Graphene功能分子在HOPG上自组装结构的密度泛函研究

Graphene自组装超分子结构,是指FTBC-Cn(n=4,6,8,12)分子有序自组装在高定向裂解石墨(HOPG)上形成的自组装超分子结构,是一种新型二维固体表面材料.其中FTBC-Cn分子是由三角形扶手椅型graphene每边添加2条含有n(n=4,6,8,12)个C原子的烷基链所形成具有曲面结构的一种分子.采用...     

The influence of solvent molecules on NMR spectrum of barbituric acid in the DMSO solution

This work shows the modification of barbituric acid (BA) chemical shifts by dimethylsulphoxide (DMSO) molecules. The discussed changes are caused by creation of the H-bonded associates formed by barbituric acid with DMSO in solution. Free molecule of barbituric acid, the cluster of BA with two DMSO molecules and two different clusters of BA with four DMSO units are taken into consideration. The chemical shifts of these systems have been calculated and the obtained results have been compared with experimental data. Theoretical calculations predict a significant downfield shift for imino protons of barbituric acid involved in intermolecular-N-H...DMSO hydrogen bonds. The influence of the solvent molecules on other nuclei chemical shifts, especially protons of barbituric acid methylene group, is also reported. The calculations have involved Hartree-Fock and several Density Functional Theory methods. All methods correctly describe experimental ¹H and ¹³C NMR spectra of barbituric acid. The best consistence between experiment and theory is observed for the BLYP functional. Four approximations of magnetic properties calculations embedded in the Gaussian’98 package have been tested. The results of the performed calculations indicate that from a practical point of view the GIAO method should be preferred.     

Two-dimensional assemblies of banana-shaped liquid crystal molecules on HOPG surface

Two-dimensional assemblies of a series of banana-shaped liquid crystal molecules, 1,3-phenylene bis[4-(4-n-alkylphenyliminomethyl) benzoates] (P-n-PIMB, n = 12, 14, 18), are investigated on a highly oriented pyrolytic graphite (HOPG) surface by using scanning tunneling microscopy (STM) at a submolecular level in an ambient environment. Two types of molecular arrangements are observed in these self-assemblies with different stripe widths that resulted from the organization of the alkyl chains. The polarization of the P-n-PIMB monolayers is exactly compensated by the adjacent lamellae with opposite bent direction. Furthermore, a bilayer structure is found in the assembly of P-18-PIMB molecules. In comparison with a gemini surfactant molecule, 4,4'-di[4-(octadecylmethylamino)styryl]-1,1'-pentamethylenebispyridinium dibromide (OPD), P-n-PIMB molecules appear in more complicated packing arrangements. The results in this paper demonstrate the effects of the molecular structures on the adlayer arrangement and will be helpful in fabricating two-dimensional molecular structures on solid surfaces.     

Advances in self-assembly and regulation of aromatic carboxylic acid derivatives at HOPG interface

Aromatic carboxylic acid self-assembly has been a hot research field for many scientists due to its strong coordination ability and flexible coordination mode.The hydrogen bond formed between aromatic carboxylic acids is a strong intermolecular force and has directionality and saturation,which plays a very important role in the self-assembly and regulation of aromatic carboxylic acids.In this review,we introduce surface organization formed by aromatic carboxylic acids with the aid of scanning tunneling microscopy(STM).These two-dimensional structures include molecular templates,host-guest systems,and photo-isomerization structures.We also emphasize the thermodynamics and dynamics,which are important research topics of current and future study.     

Molecular behavior of the aptamer HJ24 self-assembled on highly oriented pyrolytic graphite (HOPG)

Nucleic acid sensing analysis has been widely applied to the fields of food quality control, environmental monitoring, and medical diagnosis. A key step in developing effective DNA-based electrochemical biosensors is to obtain a biorecognition layer on the biosensor, which can be influenced by many factors. Hence, we constructed a series of HJ24 layers on highly oriented pyrolytic graphite to investigate the relation between the configuration of the adsorbed probe HJ24 and the redox property using atomic force microscopy and voltammetry. We used HJ24 for its diagnostic value as it specifically recognizes the SH2 domain-containing phosphatase, a critical contributor in many important signaling pathways. The results demonstrated that increasing K ions induced G-quartet oxidation peak occurrence/increase([K+]?400 mmol/L), and also resulted in the formation of more compact single strand sheets([K+]?300 mmol/L). Moreover, transitions of molecule configurations and redox currents of G-quartets were observed at low concentration [K+]=12 mmol/L, which may indicate the appearance of new configurations under this condition. Besides, by analyzing atomic force microscopy(AFM) images, it was found that the different adsorbed configurations are correlated with the HJ24 concentration, the basal configuration, and the linker group on the HJ24 sequence. This information may be useful for understanding the adsorption process of HJ24 as well as for the further development of practical applications for HJ24 films on DNA electrochemical sensors, and may ultimately help improve the diagnosis and treatment of patients with SHP2-related diseases.     

Curvature modulates the self-assembly of amphiphilic molecules

In this work, we used lattice Monte Carlo simulations and theoretical model calculations to show how the self-assembly of adsorbed amphiphilic molecules is affected by the local curvature of solid surfaces. It is found that, beyond a critical curvature value, solid surface geometry governs the spatial ordering of aggregates and may induce the morphological transitions. The simulation results show how the curvature of solid surfaces modulates the distribution of aggregates: the anisotropy in local curvature along and perpendicular to the cylindrical surfaces tends to generate orientationally ordered cylindrical micelles. To account for the morphological transitions induced by the local curvature of solid surfaces, we constructed a theoretical model which includes the Helfrich bending energy, the deformation energy of aggregates induced by solid surfaces, and the adsorption energy. The model calculations indicate that on highly curved solid surfaces the bending energy for bilayer structure sharply increases with surface curvature, which in turn induces the morphological transition from bilayer to cylindrical structure. Our results suggest that the local curvature provides a means of controlling the spatial organization of amphiphilic molecules.     

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.     

A scanning tunneling microscopy study of self-assembled nickel(II) octaethylporphyrin deposited from solutions on HOPG

The adsorption of nickel(II) octaethylporphyrin (NiOEP) from benzene and chloroform solutions on highly ordered pyrolytic graphite (HOPG) was investigated with a scanning tunneling microscope (STM) operated in ambient conditions. STM images show that NiOEP self-assembles on the graphite surface and that the molecules lie flat and form 2D lattices with spacings of 1.58 +/- 0.03 nm by 1.46 +/- 0.06 nm with a lattice angle of 69 degrees +/- 4 degrees averaged over both solvents. We were unable to eliminate the possibility that one unit cell distance is twice the above-reported distance. The corresponding molecular packing density, 4.5 +/- 0.3 x 10(13) molecules/cm(2), was essentially the same for benzene and chloroform solution deposition. These results differ somewhat from the structure revealed by high-resolution STM images of NiOEP on Au (111). The lack of apparent height (image intensity) in the constant current STM image of the alkane region of alkane-substituted metal porphyrins is attributed to a combination of changes in alkane configuration relative to the ring and associated changes in electronic coupling with HOMO and LUMO.     

Supramolecular recognition of heteropairs of lanthanide ions: a step toward self-assembled bifunctional probes

Three unsymmetrical ditopic hexadentate ligands coded for the recognition of trivalent lanthanide ions have been synthesized, L(AB), L(AC), and L(BC), where A represents a benzimidazole-pyridine-benzimidazole coordination unit, B a benzimidazole-pyridine-carboxamide one, and C a benzimidazole-pyridine-carboxylic acid moiety. Under stoichiometric 2:3 (Ln:L) conditions, these ligands self-assemble with lanthanide ions to yield triple-stranded bimetallic helicates having a sizable stability in acetonitrile: log beta(23) values for Eu are equal to 23.9 +/- 0.5 (L(AB)), 23.3 +/- 0.7 (deprotonated L(AC)), and 29.8 +/- 0.5 (deprotonated L(BC)). The crystal structure of the EuEu helicate with L(AB) shows 9-coordinate metal ions and an HHH (H stands for head) configuration of the helically wrapped ligand strands. In the presence of equimolar quantities of Ln and Ln' ions, L(AB) displays a remarkable predisposition to form HHH-heterobimetallic edifices, as proved both in the solid state by the crystal structures of the LaEu, LaTb, PrEr, and PrLu helicates and in solution by NMR spectroscopy. In all cases, the benzimidazole-pyridine-carboxamide units of the three ligands are bound to the smaller lanthanide ion, a fact further ascertained by high-resolution luminescence data on LaEu and by (1)H NMR. Analysis of the lanthanide-induced (1)H NMR shifts and of the spin-lattice relaxation times of the [LnLu(L(AB))(3)](6+) series (Ln = Ce, Pr, Nd, Sm, Eu) demonstrates the isostructural nature of the complexes in solution and that the crystal structure of LaTb is a good model for the solution structure. The selectivity of L(AB) for heteropairs of Ln(III) ions increases with increasing difference in ionic radius, resulting in 70% of the heterobimetallic species for deltar(i) = 0.1 A and up to 90% for LaLu (deltar(i) = 0.18 A), and corresponding to delta(deltaG) in the range 3-10 kJ.mol(-)(1). The origins of this stabilization are discussed in terms of the donor properties of the coordinating units and of the preferential formation of HHH isomers.     

Effect of secondary structure on the self-assembly of amphiphilic molecules: a multiscale simulation study

The self-assembly of amphiphilic molecules is of interest from a fundamental and practical standpoint. There has been recent interest in a class of molecules made from β-amino acids (which contain an additional backbone carbon atom when compared with natural amino acids). Block copolymers of β-peptides, where one block is hydrophobic and the other is hydrophilic, self-assemble into micelles. In this work, we use computer simulations to provide insight into the effect of secondary structure on the self-assembly of these molecules. Atomistic simulations for the free energy of association of a pair of molecules show that a homochiral hydrophobic block promotes self assembly compared to a heterochiral hydrophobic block, consistent with experiment. Simulations of a coarse-grained model show that these molecules spontaneously form spherical micelles.     

Effect of side-chain substituents on self-assembly of perylene diimide molecules: morphology control

Effect of side-chain substitutions on the morphology of self-assembly of perylene diimide molecules has been studied with two derivatives modified with distinctly different side-chains, N,N'-di(dodecyl)-perylene-3,4,9,10-tetracarboxylic diimide (DD-PTCDI) and N,N'-di(nonyldecyl)-perylene-3,4,9,10-tetracarboxylic diimide (ND-PTCDI). Due to the different side-chain interference, the self-assembly of the two molecules results in totally different morphologies in aggregate: one-dimensional (1D) nanobelt vs zero-dimensional (0D) nanoparticle. The size, shape, and topography of the self-assemblies were extensively characterized by a variety of microscopies including SEM, TEM, AFM, and fluorescence microscopy. The distinct morphologies of self-assembly have been obtained from both the solution-based processing and surface-supported solvent-vapor annealing. The nanobelts of DD-PTCDI fabricated in solution can feasibly be transferred to both polar (e.g., glass) and nonpolar (e.g., carbon) surfaces, implying the high stability of the molecular assembly (due to the strong pi-pi stacking). The side-chain-dependent molecular interaction was comparatively investigated using various spectrometries including UV-vis absorption, fluorescence, X-ray diffraction, and differential scanning calorimetry. Compared to the emission of ND-PTCDI aggregate, the emission of DD-PTCDI aggregate was significantly red-shifted (ca. 30 nm) and the emission quantum yield decreased about three times, primarily due to the more favorable molecular stacking for DD-PTCID. Moreover, the aggregate of DD-PTCDI shows a pronounced absorption band at the longer wavelength, whereas the absorption of ND-PTCDI aggregate is not significant in the same wavelength region. These optical spectral observations are reminiscent of the previous theoretical investigation on the side-chain-modulated electronic properties of PTCDI assembly.     

Synthesis and self-assembly of supramolecular dendritic "Bow-Ties": effect of peripheral functionality on association constants

Self-assembled polyester dendritic bow-ties with various peripheral groups were prepared, and their association constants were measured by (1)H NMR in CDCl(3). The two complementary dendrons were prepared by attachment of either a bis(adamantylurea) or a glycinylurea to the focal point of the dendron. The parent self-assembled system with benzylidene acetals on one periphery and isopropylidene acetals on the other had an association constant of 520 M(-)(1). Upon deprotection of one dendron, the association constant is increased by more than an order of magnitude as the solubility of the hydroxyl-terminated dendron in CDCl(3) is decreased. In contrast, attachment of tri(ethylene oxide) units to the periphery of one dendron lowers the association constant by almost an order of magnitude. The causes of these relatively large changes in complex strength are discussed in terms of solubility, steric effects, competitive hydrogen bonding, and the structure of the dendritic scaffold.     

Esterification in ionic liquids: the influence of solvent basicity

The second-order rate constant (k2) for the esterification of methoxyacetic acid with benzyl alcohol is reported in a range of ionic and molecular solvents. The solvent effects on esterification rate are examined by using a linear solvation energy relationship based on the Kamlet-Taft solvent scales (alpha, beta, and pi*). It is shown that the hydrogen bond basicity of the solvent is the dominant parameter in determining the esterification rate and that the best rates are achieved in low basicity solvents.     

Stereoelectronic influence of the type of bifunctional ansa-monocyclopentadienyldimethylsilylamido ligand on the molecular structures displayed by zirconium dichloride and 1,4-diphenylbutadiene complexes

A series of organozirconium dichloride and 1,4-diphenylbutadiene complexes featuring a dianionic bifunctional ligand with a cyclopentadienyl-type functionality and an appended amido N donor have been prepared and structurally characterized. [(C(5)H(4))SiMe(2)(N-t-Bu)]ZrCl(2), 1, [(C(9)H(6))SiMe(2)(N-t-Bu)]ZrCl(2), 2, and [(C(5)Me(4))SiMe(2)(N-i-Pr)]ZrCl(2), 3, were prepared in two steps, with ligand chelation accomplished by an amine elimination reaction followed by treatment of the diamido Zr intermediate with an excess of SiMe(3)Cl. X-ray structural analyses reveal that in the solid state 2 is monomeric, whereas 1 and 3 are centrosymmetric dimers linked by a pair of bridging chlorides. The level of asymmetry displayed by the central Zr(2)(micro-Cl)(2) moiety is indicated by the variation in the pair of independent bridging Zr-Cl bond distances, which are 2.618(1) and 2.657(1) A in 1 and 2.542(1) and 2.745(1) A in 3, respectively. The metathetical reactions of [Mg(C(4)H(4)Ph(2))(THF)(3)](n)() with 1, 2, 3, and [(C(5)Me(4))SiMe(2)(N-t-Bu)]ZrCl(2) proceed to afford the corresponding 1,4-diphenylbutadiene derivatives 4, 5, 6, and 7, respectively. Solution NMR data show that 6 is obtained exclusively as the supine isomer, whereas compounds 4, 5, and 7 exist as >20:1, 6:1, and 2:1 mixtures of the supine and prone isomers at ambient temperature. The molecular structures of the supine forms of 4, 5, 6, and 7 are appreciably folded (70-80 degrees ) along the line of intersection between the plane containing the Zr and the two terminal butadiene carbons and the plane of the cis-butadiene fragment. An increase in the folding is accompanied by a decrease in the difference between the average Zr-C(terminal) and Zr-C(internal) bond distances and leads to a more pronounced long-short-long C-C bond sequence within the coordinated butadiene.     

Selective self-organization of guest molecules in self-assembled molecular boxes

This article describes the synthesis and binding properties of highly selective noncovalent molecular receptors 1(3).(DEB)6 and 3(3).(DEB)6 for different hydroxyl functionalized anthraquinones 2. These receptors are formed by the self-assembly of three calix[4]arene dimelamine derivative molecules (1 or 3) and six diethylbarbiturate (DEB) molecules to give 1(3).(DEB)6 or 3(3).(DEB)6. Encapsulation of 2 occurs in a highly organized manner; that is, a noncovalent hydrogen-bonded trimer of 2 is formed within the hydrogen-bonded receptors 1(3).(DEB)6 and 3(3).(DEB)6. Both receptors 1(3).(DEB)6 and 3(3).(DEB)6 change conformation from staggered to eclipsed upon complexation to afford a better fit for the 2(3) trimer. The receptor selectivity toward different anthraquinone derivatives 2 has been studied using 1H NMR spectroscopy, X-ray crystallography, UV spectroscopy, and isothermal microcalorimetry (ITC). The pi-pi stacking between the electron-deficient center ring of the anthraquinone derivatives 2a-c and 2e-g and the relatively electron-poor melamine units of the receptor is the driving force for the encapsulation of the guest molecules. The selectivity of the hydrogen-bonded host for the anthraquinone derivatives is the result of steric interactions between the guest molecules and the calix[4]arene aromatic rings of the host.     

Intermolecular interactions in solution: elucidating the influence of the solvent

A new approach for the analysis of intermolecular interactions in a solution is proposed. The changes in the interaction energy components due to the solvent effects are estimated on the basis of the interaction energy calculated in the presence of the electric field induced in a polarizable medium, or in the field of the effective fragment potentials. Obtained results indicate a significant increase in stabilization resulting from electrostatic interactions as a result of the cooperative interactions between interacting subsystems and solvent molecules.     

The HETTAP approach: self-assembly and metal ion sensing of dumbbell-shaped molecules and clip molecules

The pentacoordinated terpyridine-phenanthroline zinc(II) complex motif, conceived along the HETTAP concept, allows the preparation of a set of multicomponent supramolecular dumbbell and clip assemblies from various bisterpyridines. All assemblies show a notable luminescence at 350-400 nm. The formation of dumbbell [Zn2(1b)2(2b)]4+ is convincingly demonstrated from the X-ray crystal structure analysis. Both dumbbell [Zn2(1b)2(2b)]4+ and clip [Zn2(1d)(2b)]4+ allow the monitoring of Hg2+ ions due to highly selective quenching of the emission that is driven by a Zn2+ --> Hg2+ exchange process, while the more-strained clip [Zn2(1d)(2c)]4+ does not undergo such metal exchange and does not show quenching of the luminescence. Consequently, these assemblies exhibit a highly selective response due solely to supramolecular effects.     

The striking influence of SWNT-COOH on self-assembled gelation

A miniscule amount of f-SWNTs remarkably improved (~17-fold) the gelation efficiency of amphiphilic molecules by triggering the formation of interconnecting self-assembled fibrillar networks (SAFIN) in supramolecular gelation.     

Disorganised self-assembled monolayers (SAMs): the incorporation of amphiphilic molecules.

A new approach for designing a voltammetric selective electrode is presented. The approach is based on the formation of a disorganised inert self-assembled monolayer (SAM), in which an amphiphilic molecule is incorporated. The latter serves as the selectivity factor, which extracts the analyte. The purpose of these experiments is to study the parameters that affect the capability of a monolayer to host amphiphiles. As model systems we focused on the incorporation of simple amphiphilic molecules (quaternary alkyl ammonium salts), electroactive amphiphiles (dialkylviologens) and a macrocycle ligand (tetramethylcyclam) into octadecyl silane monolayers formed on indium tin oxide (ITO) and purposely made disorganised alkanethiols on gold. We find that basically, the incorporation of amphiphiles into a hydrophobic inert SAM resembles a reversed stationary phase in liquid chromatography and this configuration can be used for designing selective electrodes.