Molecular Orbital Electron Research Articles

Optoelectronic and Semiconducting Properties of Conjugated Polymers Composed of Thiazolo[5,4-d]thiazole and Arene Imides Linked by Ethynylene Bridges

A set of engineered crystalline polymers containing thiazolo[5,4-d]thiazole and arene imides linked by ethynylene bridges have been modeled by means of density functional theory (periodic boundary) calculations. A large set of relevant electronic properties related to the optoelectronic and semiconductor character of these systems, such as optical band gap, frontier molecular orbital energy levels, electron affinity, ionization potential, reorganization energy, and electronic coupling between neighboring polymer chains, were obtained. We further discuss the effect of the ethynylene linkages, the presence of heteroatoms in thiazolo[5,4-d]thiazole rings, and the number of fused rings in the repeating unit on the electronic properties, for disclosing useful structure–property relationships.

Carbene →N+ Coordination Bonds in Drugs: A Quantum Chemical Study

Coordination chemistry of bonds between main group elements and electron donating ligands as in L →E (where E is electron acceptor centre like C0, Si0, N1, P1, As1, B1 and L is an electron donating N-heterocyclic carbene) has been recently gaining attention. Many important drugs have nitrogen atom as an electron acceptor center and can be represented by two general formulae: (L →N←L)⊕ and L →N-R. Divalent N1 compounds possess two lone pairs at central nitrogen and low nucleophilicity associated with them is found to be of importance. In this article, electronic structure analysis of drug molecules like picloxydine, chlorhexidine, and moroxydine was performed at B3LYP/6-311 ++G(d,p) level of theory. Evaluation of electron localization function (ELF), molecular orbitals, charge density, nucleophilicity, proton affinity and complexation energy estimation confirms the presence of coordination bonds (L →N←L)⊕ in the above mentioned drug molecules in their cationic state. Further, electronic structure analysis of drugs like clonidine, apraclonidine, brimonidine and xylazine indicated the presence of electronic structure similar to L →N-R systems.

Curved Cyclic Trimers: Orthogonal Cu–Cu Interaction versus Tetrameric Halogen Bonding

In this work, two polymorphs and a pseudopolymorph of a trinuclear copper(I) pyrazolate complex, namely, [Cu(L-Br)]3 (L-Br = 4-(4-bromophenyl)-3,5-dimethylpyrazolyl), were isolated. One of them shows remarkable molecular shape curving, which is imposed by short intermolecular CuI–CuI interaction and parallelogram-like Br4 halogen bonding. These two sets of noncovalent interactions propagate along different directions and do not interact directly with each other. Interestingly, these cooperative interactions give rise to an undulating layer in the crystal structure of one polymorph. We used a variety of theoretical methods, such as electron density distribution (e.g., atoms-in-molecules analysis and reduced-density-gradient mapping), molecular orbitals, charge analysis, electrostatic potentials, and Hirshfeld surface analysis, to demonstrate the nature and strength of multiple CuI–CuI and Br···Br bonding qualitatively and quantitatively. Moreover, preliminary calculations based on time-dependent density fu...

Effects of the charge on the structural, electronic and reactivity properties of 43 substituted N–Phenylmaleimides. A DFT study

The structural, electronic, and reactivity properties of 43 N-phenylmaleimide derivatives were studied by means of first principles theoretical calculations performed at the B3LYP/6-311+G(d,p) level of theory. Neutral, positively and negatively charged derivatives were studied. Different donor- and attractor-electron groups, attached at the ortho, meta and para positions, were selected, allowing to search for the effects of the charge on the geometrical, energetic and reactivity properties of the generated compounds. Firstly, the calculated ground state (GS) structures are in near agreement with the reported experimental X-Ray data and provide insight on some main features of the observed infrared spectra. Besides, the GS geometries show that the torsion angle, of the phenyl–maleimide rings, is an important parameter that impacts the properties of the species and of the polymeric chains, formed from such N-phenylmaleimides. It was found that the torsion angles depends on the nature (donor or attractor) of the selected group, on the position (ortho, meta, or para) on which the substitution was done, and on the charge (0e, +1e, −1e). For each compound, the effects of the charge on the: torsion angles, electronic (atomic populations and molecular orbitals) and energetic parameters (ionization energies and electron affinities) were studied. This information allows determining the chemical potentials, hardness, softness as well as the Fukui functions. Thus, the reactivity properties of these compounds were determined at this level of treatment. In neutral N-phenylmaleimides, the electrophylic attack mainly proceeds via the phenyl ring whereas the nucleophylic behavior is mostly defined by the imide group. These behaviors are enhanced on the cation and anion, respectively. Changes of these properties, produced by the substituent groups, are addressed.

Spectroscopic investigation, HOMO–LUMO energies, natural bond orbital (NBO) analysis and thermodynamic properties of two-armed macroinitiator containing coumarin with DFT quantum chemical calculations

In the present work, two-armed macroinitiator containing coumarin were synthesized, characterized by Fourier transform infrared spectroscopy and 1H nuclear magnetic resonance techniques and investigated theoretically using density functional theory (DFT) calculations. The molecular geometry, fundamental vibrational frequencies, atomic charges obtained from atomic polar tensors and Mulliken were analyzed by means of structure optimizations based on the DFT method with 6-31G+(d, p) as a basis set. The 1H chemical shifts were calculated by the gauge-including atomic orbital method and compared with available experimental data. The electronic properties, such as highest occupied molecular orbital – lowest unoccupied molecular orbital (HOMO–LUMO) energies, electron affinity, electronegativity, ionization energy, hardness, chemical potential, global softness, and global electrophilicity were calculated by using the DFT method. The electrostatic potential and molecular electrostatic potential surfaces were performed to predict the reactive sites of the two-armed macroinitiator. The energy difference between acceptor and donor and stabilization energy were determined using natural bond orbital analysis. The results show that the occurrence of intramolecular charge transfers within the polymer. Time-dependent density functional theory calculations of visible spectra were analyzed at different solvents. Finally, thermodynamic functions, such as enthalpy, heat capacity, and entropy, of the two-armed macroinitiator at different temperatures were calculated and the relationship with temperature was investigated.

Dual roles for promoting monomers to polymers: A conjugated sulfonium salt photoacid generator as photoinitiator and photosensitizer in cationic photopolymerization

ABSTRACTAn efficient strategy for comprehensive utilization of the conjugated sulfonium salt photoacid generator (PAG), namely, 3‐{4‐[4‐(4‐N,N′‐diphenylamino)‐styryl]phenyl}phenyl dimethyl sulfonium hexafluoroantimonate, was developed through photoinitiated cationic photopolymerization (CP) of epoxides and vinyl ether upon exposure to near‐UV and visible light‐emitting diodes (LEDs; e.g., 365, 385, 405, and 425 nm). Photochemical mechanisms were investigated by UV–vis spectra, molecular orbital calculations, fluorescence, cyclic voltammetry, and electron spin resonance spin‐trapping analyses. Compared with commercial PAGs, the prepared conjugated sulfonium salt generated H+, which can be used as photoinitiator. Moreover, the fluorescent byproducts from photodecomposition can be used as photosensitizer of commercial iodonium salt in the photoinitiating systems of CP. These novel D‐π‐A type sulfonium‐based photoinitiating systems are efficient (epoxide conversion = 85–90% and vinyl conversion >90%; LEDs upon exposure to 365–425 nm) even in low‐concentration initiators (1%, w/w) and low curing light intensities (10–40 mW cm−2). © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2722–2730

Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner.

Computational chemists use structure-based drug design and molecular dynamics of drug/protein complexes which require an accurate description of the conformational space of drugs. Organic chemists use qualitative chemical principles such as the effect of electronegativity on hyperconjugation, the impact of steric clashes on stereochemical outcome of reactions, and the consequence of resonance on the shape of molecules to rationalize experimental observations. While computational chemists speak about electron densities and molecular orbitals, organic chemists speak about partial charges and localized molecular orbitals. Attempts to reconcile these two parallel approaches such as programs for natural bond orbitals and intrinsic atomic orbitals computing Lewis structures-like orbitals and reaction mechanism have appeared. In the past, we have shown that encoding and quantifying chemistry knowledge and qualitative principles can lead to predictive methods. In the same vein, we thought to understand the conformational behaviors of molecules and to encode this knowledge back into a molecular mechanics tool computing conformational potential energy and to develop an alternative to atom types and training of force fields on large sets of molecules. Herein, we describe a conceptually new approach to model torsion energies based on fundamental chemistry principles. To demonstrate our approach, torsional energy parameters were derived on-the-fly from atomic properties. When the torsional energy terms implemented in GAFF, Parm@Frosst, and MMFF94 were substituted by our method, the accuracy of these force fields to reproduce MP2-derived torsional energy profiles and their transferability to a variety of functional groups and drug fragments were overall improved. In addition, our method did not rely on atom types and consequently did not suffer from poor automated atom type assignments.

ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data.

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc.

DFTB Calculation of Si Atomic Chains’ Structures and Electronic Properties

In this paper, structures and electronic properties of atomic chains with 5 to 20 silicon atoms and different atomic distances (d = 1.652 ~ 2.752Å) were calculated by the tight-binding method based on density functional theory. The results showed that the majority of the silicon atomic chains were symmetrical structures. When the number of silicon atoms was small, the silicon atomic chains were linear, when the silicon atomic chains had seven or more silicon atoms zigzag structures appeared. With the increase of the distance between atoms, atomic chains were gathering. When the number of silicon atoms was between 10 and 20, the charges on the silicon atoms appeared as a symmetrical distribution. With the increase of the number of atoms, the energy of silicon atomic chains decreased gradually. As the distance between atoms and atomic number changed, HOMO (highest occupied molecular orbital electrons) -LUMO (lowest unoccupied molecular orbital electrons) energy gap changed as well.

Room temperature photoinduced magnetism in [py.H]3[FeCl4]2Cl

Photoinduced magnetism in a homogeneous solution of [py.H]3[FeCl4]2Cl is measured by Faraday rotation in visible light (λ∼450–750 nm) at room temperature. The physics of this phenomenon may be attributed to electronic transitions caused by absorption of light. X-ray diffraction and Debye function analysis are therefore applied to find the abundant unit of molecules dissolved in the solution which are being further utilized to investigate the electronic structure and molecular orbitals by means of hybrid density function theory (B3LYP). Faraday rotation is observed at certain wavelengths consistent with energy differences of HOMO-LUMO energy levels. Thus this work puts forward a new material with certain photomagnetic properties which may be used in fabrication of room temperature magneto-optical switches.

Density Functional Theory Calculations for the Structural, Electronic, and Magnetic Properties of (Gd2O3)n0,±1 Clusters with n = 1–10

The structural stability and electronic and magnetic properties of stoichiometric (Gd2O3)n clusters with n = 1–10 were investigated using spin-polarized density functional theory through the broken-symmetry approach. Size-induced changes in the point symmetry of these clusters were observed. A large coordination number led to elongation of Gd–O bonding. Either adding an electron to or removing an electron from the ground state of a neutral cluster brought significant changes in the van der Waals volume for clusters n = 1–3. Binding energy increased with cluster size. However, the highest occupied molecular orbital–lowest unoccupied molecular orbital gap, ionization, and electron affinity fluctuated when n increased from 1 to 10. Natural population analysis and partial density of states revealed that the Gd-4f orbital hardly participated in bonding and that the Gd-5d/6s/6p orbitals were hybrid with the O-2p orbitals. The competition between Ruderman–Kittel–Kasuya–Yosida-type and superexchange-type interact...

Extended Hückel and Slater’s rule initial guess for real space grid-based density functional theory

The Extended Hückel method is commonly used as an initial guess for Gaussian basis set quantum chemistry calculations. In this work, we combine the Extended Hückel method and Slater’s rules to form an initial guess of the electron density and molecular orbitals for all-electron real-space finite element Kohn–Sham density functional theory (FE-KSDFT). With this approach, the first SCF iteration is close in energy to the converged solution, and a factor of two speedup is obtained vs. a naïve initial electron density composed of a superposition of atomic densities. In addition, because the guessed molecular orbitals are already partially self-consistent with the guess density, we can now employ less robust, but fast, block eigensolvers such as Chebyshev-filtered subspace iteration even in the first SCF iteration to achieve 2–10× further gains vs. a conventional Jacobi–Davidson eigensolver.

Oxidative Degradation of Decabromodiphenyl Ether (BDE 209) by Potassium Permanganate: Reaction Pathways, Kinetics, and Mechanisms Assisted by Density Functional Theory Calculations

This study found that decabromodiphenyl ether (BDE 209) could be oxidized effectively by potassium permanganate (KMnO4) in sulfuric acid medium. A total of 15 intermediate oxidative products were detected. The reaction pathways were proposed, which primarily included cleavage of the ether bond to form pentabromophenol. Direct oxidation on the benzene ring also played an important role because hydroxylated polybrominated diphenyl ethers (PBDEs) were produced during the oxidation process. The degradation occurred dramatically in the first few minutes and fitted pseudo-first-order kinetics. Increasing the water content decelerated the reaction rate, whereas increasing the temperature facilitated the reaction. In addition, density functional theory (DFT) was employed to determine the frontier molecular orbital (FMO) and frontier electron density (FED) of BDE 209 and the oxidative products. The theoretical calculation results confirmed the proposed reaction pathways.

Rectifying properties of oligo(phenylene ethynylene) heterometallic molecular junctions: molecular length and side group effects.

The rectifying properties of α,ω-dithiol terminated oligo(phenylene ethynylene) molecules sandwiched between heterometallic electrodes, including the molecular length and side group effects, are theoretically investigated using the fully self-consistent nonequilibrium Green's function method combined with density functional theory. The results show nonlinear variation with changes in molecule length: when the molecule becomes longer, the current decreases at first and then increases while the rectification shifts in the opposite direction. This stems from the change in molecular eigenstates and the coupling between the molecule and electrodes caused by different molecular lengths. The rectifying behavior of heterometallic molecular junctions can be attributed to the asymmetric molecule-electrode contacts, which lead to asymmetric electronic tunneling spectra, molecular eigenvalues, molecular orbitals, and potential drop at reversed equivalent bias voltages. Our results provide a fundamental understanding of the rectification of heterometallic molecular junction, and a prediction of rectifiers with different rectification properties from those in the experiment, using electrodes with reduced sizes.

Synthesis, structure and spectroscopic properties of two new cyanido-bridged trinuclear 9-atom molecular Ag[sbnd]N[tbnd]C[sbnd]Cu[sbnd]N[tbnd]C[sbnd]Au[sbnd]C[tbnd]N assembly of formula [AgCuAu(CN)3(PPh3)5](H2O)2 and a dinuclear gold–copper one-dimensional coordination polymer of formula [AuCu(CN)2(PPh3)2](H2O)2

Two new cyanido-bridged coinage metal compounds are presented. A novel hetero trinuclear Ag–Cu–Au compound of formula [AgCuAu(CN)3(PPh3)5](H2O)21 is described with bridging cyanide ligands between the metals, and terminal phosphane ligands for Cu(I) and Ag(I). Silver is tetrahedrally coordinated by 3 phosphane ligands and a bridging cyanido ligand, copper is coordinated tetrahedrally by 2 phosphanes, and 2 bridging cyanide ligands, whereas gold has a linear coordination by 2 cyanido-κC ligands. Under slightly different synthetic conditions, an alternating chain compound [AuCu(CN)2(PPh3)2](H2O)22 was found, isostructural with the related Ag–Cu compound. In 2, Cu(I) is tetrahedrally coordinated by 2 phosphane ligands and 2N atoms of the bridging cyanido ligand to the Au(I). The qualitative solid-state luminescence emission intensity of 1 is reported and compared with that of the related bimetallic Au–Cu, Ag–Cu, Ag–Ag and Ag–Au cyanido-bridged chain compounds. The luminescence of 2 was found somewhat stronger than that of 1. The electronic molecular orbitals were calculated by DFT, where a strong contribution of Cu(I) orbitals in HOMO/LUMO character of the two complexes is observed.

Rationalising molecular crystal structures using Hirshfeld surfaces

Hirshfeld surface analysis [1] has very quickly become a routine tool for rationalising and visualising intermolecular interactions in crystals. The serendipitous discovery of an intriguing and novel way to identify the space `belonging' to a molecule in a crystal has led to the development of a suite of computational tools that facilitate a deeper understanding of how molecules pack in crystals and why it makes sense that a particular crystal packing occurs [2]. We have previously used the Hirshfeld surface as a vehicle for mapping inherent shape and curvature, surface-mediated distances between closest atoms, as well as quantum mechanical properties such as molecular orbital density, electron density and electrostatic potential. Combining visualisation tools like these with quantum mechanical wavefunctions – and hence properties derived from these wavefunctions – offers a powerful and unique opportunity to investigate intuitive concepts like `electrostatic complementarity' [3]. With this in mind we have been investigating ways to subdivide Hirshfeld surfaces into discrete patches that can be identified with specific pairs of molecules in close contact in crystals, and testing different expressions to quantify our ideas on electrostatic complementarity. Coupled with this appealing visual approach we also compute the electrostatic energy of interaction between the respective molecular wavefunctions. This combination of approaches within an easy to use software package will be powerful enough to not only routinely explore and visualise the patterns of interaction exhibited by molecules in crystals, but also provide meaningful energies of interaction between relevant pairs of molecules. In this way we can readily attach some real significance – energetics – to what are more usually classified as close contacts of various kinds.

Ab initio study of electronic structure, quantum transport and optical absorption properties of polyacene quinone radical polymers

Semiempirical quantum mechanical calculations have been implemented to study the molecular structure, electronic structure, optical properties of polyacene quinone radical polymers, and the quantum transport properties are also been calculated through combination of the numerical atomic orbitals basis set method based on density functional theory with the non-equilibrium Green's function formalism. The polyacene quinone radical polymers exhibit similar elastic modulus to the carbon nanotubes. The electronic molecular orbitals and energy bands of polyacene quinone radical polymers show insulator features, with the great conjugated bonds formed in polymer molecules resulting in extreme high polarization and dielectric constants, and the Fermi energy and band-gaps of ultraviolet range are static with the variation of polymerization degree. The aluminum electrodes with crystallographic (001) surfaces have been used in the electronic transport calculations, which indicate the quantum conductance spectrum changes with the varied strain and polymerization degree, however appears no explicit change, representing large open-gap feature of insulators. Ultraviolet-visible absorption spectra show a few characteristic peaks, the positions and number of which varying with polymerization degree, predicting that polyacene quinone radical polymers, as high dielectric functional materials, could be applied to ultraviolet optoelectronic nanoscale quantum devices.

Structural and electronic properties of uranium-encapsulated Au₁₄ cage.

The structural properties of the uranium-encapsulated nano-cage U@Au14 are predicted using density functional theory. The presence of the uranium atom makes the Au14 structure more stable than the empty Au14-cage, with a triplet ground electronic state for U@Au14. Analysis of the electronic structure shows that the two frontier single-occupied molecular orbital electrons of U@Au14 mainly originate from the 5f shell of the U atom after charge transfer. Meanwhile, the bonding orbitals and charge population indicate that the designed U@Au14 nano-cage structure is stabilized by ionocovalent interactions. The current findings provide theoretical basis for future syntheses and further study of actinide doped gold nanoclusters, which might subsequently facilitate applications of such structure in radio-labeling, nanodrug carrier and other biomedical applications.

LOVO Electrons: The Special Electrons of Molecules in Positron Annihilation Process

The electrons in the lowest occupied valence orbital (LOVO) of molecules have been found to dominate the gamma-ray spectra in the positron–electron annihilation process. The mechanism of this phenomenon is revealed in the present work for the first time. Theoretical quantitative analyses are applied to all noble gas atoms and molecules CH4, O2, C6H6, and C6H14. More than 70% of LOVO electrons and less than 30% of highest occupied molecular orbital (HOMO) electrons distribute within the full width at half-maximum (FWHM) region of the momentum spectra averagely. This indicates that the LOVO electrons have at least 2 times of probabilities than the HOMO electrons within this area. The predicted positron annihilation spectra are then generally dominated by the innermost LOVO electrons instead of the outmost HOMO electrons under the plane-wave approximation.

Electronic and geometric structure of AuxCuy clusters studied by density functional theory

We have determined the stable structures of Au Cu n, Au 2 Cu n, Au 3 Cu n and Au x Cu 8-x clusters. It has been observed that Au Cu n, Au 2 Cu n and Au 3 Cu n systems have two-dimensional (2D) structures up to six atoms and they become three-dimensional (3D) afterwards. Au x Cu 8-x clusters favor 3D structures till the Au 7 Cu 1 cluster. We have found a lowest energy isomer of Au 6 Cu 2 from the literature. Bond lengths, binding energies, density of states (DOS), highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO-LUMO) gaps, ionization potential (IP) and electron affinity (EA) have been calculated for these structures using the first principles density functional theory (DFT) within the generalized gradient approximation (GGA) and the local density approximation (LDA). Generally, we have observed the overlap between s electrons of Cu and p electrons of Au near the Fermi level. Charge transfers are calculated by using the Löwdin analysis. It is observed that one Cu atom does not significantly modify the clusters which have more gold atoms. It is also seen that these clusters generally have nonmagnetic properties and results are consistent with the hybridization between s and d orbitals of Au in Au x Cu 8-x clusters.