Orientation of a benzene molecule inside a carbon nanotube

Benzene molecules confined in carbon nanotubes of varying radii are employed as semiconductors in electronic nanodevices, and their orientation determines the electrical properties of the system. In this paper, we investigate the interaction energy of all the possible configurations of a benzene molecule inside various carbon nanotubes and then we determine the equilibrium configuration. We adopt the continuous approach together with the semi-empirical Lennard-Jones potential function to model van der Waals interaction between a benzene molecule and a carbon nanotube. This approach results in an analytical expression, which accurately approximates the interaction energy and can be readily used to generate numerical data. We find that horizontal, tilted and perpendicular configurations on the axis of the carbon nanotube are all possible equilibrium configurations of the benzene molecule when the radius of the carbon nanotube is less than 5.580 Å. However, when the radius of the carbon nanotube is larger than 5.580 Å an offset horizontal orientation is the only possible equilibrium configuration of the benzene molecule. In the limiting case, the orientation of a benzene molecule on a graphene sheet can be derived simply by letting the radius of the carbon nanotube tend to infinity.     

Helium 4 dimer in nanotubes

The ground state of the helium 4 dimer is considered using the Monte Carlo technique. In a cylinder with a hard core wall, binding depends on its radius. For a small radius binding occurs as in the one-dimensional case. With an increase of the radius, the binding becomes stronger, reaches its maximum value, and then slowly diminishes. In conical geometry, that may be realized as a generalization of a cylindrical one, this dependence of the binding energy on the radius might lead to an effective force which tends to move the molecule toward the region of minimal energy. Thus, in channels, with nonhomogeneous cross-sections, the particles move easier in dimer form. In addition, the square of the momentum and of the particle separation along the cylinder axis and in the plane perpendicular to it are calculated as well.     

Theoretical investigations of the perylene electronic structure: Monomer,dimers, and excimers

The structural and electronic properties of perylene molecule, dimers, and excimers have been computationally studied. The present work represents the first systematic study of perylene molecule and dimer forms by means of long‐range corrected time‐dependent density functional theory (TDDFT) approaches. Initially, the study explores the photophysical properties of the molecular species. Vertical transitions to many excited singlet states have been computed and rationalized with different exchange‐correlation functionals. Differences between excitation energies are discussed and compared to the absorption spectrum of perylene in gas phase and diluted solution. De‐excitation energy from the relaxed geometry of the lowest excited singlet is in good agreement with the experimental fluorescence emission. Optimization of several coplanar forms of the perylene pair prove that, contrary to generalized gradient approximation (GGA) and hybrid exchange‐correlation functionals, corrected TDDFT is able to bind the perylene dimer in the ground state. Excitation energies from different dimer conformers point to dimer formation prior to photoexcitation. The fully relaxed excimer geometry belongs to the perfectly eclipsed conformation with D_2h symmetry. The excimer equilibrium intermolecular distance is shorter than the separation found for the ground state, which is an indication of stronger interchromophore interaction in the excimer state. Excimer de‐excitation energy is in rather good agreement with the excimer band of perylene in concentrated solution. The study also scans the energy profiles of the ground and lowest excited states along several geometrical distortions. The nature of the interactions responsible for the excimer stabilization is explored in terms of excitonic and charge resonance contributions. © 2015 Wiley Periodicals, Inc.     

Equilibrium density of states and thermodynamic properties of a model glass former

This paper presents an analysis of the thermodynamics of a model glass former. We have performed equilibrium sampling of a popular binary Lennard-Jones model, employing parallel tempering Monte Carlo to cover the crystalline, amorphous, and liquid regions of configuration space. Disconnectivity graphs are used to visualize the potential energy landscape in the vicinity of a crystalline geometry and in an amorphous region of configuration space. The crystalline global minimum is separated from the bulk of the minima by a large potential energy gap, leading to broken ergodicity in conventional simulations. Our sampling reveals crystalline global minima that are lower in potential energy than some of the previous candidates. We present equilibrium thermodynamic properties based on parallel tempering simulations, including heat capacities and free energy profiles, which depend explicitly on the crystal structure. We also report equilibrium melting temperatures.     

电场作用下C60富勒烯二聚体分子的几何构型与失效

By the molecular mechanics/quantum mechanics method, the geometry distortion and configuration invalidity of dimmer C60fullerene (2C60) molecule in external electric field are simulated. The effect of the electric field, with three different directions, on geometry distortion, configuration invalidity, polarization charge distribution and dipole moment for 2C60 molecule is discussed systemtically. Further the geometry distortion and invalidity of 2C60 molecule are respectively compared with those of C60 fullerene molecule in electric field. By comparison, it is shown that geometry distortion and configuration invalidity behavior of 2C60 molecule are sensitive to the direction of electric field, when the directions of the applied electric field are parallel to the bridged C-C bonds. For 2C60molecule it is very easy for the configuration of 2C60 molecule to be invalidated and the invalidity mode is very particular as well.     

Emission of thioflavin T and its off-on control in polymer membranes.

The absorption and emission spectral properties of thioflavin T (TFT+) in Nafion (Nf) and cellulose matrices have been studied. Formation of the emittive dimer is observed in both matrices. The monomer TFT+ emission is blueshifted in Nafion membrane (Nf), whereas it is red-shifted in cellulose membrane when compared with the emission in aqueous solution. The dimer emission of TFT+ in the Na+-Nf membrane undergoes off-on switching with acids and alkalis. The TFT+ molecule undergoes protonation in the H+-Nf and the protonated dye is fluorescent. The dimer emission of TFT+ is not observed in the dry H+-Nf membrane because of the protonation of the TFT+ molecule. The diffusion coefficient and the free energy of hydrophobic interaction for the TFT+ molecule in the Nf membrane are calculated. The TFT+ molecule experiences hydrophobic and electrostatic interactions in the Nf matrix, whereas it experiences a polar environment in the cellulose membrane. The 3D emission spectral studies support the formation of the emittive dimer in both Nf and cellulose matrices.     

On the effect of 4f electrons on the structural characteristics of lanthanide trihalides: computational and electron diffraction study of dysprosium trichloride

The molecular and electronic structure of dysprosium trichloride, DyCl(3), was calculated by high-level quantum chemical methods in order to learn about the effect of the partially filled 4f subshell and of the possible spin-orbit coupling on them. High-temperature electron diffraction studies of DyCl(3) were also carried out so that we could compare the computed geometry with the experimental one, after thermal corrections on the latter. Dysprosium monochloride, DyCl, and the dimer of dysprosium trichloride, Dy(2)Cl(6), were also investigated by computation. We found that the electron configuration of the 4f subshell does not influence the geometry of the trichloride monomer molecule as the ground state and first excited state molecules have the same geometry. Nonetheless, taking the 4f electrons into account in the calculation, together with the 5s and 5p electrons, is important in order to get geometrical parameters consistent with the results from experiment. Based on electron diffraction and different levels of computation, the suggested equilibrium bond length (r(e)) of DyCl(3) is 2.443(14) A, while the thermal average distance (r(g)) from electron diffraction is 2.459(11) A. The molecule is trigonal planar in equilibrium. Although the ground electronic state splits due to spin-orbit coupling, the lowering of the total electronic energy is very small (about 0.025 hartree) and the geometrical parameters are not affected. In contrast with the monomeric trichloride molecule, the bond angles of the dimer seem to be different for different electronic states, indicating the influence of the 4f electronic configuration on their structure. We carried out an anharmonic analysis of the out-of-plane vibration of the trichloride monomer and found that the vibration is considerably anharmonic at 39.5 cm(-1), compared with the 30.5 cm(-1) harmonic value.     

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide

The energy landscape of the monomer and dimer are explored for the amyloidogenic heptapeptide GNNQQNY from the N-terminal prion-determining domain of the yeast protein Sup35. The peptide is modeled by a united-atom potential and an implicit solvent representation. Replica exchange molecular dynamics is used to explore the conformational space, and discrete path sampling is employed to investigate the pathways that interconvert the most populated minima on the free energy surfaces. For the monomer, we find a rapid fluctuation between four different conformations, where a geometry intermediate between compact and extended structures is the most thermodynamically favorable. The GNNQQNY dimer forms three stable sheet structures, namely in-register parallel, off-register parallel, and antiparallel. The antiparallel dimer is stabilized by strong electrostatic interactions resulting from interpeptide hydrogen bonds, which restrict its conformational flexibility. The in-register parallel dimer, which is close to the amyloid beta-sheet structure, has fewer interpeptide hydrogen bonds, making hydrophobic interactions more important and increasing the conformational entropy compared to the antiparallel sheet. The estimated two-state rate constants indicate that the formation of dimers from monomers is fast and that the dimers are kinetically stable against dissociation at room temperature. Interconversions between the different dimers are feasible processes and are more likely than dissociation.     

Using ONIOM calculations to investigate the abilities of simple and nitrogen,boron, sulfur-doped carbon nanotubes in sensing of carbon monoxide

In this work, geometries, stabilities, and electronic properties of the carbon monoxide (CO) molecule as an adsorbent in a simple carbon nanotube (CNT) and nitrogen (N), boron (B), sulfur (S)-doped CNTs (NCNT, BCNT, and SCNT) with parallel and perpendicular configurations are fully considered using ONIOM, natural bond orbital, and quantum theory of atom in molecule (QTAIM) calculations. The adsorption energies (E_ad) demonstrate that a CO molecule could be adsorbed on the surface of the simple CNT with parallel configuration and N-doped CNT with perpendicular configuration in an exothermic process. QTAIM calculations showed the close-shell (noncovalent) interactions between the CO molecule and CNT or N, B, S-doped CNTs. In addition, the energy gap (E_g) values between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are calculated. In accordance with the results of energy gap, simple and N-doped CNTs could be used as CO sensors.     

Theoretical study on the aggregation-induced emission mechanism of anthryl-tetraphenylethene

Since the concept of aggregation-induced emission (AIE) was proposed by Benzhong Tang's research group in 2001, the exploration of the mechanism of AIE and the development of new high-performance AIE materials have been the focus and goal of this field. On the basis of a large number of experiment results, AIE mechanism has been well explained by lots of works, such as restricted intramolecular motion (RIM), J-aggregate et al. As tetraphenylethlene (TPE) molecules are stacked, the rotation of the benzene ring rotor is blocked, and the energy attenuation is released in the form of radiation, showing the AIE effect. In order to further explore the AIE effect of TPE, we performed electronic structure, spectrum simulation, and AIE mechanism calculations of the anthryl-tetraphenylethene (TPE-an) monomer and dimer in the gas phase, tetrahydrofuran (THF), and aqueous solutions at the B3LYP/6-31G** level. The calculation results show that TPE-an molecule is in a propeller-like configuration, and its fluorescence intensity is weak; compared with the monomer, the fluorescence intensity of the dimer increases by 87% in aqueous solution; the fluorescence intensity in the gas phase, THF solution, and aqueous solution gradually enhances with the increase of the degree of aggregation, which are consistent with the experimental results. The enhancement of fluorescence intensity is caused by the change of molecular structure caused by aggregation. This detailed AIE luminescence mechanism will provide theoretical guidance for AIE material design.     

Remote Effect from Boron Cluster: Tunable Photophysical Properties of o-Carborane-Based Luminogens

We proposed a new molecular design strategy that the o-carboranyl group is attached as “an innocent unit” to the remote side of luminogens to tune photophysical properties. To verify this strategy, two o-carborane-based compounds with asymmetric molecular geometry were designed and synthesized. Photophysical properties of o-carborane-based luminogens were investigated on the basis of UV-Vis spectra, photoluminescence spectra, crystal structure analysis and theoretical calculations. The results indicate that the o-carboranyl group has a slight effect on the energy gap between the ground state (S₀) and the first excited state (S₁) in the solution state but a significant effect on the energy gap between S₀ and S₁ in the solid state. Besides, the radiative and non-radiative transition processes are modulated by the o-carboranyl unit. This leads to emission quenching in the solution state but an enhanced luminous efficiency in the aggregate state with a typical aggregation-induced emission (AIE) property.     

Influence of the electric field on BN conical structures

We apply first‐principles calculations to investigate the effect of the electric field on boron nitride conical structures. The studies involve nanocones with different disclination angles. We applied fields of 0.3 V/Å and 0.6 V/Å parallel to the cone axis. It is shown that a small field does not affect the stability of such structures; however, for a larger field, a decrease of 0.1 eV/atom for all structures is observed. We also find modification in the energy gap due to the intensity of the electric field. The bandgap decreased proportionally to the intensity of the electric field, indicating that these results have consequences in the field emission properties of these structures. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Z‐Shaped Pentaleno‐Acene Dimers with High Stability and Small Band Gap

Acene‐based materials have promising applications for organic electronics but the major constrain comes from their poor stability. Herein a new strategy to stabilize reactive acenes, by fusion of an anti‐aromatic pentalene unit onto the zigzag edges of two acene units to form a Z‐shaped acene dimer, is introduced. The Z‐shaped acene dimers are extremely stable and show a small energy gap resulting from intramolecular donor–acceptor interactions. X‐ray crystallographic analysis revealed their unique geometry and one‐dimensional slip‐stack columnar structure. Besides optical and electrochemical characterizations, solution‐processed field‐effect transistors were also fabricated.     

Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Core localization and sigma* delocalization in the O 1s core-excited sulfur dioxide molecule

Electron-ion-ion coincidence measurements of sulfur dioxide at discrete resonances near the O 1s ionization edge are reported. The spectra are analyzed using a model based upon molecular symmetry and on the geometry of the molecule. We find clear evidence for molecular alignment that can be ascribed to symmetry properties of the ground and core-excited states. Configuration interaction (CI) calculations indicate geometry changes in accord with the measured spectra. For the SO(2) molecule, however, we find that the localized core hole does not produce measurable evidence for valence localization, since the transition dipole moment is not parallel to a breaking sigma* O-S bond, in contrast to the case of ozone. The dissociation behavior based upon the CI calculations using symmetry-broken orbitals while fixing a localized core-hole site is found to be nearly equivalent to that using symmetry-adapted orbitals. This implies that the core-localization effect is not strong enough to localize the sigma* valence orbital.     

An Exact Solution to the Electrostatic Interaction between an Ion-Penetrable Sphere and an Ion-Penetrable Rod

No exact solution for the free energy of electrostatic interaction for a charged sphere and rod geometry in an electrolyte solution has yet been proposed. This geometry is interesting because it can be applied to describe macromolecules interacting with a random fiber-matrix for modeling of hindered transport in diffusional systems. Here we present an analytical approach that yields an exact solution to the problem for ion-penetrable-also called "soft"-sphere and infinitely long rod. This solution is compared to a published finite-element analysis of the same system with nonpenetrable-also called "hard"-sphere and infinitely long rod maintaining a constant surface charge density restriction. For any ionic strength or ratio of rod radius to sphere radius the ion-penetrable method yields an electrostatic free energy of interaction which is lower than that given by the analysis for hard bodies. This free energy is significantly lower for most parameter value combinations and therefore suggests that one should carefully examine the system being modeled to determine if it is approximated better by a hard body or ion-penetrable body approach. Copyright 2000 Academic Press.     

The geometry of primary drainage

We show that arc menisci configuration under primary drainage in capillary tube cross sections and, by extension, in throats in the void structure of rock and soil, can be understood in terms of the computational geometry theory of medial axis analysis. The solution for arc meniscus configuration is developed for cross sections of arbitrary, simply connected polygonal shape at both entry- and over-pressure values during primary drainage for arbitrary values of wetting angle. Using this solution technique, we have obtained highly accurate solutions of entry pressure arc meniscus radius for over 21,500 throats obtained from analysis of computed tomography images in a suite of 4 Fontainebleau core samples ranging from 7.5 to 22% porosity. We show that the ratio A/P, of throat area to throat perimeter, is an excellent predictor of entry pressure meniscus radius (and hence entry pressure) for primary drainage for real pores, while inscribed radius and area equivalent radius over-predict entry pressure meniscus radius by factors of 1.5-3, and are consequently poor predictors.