Designing molecular devices by altering bond lengths

The work focuses on a theoretical approach to investigating the electric field (EF) dependence of bond-length alternation, the geometric and electronic structures of molecular wires used in the design of molecular electronic devices, the EF dependence of SCF energy, and the spatial distribution of the frontier orbitals of the molecular wires. Just as the bond length is an important influence on the conductance of the molecular wire, the dependence of the conductance on the chain length was also studied. We have also investigated how the current–voltage (I-V) characteristics change with bond length, as the bond length plays an important role in determining the conductance of molecular wires.     

Characterization of a candidate multi-pole molecular switch using computational techniques

An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G* computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M⁺ and M⁻) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between the calculated dipole moments of the M⁺ and M⁻ species shows that switching between negative and positive poles does not significantly affect the charge transfer performance of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole nanoswitch controlled by a bias voltage. Figure Electron transfer scheme and arrangement of the π-electrons in the turn-on state of the candidate multi-pole molecular switch.     

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second-order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to detection properties. Full geometry optimisation using the 6-311++G** basis set provided energetic properties, natural charges, frontier orbitals and vibrational modes. Excitation energies were obtained using time-dependent DFT. Hydrogen location and bond order contribute significantly to the electronic properties. The common cyromazine tautomer possesses the lowest energy, highest band gap energy and highest excitation energy. B3LYP/6-31G** dynamics simulations indicate each tautomer possesses a stable structure with limited rotation about the single bonds. Tautomerisation involving intramolecular hydrogen transfer influences the natural charges of neighbouring atoms and the frontier orbital properties. The excitation energies are highly correlated with band gap energies of the frontier orbitals. The calculated infrared and Raman spectra are suitable for vibrational assignments associated with the chemical structure. The tautomeric forms of cyromazine possess similar spatial properties and significant variation in electronic properties.     

Theoretical investigation of auxiliary electronic acceptors in modifying D-D-π-A sensitizers for dye-sensitized solar cells

In light of the performance of the SD2 pigments in DSSC, in order to expand the absorption spectral scope, decrease the energy difference between the highest occupied and the lowest unoccupied molecular orbitals, with SD2 dye molecular electron donor and electron acceptor as the fundamental framework, the indole fragment and thiophene derivative in the prototype dye molecule were replaced by the two π-bridges (labeled PA, PB, respectively) and the four auxiliary electron acceptors (labeled A1, A2, A3, A4, respectively). For the sake of characterizing dye molecules as thoroughly as possible in DSSC, the frontier orbital energy levels, ultraviolet absorption spectra, natural bond orbital analysis, intramolecular charge transfer, charge and hole reorganization energies, parameters influencing the short-circuit current density and the open-circuit photovoltage for these eight individual dye molecules are carried out to try to fully characterize the properties of these dye molecules. According to these computational results of physical quantities and based on the performance of these dye molecules in the above aspects, in this paper, six free molecular models were picked out to combine with titanium dioxide cluster to calculate their geometrical structures, frontier orbital distributions, electron excitation energies, ultraviolet absorption spectra and the composition of the electronic transitions in chloroform solvent with polarizable continuum model. The results of these calculations show that the PA-A2 and PB-A4 dye molecule has better properties in electron transfer and spectral absorption range before and after the adsorption on the titanium dioxide.     

History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants

Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.     

Heterogeneity of the spatial distribution of the primordial organic substance as an initial stage of biological evolution

An approach to describe the emergence of dynamics of polymerization/depolymerization of some spatially distributed prebiological structures has been analyzed, and two phases of the development of the system have been identified. In the first phase, polymerization of organic monomers occurs under the influence of external factors, and in the second one depolymerization takes place. Both processes are accompanied by “diffusive mixing” of reaction products. The dynamic equations of the system are presented. Numerical examination of the space nonuniform solution of model equations has shown that, in conditions of low stability of uniform space distribution, these solutions resolve into a number of discrete peaks of nonzero density, which are isolated from each other by free space. Such nonuniform distributions are stable when close to the bifurcation point; yet in other conditions, they can lose their stability, which entails a more pronounced nonuniformity of space dynamics. Thus, interaction of polymerization/depolymerization processes results in chaotic self-organization and leads to origination of complex and inhomogeneous (patchy) spatial structures. These structures in physical space can reflect the emergence of the spatial nonuniformity in prebiological associations, while in the distributive space of characters they can correspond to the initial steps of emergence of the first discrete domains fixed in biological evolution.     

Synthesis and density functional theoretical study of steroidal spiro-triazolidinone

The reaction of 3beta-chloro-5alpha-cholestan-6-one semicarbazone 1 with hydrogen peroxide at 0 degrees C gives 3beta-chloro-5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2 as a product. The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral data. The ab initio calculations were performed by using density functional theory (DFT) at B3LYP/6-31G* basis set in order to describe a free radical reaction mechanism. The reaction proceeds through two radical intermediates formation. The mechanism of the reaction was explained by using frontier molecular orbital (FMO), spin electronic density map, encoded electrostatic potential map and atomic charges. It was found that the localization of frontier orbitals and the flow of atomic charges of all the calculated structures support the present reaction mechanism. The molecular properties like total energy, dipole moment and hardness of each optimized structure, were also explained. Stability of all the optimized structures in this study was supported by their respective fundamental frequencies and energy minima.     

Structure and electronic properties of Alq3 derivatives with electron acceptor/donor groups at the C4 positions of the quinolate ligands: a theoretical study

The molecular structures of the ground (S(0)) and first singlet excited (S(1)) states of Alq3 derivatives in which pyrazolyl and 3-methylpyrazolyl groups are substituted at the C4 positions of the 8-hydroxyquinolate ligands as electron acceptors, and piperidinyl and N-methylpiperazinyl groups are substituted at the same positions as electron donors, have been optimized using the B3LYP/6-31G and CIS/6-31G methods, respectively. In order to analyze the electronic transitions in these derivatives, the frontier molecular orbital characteristics were analyzed systematically, and it was found that the highest occupied molecular orbital is localized on the A ligand while the lowest unoccupied molecular orbital is localized on the B ligand in their ground states, similar to what is seen for mer-Alq3. The absorption and emission spectra were evaluated at the TD-PBE0/6-31G level, and it was observed that electron acceptor substitution causes a red-shift in the emission spectra, which is also seen experimentally. The reorganization energies were calculated at the B3LYP/6-31G level and the results show that acceptor/donor substitution has a significant effect on the intrinsic charge mobilities of these derivatives as compared to mer-Alq3.     

Understanding the substituent effect on the acidity of alcohols and para-substituted phenols

We carried out Hartree–Fock (HF) and density functional theory calculations on the conjugated bases of phenols and alcohols for 23 compounds and analysed their acid–base behaviour using molecular orbital (MO) energies and their dependence on solvent effects. Despite the well-known correlation between highest-occupied MO (HOMO) energies and proton affinity (PA), we observed that HOMO energies are inadequate to describe the acid–base behaviour of these compounds. Therefore, we established a criterion to identify the best frontier MO for describing PA values and also to understand why the HOMO approach fails. The MO that fits our criterion provided very good correlations with PA values, much better than those obtained by the HOMO energies. Since the frontier MOs are those which drive the acid–base reactions in each compound, they were called frontier effective-for-reaction MOs, or FERMOs. By using the FERMO concept, the reactions that are HOMO driven, and those that are not, can be better explained, independent of the calculation method used, since both HF and Kohn–Sham methodologies lead to the same FERMO.     

Electric dipole moments of the fluorescent probes Prodan and Laurdan: experimental and theoretical evaluations

Several experimental and theoretical approaches can be used for a comprehensive understanding of solvent effects on the electronic structure of solutes. In this review, we revisit the influence of solvents on the electronic structure of the fluorescent probes Prodan and Laurdan, focusing on their electric dipole moments. These biologically used probes were synthesized to be sensitive to the environment polarity. However, their solvent-dependent electronic structures are still a matter of discussion in the literature. The absorption and emission spectra of Prodan and Laurdan in different solvents indicate that the two probes have very similar electronic structures in both the ground and excited states. Theoretical calculations confirm that their electronic ground states are very much alike. In this review, we discuss the electric dipole moments of the ground and excited states calculated using the widely applied Lippert–Mataga equation, using both spherical and spheroid prolate cavities for the solute. The dimensions of the cavity were found to be crucial for the calculated dipole moments. These values are compared to those obtained by quantum mechanics calculations, considering Prodan in vacuum, in a polarizable continuum solvent, and using a hybrid quantum mechanics–molecular mechanics methodology. Based on the theoretical approaches it is evident that the Prodan dipole moment can change even in the absence of solute–solvent-specific interactions, which is not taken into consideration with the experimental Lippert–Mataga method. Moreover, in water, for electric dipole moment calculations, it is fundamental to consider hydrogen-bonded molecules.     

Complexes of graphene nanoribbons with porphyrins and metal-encapsulated C28 as molecular rectifiers: a theoretical study

The rectification properties of porphyrin–graphene nanoflake complexes and endohedral complexes of C28 fullerene with metal atoms have been studied using the fully ab initio method. D3 dispersion-corrected PBE/-def2-SVP model was used for the optimisations and the electronic energy evaluation. In porphyrin–graphene nanoflake complexes dispersion dominates, while in the endohedral complexes of C28 dispersion does not play an important role. All studied systems do rectify. In the case of fullerenes, the rectification is possible due to the reduction in the molecular symmetry of the fullerene caused by the interaction with electrodes and the endohedral complex formation. The origin of the rectification is the asymmetrical deformation of the electron density under direct and inverse voltages which creates different currents in opposite directions. It seems that peculiar geometry of Au-TPP-Cd/NF diode is responsible for its high rectification ratio. The Cd ion is notably out of the porphyrin plane making close contact with the neighbouring electrode, increasing the asymmetry of the diode compared to other TPP/NF complexes.     

DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers

Thiadiazole derivatives have been widely employed in the areas of pharmaceutical, agricultural, industrial, and polymer chemistry. The electronic and molecular structures of thiadiazoles are of interest because they have an equal number of valence electrons and similar molecular structures to thiophenes, which are currently used in the construction of organic solar cells due to their relatively high hole mobilities and good light-harvesting properties. For this reason, the electronic properties of fluorene-1,3,4-thiadiazole oligomers warrant investigation. In the present work, the structure of fluorene-1,3,4-thiadiazole with one thiadiazole unit in the structure was analyzed. This molecule was then expanded until there were 10 thiadiazole units in the structure. The band gap, HOMO and LUMO distributions, and absorption spectrum were analyzed for each molecule. All calculations were performed by applying the B3LYP/6-31G(d) chemical model in the Gaussian 03W and GaussView software packages. The electronic properties were observed to significantly enhance as the number of monomeric units increased, which also caused the gap energy to decrease from 3.51 eV in the oligomer with just one thiadiazole ring to 2.33 eV in the oligomer with 10 units. The HOMO and LUMO regions were well defined and separated for oligomers with at least 5 monomer units of thiadiazole.

The effect of the Neolithic expansion on European molecular diversity

We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter-gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.     

Complete Demonstration of the Valence Electronic Structure Inside a Practical Organic Solar Cell Probed by Low Energy Photoemission

The complete electronic structure inside a practical organic photovoltaic (OPV) device consisting of a trilayer structure of copper‐phthalocyanine (CuPc), fullerene (C₆₀), and bathocuproine (BCP) is demonstrated using low‐energy ultraviolet photoelectron spectroscopy (LE‐UPS) and photoelectron yield spectroscopy (PYS). The molecular orbital energy alignment and electrostatic potential distribution throughout the entire device is illustrated based on the LE‐UPS results. A favorable potential gradient to carry the photogenerated holes and electrons is manifested to be built spontaneously in the CuPc and BCP layers, respectively. Furthermore, the ultrahigh sensitivity measurements of LE‐UPS clearly unveil the distributions of faint density‐of‐states in the energy‐gap region in the organic films. Substantially barrierless contacts to both electrodes are fulfilled by the existence of these gap states. The electronic structure under simulated sunlight illumination is examined for the purpose of elucidating the electronic structures inside the working devices in the open‐circuit condition. These results indicate experimentally the electronic functionalities of each organic material, in particular of the BCP buffer layer, on the cell efficiency.     

Herbarium records identify the role of long‐distance spread in the spatial distribution of alien plants in New Zealand

Aim To use herbarium records to characterize important correlates of spatial spread, areal occupancy and clustering of 100 alien plant species of conservation concern in the North and South Islands of New Zealand. Location New Zealand. Methods Using herbarium data of 6294 records representing 100 alien plant species, we assessed spatial heterogeneity in the distribution of alien species by examining the role of major urban areas as sources of sampling bias. A novel method to account for spatial biases in sampling effort was developed and applied to two simple distance metrics: nearest‐ and furthest‐neighbour spread rate. The relative importance of these two distance metrics in determining the range, areal extent and dispersion of alien species across both the North and South Islands of New Zealand was also assessed. Results The spatial distribution of herbarium records was highly clustered with a significant bias towards the more populated regions. Once sampling bias was taken into account, there was no indication that species were found closer to these urban centres than might be expected based on sampling effort. The nearest‐neighbour spread rates were usually 1–5 km yr^?1 and correlated positively with the furthest‐neighbour spread rates that were an order of magnitude higher. Range and area increased and clustering decreased with higher spread rates and longer recording time span. The spread rates divided species into five groups that were clearly distinguishable in terms of the extent of their distribution and the degree of clustering. Species occurring on both islands did not exhibit similar spread rates or spatial patterns. Main conclusions The nearest‐ and furthest‐neighbour spread rates from herbarium records can explain the area and pattern of alien plant distributions and improve the understanding of the dynamics of their spread. Five groups emerge from the spread rates in relation to a null model. Fast‐spreading plants had the widest, least clustered distribution, which suggests widespread chronic problems; slow‐spreading plants had localized, but dense, clustered distributions, indicating acutely problematic weeds. These patterns appear robust and may be useful in predicting the future patterns of spread and in planning long‐term management strategies in New Zealand.     

Dwell Time Distributions of the Molecular Motor Myosin V

The dwell times between two successive steps of the two-headed molecular motor myosin V are governed by non-exponential distributions. These distributions have been determined experimentally for various control parameters such as nucleotide concentrations and external load force. First, we use a simplified network representation to determine the dwell time distributions of myosin V, with the associated dynamics described by a Markov process on networks with absorbing boundaries. Our approach provides a direct relation between the motor’s chemical kinetics and its stepping properties. In the absence of an external load, the theoretical distributions quantitatively agree with experimental findings for various nucleotide concentrations. Second, using a more complex branched network, which includes ADP release from the leading head, we are able to elucidate the motor’s gating effect. This effect is caused by an asymmetry in the chemical properties of the leading and the trailing head of the motor molecule. In the case of an external load acting on the motor, the corresponding dwell time distributions reveal details about the motor’s backsteps.     

Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations

Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.     

Propagation of Turing patterns in a plankton model

The paper is devoted to a reaction–diffusion system of equations describing phytoplankton and zooplankton distributions. Linear stability analysis of the model is carried out. Turing and Hopf stability boundaries are found. Emergence of two-dimensional spatial structures is illustrated by numerical simulations. Travelling waves between various stationary solutions are investigated. Transitions between homogeneous in space stationary solutions and Turing structures are studied.