Huckel Theory Research Articles

Contemplating charge transport by modeling of DNA nucleobases based nano structures

Electrical charge transport through two basic strands Thymine and Adenine of DNA has been analyzed using jellium model approach. The FFT-2D computations have been performed for semi empirical Extended Huckel Theory using Atomistix Tool kit to contemplate the charge transport metrics like current and conductance. We have scrutinized the behavior of the devices in the range of -2 V–2 V for a step size of 0.2 V. A prominent observation is the drop in HLGs of Adenine and Thymine, when working as device as compared to their intrinsic values and this is comparative more visible in case of Adenine. The current in the thymine based device exhibit linear increase with voltage in spite of having low conductance. Further the broader transmission peaks represent the strong coupling of electrodes to the scattering molecule (Thymine). The NDR effect of Adenine based device for higher bias can be utilized in various future electronics applications.

Hückel theory and distinguishing between isospectral molecules: 1,4-divinylbenzene and 2-phenylbutadiene, and tetramethylenemethane and cyclobutadiene + carbon

Although Huckel molecular orbital theory (HMO) has been generally outdated as a computational method for the energetics of organic molecules, there is still much we can learn from it. This paper explores two compounds, 1,4-divinylbenzene and 2-phenylbutadiene, which, according to Huckel theory, are isospectral, i.e., they have the same eigenvalues and orbital energy levels. However, by using a small, well-defined perturbation, we show it is mathematically possible to distinguish between these two compounds. We suggest that this is a general procedure for distinguishing isospectral pairs of molecules as opposed to the two species being identical.

Graphical Representation of Hückel Molecular Orbitals

In this paper, we develop a general but very simple mathematical foundation for the predefined coefficient graphical method of Huckel molecular orbital theory (HMO). We first present the general solution for the recurrence relation of the coefficients of Huckel molecular orbitals (MOs). Subsequently, for all the three unbranched hydrocarbons, i.e., open-chain, cyclic Huckel and Mobius polyenes, different boundary conditions are explored for obtaining the MOs and their energy levels. The analytic continuation of the recurrence relation, in which one extends the domain from integral to real, allows us to analyze the symmetric properties of Huckel MOs in an elegant fashion without even knowing the actual expressions. In fact, we can use the symmetric properties to derive the Huckel MOs of the unbranched hydrocarbons and some branched hydrocarbons such as naphthalene. Consequently, this work also provides a pedagogical alternative to present the HMO model for students in an advanced physical chemistry course. Finally, the graphical approach could be a good mnemonic device for students’ comprehension of the HMO theory.

Catacondensed Chemical Hexagonal Complexes: A Natural Generalisation of Benzenoids

Catacondensed benzenoids (those benzenoids having no carbon atom belonging to three hexagonal rings) form the simplest class of polycyclic aromatic hydrocarbons (PAH). They have a long history of study and are of wide chemical importance. In this paper, mathematical possibilities for natural extension of the notion of a catacondensed benzenoid are discussed, leading under plausible chemically and physically motivated restrictions to the notion of a catacondensed chemical hexagonal complex (CCHC). A general polygonal complex is a topological structure composed of polygons that are glued together along certain edges. A polygonal complex is flat if none of its edges belong to more than two polygons. A connected flat polygonal complex determines an orientable or nonorientable surface, possibly with boundary. A CCHC is then a connected flat polygonal complex all of whose polygons are hexagons and each of whose vertices belongs to at most two hexagonal faces. We prove that all CCHC are Kekulean and give formulas for counting the perfect matchings in a series of examples based on expansion of cubic graphs in which the edges are replaced by linear polyacenes of equal length. As a preliminary assessment of the likely stability of molecules with CCHC structure, all-electron quantum chemical calculations are applied to molecular structures based on several CCHC, using either linear or kinked unbranched catafused polyacenes as the expansion motif. The systems examined all have closed shells according to Huckel theory and all correspond to minima on the potential surface, thus passing the most basic test for plausibility as a chemical species.

Room temperature high Giant Magnetoresistance graphene based spin valve and its application for realization of logic gates

In this study we carried out first principle calculations for spin dependent electronic transport in our proposed spintronic device consisting of graphene nanoribbon as scattering region with cobalt electrodes and magnesium oxide as tunneling barrier. The I–V Characteristics are calculated by using Non-Equilibrium Green's Function formalism in combination with Semi-Empirical (SE) Extended Huckel Theory (EHT) using Atomistic Tool Kit software at room temperature. The high value of GMR (Giant Magnetoresistance) is recommended for spintronic devices. The results reveal that the device shows a very high GMR ratio of 5.16×104%. The device also shows very low off state current, therefore negligible off state power consumption. The investigation of spin dependent non equilibrium transport is done by examining bias dependent transmission coefficients. Furthermore, some basic logic gates, like NOT, AND and NOR have been realized from the modeled device. The device may also find applications in data storage, magnetic field sensors etc.

Effect of Metallic Electrodes Ensemble on Charge Transport Characteristics of Cytosine Based Molecular Devices

The charge transport through molecular devices using an ensemble of metal electrodes having nucleobase cytosine as the central molecule has been envisaged using a combination of semi-empirical Extended Huckel Theory and Non Equilibrium Green Function (NEGF). FFT-2D computational approach has been effectively applied to elucidate the electron transport characteristics of these molecular devices under both equilibrium as well as non-equilibrium states. The charge transport parameters viz. Device Density of States, Transmission Spectrum, I–V curve, G–V curve and HOMO-LUMO Gap are measured to exhibit the charge transport properties. By comparing the obtained quantum transport properties, we observe that silver remains the best choice among the three electrode materials under study as the molecular device with the silver electrodes exhibits the lower HOMO-LUMO Gap with increased current and conductance for the higher bias voltages in contrast to the other two configurations which show comparatively higher value of HOMO-LUMO Gap. Hence, the molecular device with the silver electrodes has greater possibility of getting utilized as a switch in DNA based nano-electronics applications.

From Benzene to Graphene: Exploring the Electronic Structure of Single-Layer and Bilayer Graphene Using Polycyclic Aromatic Hydrocarbons

In this work, two exercises are described that are designed to teach students about the evolution and behavior of the electronic bands of graphene and bilayer graphene. These exercises involve performing extended Huckel molecular orbital theory calculations on polyacenes and polycyclic aromatic hydrocarbons. In the first exercise, students investigate how the molecular orbitals of polyacenes converge into bands as polyacene size increases. Further, students learn that long-range interactions cause frontier-orbital crossing as the size of the polyacene increases. In the second exercise, the concepts of band structures, band crossing, and k-space are explored using the results of frontier orbital calculations on π-stacked dimers of polycyclic aromatic hydrocarbons, which represent molecular analogues of layered 2D materials. The results of these calculations show how the geometry and layer–layer offset of the dimer system can affect its electronic structure, and the results can be extrapolated to provide a framework for understanding why subtle changes in the relative orientations of the layers in bilayer graphene can produce qualitative changes in the electronic properties. These calculations are easily implemented with Python or with widely available algebraic manipulation software such as Maple or Mathematica. These exercises are accessible to students who have experience with extended Huckel molecular orbital theory and are suitable for inclusion in the physical chemistry curriculum at the upper-level undergraduate or introductory graduate level.

Activity Coefficient Modeling for Aqueous Aluminum Salt Solutions in Terms of the Generalized Debye–Hückel Theory

Activity coefficients are calculated for aqueous aluminum chloride and aluminum sulfate solutions at 298 K in terms of the generalized Debye–Huckel (DH) theory using experimental static dielectric permittivity versus concentration relationships. A semiquantitative fit of the experimental data is achieved; specifically, nonmonotonic activity coefficient versus concentration trends are reproduced. The applicability of the generalized Debye–Huckel theory to fit the thermodynamic properties of 3,1 and 3,2 valence type electrolytes is shown.

Influence of long-range interactions on quantum interference in molecular conduction. A tight-binding (Hückel) approach.

When certain pairs of atoms in a π-conjugated molecule are connected with nanometer-scale source and drain electrodes, the remarkable quantum interference (QI) effect may arise. In this case, the electron transmission probability is significantly suppressed due to the QI effect. Tight-binding approaches, such as the Hückel molecular orbital (HMO) model, have revealed important features of this quantum phenomenon. However, important deviations from experiments and from more sophisticated calculations are known for a variety of cases. Here, we propose an extension of the HMO method to include non-nearest-neighbor interactions. Such long-range interactions (LRIs) are implemented in the HMO model in the form of a damping function that decays as the topological distance-the number of bonds separating two atoms-gets larger. The proposed model is further developed so that a geometric modification, i.e., the rotation around a single bond, can be taken into account. Our results show that LRI affects both the location of the antiresonance peak due to QI and the intensity of QI, even suppressing it in some cases. These results agree well with what was observed in a Density Functional based Tight-Binding (DFTB) study reported in the literature. These properties can be interpreted on the basis of a graph-theoretic path-counting model as well as the molecular orbital theory. In addition, the geometric LRI model is shown to reproduce the change of transmission as a function of rotation around the single bond separating two benzene rings in biphenyl, in agreement with what was observed in both experiment and DFTB calculation.

Anion-Specific Effects on Activity Coefficients in Aqueous Solutions of Sodium Salts: Modeling with the Extended Debye–Hückel Theory

The extended Debye–Huckel theory, which allows for concentration variation of electrolyte solution static permittivity, is employed to predict activity coefficients in aqueous solutions of sodium salts with various univalent anions (NaCl, NaBr, NaI, NaNO3, NaClO4 and NaSCN) at ambient conditions. Calculations without empirical adjustments reproduced the activity coefficients for NaI in the concentration range up to 6 mol·kg−1 and for NaSCN up to 2 mol·kg−1. In the case of other solutions, calculations underestimate water activity coefficients and overestimate mean ionic activity coefficients at concentrations beyond 0.5 mol·kg−1. In order to improve the representations, the model was extended to include ion pairing, which resulted in a better agreement between calculated activity coefficients and experimental data, especially for NaNO3. The ion pairing equilibrium constants were estimated and compared with available literature values. The extent of ion pairing was found to increase in the sequence NaI < NaSCN < NaBr < NaCl < NaClO4 < NaNO3, with violation of the Collins rule in the case of polyatomic oxygen-containing anions.

Theoretical study of some structures of titanium(IV) complexes derived from 2-, 3- and 4-hydroxyl-benzoic acids

Complexes of fluoride titanium(IV) using hydroxyl benzoic acids as ligands are known for their great interest for care of the teeth, of the oral cavity or of dentures. Their activity is closely linked to the stability of their geometry. In this paper, we studied the structures of Ti(IV) complexes derived from hydroxyl-2-benzoic acid, hydroxyl-3-benzoic and hydroxyl-4-benzoic acids by molecular modelling. Calculations by molecular mechanics, Extended Huckel Theory (EHT) calculations have enabled access to the values of steric energy, bond lengths and bond angles, torsion angles, charges, coordinates of the atoms and the total energy values. The data obtained using molecular modelling are in the same range of those obtained in literature. Both data showed an octahedral structure around the metal ion of Ti(IV) complex with a small distortion. KEY WORDS : Hydroxy benzoic acids, Ti(IV) complexes, Molecular modelling, Steric Energy, Stability Bull. Chem. Soc. Ethiop. 2018 , 32(3), 571-577. DOI: https://dx.doi.org/10.4314/bcse.v32i3.15

Comparative evaluation of NANO transport properties for DNA nucleobase based molecular junction devices.

The feasibility of electron transport conduction through a guanine base of DNA was investigated and then compared with another component of DNA, i.e., cytosine. A mathematical approach based on the jellium model using non-equilibrium Green's function combined with semi empirical extended Huckel theory was applied using the Atomistik Tool Kit. This was further used to measure significant transport parameters such as current, conductance, transmission spectra and the HOMO-LUMO gap of the suggested molecular system. An important revelation from our research work is that the cytosine-based molecular device exhibits metallic behavior with current ranging up to 70μA, and hence establishes itself as a good conductor. On the other hand, the guanine-based device is comparatively less conductive, exhibiting current in the order of 3μA. Another interesting observation about the guanine-based device is the visibility of a prominent negative differential resistance effect during the positive bias and a tunneling effect during negative bias. The uniform charge transfer through the cytosine device confirms its application as a molecular wire. The observations on the guanine-based device give better insights into its application as a memory device for nano-scale devices.

Enhanced Thermoelectric Properties of Armchair Graphene Nanoribbons with Pore Passivation

There is a need to discover efficient thermoelectric materials that can generate electricity from waste heat and could play an important role in a global sustainable energy solution. Graphene Nanoribbons have been explored for a range of pore dimensions in order to achieve better thermoelectric performance. In this paper, we investigate the thermoelectric properties of porous armchair graphene nanoribbons by introducing hydrogen atoms as passivators at the pore surfaces. The aim of this work is to study the influence of pore passivation on the thermoelectric parameters as a function of pore geometry so as to open the possibility for an optimal pore engineering which can significantly improve the thermoelectric efficiency. The results show that the phonon thermal conductivity has a very little dependence on the pore edge passivation. An improvement in thermoelectric figure of merit is achieved due to the increased values of the power factor with consistent values of thermalconductivity. The unique thermoelectric properties of graphene nanoribbons with pore passivation suggest their great potentials for nanoscale thermoelectric applications. Within ballistic transport regime, semi-empirical extended Huckel method has been used for electrical properties while Tersoff potential has been employed for phononic calculations.

Chemistry in laser-induced plasmas at local thermodynamic equilibrium

The equation of state for plasmas containing negative and positive ions of elements and molecules formed by these elements is modeled under the assumption that all ionization processes and chemical reactions are at local thermal equilibrium and the Coulomb interaction in the plasma is described by the Debye–Huckel theory. The hierarchy problem for constants of molecular reactions is resolved by using three different algorithms for high, medium, and low temperatures: the contraction principle, the Newton–Raphson method, and a scaled Newton–Raphson method, respectively. These algorithms are shown to have overlapping temperature ranges in which they are stable. The latter allows one to use the developed method for calculating the equation of state in combination with numerical solvers of Navier–Stokes equations to simulate laser-induced plasmas initiated in an atmosphere and to study formation of molecules and their ions in such plasmas. The method is applicable to a general chemical network. It is illustrated with examples of Ca–Cl and C–Si–N laser-induced plasmas.

Synthesis, characterization, electrochemical, electrical, thermal and ESIPT behaviour of oligobenzimidazoles of certain substituted benzimidazole carboxylic acids and their diode applications

A series of ESIPT active benzimidazole phenolic carboxylic acid monomers were synthesized and converted into oligomers by oxidative polycondensation using NaOCl. The structures of monomers and oligomers were confirmed with 1H, 13C NMR and FT-IR spectral analyses. The ESIPT behaviour of monomers and oligomers in DMSO solution were studied by fluorescence spectroscopy. The oligomers are showing fluorescence in the blue region with large stokes shift than the monomers, due to the extended conjugation in oligomer chain. The band gap values of monomers and oligomers were calculated using both UV–visible spectroscopy and cyclic voltametry. The band gap values of monomers were compared with theoretical band gap values obtained from DFT analysis. The electrical conductivity of iodine doped oligomers was measured using two point probe technique and are showing good correlation with the charge densities on benzimidazole nitrogen obtained from Huckel method. The dielectric properties of oligomers were measured at different frequency and temperature. The oligomer OBIPEC is showing greater dielectric constant as its monomer is having higher dipole moment (obtained from DFT) than other monomers. The p-n diodes of oligomers have shown good rectifying nature in the range −4 to 4 V. The TGA results showed that the oligomer OBIPC has highest thermal stability due to the greater the number of chain propagation sites than other oligomers.

Practical Training in Simple Hückel Theory: Matrix Diagonalization for Highly Symmetric Molecules and Visualization of Molecular Orbitals

At an advanced stage of learning quantum chemistry, undergraduate students usually encounter simple Huckel-molecular-orbital (HMO) theory, whose primitive approach gives very useful insight into the electronic structure of π-conjugated molecules. However, on one hand, computational HMO software, when programmed without using molecular symmetry, does not necessarily output chemically reasonable shapes of degenerate molecular-orbitals in benzene. On the other hand, separately inputting the molecular symmetry into the HMO calculation is mathematically redundant (i.e., duplicate information input). To solve this problem, in this study, a Microsoft Excel macro for obtaining reasonable HMOs of highly symmetric molecules such as benzene was developed. Furthermore, two other Excel macros for readily drawing quantitative contour plots of HMOs were created as student-friendly tools. The practical training in simple HMO theory proposed in the present report using these three macros will be very useful for undergradu...

Spreading Electron Density Thin: Increasing the Chromophore Size in Polyaromatic Wires Decreases Interchromophoric Electronic Coupling

The development of novel polychromophoric materials using extended polycyclic aromatic hydrocarbons as a single large chromophore holds promise for long-range charge-transfer applications in photovoltaic devices and molecular electronics. However, it is not well-understood how the interchromophoric electronic coupling varies with the chromophore size in linearly connected molecular wires. Here, we show with the aid of electrochemistry, electronic spectroscopy, density functional theory calculations, and theoretical modeling that as the number of aromatic moieties in a single chromophore increases, the interchromophoric electronic coupling decreases and may reach negligible values if the chromophore is sufficiently large. The origin of this initially surprising result becomes clear when one considers this problem with the aid of Huckel molecular orbital theory, as at the polymeric limit energies of the molecular orbitals cluster to form bands and thus the energy spacing between orbitals, and thereby the el...

Introduction to Organic Semiconductors Using Accessible Undergraduate Chemistry Concepts

Organic semiconductors (OSCs) are making great progress as active components in alternative energy and flexible electronics technologies that are of interest to many undergraduates. However, in materials governed by the confluence of multiple length scales (molecular (Angstrom), intermolecular (nm), domain (100s nm)), providing a pedagogically accessible pathway to incorporating OSCs into undergraduate education can be difficult. Here, we provide a multiscale description of OSCs that relies only on concepts covered in typical undergraduate chemistry and chemical engineering curricula: a tight-binding description of molecular orbitals using Huckel theory, the miscibility of intermolecular domains using thermodynamic principles based on the Ising spin model, the incorporation of thermal disorder of both the electronic and molecular states using the Boltzmann distribution, and a simple description of charge percolation using low-level graph theory. We illustrate these topics on a small organic molecule, 1,3,...

Synthesis, characterization, thermal, electrical and electrochemical studies of oligo nitrobenzimidazoles and their p–n diode applications

Three novel nitro oligobenzimidazoles, oligo-2-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (OBINP2), oligo-3-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (OBINP3) and oligo-4-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (OBINP4) were synthesized by oxidative polycondensation of benzimidazole monomers with NaOCl in aqueous alkaline medium. The structure of the monomers and oligomers were confirmed by FT-IR, UV–Vis, 1H and 13C NMR spectroscopic techniques. The monomer BINP2 and its oligomer are showing dual emission through excited state intramolecular proton transfer process. The band gap values of monomers and oligomers were calculated from both UV–Vis spectroscopic and cyclic voltammetric data. Theoretical band gap values of monomers obtained from DFT were compared with experimentally calculated band gap values. The electrical conductivity of I2 doped and undoped oligomers were measured using two point probe technique and are showing good correlation with the charge densities on imidazole nitrogen obtained from Huckel method. The conductivity of oligomers increases with increase in iodine vapour contact time up to 144 h. The variation of dielectric properties of oligomers has been investigated at different frequency and temperature. Among the oligomers, OBINP3 is having greater thermal stability as evidenced by its high carbine residue of around 65% at 600 °C in thermogravimetric analysis.

Rational design of metal-free organic D-π-A dyes in dye-sensitized solar cells: Insight from density functional theory (DFT) and time-dependent DFT (TD-DFT) investigations

The search for potential high efficiency dye sensitizer for dye-sensitized solar cell (DSSCs) application is still appealing at present. By manipulation of electron donor and π-bridges groups of organic dyes with multiple design strategies, we theoretically developed series of promising organic D-π-A dyes. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were used to elucidate the geometries, electronic structures, and optical features of the isolated dyes and dye-TiO2 combined system. Quantum dynamics simulation in the framework of extended Huckel theory (EHT) was carried out to simulate the interface electron transfer process across the dye/TiO2 interface. The key parameters influence the short-circuit photocurrent density and open-circuit photovoltage were analyzed in detail. Our results suggest that the dyes with further extended π-bridges has the gradually red-shifted absorption spectra and a persistent decrease of highest occupied molecular orbital (HOMO) energy. The extended π-conjugated bridges deteriorate the performance mainly because of the increased charge recombination between injected electron and electrolyte arising from the unfavorable energy alignment between dye HOMO and redox potential of electrolyte, leading to inefficient dye regeneration process. This rationalizes the experimental observation that longer π-bridge doesn't benefit the DSSCs performance. Further replacement of triphenylamine donor with carbazole or coumarin electron donor groups can shift down the HOMO level and avoid the inefficient dye regeneration issue whereas perseves other beneficial properties. The simulation performed in this work provides general design principle for experimental optimization of metal-free organic dyes towards DSSCs application.