Design of a peptide hairpin containing a central three-residue loop

The construction of a designed beta-hairpin structure, containing a central three-residue loop has been successfully achieved in the synthetic nonapeptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-(D)Ala-Leu-Phe-Val-OMe (2). The design is based on expanding the two-residue loop established in the peptide beta-hairpin Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1). Characterization of the registered beta-hairpins in peptides 1 and 2 is based on the observation of key nuclear Overhauser effects (NOEs) in CDCl(3) and CD(3)OH. Solvent titration and temperature dependence of NH chemical shifts establish the identity of NH groups involved in interstrand hydrogen bonding. In peptide 2, the antiparallel registry is maintained, with the formation of a (D)Pro-(L)Pro-(D)Ala loop, stabilized by a 5-->1 hydrogen bond between Val3 CO and Leu7 NH groups (C(13), alpha-turn) and a 3-->1 hydrogen bond between (D)Pro4 CO and (d)Ala6 NH groups (C(7), gamma-turn). NMR derived structures suggest that in peptide 2, (d)Ala(6) adopts an alpha(L) conformation. In peptide 1, the (D)Pro-(L)Pro segment adopts a type II' beta-turn. Replacement of (D)Ala (6) in peptide 2 by (L)Ala in peptide 3 yields a beta-hairpin conformation, with a central (D)Pro-(L)Pro two-residue loop. Strand slippage at the C-terminus results in altered registry of the antiparallel strands.     

Relaxation dynamics of a linear molecule in a random static medium: a scaling analysis

We present extensive molecular dynamics simulations of the motion of a single linear rigid molecule in a two-dimensional random array of fixed overlapping disklike obstacles. The diffusion constants for the center of mass translation, D(CM), and for rotation, D(R), are calculated for a wide range of the molecular length, L, and the density of obstacles, rho. The obtained results follow a master curve Drho(micro) approximately (L(2)rho)(-nu) with an exponent micro=-3/4 and 1/4 for D(R) and D(CM), respectively, that can be deduced from simple scaling and kinematic arguments. The nontrivial positive exponent nu shows an abrupt crossover at L(2)rho=zeta(1). For D(CM) we find a second crossover at L(2)rho=zeta(2). The values of zeta(1) and zeta(2) correspond to the average minor and major axis of the elliptic holes that characterize the random configuration of the obstacles. A violation of the Stokes-Einstein-Debye relation is observed for L(2)rho>zeta(1), in analogy with the phenomenon of enhanced translational diffusion observed in supercooled liquids close to the glass transition temperature.     

Two-Dimensional Planar Chromatography with a Closed Adsorbent Layer

A new two-dimensional chromatography process on closed plates is proposed. A previously described device with ethanol as a mobile phase is used to experimentally study two-dimensional thin-layer chromatography (2D TLC) on plates with 5 × 5 and 10 × 10 cm sizes. This work includes the experimental study and comparison of the following TLC versions: (1) the proposed 2D TLC version with a closed adsorbent layer with 1D separation on closed plates (an ascending mobile phase flow) and (2) conventional 2D TLC with an open adsorbent layer. The ascending version of 2D TLC with a closed adsorbent layer considerably (byR~55%) shortens the chromatographic time, especially with the use of 5 × 5 cm plates in the 2D separation version compared with the 1D version on 10 × 10 cm plates.     

Two-Dimensional Supramolecular Polymerization of a Bis-Urea Macrocycle into a Brick-Like Hydrogen-Bonded Network

We report on a dendronized bis-urea macrocycle 1 self-assembling via a cooperative mechanism into two-dimensional (2D) nanosheets formed solely by alternated urea-urea hydrogen bonding interactions. The pure macrocycle self-assembles in bulk into one-dimensional liquid-crystalline columnar phases. In contrast, its self-assembly mode drastically changes in CHCl₃ or tetrachloroethane, leading to 2D hydrogen-bonded networks. Theoretical calculations, complemented by previously reported crystalline structures, indicate that the 2D assembly is formed by a brick-like hydrogen bonding pattern between bis-urea macrocycles. This assembly is promoted by the swelling of the trisdodecyloxyphenyl groups upon solvation, which frustrates, due to steric effects, the formation of the thermodynamically more stable columnar macrocycle stacks. This work proposes a new design strategy to access 2D supramolecular polymers by means of a single non-covalent interaction motif, which is of great interest for materials development.     

Fast photodriven electron spin coherence transfer: a quantum gate based on a spin exchange j-jump

Photoexcitation of the electron donor (D) within a linear, covalent donor-acceptor-acceptor molecule (D-A(1)-A(2)) in which A(1) = A(2) results in sub-nanosecond formation of a spin-coherent singlet radical ion pair state, (1)(D(+?)-A(1)(-?)-A(2)), for which the spin-spin exchange interaction is large: 2J = 79 ± 1 mT. Subsequent laser excitation of A(1)(-?) during the lifetime of (1)(D(+?)-A(1)(-?)-A(2)) rapidly produces (1)(D(+?)-A(1)-A(2)(-?)), which abruptly decreases 2J 3600-fold. Subsequent coherent spin evolution mixes (1)(D(+?)-A(1)-A(2)(-?)) with (3)(D(+?)-A(1)-A(2)(-?)), resulting in mixed states which display transient spin-polarized EPR transitions characteristic of a spin-correlated radical ion pair. These photodriven J-jump experiments show that it is possible to use fast laser pulses to transfer electron spin coherence between organic radical ion pairs and observe the results using an essentially background-free time-resolved EPR experiment.     

A 3D QSAR study on a set of dopamine D4 receptor antagonists

The molecular alignments obtained from a previously reported pharmacophore model have been employed in a three-dimensional quantitative structure-activity relationship (3D QSAR) study, to obtain a more detailed insight into the structure-activity relationships for D(2) and D(4) receptor antagonists. The frequently applied CoMFA method and the related CoMSIA method were used. Statistically significant models have been derived with these two methods, based on a set of 32 structurally diverse D(2) and D(4) receptor antagonists. The CoMSIA and the CoMFA methods produced equally good models expressed in terms of q(2) values. The predictive power of the derived models were demonstrated to be high. Graphical interpretation of the results, provided by the CoMSIA method, brings to light important structural features of the compounds related to either low- or high-affinity D(2) or D(4) antagonism. The results of the 3D QSAR studies indicate that bulky N-substituents decrease D(2) binding, whereas D(4) binding is enhanced. Electrostatically favorable and unfavorable regions exclusive to D(2) receptor binding were identified. Likewise, certain hydrogen-bond acceptors can be used to lower D(2) affinity. These observations may be exploited for the design of novel dopamine D(4) selective antagonists.     

Lubrication theory of drag on a scanning probe in structured water, near a hydrophilic surface

The drag is evaluated, in lubrication theory, on a parabolic-cylindrical tip moving parallel to a flat sample, in water, close enough that the presumed nanometer-thick, structured-water, "interphase" coatings of both it and the sample overlap. Assuming coatings of width, w, and of viscosity, eta, much larger than bulk water's, the friction force is predicted to equal -2pietacRphi(D/2w), where R is the tip's radius of curvature, c is its speed, D is the tip-sample separation, and Phi is a universal function whose value only differs noticeably from ln(2w/D) for D < w.     

The hydrogen molecule for a two-dimensional system

The two-dimensional (2D) energy of the hydrogen molecule is carried out by the Heitler-London method. The 2D integrals (which are more localized compared to 3D ones) are performed in the light of the 3D Slater integrals. A discussion of such 2D systems is briefly outlined for doped semiconductors.     

Investigation of the partially coherent effects in a 2D Talbot interferometer

The recent use of a one-dimensional (1D) X-ray Talbot interferometer has triggered great interest in X-ray differential phase contrast imaging. As an improved version of a 1D interferometer, the development of two-dimensional (2D) grating interferometry strongly stimulated applications of grating-based imaging. In the framework of Fresnel diffraction theory, we investigated the self-image of 2D-phase gratings under partially coherent illumination. The fringe visibility of the self-image has been analyzed as a function of the spatial coherence length. From the viewpoint of self-image visibility, it is possible to find the optimal 2D grid for 2D X-ray grating interferometer imaging. Numerical simulations have been also carried out for quantitative evaluation. Results, in good agreement with theoretical analysis, indicate the spatial coherence requirements of the radiation illuminating a 2D grating interferometer. Moreover, our results can be used to optimize performances of a 2D grating interferometer and for further theoretical and experimental research on grating-based imaging systems.     

A pillared-bilayer porous coordination polymer with a 1D channel and a 2D interlayer space, showing unique gas and vapor sorption

A new 2D pillared-bilayer porous coordination polymer (PCP) has been synthesized and structurally characterized that shows selective adsorption of CO(2) over other gases (N(2), O(2), Ar, H(2), CH(4)) and guest selective single/double-step adsorption of vapor correlated to the successive confinement of adsorbates in a 1D channel and a 2D interlayer space.     

Ab initio-based all-mode two-dimensional infrared spectroscopy of a sugar molecule

To construct two-dimensional infrared (2D IR) spectra having all vibrational modes of a molecule included is still quite challenging, both experimentally and theoretically. Here we report an ab initio-based all-mode 2D IR spectra simulation approach. Using deuterated glycolaldehyde (CH2OHCDO), the smallest sugar as a model molecule, we have calculated correlation 2D IR spectrum of its entire 3N-6 (N=8) normal modes in the mid-to-far-IR region (4000-0 cm(-1)), using quantum chemical anharmonic frequency and anharmonicity computations in conjunction with time-domain third-order nonlinear response functions. The calculated 2D IR spectra were found to contain a network of structural and dynamical parameters of the molecule. It is found that certain spectral regions, once enlarged, show features that are in reasonable agreement with limited but already available single- and dual-frequency 2D IR experimental results. The extension of narrow-band 2D IR spectroscopy into the full mid-to-far-IR regime would allow us to characterize the structural distributions and dynamics of molecular complexes in condensed phases with sufficient number of parameters.     

Super flexibility of a 2D Cu-based porous coordination framework on gas adsorption in comparison with a 3D framework of identical composition: framework dimensionality-dependent gas adsorptivities

Selective synthetic routes to coordination polymers [Cu(bpy)(2)(OTf)(2)](n) (bpy = 4,4'-bipyridine, OTf = trifluoromethanesulfonate) with 2- and 3-dimensionalities of the frameworks were established by properly choosing each different solvent-solution system. They show a quite similar local coordination environment around the Cu(II) centers, but these assemble in a different way leading to the 2D and 3D building-up structures. Although the two kinds of porous coordination polymers (PCPs) both have flexible frameworks, the 2D shows more marked flexibility than the 3D, giving rise to different flexibility-associated gas adsorption behaviors. All adsorption isotherms for N(2), CO(2), and Ar on the 3D PCP are of type I, whereas the 2D PCP has stepwise gas adsorption isotherms, also for CH(4) and water, in addition to these gases. The 3D structure, having hydrophilic and hydrophobic pores, shows the size-selective and quadrupole-surface electrical field interaction dependent adsorption. Remarkably, the 2D structure can accommodate greater amounts of gas molecules than that corresponding to the inherent crystallographic void volume through framework structural changes. In alcohol adsorption isotherms, however, the 2D PCP changes its framework structure through the guest accommodation, leading to no stepwise adsorption isotherms. The structural diversity of the 2D PCP stems from the breathing phenomenon and expansion/shrinkage modulation.     

Rose‐Like Microstructures of Polyaniline by Using a Simplified Template‐Free Method under a High Relative Humidity

3‐D rose‐like microstructures of polyaniline (PANI), which are self‐assembled from 2‐D nanosheets consisted of 1‐D nanofibers, were synthesized by a template‐free method in the presence of ammonium peroxydisulfate (APS) as both oxidant and dopant under a high relative humidity of 80% for the first time. When the relative humidity increases from 25 to 80%, not only morphology of the micro/nanostructured PANI undergoes a change from 1‐D nanofibers to 2‐D nanosheets to 3‐D rose‐like microstructures, but also increase in crystallinity. It is proposed that a cooperation effect of the oriented water molecules at the vapor–water interface and difference in hydrogen bonding energies between the interface and the bulk induced by the relative high humidity results in the formation of the 3‐D rose‐like microstructures self‐assembled from 2‐D nanosheets. Moreover, the method reported may provide a simple approach for understanding self‐assembly of complex micro/nanostructures of PANI.

     

ReverseScreen3D: a structure-based ligand matching method to identify protein targets

Ligand promiscuity, which is now recognized as an extremely common phenomenon, is a major underlying cause of drug toxicity. We have developed a new reverse virtual screening (VS) method called ReverseScreen3D, which can be used to predict the potential protein targets of a query compound of interest. The method uses a 2D fingerprint-based method to select a ligand template from each unique binding site of each protein within a target database. The target database contains only the structurally determined bioactive conformations of known ligands. The 2D comparison is followed by a 3D structural comparison to the selected query ligand using a geometric matching method, in order to prioritize each target binding site in the database. We have evaluated the performance of the ReverseScreen2D and 3D methods using a diverse set of small molecule protein inhibitors known to have multiple targets, and have shown that they are able to provide a highly significant enrichment of true targets in the database. Furthermore, we have shown that the 3D structural comparison improves early enrichment when compared with the 2D method alone, and that the 3D method performs well even in the absence of 2D similarity to the template ligands. By carrying out further experimental screening on the prioritized list of targets, it may be possible to determine the potential targets of a new compound or determine the off-targets of an existing drug. The ReverseScreen3D method has been incorporated into a Web server, which is freely available at http://www.modelling.leeds.ac.uk/ReverseScreen3D .     

DB-Curve: a novel 2D method of DNA sequence visualization and representation

The large number of bases in a DNA sequence and the cryptic nature of the 4-alphabet representation make graphical visualization of DNA sequences useful for biologists. However, existing 3D graphical representations are complicated, whereas existing 2D graphical representations suffer from high degeneracy, and many features in a DNA sequence cannot be visualized clearly. This Letter introduces a novel 2D method of DNA representation: the DB-Curve (Dual-Base Curve), which overcomes some of the limitations in existing 2D graphical representations. Many properties of DNA sequences can be observed and visualized easily using a combination of DB-Curves. The new representation can avoid degeneracy completely compared to existing 2D graphical representations of DNA sequences. Unlike 3D graphical representations, no 2D projection is required for the DB-Curve, and this allows for easier analysis of DNA sequences. The DB-Curve provides a useful graphical tool for the visualization and study of DNA sequences.     

Optimization of a comprehensive two-dimensional normal-phase and reversed-phase liquid chromatography system

The present investigation is based on the evaluation of the performance of a comprehensive two-dimensional liquid chromatography (LCxLC) system during method optimization. The LCxLC set-up, operated in normal phase (NP) mode (adsorption) in the first dimension (1D) and reversed-phase (RP) mode in the second dimension (2D), is equipped with a 1D microbore silica column and a 2D monolithic C(18) column with a 10-port two position valve as the interface. A photodiode array detector is used after the 2D separation. A possible cause of peak distorsion because of the immiscibility of the mobile phases employed in the two dimensions is resolved. The optimization of the analytical run time and flow rate for both dimensions and the initial gradient in the 2D is carried out with various standard compounds. The potential and versatility of this LCxLC approach is demonstrated through the separation of 11 standard components, most of them allergens. The latter, which are characterized by a scattered distribution on the 2D space plane, underwent separation on both a hydrophobicity and polarity basis.     

Photostability via sloped conical intersections: a computational study of the excited states of the naphthalene radical cation

On the basis of an extensive ab initio electronic structure study of the ground and excited-state potential energy surfaces of the naphthalene radical cation (N*+), we propose a mechanism for its ultrafast nonradiative relaxation from the second excited state (D2) down to the ground state (D0), which could explain the experimentally observed photostability [Zhao, L.; Lian, R.; Shkrob I. A.; Crowell, R. A.; Pommeret, S.; Chronister, E. L.; Liu, A. D.; Trifunac, A. D. J. Phys. Chem. A., 2004, 108, 25]. The proposed photophysical relaxation pathway involves internal conversion from the D2 state down to the D0 state via two consecutive, accessible, sloped conical intersections (CIs). The two crossings, D0/D1 and D1/D2, are characterized at the complete active space self-consistent field (CASSCF) level. At this level of theory, the D0/D1 crossing is energetically readily accessible, while the D1/D2 CI appears too high in energy to be involved in internal conversion. However, the inclusion of dynamic correlation effects, via single point CASPT2 calculations including excitations out of the valence pi- and sigma-orbitals, lowers the D0 and D2 state energies with respect to D1. Extrapolations at the CASPT2 level predict that the D1/D2 crossing is then significantly lower in energy than with CASSCF indicating that with a higher-level treatment of dynamic correlation it may be energetically accessible following vertical excitation to D2. N*+ is proposed as one of the species contributing to a series of diffuse infrared absorption bands originating from interstellar clouds. Understanding the mechanism for photostability in the gas phase, therefore, has important consequences for astrophysics.     

Electronic interactions in a new pi-extended tetrathiafulvalene dimer

The first pi-extended tetrathiafulvalene (exTTF) dimer in which the two exTTF units are covalently connected by 1,3-dithiole rings has been obtained in a multistep synthetic procedure involving the Ullmann cross-coupling reaction by using copper(I) thiophene-2-carboxylate (CuTC). The electronic spectrum reveals a significant electronic interaction between the exTTF units. The electrochemical study carried out by cyclic voltammetry in solution and in thin-layer conditions, and the electrochemical simulation and spectroelectrochemical (SEC) measurements confirm the electronic communication and show that the oxidation of dimer 14 occurs as two consecutive 2 e(-) processes D(0)-D(0)-->D(2+)-D(0)-->D(2+)-D(2+). Theoretical calculations, performed at the B3P86/6-31G* level, confirm the experimental findings and predict that 14(2+) exists as a delocalized D(.+)-D(.+) species in the gas phase and as a localized D(2+)-D(0) species in solution (CH(3)CN or CH(2)Cl(2)). Oxidation of 14(2+) forms the tetracation 14(4+) which is constituted by two aromatic anthracene units bearing four aromatic, almost orthogonal 1,3-dithiolium cations.     

Transformation of a C-methylcalix[4]resorcinarene-based host-guest complex from a wave-like to a novel triangular brick-wall architecture

A novel 2D triangular brick-wall framework based on CMCR and bpe with included ruthenocene guest molecules is formed with time by conversion of a 1D wave-like polymer structure with an accompanying bowl-to-boat conformational change of the CMCR molecules.     

Molecular planting of a single organothiol into a “gap-site” of a 2D patterned adlayer in an electrochemical environment

The self-assembled inclusion of molecules into two-dimensional (2D) porous networks on surfaces has been extensively studied because 2D functional materials consisting of organic molecules have become an important research topic. However, the isolation of a single molecular thiol remains a challenging goal. Here, we report a method of planting and isolating organothiols onto a 2D patterned organic adlayer at an electrochemical interface. In situ scanning tunneling microscopy revealed that the phase transition of an ovalene adlayer is electrochemically induced and that the gap site created by three ovalene molecules serves as a 2D molecular template to isolate thiol molecules and to standardize the distance between them via the formation of precise selective open spaces, suggesting that electrochemical “molecular planting” opens applications for 2D patterns of isolated single organothiol molecules.

Gap sites electrochemically created in the ovalene adlayer can accept a single thiol.