Electronic Structure Of Molecules Research Articles

Квантовохимическое моделирование строения молекул иминодиуксусной кислоты и ее производных в водной среде

Проведены компьютерные вычисления атомного строения молекулы иминодиуксусной кислоты и ее гидратов в вакууме и водной среде. Показано, что учет диэлектрической проницаемости водной среды приводит к изменению длин ковалентных связей между атомами, валентных углов, эффективных зарядов и энергии связей. При этом топология химических связей изомера не изменяется. Присоединение одной молекулы воды приводит к смене позиции иона водорода, связанной с переносом его от иона кислорода к иону азота, что приводит к образованию цвиттер-структуры. Показано, присоединение молекулы воды к молекуле иминодиуксусной кислоты сопровождается возникновением трехцентровой ковалентной связи, что является физико-химическим механизмом термодинамической устойчивости цвиттер-структуры молекулы в водной среде.

Styrene butadiene rubber as a viscosity improver: Experimental investigations and quantum chemical studies

The limited viscosity range of vegetable oils restricts their effectiveness as a lubricant in numerous applications. In this work, the viscosity improvement with styrene butadiene rubber as an additive in sesame oil is studied and the results are compared with those of the commonly used viscosity improver, ethyl vinyl acetate, using a rheometer. Sesame oil/styrene butadiene rubber blends show higher increment in viscosity than sesame oil/ethyl vinyl acetate blends. The viscosity variations are further validated using Arrhenius model. A computational quantum chemical software, Gaussian 09, is used to evaluate the binding energies between molecules. Ground state electronic structures of molecules are modeled with density functional theory. Thermal properties such as flash, fire, and pour points have also been evaluated for sesame oil/styrene butadiene rubber blends. Chemical oxygen demand and biological oxygen demand are the parameters chosen to evaluate the biodegradability of sesame oil/styrene butadiene rubber blend.

Multiscale quantum-defect theory and its application to atomic spectrum

We present a multiscale quantum-defect theory based on the first analytic solution for a two-scale long range potential consisting of a Coulomb potential and a polarization potential. In its application to atomic structure, the theory extends the systematic understanding of atomic Rydberg states, as afforded by the standard single-scale quantum-defect theory, to a much greater range of energies to include the first few excited states and even the ground state. Such a level of understanding has important implications not only on atomic structure, but also on the electronic structure of molecules and on atomic and molecular interactions and reactions. We demonstrate the theory by showing that it provides an analytic description of the energy variations of the standard Coulomb quantum defects for alkali-metal atoms.

Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy.

Scanning tunneling microscopy and atomic force microscopy can provide detailed information about the geometric and electronic structure of molecules with submolecular spatial resolution. However, an essential capability to realize the full potential of these techniques for chemical applications is missing from the scanning probe toolbox: chemical recognition of organic molecules. Here, we show that maps of the minima of frequency shift-distance curves extracted from 3D data cubes contain characteristic contrast. A detailed theoretical analysis based on density functional theory and molecular mechanics shows that these features are characteristic for the investigated species. Structurally similar but chemically distinct molecules yield significantly different features. We find that the van der Waals and Pauli interaction, together with the specific adsorption geometry of a given molecule on the surface, accounts for the observed contrast.

Structural effects on the electronic characteristics of intramolecularly intercalated alkali-rubrene complexes

The geometric and electronic structures of neutral monolithium- and monosodium-rubrene (Li1 Rub and Na1 Rub) isomers are investigated and compared with monopotassium-rubrene (K1 Rub). Based on the alkali binding site, all isomers of these alkali-rubrene complexes can be subdivided into two types: intramolecularly intercalated and extramolecularly adsorbed. The minimum-energy Li1 Rub and Na1 Rub are intercalated structures, whereas the minimum-energy K1 Rub is adsorbed. The fact that the intercalated Li1 Rub and Na1 Rub structures are energetically favorable over the adsorbed ones can be explained by two energy rules. First, “double” proximity of the intercalating alkali element to a pair of phenyl side groups enormously reduces the total energy. Second, accommodation of a minuscule intercalant does not significantly deform the carbon frame and, thus, increases the energy only by a small amount. Additionally, the peculiar effects of intramolecular intercalation on the electronic structures of molecules are also studied in this simulation of monoalkali intercalation. In the monoalkali-intercalated rubrene complex, only one of the two pairs of phenyl groups of rubrene is intercalated, intentionally leaving another pair pristine, which facilitates the comparison of electronic structures between the intercalated and pristine pairs of phenyl side groups in a single molecule. The uniformity of chemical environments of the phenyl groups of the intercalated Li1 Rub/Na1 Rub is deteriorated by the incorporation of the intercalant, and leads to their spectral characteristics in contrast to K1 Rub. In particular, the introduction of the intercalant promotes the carbon 2p orbitals of the intercalated phenyl pair to take part in the electronic structures of the HOMO and LUMO peaks of Li1 Rub/Na1 Rub. The unpaired electron in the HOMO is delocalized over the backbone with higher probability of distributing over the central two fused rings than over the outer two.

A quantum chemical study of aluminum–nitrogen bonds in three-coordinate aluminum compounds

DFT and HF methods implemented in the PC GAMESS-Firefly program package are employed to calculate the spatial and electronic structures of molecules of three-coordinate aluminum compounds with Al–N bonds. NBO and AIM methods are applied to determine the main characteristics of Al–N and N–C bonds in these molecules. It is shown that Al and N atoms interact with each other as closed shell atoms. The N–C bonds are close to covalent ones.

Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated pi electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.

Themodynamics of adsorption and patterns of the gas-chromatographic retention of cyclic amines on surfaces of graphitized thermal carbon black

The thermodynamic characteristics of adsorption (TCA) of aniline, cyclohexylamine, and some of their derivatives on surfaces of graphitized thermal carbon black (GTC) are experimentally determined under conditions of gas-adsorption chromatography. It is concluded that the TCA values for the studied compounds depend to a large extent on the features of the geometrical and electronic structure of molecules in the gas phase. The effect of the sp3-sp2-rehybridization of nitrogen atoms upon moving from molecules of unsubstituted aniline to N-methyl- and N,N-dimethylanilines are determined, along with the ortho-effects in 2-methyland 2,6-dimethylanilines on the TCA values. It is shown that the above intramolecular effects result in nonadditive contributions to the energy of adsorption of the NH2-group in the a number of the studied compounds. Values of the thermal component of adsorption entropy are calculated, allowing conclusions on the physical state of the molecules of the studied compounds in the field of GTC adsorption forces. The mobility of adsorbate molecules is estimated using models of delocalized and localized adsorption. It is shown that in the series of ortho-meta-para-substituted anilines, the para-isomer is characterized by the highest values of retention on GTC, while the relative order of ortho- and meta-isomer elution is determined by the Van der Waals sizes of substituents in aromatic rings. A conclusion is reached on the high structural selectivity of a GTC surface in respect to positional isomers in the series of studied aniline derivatives.

The Influence of Magnetic Properties and Electronic Structure of Molecules on Motor Fuel Operating Characteristics by Example of n-Alkanes

The Influence of Magnetic Properties and Electronic Structure of Molecules on Motor Fuel Operating Characteristics by Example of n-Alkanes

The fluorescence and electronic structure of phenyl-substituted tetraazachlorin molecules

The effect of the addition of phenyl groups to pyrrole rings of tetraazachlorins, a new class of tetrapyrroles, on the photophysical properties and electronic structure of the molecules has been investigated by a complex of experimental and theoretical methods. Characteristics of fluorescence at 293 and 77 K have been determined for phenyl-substituted tetraazachlorins. The objects of this study include unsubstituted tetraazaporphine. The introduction of phenyl groups affords a marked increase in the fluorescence quantum yield. For tetraazaporphine and phenyl-substituted tetraazachlorins, fluorescence buildup occurs as the temperature is decreased from 293 to 77 K, but to a lesser extent than for tetraazachlorins having no phenyl groups, which were earlier studied by the authors. The fluorescence buildup mechanism is discussed. The singlet oxygen generation quantum yield has been determined for the tetrapyrroles examined. This characteristic increases upon tetrapyrrole is phenylation. The electronic structure and absorption spectra of unsubstituted porphine and chlorin, tetraazaporphine, tetraazachlorin, octaphenyltetraazaporphine, and tetramethylhexaphenyltetraazachlorin have been calculated by the INDO/Sm method (original modification of the INDO/S method) with molecular geometry optimization using DFT. The results of the quantum-chemical calculation of the absorption spectra are in good agreement with experimental data for transitions to the lowest excited electronic states Qx(S1) and Qy(S2).

Calculating X-ray Absorption Spectra of Open-Shell Molecules with the Unrestricted Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator.

X-ray absorption spectroscopy (XAS) is a powerful tool that provides information about the electronic structure of molecules via excitation of electrons from the K-shell core region to the unoccupied molecular levels. These high-lying electronic core-excited states can be accurately calculated using the algebraic-diagrammatic construction scheme of second order ADC(2) by applying the core-valence separation (CVS) approximation to the ADC(2) working equations. For the first time, an efficient implementation of an unrestricted CVS-ADC(2) variant CVS-UADC(2) is presented for the calculation of open-shell molecules by treating α and β spins separately from each other. The potential of the CVS-UADC(2) method is demonstrated with a set of small organic radicals by comparison with standard TD-DFT/B3LYP values and experimental data. It turns out that the extended variant CVS-UADC(2)-x, in particular, provides the most accurate results with errors of only 0.1% compared to experimental values. This remarkable agreement justifies the prediction of yet nonrecorded experimental XAS spectra like the one of the anthracene cation. The cation exhibits additional peaks due to the half-filled single-occupied molecular orbital, which may help to distinguish cation from the neutral species.

Gate-count estimates for performing quantum chemistry on small quantum computers

As quantum computing technology improves and quantum computers with a small but non-trivial number of N > 100 qubits appear feasible in the near future the question of possible applications of small quantum computers gains importance. One frequently mentioned application is Feynman's original proposal of simulating quantum systems, and in particular the electronic structure of molecules and materials. In this paper, we analyze the computational requirements for one of the standard algorithms to perform quantum chemistry on a quantum computer. We focus on the quantum resources required to find the ground state of a molecule twice as large as what current classical computers can solve exactly. We find that while such a problem requires about a ten-fold increase in the number of qubits over current technology, the required increase in the number of gates that can be coherently executed is many orders of magnitude larger. This suggests that for quantum computation to become useful for quantum chemistry problems, drastic algorithmic improvements will be needed.

QT-AIM analysis of neutral pterin and its anionic and cationic forms

Abstract Quantum theory of atoms in molecules (QT-AIM) allows detailed insight into the electronic structure of molecules by analysis of the gradient vector field of the electronic density distribution function. First results of a QT-AIM analysis of neutral pterin as well as its anionic and cationic forms in aqueous solution are reported based on density functional theory using B3LYP/6–311+G(2d,p)//6–31G(d) level of theory. Besides reporting QT-AIM results of the atomic partial charges and bond orders of the molecules, their electron density functions, Laplacians and electrostatic potential functions are also shown. The results demonstrate the rather extensive delocalization of both negative and positive extra charges predominantly over the pyrimidine moiety of the pterin ring system and allow a precise quantitation of the effects of addition or elimination of a proton on the bonding structure. Quantum chemical techniques in combination with QT-AIM procedures are thus well-suited to describing the bonding structure as well as the major atomic and bonding features of neutral pterin and its cationic and anionic forms. Moreover, the data demonstrate that the chosen level of theory yields chemically reasonable results while not being computationally too expensive, thus providing a sound basis for further theoretical chemical work on pteridines.

Orientational order and polarizability of molecules in a nematic liquid crystal

The influence of the orientational order of molecules in a nematic liquid crystal on the mean value and anisotropy Δγ of the molecular polarizability has been studied in the framework of the molecular sta� tistical approach with allowance for the perturbation of the electronic structure of molecules due to the change in the conformation of their aromatic core and intermolecular interactions. Experimental depen� dences of and Δγ on the molecular orientational order parameter S have been derived, and their specific features for the known objects have been explained. The possibility of separating the contributions of opposite signs to the dependence Δγ(S) due to the change in the conformation of molecules and intermolecular inter� actions has been shown using nematic MBBA as an example.

Tunable single and dual emission behavior of imidazole fluorophores based on D-π-A architecture

• A series of imidazole derivatives were synthesized and characterized. • Influence of solvent polarity on spectral behavior was investigated. • Kamlet–Taft and Catalán solvent parameters were used to analyze the solvatochromism. • Interplay between LE and ICT state was analyzed. • TD-DFT method was used to study the geometric and electronic structure of molecules. A series of three D-π-A molecules containing 4,5-diphenyl-1H-imidazole moiety as the donor (D) with cyanoacetic acid, rhodanine-3-acetic acid and 4-nitrophenyl acetonitrile as the acceptor (A) connected by a biphenyl bridge have been synthesized and characterized. Crystallography of BIC shows C4-phenyl group to be twisted nearly perpendicular to the imidazole unit and the remaining groups are in plane. The absorption spectra of the compounds are dominated by intramolecular charge transitions that arise from the imidazole core to the acceptor groups. The compounds display distinct dual and single emission behavior in different solvent environments, namely locally excited (LE ∼ 430 nm) and intramolecular charge transfer (ICT ∼ 550 nm). The Lippert–Mataga analysis suggested that the excited state dipole moment of ICT band is higher than the LE band. The influence of general and specific solvent effects on photophysical properties of the fluorophores was discussed with Catalán four parameter and Kamlet–Taft three parameter solvent scales. These results suggest that the major influence from solvent dipolarity takes part in a prominent role on changing the emission behavior of the compounds. The quantum yield of the compounds ranged between 0.07 and 0.55 in different solvents and it was shown to depend on the substitution pattern most notably that based on acceptor groups. All the compounds exhibit two lifetimes in the singlet excited state corresponding to LE state (short lived) and ICT state (long lived). In addition, the triplet state absorption properties of the compounds are also investigated by transient absorption measurement. The geometric structure and electronic structure of the molecules in the ground state is studied with DFT methods, whereas the energies of the lowest singlet excited states are calculated by employing TD-DFT methods. The results show that most prominent bands in acetonitrile solvent with higher oscillator strength for BIC, BIN and BIR are due to LE.

QSAR in the study of mechanisms of biological activity of acetone in vitro

Using computer calculation of descriptors of the electronic structure of molecules of acetone and phytohormones—ethylene, indoleacetic acid (IAA), benzylaminopurine (BAP), naphthalene acetic acid (NAA), abscisic acid (ABA), and gibberellic acid (GA)—the similarity of the activity of acetone with that of a number of phytohormones was found. The results of computer simulation were tested in biological experiments. The acetone bioactivity in vitro is also manifested in the possibility of dissolution of the cell walls and release of endogenous phytohormones in the formation of CO2, which activates photosynthesis. An assumption is made about the integrated action of these mechanisms.

Why Did the Electron Cross the Road? A Scanning Tunneling Microscopy (STM) Study of Molecular Conductance for the Physical Chemistry Lab

A series of experiments employing scanning tunneling microscopy (STM) have been developed for the physical chemistry laboratory. These experiments are designed to engage students in cutting edge research techniques while introducing and reinforcing topics in physical chemistry, quantum mechanics, solid-state chemistry, and the electronic structure of molecules and materials. In the first of three experiments, students are introduced to the basics of STM operation while imaging and conducting spectroscopy on the highly oriented pyrolytic graphite (HOPG) surface. Images of the surface are used to determine the crystal structure of the material, and scanning tunneling spectroscopy is used to determine the electronic properties of the material and study the tunneling phenomenon. In the second experiment, the students image the Au(111) surface as well as a series of alkanethiol self-assembled monolayers (SAMs) of different chains lengths on the Au(111) surface. They examine the structural and electronic properties of the metal surface and the adlattice structure of the film. Finally, in the third experiment, the students examine the conductance of molecules adsorbed onto the Au(111) surface, including the alkanethiol SAMs and a thiol-tethered porphyrin molecule or a dimercaptostilbene embedded into the SAM matrix. By measuring the tunneling efficiency and spectroscopic characteristics of these molecules, the students can explore the relationship between chemical structure and charge transport efficiency. The experiments provide advanced chemistry students an opportunity to view and study materials at the atomic and molecular length scales and provide an opportunity to apply their understanding of quantum mechanical concepts to real systems.

Study of geometry and electronic structure of molecules, cation-radicals, and anion-radicals of nitromethane, dimethylnitramine, and ethyl nitrate

The geometry of cation-radicals and anion-radicals of nitromethane, dimethylnitramine, and ethyl nitrate have been computed by means of modern quantum-chemical methods. Their electron affinities and ionization potentials have been determined. The validity of the results has been confirmed by comparison with the experiment.

A quantum chemical study of alkoxy derivatives of three-coordinate aluminum

DFT and HF methods using the PC GAMESS-Firefly program are employed to calculate the spatial and electronic structures of molecules: alkoxy derivatives of aluminum. By NBO and AIM methods the main characteristics of Al-O, C-O, and Al-X bonds in these molecules are determined. It is shown that Al and O atoms interact with each other as atoms with closed shells. The C-O bonds are close to covalent, whereas the Al-X bonds are the intermediate type bonds.

State-Specific Embedding Potentials for Excitation-Energy Calculations.

Embedding potentials are frequently used to describe the effect of an environment on the electronic structure of molecules in larger systems, including their excited states. If such excitations are accompanied by significant rearrangements in the electron density of the embedded molecule, large differential polarization effects may take place, which in turn can require state-specific embedding potentials for an accurate theoretical description. We outline here how to extend wave function in density functional theory (WF/DFT) methods to compute the excitation energies of a molecule in a responsive environment through the use of state-specific density-based embedding potentials constructed within a modified subsystem DFT approach. We evaluate the general expression of the ground- and excited-state energy difference of the total system both with the use of state-independent and state-dependent embedding potentials and propose some practical recipes to construct the approximate excited-state DFT density of the active part used to polarize the environment. We illustrate these concepts with the state-independent and state-dependent WF/DFT computation of the excitation energies of p-nitroaniline, acrolein, methylenecyclopropene, and p-nitrophenolate in various solvents.