Turnover numbers, turnover frequencies, and overpotential in molecular catalysis of electrochemical reactions. Cyclic voltammetry and preparative-scale electrolysis

The search for efficient catalysts to face modern energy challenges requires evaluation and comparison through reliable methods. Catalytic current efficiencies may be the combination of many factors besides the intrinsic chemical properties of the catalyst. Defining turnover number and turnover frequency (TOF) as reflecting these intrinsic chemical properties, it is shown that catalysts are not characterized by their TOF and their overpotential (η) as separate parameters but rather that the parameters are linked together by a definite relationship. The log TOF-η relationship can often be linearized, giving rise to a Tafel law, which allows the characterization of the catalyst by the value of the TOF at zero overpotential (TOF(0)). Foot-of-the-wave analysis of the cyclic voltammetric catalytic responses allows the determination of the TOF, log TOF-η relationship, and TOF(0), regardless of the side-phenomena that interfere at high current densities, preventing the expected catalytic current plateau from being reached. Strategies for optimized preparative-scale electrolyses may then be devised on these bases. The validity of this methodology is established on theoretical grounds and checked experimentally with examples taken from the catalytic reduction of CO(2) by iron(0) porphyrins.     

2′,5′-二氢-1′H-吡咯骈[3′,4′:1,2]][60]富勒烯衍生物的合成

以甘氨酸乙酯盐酸盐与取代的苯甲醛为原料,制得了一系列亚胺,然后用亚胺与C(60)反应,得到带有不同取代基的吡咯烷骈[60]富勒烯衍生物.经~1H NMR,~(13)C NMR,FT-IR,UV-vis以及TOF-SIMS等方法对所得化合物结构进行了表征,并进行了产物的生物活性测试.     

Rational design of the pore system within the framework aluminium alkylenediphosphonate series

We report here on the solvothermal synthesis and crystal structure of the hybrid organic-inorganic framework material Al(2)[O(3)PC(3)H(6)PO(3)](H(2)O)(2)F(2).H(2)O (orthorhombic, Pmmn, a = 12.0591(2) A, b = 19.1647(5) A, c = 4.91142(7) A, Z = 4), the second member of the Al(2)[O(3)PC(n)H(2n)PO(3)](H(2)O)(2)F(2).H(2)O series. The structure consists of corrugated chains of corner-sharing AlO(4)F(2) octahedra in which alternating AlO(4)F(2) octahedra contain two fluorine atoms in a trans or a cis configuration. The diphosphonate groups link the chains together through Al-O-P-O-Al bridges and through the propylene groups to form a three-dimensional framework structure containing a one-dimensional channel system. The linkage of the corrugated inorganic Al-O-P layers within the structure results in the formation of two types of channel that differ in size, shape and composition. The smaller channel is unoccupied; the larger channel is more elongated and contains two extra-framework water molecules per unit cell. A computational investigation into the driving force that controls the stacking arrangement of the Al-O-P inorganic layers within this series of compounds reveals that the stacking is found to be controlled by thermodynamic factors, arising chiefly from the conformation of the organic linker molecule used to connect the inorganic sheets. It is found that the registration of the inorganic layers can be engineered by selecting an appropriate, simple organic spacer or linker alkyl chain, where an even number of carbon atoms in the alkyl chain directs formation of aligned, stacked, inorganic sheets (AAAAAA), and an odd number directs formation of unaligned, stacked sheets (ABABAB) and the formation of one or two channel types in the resultant structure, respectively. This combination of alkyl-chain linkers in conjunction with corrugated inorganic layers is an effective tool to rationally design the pore system of hybrid framework materials.     

Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling

The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.     

Supramolecular framework with two different kinds of channels via self-assembly of 1D coordination polymers in a prismatic manner

Slow diffusion of Cu(ClO4)2 with p-C6H4(SiMe2(4-Py))2 yields a supramolecular framework consisting of two kinds of channels via self-assembly of a 1D double-stranded chain in a prismatic fashion. The channel has a 11 x 11 A2 cross section (Cu...C = 11.13 A) with a 6 x 6 A2 square pore. The channels are infinitely arranged, resulting in another kind of channel with similar pores. Thus, two different kinds of channels with different solvate molecules coexist in a 1:2 ratio. Weak C-H...pi interaction may be one of the driving forces in the assembly of the prismatic channel structure.     

Targeted molecular dynamics of an open-state KcsA channel

Pore opening of KcsA channel is studied using targeted molecular dynamics simulations. Conformational changes of the protein are determined, starting from the crystallized refined 2.0 A structure (pdb 1K4C) determined in x-ray experiments and arriving to the open-state structure constructed on the basis of electron paramagnetic resonance spectroscopic data (pdb 1JQ1). Our results corroborate the essential role played by the terminal residues located on the transmembrane helices M2 which were not taken into account at that time. The aperture mechanism of the channel appears to be ziplike. A small constraint (approximately equal to 5 x 10(-2) kcal mol(-1) A(-2) per C(alpha)) applied to the terminal residues located on the intracellular side is sufficient to initialize the pore opening at the innermost part of the gate, but additional constraint must be applied to definitely complete the pore aperture. The open structure is proved to be a metastable state since releasing the constraint leads to another relaxed open conformation which seems to reach stability.     

In silico models for the human alpha4beta2 nicotinic acetylcholine receptor

The neuronal alpha4beta2 nicotinic acetylcholine receptor (nAChR) is one of the most widely expressed nAChR subtypes in the brain. Its subunits have high sequence identity (54 and 46% for alpha4 and beta2, respectively) with alpha and beta subunits in Torpedo nAChR. Using the known structure of the Torpedo nAChR as a template, the closed-channel structure of the alpha4beta2 nAChR was constructed through homology modeling. Normal-mode analysis was performed on this closed structure and the resulting lowest frequency mode was applied to it for a "twist-to-open" motion, which increased the minimum pore radius from 2.7 to 3.4 A and generated an open-channel model. Nicotine could bind to the predicted agonist binding sites in the open-channel model but not in the closed one. Both models were subsequently equilibrated in a ternary lipid mixture via extensive molecular dynamics (MD) simulations. Over the course of 11 ns MD simulations, the open channel remained open with filled water, but the closed channel showed a much lower water density at its hydrophobic gate comprised of residues alpha4-V259 and alpha4-L263 and their homologous residues in the beta2 subunits. Brownian dynamics simulations of Na+ permeation through the open channel demonstrated a current-voltage relationship that was consistent with experimental data on the conducting state of alpha4beta2 nAChR. Besides establishment of the well-equilibrated closed- and open-channel alpha4beta2 structural models, the MD simulations on these models provided valuable insights into critical factors that potentially modulate channel gating. Rotation and tilting of TM2 helices led to changes in orientations of pore-lining residue side chains. Without concerted movement, the reorientation of one or two hydrophobic side chains could be enough for channel opening. The closed- and open-channel structures exhibited distinct patterns of electrostatic interactions at the interface of extracellular and transmembrane domains that might regulate the signal propagation of agonist binding to channel opening. A potential prominent role of the beta2 subunit in channel gating was also elucidated in the study.     

Bis(isoquinoline N-oxide) pincers as a new type of metal cation dual channel fluorosensor

[structure: see text] A new type of donor-spacer-acceptor podand system has been synthesized and proved as an efficient dual channel fluorosensor for Li+, Mg2+, and Ca2+. The known ability for the N-oxide function to bind Lewis acids is the key step in the appearance of a new emitting charge-transfer (CT) excited state. The occurrence of this CT state for alkaline earth (Mg2+ and Ca2+) and not for alkaline metals (Li+) provided a new type of dual channel fluorosensors.     

Recent progress in computational approaches to studying the M2 proton channel and its implication to drug design against influenza viruses

For quite a long period of time in history, many intense efforts have been made to determine the 3D (three-dimensional) structure of the M2 proton channel. The reason why the M2 proton channel has attracted so many attentions is because (1) it is the key for really understanding the life cycle of influenza viruses, and (2) it is indispensable for conducting rational drug design against the flu viruses. Recently, the long-sough 3D structures of the M2 proton channels for both influenza A and B viruses were consecutively successfully determined by the high-resolution NMR spectroscopy (Schnell J.R. and Chou, J.J., Nature, 2008, 451: 591-595; Wang, J., Pielak, R.M., McClintock, M.A., and Chou, J.J., Nature Structural & Molecular Biology, 2009,16: 1267-1271). Such a milestone work has provided a solid structural basis for in-depth understanding the action mechanism of the M2 channel and rationally designing effective drugs against influenza viruses. This review is devoted to, with the focus on the M2 proton channel of influenza A, addressing a series of relevant problems, such as how to correctly understand the novel allosteric inhibition mechanism inferred from the NMR structure that is completely different from the traditional view, what the possible impacts are to the previous functional studies in this area, and what kind of new strategy can be stimulated for drug development against influenza.     

Synthesis and characterisation of (C4N2H12)(UO2)2(PO3H)2(PO2(OH)H)2: a three dimensionally connected actinide framework

The material (C4N2H12)(UO2)2(PO3H)2(PO2(OH)H)2 (MUPH-1) has been prepared hydrothermally; it is a three dimensional structure consisting of four intersecting elliptical shaped one-dimensional channels, the largest channel has dimensions of 13.1 x 7.2 A.     

Structure-based prediction of the conductance properties of ion channels

The HOLE procedure allows the prediction of the absolute conductance of an ion channel model from its structure. The original prediction method uses an empirically corrected Ohmic method. It is most successful, with predictions being reliable to within a factor of two. A new modification of the procedure is presented in which the self-diffusion coefficients of water molecules from molecular dynamics simulation are used to replace the empirical correction factor. A "prediction" of the conductance for the porin OmpF by the new method is made and shown to be very close to the experimental value. HOLE also allows the prediction of the effect that the addition of non-electrolyte polymers will have on channel conductance. The method has great potential to yield structural information from data provided by single channel recordings but needs further validation by making measurements on channels of known structure. Preliminary results are given of single channel records establishing the effects of non-electrolytes on the conductance of gramicidin D channels. As an example of the potential uses of the procedure application is made to examine the oligomerization of alpha-toxin (alpha-hemolysin) channels. A model for the alpha-toxin hexamer, based on the crystal structure for the heptamer, is generated using molecular mechanics methods. The compatibility of the structures with single channel conductance data is assessed using HOLE.     

Gating Mechanism of the Voltage-Gated Proton Channel Studied by Molecular Dynamics Simulations

The voltage-gated proton channel Hv1 has important roles in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The Hv1 channel has also been found to be highly expressed in cell lines and tissue samples from patients with breast cancer. A high-resolution closed-state structure has been reported for the mouse Hv1 chimera channel (mHv1cc), solved by X-ray crystallography, but the open-state structure of Hv1 has not been solved. Since Hv1 is a promising drug target, various groups have proposed open conformations by molecular modeling and simulation studies. However, the gating mechanism and the open-state conformation under the membrane potential are still debate. Here, we present a molecular dynamics study considering membrane potential and pH conditions. The closed-state structure of mHv1cc was used to run molecular dynamics (MD) simulations with respect to electric field and pH conditions in order to investigate the mechanism of proton transfer. We observed a continuous hydrogen bond chain of water molecules called a water-wire to be formed through the channel pore in the channel opening, triggered by downward displacement of the S2 helix and upward movement of the S4 helix relative to other helices. Due to the movement of the S2 and S4 helices, the internal salt bridge network was rearranged, and the hydrophobic gating layers were destroyed. In line with previous experimental and simulation observations, our simulation results led us to propose a new gating mechanism for the Hv1 proton channel, and may provide valuable information for novel drug discovery.     

盐酸戈洛帕米的合成

以2-(3,4,5-三甲氧基苯基)乙腈和2-(3,4-二甲氧基苯基)-N-甲基乙胺为起始原料,经亲核取代反应和成盐反应合成了一种钙通道阻滞剂——盐酸戈洛帕米,其结构经1HNMR和MS确证。     

固载型光化学传感器的形貌及结构对检测Hg2+性能的影响

采用氨丙基三乙氧基硅烷(APTES)、异氰酸酯基三乙氧基硅烷(Tri)及纳米金颗粒作为连接体,纯硅中孔分子筛HMS作为无机载体,以分子改造后的染料罗丹明B(RhB)作为有机分子,制得3种固载型光化学传感器,用于检测水中的Hg2+.采用扫描电子显微镜(SEM)、透射电子显微镜(TEM)、N2物理吸附和傅里叶变换红外光谱(FTIR)对材料进行表征,并利用荧光光谱检测水溶液中的Hg2+.结果表明,3种连接体均成功地将有机分子RhB固载到HMS上,所制备的固载型光化学传感器均能够检测水溶液中的Hg2+.研究发现,固载后样品的表面形貌及孔道结构对其检测能力产生影响,具有完好表面形貌及孔道结构的样品RhB-Au-HMS对于Hg2+的检测能力最强,内部孔道坍塌的样品RhB-APTES-HMS对于Hg2+的检测能力最弱.     

The close-packed triple helix as a possible new structural motif for collagen

The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of v _CP =?43.3°. Contrary to the conventional notion, we suggest that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the difficulties for the current understanding of the structure of collagen are reviewed: The ambiguity in assigning crystal structures for collagen-like peptides, and the failure to satisfactorily calculate circular dichroism spectra. Further, the proposed new geometrical structure for collagen is better packed than both the 10/3 and the 7/2 structure. A feature of the suggested collagen structure is the existence of a central channel with negatively charged walls. We find support for this structural feature in some of the early x-ray diffraction data of collagen. The central channel of the structure suggests the possibility of a one-dimensional proton lattice. This geometry can explain the observed magic angle effect seen in NMR studies of collagen. The central channel also offers the possibility of ion transport and may cast new light on various biological and physical phenomena, including biomineralization.     

无机微孔晶体AlPO_4-CJ_1合成与性能研究Ⅰ.

自从八十年代美国UCC首次合成出非硅铝酸盐的AlPO_4-n系列分子筛以米,由于其特殊的骨架结构和物化性质,引起人们的广泛重视.我们用乙二胺基乙醇作模板剂合成出AlPO_4-CJ_1.经多晶X射线衍射,红外光谱及扫描电镜等结构表征,证明其为纯的,新型无机微孔晶体,吸附实验证明其具有4(?)的孔道.AlPO_4-CJ_1的制备:反应物摩尔配比:1.0Al_2O_3:1.0F_2O_5:(1.0-1.8)乙二胺基乙醇:(90-120)H_2O.以铝源[硫酸铝水溶液(含Al_2O_37.04％)];磷源(磷酸铵);有机胺;水的次     

Control of structures and sorption properties of ionic crystals of A2[Cr3O(OOCC2H5)6(H2O)3]2[alpha-SiW12O40] (A = Na, K, Rb, NH4, Cs, TMA)

The complexation of Keggin-type polyoxometalate [alpha-SiW 12O 40] (4-), macrocation [Cr 3O(OOCC 2H 5) 6(H 2O) 3] (+), and monovalent cation A (+) forms ionic crystals of A 2[Cr 3O(OOCC 2H 5) 6(H 2O) 3] 2[alpha-SiW 12O 40]. nH 2O [A = Na ( 1a), K ( 2a), Rb ( 3a), NH 4 ( 4a), Cs ( 5a), and tetramethylammonium (TMA) ( 6a)]. Single crystal (1a- 4a and 6a) and powder (5a) X-ray analyses have shown that the ionic crystals possess 2D layers of polyoxometalates and macrocations. Compounds 2a- 5a had almost the same structure, while the layers in 1a and 6a stack in different ways. The structures and sorption properties of 2b- 5b are investigated in more detail. The interlayer distances of guest free phases 2b- 5b increase with the increase in the ionic radii of the monovalent cations, which reside between the layers. Compounds 2b- 5b possess hydrophobic and hydrophilic channels, which exist between the layers and through the layers, respectively. The volumes of the hydrophobic channels increase in the order of 2b < 3b approximately 4b < 5b, and those of the hydrophilic channels increase in the order of 2b < or = 3b < or = 4b < 5b. Single-crystal X-ray structure analyses of 2a- 4a have shown that the water of crystallization resides in the hydrophilic channel. It is probable that the water of crystallization in 5a resides in the hydrophilic channel in the same manner as those in 2a- 4a since 2a- 5a have almost the same structure. The water vapor sorption profiles of 2b- 5b are approximately reproduced by a linear driving force model. Therefore, water molecules sorbed in 2b- 5b probably reside in the hydrophilic channel. The n-propanol sorption profiles are reproduced by the summation of the linear driving force model, showing that two independent barriers exist in the n-propanol sorption. The in situ IR spectra of n-propanol sorbed showed the presence of two n-propanol species. These data show that n-propanol is sorbed into both hydrophilic and hydrophobic channels. Compound 5b sorbs halocarbons in the hydrophobic channel, while 2b- 4b exclude them.     

First example of an ice-like water hexamer boat tape structure in a supramolecular organic host

A T6(2) tape of hydrogen bonded water molecules in boat cyclohexane conformation resides in the channel structure of a dibromophloroglucinol (DBPG) host; water escapes at 40-90 degrees C but is readily re-absorbed by the sponge-like apohost.     

A pH-tunable nanofluidic diode: electrochemical rectification in a reconstituted single ion channel

We report pH-dependent electrochemical rectification in a protein ion channel (the bacterial porin OmpF) reconstituted on a planar phospholipid membrane. The measurements performed at single-channel level show that the electric current is controlled by the protein fixed charge and it can be tuned by adjusting the local pH. Under highly asymmetric pH conditions, the channel behaves like a liquid diode. Unlike other nanofluidic devices that display also asymmetric conductance, here the microscopic charge distribution of the system can be explored by using the available high-resolution (2.4 A) channel crystallographic structure. Continuum electrostatics calculations confirm the hypothesized bipolar structure of the system. The selective titration of the channel residues is identified as the underlying physicochemical mechanism responsible for current rectification.     

Selective and rapid water transportation across a self-assembled peptide-diol channel via the formation of a dual water array

Achieving superfast water transport by using synthetically designed molecular artifacts, which exclude salts and protons, is a challenging task in separation science today, as it requires the concomitant presence of a proper water-binding site and necessary selectivity filter for transporting water. Here, we demonstrate the water channel behavior of two configurationally different peptide diol isomers that mimic the natural water channel system, i.e., aquaporins. The solid-state morphology studies showed the formation of a self-assembled aggregated structure, and X-ray crystal structure analysis confirmed the formation of a nanotubular assembly that comprises two distinct water channels. The water permeabilities of all six compounds were evaluated and are found to transport water by excluding salts and protons with a water permeability rate of 5.05 × 10⁸ water molecules per s per channel, which is around one order of magnitude less than the water permeability rate of aquaporins. MD simulation studies showed that the system forms a stable water channel inside the bilayer membrane under ambient conditions, with a 2 × 8 layered assembly, and efficiently transports water molecules by forming two distinct water arrays within the channel.

A 1,2-diol-linked peptide forms a self-assembled channel in the lipid bilayer membrane. The channel allows rapid transport of water by excluding proton and salts.