Ab Initio Quantum Mechanical Calculations Research Articles

Theoretical and experimental investigations on the nonlinear optical properties of gold(III) dithiolene complexes

Degenerate four-wave mixing (DFWM) experiments have been performed to determine the third-order nonlinear optical (NLO) susceptibilities (χ(3)) of gold(III) maleimide dithiolate tetraphenylphosphonium, (PPh4)[Au(midt)2], (Au-P) and gold(III) maleimide dithiolate melamine melaminium hybrid solvate, (C3N6H6)(C3N6H7+)[Au(midt)2]−·2DMF·2H2O, (Au-Mel). Ab-initio quantum mechanical calculations (time-dependent Hartree–Fock (TDHF) method) of Au-P and Au-Mel have been carried out to compute the electric dipole moment (μ), the dispersion-free and frequency-dependent dipole polarizability (α) and the second hyperpolarizability (γ) values. These theoretical calculations are in good agreement with the experimentally obtained results by the DFWM technique. All the investigations show clearly the effect played by the counter ion on the resulting NLO properties of the two gold complexes.

Internal energy and parameters of the order-disorder phase transition in titanium monoxide TiO y

Quantum-mechanical ab initio calculations are used to simulate the free energy functions for titanium monoxide TiO y . The effect of the long-range order of the Ti5O5 type superstructure on the internal energy of the compound is studied by the supercell method. The dependences of the configuration entropy and free energy on the long-range order parameter are determined. It is found that the order-disorder phase transition in titanium monoxide must occur in accordance with the mechanism of the first-order phase transition with a critical value of the long-range order parameter of 0.971. The calculated parameters of the phase transition are compared with the experimental data and the results obtained using the model of point charges and by calculating the Madelung energy. It is concluded that the short-range order and the phonon entropy must be taken into account in calculating the equilibrium phase diagrams for strongly nonstoichiometric compounds.

Amino, ammonio and aminioethenes: a theoretical study of their structure and energetics

We have performed high level ab initio quantum mechanical calculations for aminoethene and the three isomeric 1,1- (Z)- or (E)-1,2-diaminoethenes as well as their singly and doubly charged cations derived by loss of electrons and/or upon protonation. Gas phase molecular structures were computed at the MP2/6-311+G(3df,2p) level. Standard molar enthalpies of formation in the gas phase, at T = 298.15 K were estimated using the G3 composite method and atomization, isodesmic and homodesmotic reactions. Other energetic parameters were also calculated at the G3 level: proton affinities, basicities and adiabatic ionization enthalpies. Theoretical and experimental data are compared. The reported experimental data refer only to aminoethene wherein the standard molar enthalpy of formation has a considerable uncertainty, although the molecular structure is well-established. There are no such data, neither structural nor thermochemical, for any of the three isomeric diaminoethenes. Isoelectronic comparisons are made. For example, the diprotonated diaminoethenes are isoelectronic to isobutene and (Z)- and (E)-butene, while the doubly ionized diaminoethenes are likewise related to trimethylenemethane and 1,3-butadiene.

Core hole screening and decay rates of double core ionized first row hydrides

Because of the high intensity, X-ray free electron lasers allow one to create and probe double core ionized states in molecules. The decay of these multiple core ionized states crucially determines the evolution of radiation damage in single molecule diffractive imaging experiments. Here we have studied the Auger decay in hydrides of first row elements after single and double core ionization by quantum mechanical ab initio calculations. In our approach the continuum wave function of the emitted Auger electron is expanded into spherical harmonics on a radial grid. The obtained decay rates of double K-shell vacancies were found to be systematically larger than those for the respective single K-shell vacancies, markedly exceeding the expected factor of two. This enhancement is attributed to the screening effects induced by the core hole. We propose a simple model, which is able to predict core hole decay rates in molecules with low Z elements based on the electron density in the vicinity of the core hole.

Automated development of force fields for the calculation of thermodynamic properties: acetonitrile as a case study

Force fields for engineering applications are often parameterised using strategies based on quantum mechanical ab initio calculations and thermodynamic properties from experiment. An automated procedure for adjusting molecular model parameters to experimental thermodynamic property data is introduced. The process accelerates the development of molecular models by an efficient use of parallel computing power and an autonomous progress of the model development without any user interaction. As a case study, the procedure is applied to the parameterisation of a molecular model for acetonitrile. The resulting model reproduces vapour–liquid equilibrium data of acetonitrile with an accuracy of 0.1% for the saturated liquid density, 4.9% for the vapour pressure and 3.7% for the enthalpy of vaporisation. These accuracies are superior to data obtained with previously published force fields for acetonitrile.

Spatial and temporal interference during the ionization of H by few-cycle XUV laser pulses

We have investigated the ionization of H atoms by few-cycle XUV laser pulses, in particular the interference between electronic wave packets emitted at different time moments (temporal interference), and the interference between wave packets emitted at the same time, but following different paths (spatial interference). During the spatial interference, under appropriate conditions, the holographic mapping (HM) of the target atom's state is achieved, which has the potential to become a powerful tool to study atomic structure. First, by using classical trajectory Monte Carlo calculations, we have confirmed the existence of two distinct types of electron trajectories, which contribute to the formation of the HM interference pattern. Then, by using ab initio quantum-mechanical calculations, we have studied how the shape of the HM pattern is influenced by the laser pulse parameters. Finally, we have identified the optimal laser pulse parameters for the observation of the HM interference in the case of atomic species with an ionization potential close to 0.5 a.u.

Natural gas storage on silicon, carbon, and silicon carbide nanotubes: a combined quantum mechanics and grand canonical Monte Carlo simulation study

Grand canonical Monte Carlo (GCMC) simulation combined with ab initio quantum mechanics calculations were employed to study methane storage in homogeneous armchair open-ended single-walled silicon nanotubes (SWSiNTs), single-walled carbon nanotubes (SWCNTs), and single-walled silicon carbide nanotubes (SWSiCNTs) in triangular arrays. Two different groups of nanotubes were studied: the first were (12,12) SiNTs, (19,19) CNTs, and (15,15) SiCNTs and the second were (7,7) SiNTs, (11,11) CNTs, and (9,9) SiCNTs with the diameters of 26 and 15 A for the first and second groups, respectively. The simulations were carried out at different thermodynamic states. The potential energy functions were calculated using ab initio quantum mechanics and then fitted with (12,6) Lennard–Jones potential model as a bridge between first-principles calculations and GCMC simulations. The absolute, excess, and delivery adsorption isotherms of methane were calculated for two groups of nanotubes. The specific surface area and the isosteric heat of adsorption were computed. The radial distribution functions for the adsorbed molecules on different nanotubes were also calculated. Different isotherm models were fitted with the simulation adsorption data. According to the results, the excess uptake value of methane adsorption in (11,11) CNT array exceeded the US Department of Energy target (180 V/V at 298 K and 35 bar). The results also indicate that SiNTs and SiCNTs are not desirable materials compared with corresponding CNTs for natural gas storage.

Non-unique Lennard-Jones Parameter Problem with a Monatomic Cation

In molecular mechanical force fields, a monatomic ion is represented as a charged van der Waals particle that interacts with all atoms of the molecular system. The Coulomb potential normally specifies the electrostatic interaction of the charge. The Lennard-Jones (LJ) potential expresses the pair-wise exchange-repulsion and dispersion interactions between atoms i and j with the well depth eij and the distance Rmin,ij at which the potential reaches the minimum. Following the Lorentz-Berthelot combination rule, the charge and the dispersion parameters, e and Rmin, define the force field of a monatomic ion. 1 The force field parameters are optimized to reproduce experimental findings through molecular simulations. Various experimental and theoretical data have been considered; a partial list includes the free energy of hydration, the entropy of hydration, the radial distribution function of water oxygen atoms around the ion, the lattice constant and the lattice energy of ionic crystals, osmotic coefficients, and geometric and energetic data from ab initio quantum mechanical calculations of monohydrates to water clusters of ions. 2-8 Unfortunately, it has been difficult to determine a

Theoretical study on the CH⋯NC hydrogen bond interaction in thiophene-based molecules

Results on a detailed investigation of the CH⋯NC hydrogen bond interaction in functional thiophene-based molecules are presented by employing quantum-mechanical ab initio and DFT-based calculations. Dimers of 1-cyano-thiophene are studied to evaluate the influence of the computational method, of the chosen basis set and of substitution in 3-position on the structure and stability of the hydrogen bond. Furthermore, we focus on the intermolecular hydrogen bond in a chain of α,ω-dicyano-β,β′-dibutylquarterthiophene (DCNDBQT) molecule, which was found to be a promising organic semiconducting material for thin-film organic field-effect transistors. In particular, the intermolecular structure and the electronic properties of the material are determined employing the efficient SCC-DFTB method. We demonstrate the highly local character of the hydrogen and found that the weak CH⋯NC interaction links the molecules into extended ribbons perpendicular to the support.

Measurement of Binary Diffusion Coefficients for Neon–Argon Gas Mixtures Using a Loschmidt Cell Combined with Holographic Interferometry

The paper reports on experimental binary diffusion coefficient data of neon–argon gas mixtures. Measurements were performed in the temperature range between 293.15 K and 333.15 K and for pressures between 1 bar and 10 bar over almost the whole composition range using a Loschmidt diffusion cell combined with holographic interferometry. The thermostated Loschmidt cell is divided into two half-cells, which can be separated and connected by a sliding plate. Prior to the measurements, two different pure gases are filled into the two half-cells. After starting the diffusion process, the temporal change of the partial molar densities, or rather of the refractive index of the gases, is detected in both half-cells using two holographic interferometers. With this apparatus, the temperature, pressure, and concentration dependence of the binary diffusion coefficient can be determined. The relative uncertainty of a diffusion measurement is between 0.4 % and 1.4 % depending on the pressure. The experimental data are compared with data from the literature and with new theoretical data based on quantum-mechanical ab initio calculations combined with the kinetic theory of gases. Due to a systematic error, the concentration dependence determined in the upper half-cell shows deviations from the theoretical values and from most of the literature data. The concentration, temperature, and pressure dependence obtained from the data from the lower half-cell, however, are in very good agreement with available data. The product of the binary gas diffusion coefficient and the molar density of the gas mixture shows no significant dependence on pressure for the studied neon–argon noble gas system.

On the quantum theory of molecules

Transition state theory was introduced in 1930s to account for chemical reactions. Central to this theory is the idea of a potential energy surface (PES). It was assumed that such a surface could be constructed using eigensolutions of the Schrödinger equation for the molecular (Coulomb) Hamiltonian but at that time such calculations were not possible. Nowadays quantum mechanical ab initio electronic structure calculations are routine and from their results PESs can be constructed which are believed to approximate those assumed derivable from the eigensolutions. It is argued here that this belief is unfounded. It is suggested that the potential energy surface construction is more appropriately regarded as a legitimate and effective modification of quantum mechanics for chemical purposes.

Quantum mechanical study of energetics and mechanisms of cis–trans isomerization of some four-membered heterocycles

Ab initio quantum mechanical calculations using density functional (B3LYP) method and 6-311G** basis set have been performed on two cis and trans conformers of 2,4-diphenyl thietane dioxide (DPTD), 2,4-diphenyl thietane (DPT), 2,4-diphenyl azetidine (DPA) and 2,4-diphenyl oxetane (DPO). The calculated stability energy for cis–trans isomerization in gas phase and in different solvents such as benzene, DMSO, water and methanol indicated that the cis conformer is more stable than trans in all above-mentioned compounds about 11–2 kcal mol−1. In the next step, a transition states for cis–trans inter-conversion for all four-membered heterocycles (DPTD, DPT, DPA and DPO) were proposed in methanol as solvent. Thermodynamic functions such as standard enthalpies of isomerization (∆Hoiso), standard entropy of isomerization (∆Soiso) and standard Gibbs free energy of isomerization (∆Goiso) for all studied compounds were also evaluated. The calculation showed that the conversion of trans to cis isomer is exothermic and spontaneous. In all calculations, solvent effects were considered using a polarized continuum model.

ENERGY RELAXATION OF HELIUM ATOMS IN ASTROPHYSICAL GASES

We report accurate parameters describing energy relaxation of He atoms in atomic gases, important for astrophysics and atmospheric science. Collisional energy exchange between helium atoms and atomic constituents of the interstellar gas, heliosphere, and upper planetary atmosphere has been investigated. Energy transfer rates, number of collisions required for thermalization, energy distributions of recoil atoms, and other major parameters of energy relaxation for fast He atoms in thermal H, He, and O gases have been computed in a broad interval of energies from 10 meV to 10 keV. This energy interval is important for astrophysical applications involving the energy deposition of energetic atoms and ions into atmospheres of planets and exoplanets, atmospheric evolution, and analysis of non-equilibrium processes in the interstellar gas and heliosphere. Angular- and energy-dependent cross sections, required for an accurate description of the momentum-energy transfer, are obtained using ab initio interaction potentials and quantum mechanical calculations for scattering processes. Calculation methods used include partial wave analysis for collisional energies below 2 keV and the eikonal approximation at energies higher than 100 eV, keeping a significant energy region of overlap, 0.1-2 keV, between these two methods for their mutual verification. The partial wave method and the eikonal approximation excellently match results obtained with each other as well as experimental data, providing reliable cross sections in the astrophysically important interval of energies from 10 meV to 10 keV. Analytical formulae, interpolating obtained energy- and angular-dependent cross sections, are presented to simplify potential applications of the reported database. Thermalization of fast He atoms in the interstellar gas and energy relaxation of hot He and O atoms in the upper atmosphere of Mars are considered as illustrative examples of potential applications of the new database.

Molecular Rotors: What Lies Behind the High Sensitivity of the Thioflavin-T Fluorescent Marker

Thioflavin-T (ThT) can bind to amyloid fibrils and is frequently used as a fluorescent marker for in vitro biomedical assays of the potency of inhibitors for amyloid-related diseases, such as Alzheimer's disease, Parkinson's disease, and amyloidosis. Upon binding to amyloid fibrils, the steady-state (time-integrated) emission intensity of ThT increases by orders of magnitude. The simplicity of this type of measurement has made ThT a common fluorescent marker in biomedical research over the last 50 years. As a result of the remarkable development in ultrafast spectroscopy measurements, researchers have made substantial progress in understanding the photophysical nature of ThT. Both ab initio quantum-mechanical calculations and experimental evidence have shown that the electronically excited-state surface potential of ThT is composed of two regimes: a locally excited (LE) state and a charge-transfer (CT) state. The electronic wave function of the excited state changes from the initial LE state to the CT state as a result of the rotation around a single C-C bond in the middle of the molecule, which connects the benzothiazole moiety to the dimethylanilino ring. This twisted-internal-CT (TICT) is responsible for the molecular rotor behavior of ThT. This Account discusses several factors that can influence the LE-TICT dynamics of the excited state. Solvent, temperature, and hydrostatic pressure play roles in this process. In the context of biomedical assays, the binding to amyloid fibrils inhibits the internal rotation of the molecular segments and as a result, the electron cannot cross into the nonradiative "dark" CT state. The LE state has high oscillator strength that enables radiative excited-state relaxation to the ground state. This process makes the ThT molecule light up in the presence of amyloid fibrils. In the literature, researchers have suggested several models to explain nonradiative processes. We discuss the advantages and disadvantages of the various nonradiative models while focusing on the model that was initially proposed by Glasbeek and co-workers for auramine-O to be the best suited for ThT. We further discuss the computational fitting of the model for the nonradiative process of ThT.

Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation and NLO, HOMO–LUMO, NBO analysis of organic 2,4,5-trichloroaniline

In this work, the experimental and theoretical study on the molecular structure and vibrational spectra of 2,4,5-trichloroaniline (C6H4NCl3, abbreviated as 2,4,5-TClA) were studied. The FT-IR and FT-Raman spectra were recorded. The molecular geometry and vibrational frequencies in the ground state were calculated by using the Hartree–Fock (HF) and density functional theory (DFT) methods (B3LYP) with 6-311++G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of 2,4,5-TClA with calculated results by HF and DFT indicates that B3LYP is superior to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4,5-TClA molecule may have microscopic nonlinear optical (NLO) behavior with non-zero values. Mulliken atomic charges of 2,4,5-TClA was calculated and compared with aniline and chlorobenzene molecules. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations

Molecular dynamics (MD) simulations have been performed in order to investigate the properties of [C n mim+][Tf2N−] (n = 4, 8, 12) ionic liquids (ILs) in a wide temperature range (298.15−498.15 K) and at atmospheric pressure (1 bar). A previously developed methodology for the calculation of the charge distribution that incorporates ab initio quantum mechanical calculations based on density functional theory (DFT) was used to calculate the partial charges for the classical molecular simulations. The wide range of time scales that characterize the segmental dynamics of these ILs, especially at low temperatures, required very long MD simulations, on the order of several tens of nanoseconds, to calculate the thermodynamic (density, thermal expansion, isothermal compressibility), structural (radial distribution functions between the centers of mass of ions and between individual sites, radial-angular distribution functions) and dynamic (relaxation times of the reorientation of the bonds and the torsion angles, self-diffusion coefficients, shear viscosity) properties. The influence of the temperature and the cation's alkyl chain length on the above-mentioned properties was thoroughly investigated. The calculated thermodynamic (primary and derivative) and structural properties are in good agreement with the experimental data, while the extremely sluggish dynamics of the ILs under study renders the calculation of their transport properties a very complicated and challenging task, especially at low temperatures.

Solid-State 13C NMR Investigations of Cyclophanes: [2.2]Paracyclophane and 1,8-Dioxa[8](2,7)pyrenophane

Solid-state NMR (ssNMR) and ab initio quantum mechanical calculations are used in order to understand and to better characterize the molecular conformation and properties of [2.2]paracyclophane and 1,8-dioxa[8](2,7)pyrenophane. Both molecules are cyclophanes, consisting of an aromatic ring assembly and a cyclic aliphatic chain connected to both ends of the aromatic portion. The aliphatic chain causes curvature in the six-membered aromatic ring structures. This led us to examine how the ring strain due to curvature affects the chemical shifts. Using X-ray structures of both [2.2]paracyclophane and 1,8-dioxa[8](2,7)pyrenophane as our starting model, we calculate the chemical shielding tensors and compare these data with those collected from the (13)C ssNMR FIREMAT experiment. We define curvature of [2.2]paracyclophane and 1,8-dioxa[8](2,7)pyrenophane using the π-orbital axis vector (POAV) pyramidalization angle (θ(p)).

Structural, electronic, and hyperfine properties of pure and Ta-dopedm-ZrO2

A combination of experiments and ab initio quantum-mechanical calculations has been applied to examine electronic, structural, and hyperfine interactions in pure and Ta-doped zirconium dioxide in its monoclinic phase ($m$-ZrO${}_{2}$). From the theoretical point of view, the full-potential linear augmented plane wave plus local orbital (APW+lo) method was applied to treat the electronic structure of the doped system including the atomic relaxations introduced by the impurities in the host in a fully self-consistent way using a supercell approach. Different charge states of the Ta impurity were considered in the study and its effects on the electronic, structural, and hyperfine properties are discussed. Our results suggest that two different charge states coexist in Ta-doped $m$-ZrO${}_{2}$. Further, ab initio calculations predict that depending on the impurity charge state, a sizeable magnetic moment can be induced at the Ta-probe site. This prediction is confirmed by a new analysis of experimental data.

Is there an exact potential energy surface?

Transition state theory was introduced in the 1930s to account for chemical reactions. Central to this theory is the idea of a potential energy surface (PES). It was assumed that quantum mechanical computation, when it became possible, would yield such surfaces, but for the time being they would have to be constructed empirically. The approach was very successful. Nowadays, quantum mechanical ab initio electronic structure calculations are possible and from their results PESs can be constructed. Such surfaces are now widely used in the explanation of chemical reactions in place of the traditional empirical ones. It is argued here that theoretical basis of such PESs is not quite as clear as is usually assumed and that, from a quantum mechanical perspective, certain puzzles remain.

Influence of a methyl substituent on the Raman spectrum of but-3-enyl methyl ether

The Raman spectrum of but-3-enyl methyl ether, CH2CHCH2CH2OCH3 is reported and compared with those of its homologues in which a methyl group is substituted for a hydrogen atom on one of the carbon atoms of the alkenyl chain. Attention is focused on the influence of this methyl group on the bands in the spectrum associated with specific CH, skeletal stretching and bending vibrations. The use of ab initio DFT quantum mechanical calculations to assist in making these assignments reveals a high degree of mode-mixing in the skeletal vibrations. The value of model studies of this kind in refining the correlations between the presence and absence of specific bands in a Raman spectrum with molecular structure is emphasised.