Molecular Model Systems Research Articles

Translational Dynamics of One-Dimensional Fullerene Chains Encapsulated Inside Single-Walled Carbon Nanotubes

Fullerenes inserted in single-walled carbon nanotubes, the so-called “peapods,” provide scientists with an exceptional molecular model system to study one-dimensional physics and confinement. In this communication, we present recent inelastic neutron scattering measurements concerning the translational dynamics of this one-dimensional system. The recent synthesis of a large amount of two-dimensional oriented samples allows us to extract the sole contribution of the inserted C60 chains. The related quasi-elastic-like peak evolves with the temperature but never shows an additional inelastic contribution when lowering temperature, indicating that carbon peapod is a true one-dimensional system down to low temperatures.

Binding of styrene on silicon (111)-7 × 7 surfaces as a model molecular electronics system

Styrene on Si(111)-7 × 7 surfaces was investigated as a model molecular electronics system to study the effects of conjugation to the semiconductor surface. Scanning tunneling microscopy imaging, combined with theoretical images show that styrene molecules bind in a [4 + 2] cycloaddition mode, binding at the terminal C of the vinyl substituent and a C on the phenyl ring. These single molecule results are consistent with those of ensembles of molecules as obtained by high resolution electron energy loss spectroscopy. For styrene on Si(111)-7 × 7, the aromaticity of the phenyl ring is broken and the conjugated π-system does not extend to the silicon surface, potentially hindering conduction between molecule and surface. However, styrene does retain a conjugated π-system after binding, as is evident in the π-π* shakeup transition in the C 1s x-ray photoelectron spectra as well as UV photoemission spectra. This suggests that styrene-type molecules, when bonded to Si surfaces, do not maintain ready conduction between molecule and surface.

Effect of discontinuities in Kohn-Sham-based chemical reactivity theory

We provide a new derivation of a formula for the Fukui function of density functional chemical reactivity theory which incorporates the discontinuities in the Kohn-Sham reference system. Orbital relaxations are described in terms of the exchange-correlation (XC) kernel, i.e., the derivative of the XC potential with respect to the density and it is shown that in order to correctly measure the reactivity toward a nucleophilic reagent a discontinuity of the XC kernel has to be taken into account. The importance of this finding is illustrated in model molecular systems.

Tuning Structural and Mechanical Properties of Two-Dimensional Molecular Crystals: The Roles of Carbon Side Chains

A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

Assessment of density functional theory for bonds formed between rare gases and open-shell atoms: a computational study of small molecules containing He, Ar, Kr and Xe

The validity of the description of the DFT approximations currently implemented in plane wave DFT codes (LDA, GGA, meta-GGA, hybrid, GGA + empirical dispersion correction) for interactions between rare gases and open-shell atoms which form materials is poorly known. We have performed a first assessment of the accuracy of these functionals for the description of the bonds formed by helium, argon, krypton and xenon with various open-shell atoms. This evaluation has been done on model molecular systems for which precise experimental data are available and reference post-Hartree-Fock calculations (CCSD(T) using large basis sets) are feasible. The results show that when the rare gas atom shares density with the neighbouring atoms, the GGA functionals yield good geometries and qualitatively correct binding energies, even if these are quite significantly overestimated. The use of hybrid functionals enables us to obtain good geometries and satisfactory binding energies. For compounds in which the rare gas atom forms weak dispersive-like bonding, the accuracy yielded by the various functionals is not as good. No functional gives satisfactory binding energies for all the compounds investigated. Several GGA and hybrid functionals yield correct geometries, even if some isomers are not obtained. One GGA functional (PBE) yields qualitatively correct results for the compounds of the three rare gases and several hybrid functionals give satisfactory energies for He compounds. The addition of an empirical dispersive correction improves the results on association compounds, but several isomers are not found.

Analysis of phase transitions in molecular solids: quantitative assessment of phonon-mode vs intra-molecular spectral data

The efficacy of phonon-mode spectral data (20–400 cm−1) in identifying and characterising phase transitions is for the first time compared directly with traditional “fingerprint” intra-molecular spectral data (400–3800 cm−1) for a model molecular system, using a range of statistical approaches and algorithms. Both data sets were collected in the same experiment, allowing a direct comparison. We find that phonon-mode data offer a reliable method of identifying phase transitions, whereas the intra-molecular are inherently unsuitable. Our results are likely to apply widely to solid-solid transformations.

Model of Self Reproducing Vesicles

Evolution of molecular assemblies toward a cellular life in prebiotic world is fascinating research filed in soft matter science. So far extensive investigations have been performed to construct molecular model system which expresses similar dynamics as those of a life system using well-defined organic molecules. Especially modeling of a self-reproducing vesicular system is a key concept to understand origin of the cellular life. In typical self-reproducing vesicle systems, membrane precursors are converted into membrane molecules with the help of a catalyst and the membrane molecules induce the formation of daughter vesicles. The self-reproducing vesicle systems have two pathways for the topology transition, the birthing and the budding. In the birthing pathway, new synthesized membrane molecules form daughter vesicles inside a mother vesicle. When the daughter vesicle grows to a certain size, it extrude through the membrane of the mother vesicle to the environment. On the other hand, in the budding pathway, the mother vesicle deforms to pear-like shape and is divided into two independent vesicles. We established a model self-reproducing vesicle system without the membrane molecule synthesis route. The model vesicle composed of cylinder- and inverse-cone-shaped lipids formed inclusion vesicles inside the mother vesicle and the inclusion vesicles were then expelled by a temperature cycling. By changing the vesicle composition, the mother vesicles showed the budding type self-reproduction pathway. A key concept of this system is the coupling of the main-chain transition and the shape of lipids.

Molecular early main group metal hydrides: synthetic challenge, structures and applications

Within the general area of early main group metal chemistry, the controlled synthesis of well-defined metal hydride complexes is a rapidly developing research field. As group 1 and 2 metal complexes are generally highly dynamic and lattice energies for their [MH](∞) and [MH(2)](∞) salts are high, the synthesis of well-defined soluble hydride complexes is an obvious challenge. Access to molecular early main group metal hydrides, however, is rewarding: these hydrocarbon-soluble metal hydrides are highly reactive, have found use in early main group metal catalysis and are potentially also valuable molecular model systems for polar metal hydrides as a hydrogen storage material. The article focusses specifically on alkali and alkaline-earth metal hydride complexes and discusses the synthetic challenge, molecular structures, reactivity and applications.

A Collaborative Molecular Modeling Environment Using a Virtual Tunneling Service

Collaborative researches of three-dimensional molecular modeling can be limited by different time zones and locations. A networked virtual environment can be utilized to overcome the problem caused by the temporal and spatial differences. However, traditional approaches did not sufficiently consider integration of different computing environments, which were characterized by types of applications, roles of users, and so on. We propose a collaborative molecular modeling environment to integrate different molecule modeling systems using a virtual tunneling service. We integrated Co-Coot, which is a collaborative crystallographic object-oriented toolkit, with VRMMS, which is a virtual reality molecular modeling system, through a collaborative tunneling system. The proposed system showed reliable quantitative and qualitative results through pilot experiments.

Temporal analysis of nonresonant two-photon coherent control involving bound and dissociative molecular states

We theoretically study the control of two-photon excitation to bound and dissociative states in a molecule induced by trains of laser pulses, which are equivalent to certain sets of spectral phase modulated pulses. To this end, we solve the time-dependent Schr\"odinger equation for the interaction of molecular model systems with an external intense laser field. Our numerical results for the temporal evolution of the population in the excited states show that, in the case of an excited dissociative state, control schemes, previously validated for the atomic case, fail due to the coupling of electronic and nuclear motion. In contrast, for excitation to bound states the two-photon excitation probability is controlled via the time delay and the carrier-envelope phase difference between two consecutive pulses in the train.

Yukawa-field approximation of electrostatic free energy and dielectric boundary force

A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends nontrivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation.

Tunneling Currents That Increase with Molecular Elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.

Plant‐mediated facilitation between a leaf‐feeding and a phloem‐feeding insect in a brassicaceous plant: from insect performance to gene transcription

Summary1. Plants face threats from a variety of herbivorous insects and can use induced responses to defend themselves against these attackers. Induced responses are mediated by signal transduction involving phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Cross‐talk between signal transduction pathways triggered by attackers with contrasting feeding styles allows plants to fine‐tune defences. A central question in this emerging field is to understand how responses to single attackers interfere with responses to other attackers, especially by integratively addressing molecular and ecological aspects.2. We examined the plant‐mediated interactions between the leaf‐chewing Pieris brassicae and the phloem‐sucking Brevicoryne brassicae, and their respective parasitoids Cotesia glomerata and Diaeretiella rapae, when feeding simultaneously, sequentially or in isolation on the brassicaceous ecological model plant Brassica oleracea. We analysed the underlying defence mechanisms in the plant. Levels of the phytohormones JA and SA transcriptional responses of a number of selected defence‐related genes and secondary plant compounds were quantified at different time points during the single and multiple infestations.3. The caterpillars developed faster and reached a larger body mass on plants previously attacked by aphids. Aphids initially developed faster on plants with caterpillars, although the moment of moulting to adults was independent of the presence of caterpillars. Both parasitoid species performed better under multiple‐infestation scenarios than in single‐herbivore situations.4. On plants attacked by aphids, the JA levels were tenfold lower than on undamaged plants or plants with caterpillars. Additionally, the low transcript levels of LOX and MYC, genes coding for a JA biosynthesis‐related enzyme and a transcription factor, respectively, in aphid‐infested plants, suggest that the facilitation of the caterpillar performance was mediated by interference in signal transduction. Levels of carbon and nitrogen and secondary plant compounds (glucosinolates) did not differ significantly between treatments, suggesting that these compounds did not mediate the facilitation.5. Our data show that the leaf chewer and phloem feeder asymmetrically interact not via competition as would be expected from interspecific herbivores but instead via facilitation; the phloem feeder attenuated JA‐related plant defences, thus facilitating the growth and development of the leaf chewers. In linear bitrophic systems, interactions between JA and SA signalling pathways have been proposed to allow plants to fine‐tune their defences, but if facilitation frequently occurs in interspecific interguild interactions among herbivores this may represent an important constraint for plant defences. Such a constraint might be reduced if, as in our model system, parasitoids also benefit from interactions between interguild hosts and nonhosts, but parasitoids are rarely considered in model molecular systems to assess the impact of herbivore‐induced plant defences.

Low-temperature phases obtained by linear programming: An application to a lattice system of model chiral molecules

A convenient, Peierls-type approach to obtain low-temperature phases is to use the method of an m-potential. In this paper we show that, for more complex systems where it may be rather difficult to rewrite the Hamiltonian as an m-potential and whose configurations are subject to linear constraints, the verification of the Peierls condition can be reformulated as a linear programming problem. Before introducing this novel strategy for a general lattice system, we compare it with the m-potential method for a specific model molecular system consisting of an equimolar mixture of a chiral molecule and its non-superimposable mirror image that occupy all the sites of a honeycomb lattice. In one range of interactions, we prove that a racemic low-temperature phase occurs (containing equal numbers of each enantiomer). However, in a neighboring range of interactions, we show that a homochiral low-temperature phase (containing a single enantiomer) exists, and thus chiral segregation occurs in the system. Our linear programming technique yields these results in wider ranges of interactions than the m-potential method.

A density functional study on dielectric properties of acrylic acid grafted polypropylene

Influence of acrylic acid grafting of isotactic polypropylene on the dielectric properties of the polymer is investigated using density functional theory (DFT) calculations, both in the molecular modeling and three-dimensional (3D) bulk periodic system frameworks. In our molecular modeling calculations, polarizability volume, and polarizability volume per mass which reflects the permittivity of the polymer, as well as the HOMO-LUMO gap, one of the important measures indicating the electrical breakdown voltage strength, were examined for oligomers with various chain lengths and carboxyl mixture ratios. When a polypropylene oligomer is grafted with carboxyl groups (cf. acrylic acid), our calculations show that the increase of the polarizability volume α' of the oligomer is proportional to the increase of its mass m, while the ratio α'/m decreases from the value of a pure polymer when increasing the mixture ratio. The decreasing ratio of α'/m under carboxyl grafting indicates that the material permittivity might also decrease if the mass density of the material remains constant. Furthermore, our calculations show that the HOMO-LUMO gap energy decreases by only about 15% in grafting, but this decrease seems to be independent on the mixture ratio of carboxyl. This indicates that by doping polymers with additives better dielectric properties can be tailored. Finally, using the first-principles molecular DFT results for polarizability volume per mass in connection with the classical Clausius-Mossotti relation, we have estimated static permittivity for acrylic acid grafted polypropylene, assuming the structural density keeping constant under grafting. The computed permittivity values are in a qualitative agreement with the recent experiments, showing increasing tendency of the permittivity as a function of the grafting composition. In order to validate our molecular DFT based approach, we have also carried out extensive three-dimensional bulk periodic first-principles total-energy calculations in the frameworks of the density functional theory and density functional perturbation theory (DFPT) for crystalline acrylic acid grafted polypropylene. Interestingly, the computed electronic and dielectric properties behave very similarly between the simplified molecular DFT modeling and the more realistic 3D bulk periodic DFPT method. In particular, the static permittivity values [ε(r)(0)] from the molecular DFT-Clausius-Mossotti modeling are in excellent agreement with the high-frequency dielectric constant values (ε(∞)) from the DFPT method. This obviously implies that the chain-to-chain interaction to dielectric and electronic properties of acrylic acid polypropylene, to a first approximation, can be neglected, therefore justifying the usage of molecular DFT modeling in our calculations.

Physiologic and anatomic characterization of the brain surface glia barrier of Drosophila.

Central nervous system (CNS) physiology requires special chemical, metabolic, and cellular privileges for normal function, and blood-brain barrier (BBB) structures are the anatomic and physiologic constructs that arbitrate communication between the brain and body. In the vertebrate BBB, two primary cell types create CNS exclusion biology, a polarized vascular endothelium (VE), and a tightly associated single layer of astrocytic glia (AG). Examples of direct action by the BBB in CNS disease are constantly expanding, including key pathophysiologic roles in multiple sclerosis, stroke, and cancer. In addition, its role as a pharmacologic treatment obstacle to the brain is long standing; thus, molecular model systems that can parse BBB functions and understand the complex integration of sophisticated cellular anatomy and highly polarized chemical protection physiology are desperately needed. Compound barrier structures that use two primary cell types (i.e., functional bicellularity) are common to other humoral/CNS barrier structures. For example, invertebrates use two cell layers of glia, perineurial and subperineurial, to control chemical access to the brain, and analogous glial layers, fenestrated and pseudocartridge, to maintain the blood-eye barrier. In this article, we summarize our current understanding of brain-barrier glial anatomy in Drosophila, demonstrate the power of live imaging as a screening methodology for identifying physiologic characteristics of BBB glia, and compare the physiologies of Drosophila barrier layers to the VE/AG interface of vertebrates. We conclude that many unique BBB physiologies are conserved across phyla and suggest new methods for modeling CNS physiology and disease.

Bias effects on the electronic spectrum of a molecular bridge

In this paper the effect of bias and geometric symmetry breaking on the electronic spectrum of a model molecular system is studied. Geometric symmetry breaking can either enhance the dissipative effect of the bias, where spectral peaks are disabled, or enable new excitations that are absent under zero bias conditions. The spectral analysis is performed on a simple model system by solving for the electronic response to an instantaneously impulsive perturbation in the dipole approximation. The dynamical response is extracted from the electronic equations of motion as expressed by the Keldysh formalism. This expression provides for the accurate treatment of the electronic structure of a bulk-coupled system at the chosen model Hamiltonian electronic structure level.

Response signal in a femtosecond pump-probe experiment in a condensed medium with account of the memory induced by the relaxation medium

For a model molecular system with one vibrational degree of freedom and three electronic states coupled by pump and probe laser pulses in a condensed medium, the response signal in a femtosecond pump-probe experiment is calculated. The potential curves of all three states are described by the Morse potential. Calculations are performed using two qualitatively different approaches to describing the medium-induced relaxation: with memory of the relaxation process and without memory (Markovian approximation). The temporal evolution of the vibrational wave packet in the intermediate electronically excited state is described using a master equation for the density matrix of the molecular system, which is derived within the framework of the Nakajima-Zwanzig formalism. It is demonstrated that, at short delay times, when the proposed approach is applicable, taking into account memory effects can substantially change the form of the pump-probe experiment signal in comparison with the signal calculated in the Markovian approximation.

Double excitations in correlated systems: A many–body approach

A coherent approach to the description of double excitations in correlated materials is presented: We derive stringent mathematical conditions on the algebraical structure of the Bethe-Salpeter and time-dependent density functional theory kernels that avoid the occurrence of spurious and nonphysical excitations. We discuss how these conditions need to be respected at any level of approximation, including the commonly used local density and static screening approximations. We propose a correlated kernel for the Bethe-Salpeter equation, and we illustrate several aspects of our approach with numerical calculations for model molecular systems.

The heat conductivity of liquid crystal phases of a soft ellipsoid string-fluid evaluated by molecular dynamics simulation

We have applied a nonequilibrium molecular dynamics heat flow algorithm to calculate the heat conductivity of a molecular model system, which forms uniaxial and biaxial nematic liquid crystals. The model system consists of a soft ellipsoid string-fluid where the ellipsoids interact according to a repulsive version of the Gay-Berne potential. On compression, this system forms discotic or calamitic uniaxial nematic phases depending on the dimensions of the molecules, and on further compression a biaxial nematic phase is formed. In the discotic nematic phase, the heat conductivity has two components, one parallel and one perpendicular to the director, where the last mentioned component is the largest one. This order of magnitudes is reversed in the calamitic nematic phase. In the biaxial nematic phase there are three components of the heat conductivity, one in the direction around which the long axes of the molecules are oriented, this is the largest component, another one in the direction around which the normals of the broadsides of the molecules are oriented, this is the smallest component, and one in the direction perpendicular to these two directions with a magnitude in between those of the first mentioned components. The relative magnitudes of the components of the heat conductivity span a fairly wide interval so it should be possible to use the model to parameterise experimental data.