Energetics and molecular biology of active transport in bacterial membrane vesicles.

Bacterial membrane vesicles retain the same sidedness as the membrane in the intact cell and catalyze active transport of many solutes by a respiration-dependent mechanism that does not involve the generation of utilization of ATP or other high-energy phosphate compounds. In E. coli vesicles, most of these transport systems are coupled to an electrochemical gradient of protons (deltamuH+, interior negative and alkaline) generated primarily by the oxidation of D-lactate or reduced phenazine methosulfate via a membrane-bound respiratory chain. Oxygen or, under appropriate conditions, fumarate or nitrate can function as terminal electron acceptors, and the site at which deltamuH+ is generated is located before cytochrome b1 in the respiratory chain. Certain (N-dansyl)aminoalkyl-beta-D-galactopyranosides (Dns-gal) and N(2-nitro-4-azidophenyl)aminoalkyl 1-thio-beta-D-galactopyranosides (APG) are competitive inhibitors of lactose transport but are not transported themselves. Various fluorescence techniques, direct binding assays, and photoinactivation studies demonstrate that the great bulk of the lac carrier protein (ca. 95%) does not bind ligand in the absence of energy-coupling. Upon generation of a deltamuH+ (interior negative and alkaline), binding of Dns-gal and APG-dependent photoinactivation are observed. The data indicate that energy is coupled to the initial step in the transport process, and suggest that the lac carrier protein may be negatively charged.     

Lithographic compartmentalization of emulsion droplet templates for microparticles with multiple nanostructured compartments

Complicated functional microparticles with complex nanostructured compartments have been synthesized from emulsion templates by lithographic compartment allocations. Our 'top-down-bottom-up' hybrid method will provide additional material engineering capability for the synthesis of advanced functional microparticles.     

Influence of functional groups on charge transport in molecular junctions

Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO(2), OCH(3), CH(3), CCl(3), and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can be predicted from its known electronic effect (whether it is sigma/pi donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than the experimental values, but good agreement is obtained after correcting for self-interaction and image charge effects.     

Walljet electrochemistry: quantifying molecular transport through metallopolymeric and zirconium phosphonate assembled porphyrin square thin films

By employing redox-active probes, condensed-phase molecular transport through nanoporous thin films can often be measured electrochemically. Certain kinds of electrode materials (e.g. conductive glass) are difficult to fabricate as rotatable disks or as ultramicroelectrodes-the configurations most often used for electrochemical permeation measurements. These limitations point to the need for a more materials-general measurement method. Herein, we report the application of walljet electrochemistry to the study of molecular transport through model metallopolymeric films on indium tin oxide electrodes. A quantitative expression is presented that describes the transport-limited current at the walljet electrode in terms of mass transport through solution and permeation through the film phase. A comparison of the film permeabilities for a series of redox probes measured using the walljet electrode and a rotating disk electrode establishes the accuracy of the walljet method, while also demonstrating similar precision for the two methods. We apply this technique to a system consisting of zirconium phosphonate assembled films of a porphyrinic molecular square. Transport through films comprising three or more layers is free from significant contributions from pinhole defects. Surprisingly, transport through films of this kind is 2-3 orders of magnitude slower than through films constructed via interfacial polymerization of nearly identical supramolecular square building blocks (Keefe; et al. Adv. Mater. 2003, 15, 1936). The zirconium phosphate assembled films show good size exclusion behavior. The details of the observed dependence of permeation rates on probe molecule size can be rationalized with a model that assumes that the walls of the squares are slightly tilted from a strictly vertical geometry, consistent with atomic force microscopy measurements, and assumes that the individual wall geometries are locked by rigid interlayer linkages.     

Coulomb-hole-Hartree-Fock functional for molecular systems

We have extended to molecules a density functional previously parametrized for atomic computations. The Coulombhole-Hartree-Fock functional, introduced by Clementi in 1963, estimated the dynamic correlation energy by the computation of a Hartree-Fock type single-determinant wavefunction, where the Hartree-Fock potential was augmented with an effective potential term, related to a hard Coulomb hole enclosing each electron. The method was later revised by S. Chakravorty and E. Clementi, Phys. Rev. A, 38 (1989) 2290, so that a Yukawa-type soft Coulomb hole replaced the previous hard hole. Atomic correlation energies, computed for atoms with Z = 2 to 54, as well as for a number of excited states, validated the method. In this work we have parametrized for molecules a function which controls the width of the soft Coulomb hole by fitting the first and second atomic ionization potentials of atoms with 1 Z 18 and the binding energies of a few diatomic molecules. The parametrization was successfully validated by computing the dissociation energy for a number of molecules. A few-determinant version of the Coulomb-Hartree-Fock method (CHF-N) necessary to account for the non-dynamic correlation correction and to ensure proper dissociation products, is briefly discussed with reference to a previous proposal by G.C. Lie and E. Clementi, J. Chem. Phys., 60 (1974) 1275 and 60 (1974) 1288.     

Accurate calculation of transport properties for organic molecular semiconductors with spin-component scaled MP2 and modern density functional theory methods

At ambient temperatures, intermolecular hopping of charge carriers dominates the field effect mobility and thus the performance of organic molecular semiconductors for organic-based electronic devices. We have used a wide variety of modern and accurate computational methods to calculate the main parameters associated with charge transport, taking oligoacenes, and its derivatives as the exemplary organic materials. We tackle the problem from a combined inter- and intramolecular approach, in which the parameters are calculated for an isolated single molecule concomitantly with the stability of the dimers found in experimentally determined crystalline structures. Considering that most of the future applications within the field would need a full understanding of the transport mechanism, we assess the reliability of the methods to be employed according to the nature of the problem. Finally, we perform a computationally guided molecular engineering of a new set of materials derived from tetracene (rubrene and highly twisted oligoacenes) which allows to robustly anticipate the reasons for their expected performance in organic-based electronic devices.     

An efficient nonequilibrium Green's function formalism combined with density functional theory approach for calculating electron transport properties of molecular devices with quasi-one-dimensional electrodes

An efficient self-consistent approach combining the nonequilibrium Green's function formalism with density functional theory is developed to calculate electron transport properties of molecular devices with quasi-one-dimensional (1D) electrodes. Two problems associated with the low dimensionality of the 1D electrodes, i.e., the nonequilibrium state and the uncertain boundary conditions for the electrostatic potential, are circumvented by introducing the reflectionless boundary conditions at the electrode-contact interfaces and the zero electric field boundary conditions at the electrode-molecule interfaces. Three prototypical systems, respectively, an ideal ballistic conductor, a high resistance tunnel junction, and a molecular device, are investigated to illustrate the accuracy and efficiency of our approach.     

Engineering molecular crystals with abnormally weak cohesion

Adding astutely placed methyl groups to hexaphenylbenzene increases molecular weight but simultaneously weakens key C-H···π interactions, thereby leading to decreased enthalpies of sublimation and showing that materials with abnormally weak cohesion can be made by identifying and then obstructing interactions that help control association.     

A synthetic DNA walker for molecular transport

Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. Real-time monitoring of specific bidirectional walker movement is achieved via multiplexed fluorescence quenching.     

Playing with organic radicals as building blocks for functional molecular materials

The literature has shown numerous contributions on the synthesis and physicochemical properties of persistent organic radicals but there are a lesser number of reports about their use as building blocks for obtaining molecular magnetic materials exhibiting an additional and useful physical property or function. These materials show promise for applications in spintronics as well as bistable memory devices and sensing materials. This critical review provides an up-to-date survey to this new generation of multifunctional magnetic materials. For this, a detailed revision of the most common families of persistent organic radicals-nitroxide, triphenylmethyl, verdazyl, phenalenyl, and dithiadiazolyl-so far reported will be presented, classified into three different sections: materials with magnetic, conducting and optical properties. An additional section reporting switchable materials based on these radicals is presented (257 references).     

Transition functional schemes for molecular transition energies

Two different transition functionals are used to calculate the first and second ionization potentials of water. The results compare favourably with more costly E _scf results. Methods of dealing with convergence problems are discussed.     

多羧基小分子化合物诱导阳离子囊泡聚集的研究

研究了由阳离子型肽脂质溴化N,N-二-十六烷基-Na-6-三甲胺基己酰基-L-丙氨酰胺(N+C5Ala2C16)形成的阳离子囊泡,在加入含羧基小分子化合物后形成的聚集。考察了乙二胺四乙酸(EDTA)加入到囊泡中后吸光值随时间的变化。结果表明:当EDTA增加到一定浓度时可以引起由阳离子囊泡的聚集;在加入Ca2+后,阳离子囊泡聚集体得到分散;借助电子显微镜观察到了囊泡的聚集和分散。超滤后,用高效液相色谱法确定了囊泡结合的EDTA量。考察了不同pH条件下EDTA对囊泡聚集的影响,当EDTA等含多羧基小分子化合物羧基解离数为三个或以上时能够引起囊泡的聚集,而少于三个时囊泡不能发生聚集。     

Polyacrylamide gels with electrostatic functional groups for the molecular imprinting of lysozyme

The system of polyacrylamide incorporated with methacrylic acid and 2-(dimethylamino)ethyl methacrylate was studied for the possibility of imprinting of lysozyme. The results show that approximately 27% (w/w) of the lysozyme template was not able to be extracted from the molecularly imprinted acrylamide polymers. The amount of the lysozyme template able to be extracted was increased by the addition of methacrylic acid. The molecularly imprinted polymer (MIP), which was prepared with 0.573 M acrylamide, 0.573 M methacrylic acid and 0.573 M 2-(dimethylamino)ethyl methacrylate at a total solution concentration of 20% (w/w), was able to adsorb 83% more lysozyme than the non-imprinted polymer. Selectivity of MIP was also studied.     

Investigating charge transport in molecular switches with neural networks

The control of charge transport on a polymer chain by impurity molecules working as switches is studied. Charge propagation is estimated using a backpropagation neural network approach. The supervised learning is accomplished using theoretical results in which the chain is modeled by a tight-binding Hamiltonian extended to include the effects of an external electric field. The charge transport through the sites that work like a switch is analyzed by the numerical integration of the equations of motion. For a donor–acceptor pair of impurities, we found that the chain offers a wide range of devices, from simple switches to perfect molecular rectifiers. The influence of the parameters of the molecules on the charge transport, the role of the length of separation between the sites where the impurity molecules bond, as well as the changes they must undergo to characterize each kind of molecular switch are determined. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1060–1066, 1999     

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of L?wdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.     

An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins

A procedure for determining the extent of phosphorylation at individual sites of multiply phosphorylated proteins was developed and applied to two polyphosphorylated proteins. The protocol, using simple chemical (Fischer methyl-esterification) and enzymatic (phosphatase) modification steps and an accessible isotopic labeling reagent (methyl alcohol-d(4)), is described in detail. Site-specific phosphorylation stoichiometries are derived from the comparison of chemically identical but isotopically distinct peptide species analyzed by microspray liquid chromatography-mass spectrometry (microLC-MS) using a Micromass Q-TOF2 mass spectrometer. Ten phosphorylation sites were unambiguously identified in tryptic digests of both proteins, and phosphorylation stoichiometries were determined for eight of the ten sites using the isotope-coded strategy. The extent of phosphorylation was also estimated from the mass spectral peak areas for the phosphorylated and unmodified peptides, and these estimates, when compared with stoichiometries determined using the isotope-coded technique, differed only marginally (within approximately 20%).     

Electronic transport through molecular junctions with nonrigid molecule-leads coupling

The Landauer-type formulation of current through a molecular junction with electronic-nuclear coupling introduced by Troisi et al. [J. Chem. Phys. 118, 6072 (2003)] is generalized to account for the dependence of the molecule-leads coupling terms on the nuclear coordinates. Although this electronic-nuclear coupling is external to the molecule there is no need to extend the molecular subspace when projection operators are employed for calculations of the current through the junction. A test case of a conductor with vibrating contacts to the leads is studied numerically. It is demonstrated that contact vibrations lead to inelastic contributions to the current and to characteristic features in the I-V curve and its derivatives, similar to the ones observed for internal (molecular) electronic-nuclear coupling.     

Simulations of optically switchable molecular machines for particle transport

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first‐generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene‐derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on‐the‐fly photodynamics, excited‐state surface‐hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating‐occupation configuration interaction as the QM part and the OPLSAA‐L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi‐molecule arrangements. Our results provide valuable design guidelines for cilia‐driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium‐target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.