1 protease to develop and validate this method. Drug design is always initiated with a protein-ligand structure, and such success with unbound protein structures is remarkable - particularly in the case of HIV-1 protease, which has a large conformational change upon binding. This technique holds the promise of successful computer-based drug design before bound crystal structures are even discovered, which can mean a jump-start of 1-3 years in tackling some medically relevant systems with computational methods.     

Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands

Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP‐regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP‐competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2‐phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first‐generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules’ effects on Hsp90 enzymatic, conformational, co‐chaperone and client‐binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary.     

Synthesis of β‐Cyclodextrin Containing Copolymer via “Click” Chemistry and Its Self‐Assembly in the Presence of Guest Compounds

We report the synthesis of a hydrophilic copolymer with one polyethylene glycol (PEG) block and one β‐cyclodextrin (β‐CD) containing block by a “click” reaction between azido‐substituted β‐CD and propargyl flanking copolymer. ¹H NMR study suggested a highly efficient conjugation of β‐CD units by this approach. The obtained copolymer was used as a host macromolecule to construct assemblies in the presence of hydrophobic guests. For assemblies containing a hydrophobic polymer, their size can be simply adjusted by simply changing the content of hydrophobic component. By serving as a guest molecule, hydrophobic drugs can also be loaded accompanying the formation of nanoparticles, and the drug payload is releasable. Therefore, the copolymer synthesized herein can be employed as a carrier for drug delivery.     

Astemizole tetra­chloro­cuprate(II)

The structure of {3‐[(4‐fluoro­phenyl)­methyl]‐1H‐benzimidazol‐2‐ylidene}{1‐[2‐(4‐meth­oxy­phenyl)­ethyl]‐4‐piperidin‐1‐io}ammonium tetra­chloro­cuprate(II), (C₂₈H₃₃FN₄O)[CuCl₄], contains diprotonated cations of astemizole hydrogen bonded to three Cl atoms in two different CuCl₄^2? anions, with Cl?N distances in the range 3.166 (4)–3.203 (4) Å. The geometry around copper is flattened tetrahedral with significantly different Cu—Cl distances which lie in the range 2.1968 (14)–2.2861 (12) Å. The phenyl­ethyl C atoms of the (4‐methoxy­phenyl­)ethyl group are disordered indicating the presence of two conformers in the crystals.     

Hydrogen bonding in N,N,N′,N′‐tetra­methyl­ethyl­ene­di­ammonium bis­(benzene­selenol­ate)

The crystal structure of the title compound, [Me₂NHC₂H₄NHMe₂][SePh]₂ or C₆H₁₈N₂²⁺·2C₆H₅Se^?, reveals hydrogen bonding between the benzene­seleno­late anions and the tetra­methyl­ethyl­ene­di­ammonium cations. The asymmetric unit contains one formula unit of the title compound. The two Se?H distances are 2.22 (4) and 2.34 (4) Å.