General mechanism for inchworm nanoscale track walkers: analytical theory and realistic simulation

Nanomotors capable of directed transportation along an unlimited linear track are being vigorously pursued both theoretically and experimentally. This study generalizes a previously proposed mechanism for nanoscale track walkers by explicitly treating key molecular details of the walker-track systems. An energy-diagram analysis identifies pathways of energy flow through the walker's movement cycle, and thereby enables us to develop an analytical theory for the track-walking mechanism. Realistic simulations of the walker's movement cycles are also conducted. The results show that the walker's directionality, run length, and speed depend critically on several key dimensional parameters of the walker-track systems. Most notably, the walker's performance as a function of the binding site interval of the track exhibits an oscillating pattern, which is accurately reproduced by the analytical theory. The wealth of nanocontrol mechanisms identified in the proposed track-walker systems not only provides a framework for optimizing performance of the walker, but also clarifies major requirements for future experimental implementation.     

Walking molecules

Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references).     

Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track

We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s⁻¹ in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pK_a values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.     

一种具有梯状链结构有机模板硫酸铽的合成、结构表征以及荧光性质

本文采用溶剂热法合成了一种具有梯状链结构新的有机模板硫酸铽盐:(C2H8N)[Tb(SO4)2.H2O](1),并通过X-射线衍射、红外、热重及元素分析对其进行了表征。该晶体属于单斜晶系,P21/n空间群。其中a=0.568 1(3)nm,b=1.972 7(10)nm,c=0.862 7(4)nm,β=90.658(6)°,V=0.966 7(8)nm3,Z=4。化合物1的骨架结构由TbO8多面体和SO4四面体构成。S(1)和S(2)与Tb(1)相连接,通过3个S-O-Tb连接构成双链,而相邻的双链通过μ3-O(O5)连接形成一个新的梯状链。     

含氮杂茂配体的类茂配合物NpCpTiCl_2催化乙烯聚合研究

茂金属催化烯烃聚合时不仅须大量甲基铝氧烷(MAO)作助催化剂,而且其稳定性较差,结构修饰困难,这都一定程度上限制了茂金属催化剂的发展.近几年来,将非环戊二烯类配体与IVB 族金属作用形成的配合物应用于催化烯烃聚合的研究大量出现[1],其中非环戊二烯配体有脒化物[2,3]、酰胺基[4,5]、NFDA3唑啉[6]、卟啉[7 ]、烷氧基[8]、芳氧基[9～11]、和β-二酮[12,13]、8-羟基喹啉[14～16]等.这些非茂配合物均可催化乙烯或丙烯聚合,但活性都较低.我们曾制备了含配位原子为氧或氮的非环戊二烯基配体的半茂配合物,即茂金属中一个环戊二烯基配体被非环戊二烯基配体取代,使金属中心与一个茂和一个非茂配体配位而形成的桥连或非桥连型的配合物[17,18].这类配合物不仅稳定性好,而且消耗的助催化剂量较少,活性高,对所得聚合物的结构有一定的控制作用.桥连型半茂配合物以“限制几何构型”催化剂为代表[16,19～20 ],非桥连型半茂配合物的报道较少,如CpTi(OiPr)Me2和CpTi(OAr)X2 [21 ,22].我们选择氮杂茂类配体为非环戊二烯阴离子配体,氮杂茂环以一价阴离子的形式与金属中心钛配位,与另一个环戊二烯阴离子形成类茂型配合物.这种类茂配合物易于制备, 稳定性好,而且消耗的助催化剂量较小.     

Synthesis, characterisation and molecular structure of Re(III) 2-oxacyclocarbenes stabilised by a benzoyldiazenido ligand

A family of new Fischer-type rhenium(III) benzoyldiazenido-2-oxacyclocarbenes of formula [(ReCl2[eta1-N2C(O)Ph][=C(CH2)nCH(R)O](PPh3)2][n = 2, R = H (2), R = Me (3); n = 3, R = H (4), R = Me (5)] have been prepared by reaction of [ReCl2[eta2-N2C(Ph)O](PPh3)2] (1) with omega-alkynols, such as 3-butyn-1-ol, 4-pentyn-1-ol, 4-pentyn-2-ol, 5-hexyn-2-ol in refluxing THF. The correct formulation of the carbene derivatives 2-5 has been unambiguously determined in solution by NMR analysis and confirmed for compounds 2-4 by X-ray diffraction methods in the solid state. All complexes are octahedral with the benzoyldiazenido ligand, Re[N2C(O)Ph], adopting a "single bent" conformation. The coordination basal plane is completed by an oxacyclocarbene ligand and two chlorine atoms. Two triphenylphosphines in trans positions with respect to each other complete the octahedral geometry around rhenium. The reactivity of 1 towards different alkynes and alkenes including propargyl- and allylamine has been also studied. With propargyl amine, monosubstituted or bisubstituted complexes, [(ReCl2[eta1-N2C(O)Ph][eta1-NH2CH2C triple bond CH]n(PPh3)(3-n)][n= 1 (6); n = 2 (7)], have been isolated depending on the reaction conditions. In contrast, the reaction with allylamine gave only the disubstituted complex [(ReCl2[eta1-N2C(O)Ph][eta1-NH2CH2CH=CH2]2(PPh3)] (8). The molecular structure of the monosubstituted adduct has been confirmed by X-ray analysis in the solid state.     

Syntheses and skeletal transformations of NCNH- and NCN-bridged tetrairidium(III) cages

The diiridium complex [Cp*IrCl2]2 (Cp* = eta5-C5Me5) reacts with 2 equiv of Na(NCNH) at room temperature to afford the 16-membered macrocyclic tetrairidium complex [Cp*IrCl(mu2-NCNH-N,N')]4 (1a). Treatment of 1a with 4 equiv of triethylamine at room temperature leads to the formation of the "C3-elongated cubane-like" tetrairidium complex [Cp*Ir(mu3-NCN-N,N,N')3(IrCp*)3(mu3-NCN-N,N,N)] (2) as the major product, which is further converted into the cubane-type complex [Cp*Ir(mu3-NCN-N,N,N)]4 (3) on refluxing in p-xylene. The molecular structures of [Cp*IrI(mu3-NCNH-N,N')]4.C7H8 (1b.C7H8), 2.0.5C7H8, and 3 have been determined by X-ray analyses.     

Hydrothermal synthesis,structures, and magnetic properties of three novel 5-aminoisophthalic acid ligand bridged transition metal cation polymers

Three novel 5-aminoisophthalic acid (AIP) bridged polymers [Co(C(8)NH(5)O(4))(H(2)O)](n)() (1), [Ni(C(8)NH(5)O(4))(H(2)O)(2)](n)() (2), and [Zn(C(8)NH(5)O(4))(H(2)O)](n)() (3) were synthesized by hydrothermal reactions and characterized by IR, Raman, elemental analysis, ESR, and magnetic measurements. X-ray single-crystal analyses were carried out for [Co(C(8)NH(5)O(4))(H(2)O)](n)() (1), which crystallizes in the triclinic system, space group P1 macro, with a = 6.477(1) A, b = 7.130(1) A, c = 9.826(2) A, alpha = 108.9(1) degrees, beta = 93.97(3) degrees, gamma = 98.82(3) degrees, and Z = 2; for [Ni(C(8)NH(5)O(4))(H(2)O)(2)](n)() (2), in the triclinic system, space group P1 macro, a = 6.425(1) A, b = 8.115(2) A, c = 10.146(2) A, alpha = 113.09(3)(o), beta = 99.64(3)(o), gamma = 98.90(3)(o), and Z = 2; and for [Zn(C(8)NH(5)O(4))(H(2)O)](n)() (3), in the monoclinic system, space group P2(1)/n, a = 9.044(1) A, b = 8.264(1) A, c = 11.646(1) A, beta = 100.77(1) degrees, and Z = 4. The single X-ray diffraction studies reveal that 1 consists of an infinite honeycomb layer formed by four crystallographically independent motifs packed alternatively together; 2 consists of an infinite neutral railroad-like linear polymer, and 3 consists of infinite layers of alternating four-coordinated Zn(II) cations and AIP ligands. Finally, they are all packed into beautiful three-dimensional frameworks through complicated hydrogen bonding. Antiferromagnetic and ferromagnetic behaviors were observed for 1 and 2 from the magnetic measurements.     

Mechanisms,Methods of Tracking and Applications of DNA Walkers: A Review

In recent years, DNA nanotechnology expanded its scope from structural DNA nanoarchitecture towards designing dynamic and functional nanodevices. This progress has been evident in the development of an advanced class of DNA nanomachines, the so-called DNA walkers. They represent an evolution of basic switching between distinctly defined states into continuous motion. Inspired by the naturally occurring walkers such as kinesin, research on DNA walkers has focused on developing new ways of powering them and investigating their walking mechanisms and advantages. New techniques allowing the visualization of walkers as single molecules and in real time have provided a deeper insight into their behavior and performance. The construction of novel DNA walkers bears great potential for applications in therapeutics, nanorobotics or computation. This review will cover the various examples and breakthrough designs of recently reported DNA walkers that pushed the limits of their performance. It will also mention the techniques that have been used to investigate walker nanosystems, as well as discuss the applications that have been explored so far.     

Amino acid and peptide bioconjugates of copper(II) and zinc(II) complexes with a modified N,N-bis(2-picolyl)amine ligand

Four chelating nitrogen ligands 2-5 derived from N,N-bis(2-picolyl)amine (bpa, 1) were synthesized, namely, (PyCH(2))(2)N-CH(2)-p-C(6)H(4)-CO(2)R (R = Me, 2, and R = H, 3) and (PyCH(2))(2)N-(CH(2))(n)-CO(2)H (n = 2, 4, and n = 5, 5). Amino acid conjugates 6 and 7 were formed by condensation of 3 with H-Phe-OMe and H-betaAla-OMe, respectively. Cu(II) and Zn(II) complexes of 1-7 were prepared and fully characterized. The X-ray structures of 1(Zn), 2(Zn), 4(Cu), and 7(Cu) were determined. The Zn complexes 1(Zn) and 2(Zn) as well as 7(Cu) show a distorted trigonal bipyramidal coordination environment in the solid state. An octahedral complex is observed for 4(Cu) which forms chains along the crystallographic b axis by intermolecular coordination of the carboxylic acid to the metal ion of a neighboring complex. Ligand 3 was used to prepare the peptide bioconjugate 8 (3-Ahx-Pro-Lys-Lys-Lys-Arg-Lys-Phe-NH(2)) with a nuclear localization signal (nls) heptapeptide by solid phase synthesis. Cu(II) and Zn(II) complexes of 8 were synthesized in situ and studied by FAB-MS, ESI-MS, UV/vis, and EPR (for 8(Cu)), and FAB-MS, ESI-MS, and NMR (for 8(Zn)). All spectroscopic results clearly support metal coordination to the bpa ligand in the bioconjugates 8(M), even in the presence of other potential ligands from amino acid side chains of the peptide. We suggest metal-peptide conjugates like 8(M) as artificial metallochaperones because they have the potential to deliver metal ions to specific compartments in the cell as determined by the peptide moieties.     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

Controlled Ethylene Polymerization Catalyzed by Cp$\rm{{_{2}^{\ast}}}$ZrBu2/[Ph3C] [B(C6F5)4]/iBu4Al2O above Room Temperature

The ternary system composed of Cp ZrBu₂ (Cp*=Me₅Cp), [CPh₃][B(C₆F₅)₄], and tetraisobutyldialuminoxane (TIBAO) catalyzed the polymerization of ethylene in a controlled fashion at temperatures up to 60 °C. The consumption of ethylene remained constant during the polymerization process, the molecular weight of the polyethylene increased linearly with time, and polydispersity indexes down to 1.3 were obtained. Characterization of the polyethylene by ¹³C‐NMR and FT‐IR spectroscopy did not indicate any branching or CC linkages, even for polymer produced at 40 °C or above. The linear and saturated polymer structure is due to the absence of β‐hydride transfer, β‐hydride elimination and chain walking during the polymerization. The absence of termination reactions is consistent with the system's demonstrated controlled polymerization.     

混合阴、阳离子表面活性剂溶液中的分子相互作用和相分离

混合阴、阳离子表面活性剂的表面活性比单一组份的表面活性高得多[1]．多年来，该体系的界面化学性质得到了广泛的研究［1，2］．但是，一旦该体系在水溶液中的浓度超过其临界胶团浓度（cmc）后，就将沉淀[3]或分层［2，4］，从而失去其表面活性．后来发现卜，司，在某些情况下，阴、阳离子混合表面活性剂的沉淀现象有所改善；但一直不易找到在相当大浓度范围内仍不分层的阴、阳离子表面活性剂混合体系．本文较为简明、系统地讨论了阴、阳离子表面活性剂的相互作用与沉淀或分相的关系．这对于该体系的深入研究以及实际应用，具有积极的意义…     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

Reversed-phase liquid chromatography in-line with negative ionization electrospray mass spectrometry for the characterization of the disulfide-linkages of an immunoglobulin gamma antibody

In this report, we present a new approach for the determination of the disulfide bond connectivity in proteins using negative ionization mass spectrometry of nonreduced enzymatic digests. The mass spectrometric analysis in negative ion mode was optimized to allow in-line analysis coupled directly to the HPLC system used for the separation of the peptides resulting from enzymatic digestion. We determined the disulfide structure of a human immunoglobulin gamma 2 (IgG2) antibody containing 18 unique cysteine residues linked via 11 unique disulfide bonds. The efficiency of the gas-phase dissociation of disulfide-linked peptides using negative electrospray ionization was evaluated for an ion trap mass spectrometer and an orthogonal acceleration time-of-flight mass spectrometer. Both mass spectrometry techniques provided efficient in-source fragmentation for the identification of the disulfide-linked peptides of the antibody. Both instruments were limited in the number of disulfide bonds that could be dissociated. Seven of the 11 unique disulfide linkages have been determined, including the linkage of the light chain to the heavy chain. Only the disulfide connectivity of the hinge peptide H6H7H8H9 (C6C7VEC8PPC9PAPPVAGPSVFLFPPKPK) could not be determined (numbering the cysteine residues sequentially from the N-terminus and labeling the heavy chain cysteines "H" and the light chain cysteines "L"). However, we identified the dimer of peptide C6C7VEC8PPC9PAPPVAGPSVFLFPPKPK linked via four disulfide bonds based on the unique molecular weight of this dipeptide. The established linkages were H1 to H2, H10 to H11, H12 to H13, L1 to L2, L3 to L4, and L5 to H3H4. The intrachain linkages of the light chain (L1 to L2, L3 to L4), and heavy chain (H10 to H11, H12 to H13) domains were identical to the linkages found in IgG1 antibodies.     

Molecular length, monolayer density, and charge transport: lessons from Al-AlOx/alkyl-phosphonate/Hg junctions

A combined electronic transport-structure characterization of self-assembled monolayers (MLs) of alkyl-phosphonate (AP) chains on Al-AlOx substrates indicates a strong molecular structural effect on charge transport. On the basis of X-ray reflectivity, XPS, and FTIR data, we conclude that "long" APs (C14 and C16) form much denser MLs than do "short" APs (C8, C10, C12). While current through all junctions showed a tunneling-like exponential length-attenuation, junctions with sparsely packed "short" AP MLs attenuate the current relatively more efficiently than those with densely packed, "long" ones. Furthermore, "long" AP ML junctions showed strong bias variation of the length decay coefficient, β, while for "short" AP ML junctions β is nearly independent of bias. Therefore, even for these simple molecular systems made up of what are considered to be inert molecules, the tunneling distance cannot be varied independently of other electrical properties, as is commonly assumed.     

Sulfone-linked paracyclophanes via macrocyclic aromatic thioethers: synthetic and structural investigations

Reaction of 4,4'-sulfonylbis(benzenethiol) with 4,4'-dichlorodiphenylsulfone under pseudo-high-dilution conditions leads to macrocyclic thioethersulfones [-S-Ar-SO2-Ar-]n (Ar = 1,4-phenylene). These include a highly strained [1+1] cyclodimer (n = 2), a cyclotrimer resulting from thioetherexchange reactions, and a [2+2] cyclotetramer which can adopt two entirely different conformations in the crystalline state, one having molecular D2d ("tennis-ball-seam") symmetry. The same type of reaction is successful using 4,4'-thiobis(benzenethiol) instead of 4,4'-sulfonylbis(benzenethiol) and affords macrocycles with a higher ratio of thioether to sulfone linkages. Exhaustive oxidation of macrocyclic thioethersulfones with hydrogen peroxide affords a series of sulfone-linked paracyclophanes, [-Ar-SO2-]4, [-Ar-SO2-]6, [-Ar-SO2-]8 and [-Ar-SO2-]12. Single crystal X-ray analysis reveals [Ar-SO2-]4 to be a near-perfect square box, whilst the cyclic hexamer [-Ar-SO2-]6 adopts a much more irregular conformation. and [-Ar-SO2-]8 displays a "double-box" structure clearly related to that of [Ar-SO2-]4.     

Di- and tetranuclear copper(I) complexes containing phenylaminobis(phosphonite), PhN{P(OC6H4OMe-o)2}2, and their reactivity toward bipyridyl ligands

The aminobis(phosphonite) PhN(P(OC6H4OMe-o)2)2 (PNP; 1) reacts with 2 equiv of CuI to give a binuclear complex, Cu2(mu2-I)2(NCCH3)2(mu-PNP) (2), whereas similar reactions with CuCl and CuBr furnish tetranuclear "ladder"-type complexes, Cu4(mu2-X)2(mu3-X)2(mu-PNP)2 (3, X = Cl; 4, X = Br), in excellent yield. The complex 2 when heated under vacuum turns into the tetranuclear complex 5 in a reversible fashion. Similarly, the complexes 3 and 4 on dissolution in CH3CN dissociate reversibly into the corresponding binuclear complexes from which the tetrameric complexes can be readily regenerated. Treatment of 2 with excess of pyridine produces the heterosubstituted derivative, Cu2(mu2-I)2(C5H5N)2(mu-PNP) (6). The interaction of 2 with 2,2'-bipyridine in 1:1 and 1:2 ratios produces the mono- and disubstituted derivatives, Cu2(mu2-I)I(C10H8N2)(mu-PNP) (7) and [Cu2(mu2-I)(C10H8N2)2(mu-PNP)]I (8), respectively. The chloro and bromo analogues of 7 are prepared by treating the tetranuclear derivatives 3 and 4 with 2,2'-bipyridine. Reaction of 2 with 4,4'-bipyridine in the presence of AgOTf gives the cationic complex [Cu4(NCCH3)4(C10H8N2)2(mu-PNP)2](OTf)4 (9), whereas the complex [Cu2(NCCH3)2(mu-PNP)2](OTf)2 (10) was obtained from the reaction of 2 with 1 equiv of 1 and AgOTf. The reactions of 3 and 4 with 2 equiv of 4,4'-bipyridine in acetonitrile afford one-dimensional copper(I) coordination polymers [Cu2(mu2-X)2(mu-PNP)(C10H8N2)]n (13, X = Cl; 14, X = Br). The molecular structures of 2-4, 6-8, 12, and 14 are confirmed by X-ray crystallography.