Phase switching of a single isomeric molecule and associated characteristic rectification

Variations in molecular electronic structures related to conformational change are exceedingly attractive because of their key role in the understanding and development of functional processes in molecular electronics and biology. We observed, for the first time, the novel phase switching of a photoactive isomeric molecule, N-(2-mercaptoethyl)-4-phenylazobenzamide (Azo molecule) at a single-molecule level, which exhibits a distinctive change in the conductive characteristic under scanning tunneling microscope (STM) measurement. In comparison with the results obtained by the measurement of photoactive isomerization of the isolated Azo molecule, which was performed also for the first time, the observed characteristics are attributed to the results of the trans and cis phase transformation of the Azo molecule, under the condition of an external electric field and current flow. A specific point is that the potential landscape of the system is controllable by the electric field and provides a conformational stability with asymmetric bias dependence resulting in rectification.     

Exploring the possibilities to control the molecular switching properties and dynamics: A field-switchable rotor-stator molecular system

A bistable, dipolar stator-rotor molecular system-candidate for molecular electronics is investigated. We demonstrate that it is possible to control the intramolecular torsional states and dynamics in this system by applying an appropriate additional electric field (instead of biasing one), achieving fine tuning and modulation of the relevant properties. The electric field effects on the quantities responsible for torsional dynamics (potential energy surface, potential barrier height, quantum and classical transition probabilities, correlation time, HOMO-LUMO gap) are studied from first principles. Our results indicate that it is possible to artificially stabilize the metastable conformational state of the studied molecule. The importance of this is evident, as the current-voltage characteristics of the metastable state are clearly distinguishable from the current-voltage characteristics of the two stable states. We report for the first time exact calculations related to the possibilities to control the thermally induced stochastic switching, and reduce the noise in a practical application. Thus, we believe that the molecule studied in this paper could operate as a field-switchable molecular device under real conditions.     

Au(111)表面Verdazyl自由基的构象转换

Pure organic radical molecules on metal surfaces are of great significance in exploration of the electron spin behavior. However, only a few of them are investigated in surface studies due to their poor thermal stability. The adsorption and conformational switching of two verdazyl radical molecules, namely, 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-2-yl)-6-oxoverdazyl (B2P) and 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-4-yl)-6-oxoverdazyl (B4P), are studied by scanning tunneling microscopy (STM) and density functional theory (DFT). The adsorbed B2P molecules on Au(111) form dimers, trimers and tetramers without any ordered assembly structure in which two distinct appearances of B2P in STM images are observed and assigned to be its "P" and "T" conformations. The "P" conformation molecules appear in the STM image with a large elliptical protrusion and two small ones of equal size, while the "T" ones appear with a large protrusion and two small ones of different size. Likewise, the B4P molecules on Au(111) form dimers at low coverage, strip structure at medium coverage and assembled structure at high coverage which also consists of above-mentioned two conformations. Both B2P molecules and B4P molecules are held together by weak intermolecular interaction rather than chemical bond. STM tip induced conformational switching of both verdayzl radicals is observed at the bias voltage of +2.0 V. The "T" conformation of B2P can be switched to the "P" while the "P" conformation of B4P can be switched to the "T" one. For both molecules, such a conformational switching is irreversible. The DFT calculations with Perdew-Burke-Ernzerhof version exchange-correlation functional are used to optimize the model structure and simulate the STM images. STM images of several possible molecular conformations with different isopropyl orientation and different tilt angle between verdazyl radical and Au(111) surface are simulated. For conformations with different isopropyl orientation, the STM simulated images are similar, while different tilt angles of verdazyl radical lead to significantly different STM simulated images. Combined STM experiments and DFT simulations reveal that the conformational switching originates from the change of tilting angle between the verdazyl radical and Au(111) surface. The tilt angles in "P" and "T" conformations are 0° and 50°, respectively. In this study, two different adsorption conformations of verdazyl radicals on the Au(111) surface are presented and their exact adsorption structures are identified. This study provides a possible way to study the relationship between the electron spin and configuration conversion of pure organic radical molecules and a reference for designing more conformational switchable radical molecules that can be employed as interesting molecular switches.     

A programmable molecular diode driven by charge-induced conformational changes

The 3-nitro-2-(3'-nitro-2'-ethynylpyridine)-5-thiopyridine molecule shows charge-induced conformational switching and a rectifying behavior with a charge-induced controllable switching. This device can be used as a memory operated with an external field interacting with one of the rings local dipole. Alternatively, the molecule can be used as a nano-actuator controlling the rotation of the ring by charging the molecule with a bias voltage.     

Electric field induced switching behaviors of monolayer-modified silicon surfaces: surface designs and molecular dynamics simulations

Electric field induced switching behaviors of a series of low-density omega-carboxyalkyl modified H-Si(111) and the mixed omega-carboxyalkyl/alkyl covered H-Si(111) have been simulated by using molecular dynamics (MD) simulation techniques. The external electric fields may drive surface-confined molecules to reversibly change conformations between the all-trans (switching "on") and the mixed trans-gauche (switching "off") states. Such surfaces switch wettabilities between the hydrophilic state and the moderately hydrophobic state. It has been found in broad ranges of intensities of applied electric fields, -2.0 x 10(9) V/m < or = E(down) < or = 0 and 1.8 x 10(9) V/m < or = E(up) < or = 7.3 x 10(9) V/m, both the low-density (11.1%-33.3%) omega-carboxyalkyl and the mixed omega-carboxyalkyl/alkyl (in mole fraction of 0.4 < or = N(carboxyalkyl) : N(alkyl) < or = 3.0) monolayers covering H-Si(111) exhibit conformational switching in the aqueous medium. The critical intensity of the electric field, E(up) = 1.8 x 10(9) V/m, which is required to trigger the switches is observed by our MD simulations and further rationalized by a thermodynamical model. Some important factors in the control of switching performances, such as the steric hindrances, the formation of the electric double layer at the monolayer/electrolyte solution interface, the hydration effects of carboxylate anions, the components of surrounding electrolyte solutions, as well as the rigidity of surface-confined chains are elucidated. The lower ionic strength and additions of acetonitrile molecules in the surrounding aqueous solution can reduce the value of critical intensity of the electric field and hence facilitate the realization of switching. Some practical considerations in construction and optimum design of switching surfaces are also suggested.     

Computational analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) (TSAO) as HIV-1 reverse transcriptase inhibitors: relevance of conformational properties on the inhibitory activity

We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.     

The influence of layer curvature on switching in ferroelectric B2 phases of liquid crystals having bent-shape molecules

In the B₂ phase of liquid crystalline compounds with bent-shape molecules ferroelectric switching can occur either by molecular rotation on the cone or by rotation of the molecule about its long axis (so-called chirality flipping), or by both mechanisms simultaneously. When the smectic layers of the B₂ phase are non-deformed and parallel the rotation of molecules under an external electric field occurs readily on the surface of the cone, while rotation around the long molecular axis is hindered by an energy barrier. Imposed deformation of smectic layers leads to interaction between local layer curvatures and molecular orientation, which results in the energy barrier hindering the molecular rotation by a cone. For appropriate constants describing this interaction the energy barrier can be so high that chirality flipping becomes the principal switching mode. An increase in the electric field can eliminate layer curvature, and therefore the energy barrier, so that switching with molecular rotation on the cone becomes possible. In the present contribution these mechanisms of switching are discussed and the influence of layer curvature on the switching mode is demonstrated.     

Enhanced role of Al or Ga-doped graphene on the adsorption and dissociation of N2O under electric field

To find an effective strategy for the capture and decomposition of nitrous oxide (N(2)O) is very important in order to protect the ozone layer and control the effects of global warming. Based on first-principles calculations, such a strategy is proposed by the systemic study of N(2)O interaction with pristine and Al (or Ga)-doped graphene, and N(2)O dissociation on the surface of Al (or Ga)-doped graphene in an applied electric field. The calculated adsorption energy value shows the N(2)O molecule more firmly adsorbs on the surface of Al (or Ga)-doped graphene than that of pristine graphene, deriving from a stronger covalent bond between the N(2)O molecule and the Al (or Ga) atom. Furthermore, our study suggests that N(2)O molecules can be easily decomposed to N(2) and O(2) with the appropriate electric field, which reveals that Al-doped graphene may be a new candidate for control of N(2)O.     

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.     

Electric field-derived point charges to mimic the electrostatics in molecular crystals

Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.     

Small Janus dimer as electric field manipulated molecular clam switch and electric information storage unit

A small Janus molecular dimer, as external electric field (F_z) manipulated both a molecular clam switch and a novel electric information storage unit, is found by quantum chemical computations for the first time. The molecular clam switching is intriguing and reversible. A critical F_z value of 95 × 10⁻⁴ au causes a dramatically open change in conformation from Closed form to Open form. And a small reversed electric field of F_z = −10 × 10⁻⁴ au performs a close change from Open form to Closed form. In the switching process, owing to the existence of a great electric dipole moment (μ) contrast between 0 and 22.13 D, the molecular clam switch may serve as an electric information storage unit. Gratifyingly, the reading, writing, and erasing of binary information on the electric information storage unit are easy. And further calculations show that Janus graphene fragment dimer can also serve as a molecular clam switch. Thus, this work proposes a new molecular switch prototype in the invention of artificial molecular machines, and a novel electric information storage unit in the field of molecular electronics.     

Labeling of DNA via rearrangement of S-2-aminoethyl phosphorothioates to N-(2-mercaptoethyl)phosphoramidates

The reaction of phosphorothioates in DNA with 2-bromoethylammonium bromide results in S-2-aminoethyl phosphorothioates, which can rearrange to N-(2-mercaptoethyl)phosphoramidates providing a facile method for the generation of site-specific thiol labeling of DNA sequences. The applicability of this method was demonstrated by conjugation of the thiolated DNA sequence with Na-(3-maleimidylpropionyl) biocytin and Alexa Fluor 546 C5-maleimide.     

Electrical switching of DNA monolayers investigated by surface plasmon resonance

The switching of DNA monolayers between a "lying" and a "standing" state initiated by applying electric field, and the subsequent DNA hybridization at different states were investigated in a contactless, label-free mode by surface plasmon resonance (SPR) technique. The results showed that the strength of the electric field and surface coverage could influence the switching of DNA monolayers. In addition, it was found that DNA hybridization efficiency could be enhanced or decreased when DNA probes stood straight up or lay flat on the gold surface, depending on the potential of the gold substrate. The enhancement of DNA hybridization efficiency reached the maximum when surface coverage reached 5.87 x 10(12) molecules/cm(2) and the potential of gold substrate was more negative than -0.7 V (versus ITO-coated glass). The research may be helpful for the construction of sensitive biosensors, biochips, and nanoscale electronic devices.     

Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulation

The morphogenic opiate pentapeptide leucine-enkephalin (lenk) in a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer is studied using NMR spectroscopy and molecular dynamics simulation. Contrary to the frequent assumption that the peptide attains a single fixed conformation in the presence of membranes, we find that the lenk molecule is flexible, switching between specific bent conformations. The constraints to the orientation of the aromatic rings that are identified by the NMR experiment are found by the MD simulation to be related to the depth of the peptide in the bilayer. The motion of the N-H vectors of the peptide bonds with respect to the magnetic field direction as observed by MD largely explain the magnitude of the observed residual dipolar coupling (RDC), which are much reduced over the static (15)N-(1)H coupling. The measured RDCs are nevertheless significantly larger than the predicted ones, possibly due the absence of long-time motions in the simulations. The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms.     

Cyclohexane in nanotubes: Direct chair–chair interconversion

DFT PBE/3ζ study of conformational transformations of cyclohexane inside nanotubes with chirality indices of (8,0) and (5,5) showed that the encapsulated molecule is characterized by shortened C–C bonds, some electric charge, and reduced barrier to chair–chair interconversion in comparison to the free molecule. Unlike free cyclohexane, no twist conformer as intermediate minimum on the potential energy surface was localized for the encapsulated molecule.     

Determination of potential-energy surface of molecules in an applied field on the basis of virial relations

The quantum-mechanical virial theorem (in diagonal and nondiagonal forms) for molecules in an external, weak, uniform electric field is used for obtaining the analytical expression of the potentialenergy surface in the Hartree–Fock–Roothaan one-determinantal approximation. The polarizability tensor components of the H₂O molecule are computed on this basis. The dependence of basing the atomic orbitals upon the intensity of the applied field lead to good coincidence of results with the data of near Hartree–Fock calculations.     

Functionality in single-molecule devices: model calculations and applications of the inelastic electron tunneling signal in molecular junctions

We analyze how functionality could be obtained within single-molecule devices by using a combination of non-equilibrium Green's functions and ab initio calculations to study the inelastic transport properties of single-molecule junctions. First, we apply a full non-equilibrium Green's function technique to a model system with electron-vibration coupling. We show that the features in the inelastic electron tunneling spectra (IETS) of the molecular junctions are virtually independent of the nature of the molecule-lead contacts. Since the contacts are not easily reproducible from one device to another, this is a very useful property. The IETS signal is much more robust versus modifications at the contacts and hence can be used to build functional nanodevices. Second, we consider a realistic model of a organic conjugated molecule. We use ab initio calculations to study how the vibronic properties of the molecule can be controlled by an external electric field which acts as a gate voltage. The control, through the gate voltage, of the vibron frequencies and (more importantly) of the electron-vibron coupling enables the construction of functionality: nonlinear amplification and/or switching is obtained from the IETS signal within a single-molecule device.     

Ambient Bistable Single Dipole Switching in a Molecular Monolayer

Reported here is a molecular dipole that self‐assembles into highly ordered patterns at the liquid‐solid interface, and it can be switched at room temperature between a bright and a dark state at the single‐molecule level. Using a scanning tunneling microscope (STM) under suitable bias conditions, binary information can be written at a density of up to 41 Tb cm^?2 (256 Tb/in²). The written information is stable during reading at room temperature, but it can also be erased at will, instantly, by proper choice of tunneling conditions. DFT calculations indicate that the contrast and switching mechanism originate from the stacking sequence of the molecular dipole, which is reoriented by the electric field between the tip and substrate.     

Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.