Propionaldehyde: ab initio and semi-empirical calculations

The internal rotation of propionaldehyde about the 1–2 bond has been studied by means of ab initio calculations. The most stable conformer has methyl and carbonyl eclipsed. Increasing the 1–2 dihedral angle to 60°, 120°, and 180° gives energies of 1.7, 0.4, and 0.7 Kcal/mol, respectively. The agreement with force field calculations and with experiment is reasonable.     

Ionization of aqueous cations: photoelectron spectroscopy and ab initio calculations of protonated imidazole

Photoelectron spectroscopy and ab initio calculations employing a nonequilibrium polarizable continuum model were employed for determining the vertical ionization potential of aqueous protonated imidazole. The experimental value of 8.96 eV is in in excellent agreement with calculations, which also perform quantitatively for ionization of aqueous alkali cations as benchmark species. The present results show that protonation of imidazole increases its vertical ionization potential up in water by 0.7 eV, which is significantly larger than the resolution of the experiment or the error of the calculation. This combined experimental and computational approach may open the possibility for quantitatively analyzing the protonation state of histidine, of which imidazole is the titratable side chain group, in aqueous peptides and proteins.     

Photodissociation of warm water: ab initio calculations of the room-temperature absorption spectrum

This Letter presents cross sections of water in the second absorption band obtained from quantum mechanical calculations. A Monte-Carlo sampling over the initial rotational state is applied in order to calculate the cross section for water at a temperature of 300 K (warm water). This makes a fair comparison with the experimental spectrum, only available for water at room temperature, possible. The overall rotation of the water molecule is treated exactly. The inclusion of initial rotational motion, which reduces the resonance structure in the spectrum, significantly improves the agreement between theory and experiment.     

F K-edge X-ray absorption near-edge structure (XANES) of AlF3 polymorphs: combining ab initio calculations with Walsh correlation diagrams

The X-ray absorption near-edge structures (XANES) at the F K-edge of alpha-AlF(3), beta-AlF(3) and a tetragonal AlF(3) phase are analysed by a combination of ab initio calculations with the FEFF8 code and a phenomenological discussion of local molecular orbital (MO) symmetries at the absorbing fluorine atoms. By means of a Walsh correlation diagram it is shown that the two intense absorption bands observed at the F K-edges of the AlF(3) polymorphs can be interpreted as transitions to anti-bonding MOs in [Al-F-Al]-units that have C(2v) and D(infinity h) point group symmetries. The energies of both anti-bonding orbitals are very insensitive to the angle between the Al-F bonds, which explains the close similarity of the XANES signatures from the three polymorphs. The FEFF8 analysis shows that the increased broadening of the XANES structure for beta-AlF(3) and the tetragonal AlF(3) phase is due to the superposition of the individual absorption spectra from the crystallographically distinct F species. The interpretation in terms of local MOs provides for the first time a "chemically intuitive" approach to investigations of solid fluorides by XANES spectroscopy and provides a simple conceptual framework for the discussion of the electronic structure in AlF(3) materials.     

Photophysics of indole-2-carboxylic acid in an aqueous environment studied by fluorescence spectroscopy in combination with ab initio calculations

The photo-physics and -chemistry of indoles are known to be highly complex and strongly dependent on their precise molecular structure and environment. Combination of spectroscopic analysis with quantum chemical calculations should be a powerful tool to unravel precise excited state deactivation mechanisms. At the same time, combined studies are seldom and likely far from trivial. In this work we explore the feasibility of combining spectroscopic and quantum-chemical data into one consistent model. The molecule of choice is indole-2-carboxylic acid (ICA) in aqueous media. Excited state dynamics are determined by time-resolved fluorescence experiments, while excited state reaction pathways of ICA-H(2)O clusters are explored by ab initio calculations.     

Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations

Proton transfer reactions were studied in all titratable pairs of amino acid side chains where, under physiologically reasonable conditions, one amino acid may function as a donor and the other one as an acceptor. Energy barriers for shifting the proton from donor to acceptor atom were calculated by electronic structure methods at the MP2/6-31++G(d,p) level, and the well-known double-well potentials were characterized. The energy difference between both minima can be expressed by a parabola using as argument the donor-acceptor distance R(DA). In this work, the fit parameters of the quadratic expression are determined for each donor-acceptor pair. Moreover, it was found previously that the energy barriers of the reactions can be expressed by an analytical expression depending on the distance between donor and acceptor and the energy difference between donor and acceptor bound states. The validity of this approach is supported by the extensive new data set. This new parameterization of proton transfer barriers between titratable amino acid side chains allows us to very efficiently estimate proton transfer probabilities in molecular modelling studies or during classical molecular dynamics simulation of biomolecular systems.     

A simple treatment of intermolecular interactions: Synthesis of ab initio calculations and combination rules

A new technique for a simple and efficient treatment of intermolecular interactions is proposed and tested. The method is based on an approximation of the first order SCF term E_SCF⁽¹⁾ which is the most structured contribution to the total interaction. E_SCF⁽¹⁾ is represented by a site–site potential V of (exp, 1/R)-type, which accounts for the exchange plus penetration and the long range Coulomb forces (by means of a point charge model). The individual contributions to V are obtained by means of combination rules from corresponding site parameters of interacting molecules. The site parameters are consequently molecular and not intermolecular properties and can conveniently be determined by probing a molecule with appropriate test particles. Site parameters are reported for He, Ne, Ar, N₂, CO, CO₂, CS₂, and HCl. Comprisons show close agreement of V with E which in turn is close to ΔE_SCF if polarization and charge transfer effects are small.     

吡啶甲酸分子平衡构型的ab initio理论研究

本文用能量梯度法TEXAS从头计算程序,选取4-21G(,N原子含极化d轨道)基组,对α-,β-吡啶甲酸分子的平衡几何构型进行了全优化计算,二套基组的理论优化表明,三个吡啶甲酸分子都具有平面的平衡构型,其计算键长经4-21G 基组的标准经验校正值校正后,所得的理论预测平衡几何构型与X射线单晶衍射实验结果有很好的一致性.对部分键长以及羧基与吡啶华平面的二面角中出现的差异进行了讨论.     

Adsorption of polyacrylic acid on aluminium oxide: DRIFT spectroscopy and ab initio calculations

Diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy was used to study the adsorption process of the water-soluble polyacrylic acid (PAA) polymer on hydrous δ-Al₂O₃. Vibrational assignment of PAA, sodium polyacrylate, (Na–PA) and the PA-oxide surface complex was achieved by comparison of observed band position and intensity in the DRIFT spectra with wavenumbers and intensities from ab initio quantum mechanical calculations. The presented data of polyacrylic acid suggest that IR data calculated ab initio on relatively short oligomers (quantum-mechanical oligomer approach) may provide valuable information regarding the interpretation of polyelectrolyte infrared spectra. Batch adsorption experiments were performed to sorb PAA onto the δ-Al₂O₃ surface. The results obtained from DRIFT studies were compared with adsorption isotherm experiments in order to relate the level of PAA coverage to the nature of the surface complex. Ab initio molecular orbital calculations on PAA/Al₂O₃ clusters were used to model possible surface complexes. Strong correlation were found between theoretical and observed DRIFT frequencies of the antisymmetric R-COO⁻ vibration. A number of possible configurations of the polyacrylic acid/aluminate surface complex were tested via ab initio calculations. These possible configurations included different di-aluminium octahedral Al³⁺ surface models. Results obtained from adsorption isotherm experiments, DRIFT spectra and ab initio calculations indicate that the carboxylate oxygens bridge an Al³⁺-octahedral dimer [Al₂(OH)₂4(H₂O)2(OH)] in a ligand-exchange inner sphere complex.     

Electronic structure of the spinel Li4Ti5O12 studied by ab initio calculations and X-ray absorption spectroscopy

The electronic structure of the spinel compound Li₄Ti₅O₁₂, used as anode material in Li-ion batteries, is studied both theoretically and experimentally. The partial densities of occupied and vacant s, p and d electronic states were calculated for Li, Ti and O, using the linear augmented plane wave formalism (LAPW) in order to obtain information on the chemical bond. X-ray absorption spectra were recorded at the Ti L₂₃, Ti K and O K absorption edges and calculated within the dipolar approximation by considering both the electronic ground state and the effect of core holes. The atomic origin of the observed main peaks is analysed from the comparison between the experimental and calculated spectra. We show that the two types of lithium in Li₄Ti₅O₁₂ which are found in tetrahedral and octahedral sites could be distinguished by X-ray absorption spectroscopy. We suggest to use such a technique for the investigation of Li-insertion mechanisms in lithium titanate spinels.     

Probing photophysical and photochemical processes of benzoic acid from ab initio calculations

The CASSCF and DFT methods have been used to determine geometric and electronic structures of the benzoic acid monomer in the S(0), S(1), S(2), T(1), and T(2) electronic states. The S(1)/T(2)/T(1) three-surface intersection was found by the state-averaged CASSCF calculations, which, in combination with features of the five lowest electronic states, provides new insights into photophysical processes of the benzoic acid monomer. The potential energy profiles of the alpha C-C and C-O bond fissions as well as decarboxylation reaction in different electronic states have been determined for the benzoic acid monomer. The alpha C-O bond cleavage starts from the T(2) state and leads to the fragments of C(6)H(5)CO(X(2)A') and OH(X(2)Pi) in the ground state, which is predicted to be the most possible channel upon photoexcitation of the benzoic acid monomer at 270 nm or shorter wavelengths.     

Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions

Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.     

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.     

Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations

Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.     

Optical absorption and luminescence energies of F centers in CaO from ab initio embedded cluster calculations

We calculated the optical absorption and luminescence energies of electrons trapped at oxygen vacancies in CaO using a consistent embedded cluster method which accounts for the long-range polarization effects and partial covalence of CaO. Optical absorption and luminescence energies of neutral (F center) and positively charged (F+ center) vacancies are calculated by means of time dependent density functional theory using the B3LYP exchange-correlation density functional. Our results demonstrate that using large basis sets to describe a diffuse nature of excited states, and properly accounting for long-range polarization induced by charged and excited defect states, is crucial for accurate predictions of optical excitation and luminescence energies of these defects.     

Hyperfine interactions in aqueous solution of Cr3+: an ab initio molecular dynamics study

We performed an ab initio molecular dynamics simulation of the paramagnetic transition metal ion Cr³⁺ in aqueous solution. Isotropic hyperfine coupling constants between the electron spin of the chromium ion and nuclear spins of all water molecules have been determined for instantaneous snapshots extracted from the trajectory. The coupling constant of first sphere oxygen, A _iso(¹⁷O_I)=1.9±0.3 MHz, is independent on Cr–O_I distance but increases with the tilt angle for the water molecule approaching 180°. First sphere hydrogen spins have A _iso(¹ H_I)=2.1±0.2 MHz which decreases with increasing tilt angle and shows a Cr–H_I distance dependence. The hyperfine coupling constants for second sphere ¹⁷O is negative and an order of magnitude smaller (−0.20±0.02 MHz) compared to first sphere.     

Understanding solvation in hydrofluoroalkanes: ab initio calculations and chemical force microscopy

Understanding solvation in hydrofluoroalkane (HFA) propellants is of great importance for the development of novel pressurized metered-dose inhaler (pMDI) formulations. HFA-based pMDIs are not only the most widely used inhalation therapy devices for treating lung diseases, but they also hold promise as vehicles for the systemic delivery of biomolecules to and through the lungs. In this work we propose a combined microscopic experimental and computational approach to quantitatively relate the chemistry of moieties to their HFA-philicity. Binding energy calculations are used to determine the degree of interaction between a propellant HFA and candidate fragments. We define a new quantity, the enhancement factor E, which also takes into account fragment-fragment interactions. This quantity is expected to correlate well with the solubility and the ability of the moieties of interest to impart stability to colloidal dispersions in HFAs. We use a methyl-based (CH) segment and its fluorinated analog (CF) to test our approach. CH is an important baseline case since it represents the tails of surfactants in FDA-approved pMDIs. CF was chosen due to the improved solubility and ability of this chemistry to stabilize aqueous dispersions in HFAs. Adhesion force from Chemical Force Microscopy (CFM) is used as an experimental analog to the binding energy calculations. The force of interaction between a chemically modified AFM tip and substrate is measured in a model HFA, which is a liquid at ambient conditions. Silanes with the same chemistry as the fragments used in the ab initio calculations allow for direct comparison between the two techniques. The CFM results provide an absolute scale for HFA-philicity. Single molecule (pair) forces calculated from the CFM experiments are shown to be in very good agreement to the E determined from the ab initio calculations. The ab initio calculations and CFM are corroborated by previous experimental studies where propellants HFAs are seen to better solvate the CF functionality.