Ab Initio Quantum Chemical Calculations Research Articles

Intermolecular Dynamics of Positively and Negatively Charged Aromatics and Their Isoelectronic Neutral Analogs in Aqueous Solutions.

In this study, we investigated the temperature dependence of intermolecular vibrations and orientational dynamics in the aqueous solutions of imidazole hydrochloride, imidazole, sodium triazolide, and triazole using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES) and steady-state Raman spectroscopy. The difference low-frequency Raman spectra under 250 cm-1 of the aqueous solutions relative to the neat water showed that the spectral shoulder in the high-frequency region at 60-100 cm-1, assigned to the libration of an aromatic ring, was higher in frequency for the imidazolium cation but lower for the triazolide anion than those of the respective neutral aromatics. The results of the ab initio quantum chemistry calculations of the clusters of the aromatics and water molecule(s) were consistent with the experimental spectra of the aqueous solutions. Further, the results of the temperature-dependent experiments showed that the signal intensity in the low-frequency region below 50 cm-1 increased for all solutions with an increase in temperature. In contrast, the spectral density in the high-frequency region above 80 cm-1 exhibited almost no shift for the 1.0 M solutions, while a significant red shift was observed for the 5.0 M solutions. In addition, the temperature-dependent densities, viscosities, and surface tensions were characterized for the aqueous aromatic solutions from 293 to 353 K.

Ab initio development of generalized Lennard-Jones (Mie) force fields for predictions of thermodynamic properties in advanced molecular-based SAFT equations of state.

A methodology for obtaining molecular parameters of a modified statistical associating fluid theory for variable-range interactions of Mie form (SAFT-VR Mie) equation of state (EoS) from ab initio calculations is proposed for non-associative species that can be modeled as single spherical segments. The methodology provides a strategy to map interatomic or intermolecular potentials obtained from ab initio quantum-chemistry calculations to the corresponding Mie potentials that can be used within the SAFT-VR Mie EoS. The inclusion of corrections for quantum and many-body effects allows for an excellent, fully predictive description of the vapor-liquid envelope and other bulk thermodynamic properties of noble gases; this description is of similar or superior quality to that obtained using SAFT-VR Mie with parameters regressed in the traditional way using experimental thermodynamic-property data. The methodology is extended to an anisotropic species, methane, where similar levels of accuracy are obtained. The efficacy of using less-accurate quantum-chemistry methods in this methodology is explored, showing that these methods do not provide satisfactory results, although we note that the description is nevertheless substantially better than those obtained using the conductor-like screening model for describing real solvents (COSMO-RS), the only other fully predictive ab initio method currently available. Overall, the reliance on thermophysical data is completely dispensed with, providing the first extensible, wholly predictive SAFT-type EoSs.

The features of haloacetic acid oxidation that contribute to stratospheric ozone depletion

Environmental context Due to The Montreal Protocol, stratospheric ozone concentration is slowly regenerating, however, the recovery rate is slower than predicted by photochemical models. FTIR spectroscopy together with quantum chemical calculations confirmed that ozone reacts with halogenated acids adsorbed at a model aerosol surface. Reactions occur at low temperatures without photochemical activation with formation of halogen oxides that are known to promote catalytic cycles of ozone depletion. Abstract The present work addresses the problem of stratospheric ozone depletion. While gas phase and photochemically induced reactions of ozone are well studied, the mechanisms of heterogeneous O3 interactions with different halogenated species still remain uncertain. An in situ FTIR investigation of low-temperature heterogeneous reactions of ozone and haloacetic acids in conditions close to stratospheric was performed and supported by ab initio quantum chemical calculations. Products of ozone reaction with differently chlorine and bromine-substituted acetic acids were identified and possible reactions pathways were suggested. Ozone can attach to a carbon atom to release a halogen atom that forms a halogen oxide. Halogen oxide in its turn can take part in the catalytic cycles of ozone depletion. Suggested reaction pathways leading to the additional release of the chlorine oxides can enhance the atmospheric models that calculate ozone concentration.

Atmospheric chemistry of sevoflurane radical: A degradation reaction mechanism in the presence of NO from a theoretical perspective

Ab initio quantum chemistry calculations were performed to investigate the degradation reaction mechanism of sevoflurane radical in the presence of NO. The geometries of all the species were optimized using B3LYP/6–311++G(d, p) method. Single point energies were further calculated using QCISD(T)/6-311G(d, p). Three pathways P(1), P(2) and P(3) were found and six reaction steps were analyzed with the Gibbs barriers of 3.16, 39.45, 53.64, 49.64, 156.16 and 78.47 kJ/mol, respectively. The corresponding rate constants were also calculated. The results show that Reaction 3 is a rate-determining step of (CF3)2CHOC(O)F formation using QCISD(T)//B3LYP methods. However, this rate-determining step is probably affected by methodology errors. Reaction 6 is a rate-determining one resulting in the formation of (CF3)2CO and HCOF. These findings are helpful for understanding the atmospheric chemistry of sevoflurane radical degradation process.

Dipole–Dipole Polarizability of the Cadmium 1S0 State Revisited

Experimental results and high-level quantum chemical ab initio calculations of the static polarizability $\alpha_0=\alpha(\omega=0)$ of the cadmium ${^1S_0}$ state are still in marked disagreement. Here we analyze this discrepancy by using experimentally determined dipole oscillator strength distributions (DOSD). It will be shown that within this procedure the experimentally determined static polarizability $\alpha_0$ will shift from $49.7 \pm 1.6~$au to considerably lower values. We now conclude an experimentally determined polarizability of $\alpha_0=47.5 \pm 2.0~$au in much better agreement with the latest calculations of $\alpha_0 \approx 46~$au.

The dehydrogenation of butane on metal-free graphene

The dehydrogenation of alkane feedstock to produce alkenes is a significant and energy intensive industrial process, generally occurring on metals and metal oxides. Here, we investigate a catalytic mechanism for the dehydrogenation of butane on single-layer, metal-free graphene using a combination of ab initio quantum chemical calculations and adsorption microcalorimetry. Dispersion-corrected Density Functional Theory (DFT) is employed to calculate transition states and energy minima that describe the reaction pathways connecting butane to the two possible products, but-1-ene and but-2-ene. The deprotonations occur with moderate energy barriers in the 0.54 eV-0.69 eV range. A strong agreement is observed between the results of the adsorption energies calculated by DFT (0.40 eV) and the measured differential heat of adsorption of n-butane on a graphitic overlayer. We conclude that the active-site for this catalytic reaction is a metal-free graphene vacancy, created by removing a carbon atom from a single-layer graphene sheet.

Chemical shielding and electric field gradient tensors of disodium 5′-adenosine triphosphate trihydrate determined by solid-state NMR spectroscopy and ab initio calculations

The tri-phosphate and sodium ion environments in well crystallized disodium 5′adenosine triphosphate trihydrate (ATP•3H2O) are investigated using high-resolution solid-state NMR spectroscopy and ab initio calculations. The six inequivalent phosphorus sites resolved in 31P MAS spectra have been assigned on the basis of experimentally obtained results and theoretical ab initio quantum chemical calculations of 31P chemical shielding tensors with increased numerical accuracy. Aided by 31P-31P dipolar connectivity established in DQ-SQ correlation experiment and DFT calculations carried out at the B3LYP/(aug-cc-pDVZ(3s,2p,1d), 6–31G(d,p)) level, phosphorus resonance assignments in MAS spectra have been made and the 31P chemical shielding anisotropies and tensor orientations in the molecule-fixed frame have been determined. 31P shielding tensors are found to be oriented with the most shielded direction nearly perpendicular to the O-P-O plane involving the two adjoining oxygens. The complete resolution of the four sodium sites has been achieved from 3Q-MAS experiments performed at 7.05 T and this has enabled 23Na quadrupole parameters to be determined experimentally and compared with theoretical calculations. Besides aiding a partial resonance assignment of the 23Na 3Q-MAS spectrum, our HF/6–311++G(2d,2p) calculations of 23Na EFG tensors show that for two sodium sites which are tightly coordinated the orientation of the EFG tensor is distinct. These exhibit unique directions along which the field gradient is the smallest and largest.

Characterizing the E⊗e Jahn–Teller Potential Energy Surfaces by Differential Geometry Tools

The term ‘mathematical chemistry’ is mostly associated with applications of graph theory in topological issues of 3D chemical structures, thought of as a collection of atoms as dots and bonds as lines. We propose here new directions in this field, coming from the side of theoretical chemistry approached with modern computational tools. Possible challenges are proposed in using ancillary tools of differential geometry for examining the potential energy surfaces of certain specific structural prototypes. Concretely, we describe here the geodesics on the surfaces related to the potential energy functions of the so-called E⊗e Jahn–Teller effect, a spontaneous symmetry-breaking phenomenon also known as a case of conical intersection. To illustrate the case, first-principles (ab initio) quantum chemical calculations are performed on the cyclo-propenyl molecular radical C3H3.

A theoretical investigation into the comparative adsorption between dissolved oxygen and oxygenate species on zeolite 3.7 Å during aviation fuel treatment for thermal stability improvement

In this work we present a theoretical investigation to promote our understanding of the underlying processes of chabazite supported fuel treatment to improve thermal stability at the laboratory scale. It has been shown in prior work that zeolites can remove oxygenated heteroatomic species as well as molecular oxygen from fuel. This work investigates the molecular interaction of the aforementioned species with zeolite to provide a theoretical framework to robustly describe the experimentally observed behaviour. The ab initio quantum chemistry calculations show that a variety of interactions can occur. This work correlates observed enthalpy changes between different oxygenated species and oxygen to their propensity to be removed from the fuel during zeolite treatment which can act as a predictor for the propensity of contaminants to be removed by the zeolite.

Theoretical analysis of the role of complex transition dipole phase in XUV transient-absorption probing of charge migration.

We theoretically investigate the role of complex dipole phase in the attosecond probing of charge migration. The iodobromoacetylene ion (ICCBr+) is considered as an example, in which one can probe charge migration by accessing both the iodine and bromine ends of the molecule with different spectral windows of an extreme-ultraviolet (XUV) pulse. The analytical expression for transient absorption shows that the site-specific information of charge migration is encoded in the complex phase of cross dipole products for XUV transitions between the I-4d and Br-3d spectral windows. Ab-initio quantum chemistry calculations on ICCBr+ reveal that there is a constant π phase difference between the I-4d and Br-3d transient-absorption spectral windows, irrespective of the fine-structure energy splittings. Transient absorption spectra are simulated with a multistate model including the complex dipole phase, and the results correctly reconstruct the charge-migration dynamics via the quantum beats in the two element spectral windows, exhibiting out-of-phase oscillations.

Charge ordering in Ir dimers in the ground state of Ba5AlIr2O11

It has been well established experimentally that the interplay of electronic correlations and spin-orbit interactions in ${\mathrm{Ir}}^{4+}$ and ${\mathrm{Ir}}^{5+}$ oxides results in insulating ${J}_{\mathrm{eff}}=1/2$ and ${J}_{\mathrm{eff}}=0$ ground states, respectively. However, in compounds where the structural dimerization of iridium ions is favorable, the direct Ir $d\text{\ensuremath{-}}d$ hybridization can be significant and takes a key role. Here, we investigate the effects of direct Ir $d\text{\ensuremath{-}}d$ hybridization in comparison with electronic correlations and spin-orbit coupling in ${\mathrm{Ba}}_{5}{\mathrm{AlIr}}_{2}{\mathrm{O}}_{11}$, a compound with Ir dimers. Using a combination of ab initio many-body wave-function quantum chemistry calculations and resonant inelastic x-ray scattering experiments, we elucidate the electronic structure of ${\mathrm{Ba}}_{5}{\mathrm{AlIr}}_{2}{\mathrm{O}}_{11}$. We find excellent agreement between the calculated and the measured spin-orbit excitations. Contrary to expectations, the analysis of the many-body wave function shows that the two Ir (${\mathrm{Ir}}^{4+}$ and ${\mathrm{Ir}}^{5+}$) ions in the ${\mathrm{Ir}}_{2}{\mathrm{O}}_{9}$ dimer unit in this compound preserve their local ${J}_{\mathrm{eff}}$ character close to 1/2 and 0, respectively. The local point group symmetry at each of the Ir ions plays an important role, significantly limiting the direct $d\text{\ensuremath{-}}d$ hybridization. Our results emphasize that minute details in the local crystal field environment can lead to dramatic differences in the electronic states in iridates and $5d$ oxides in general.

Theoretical prediction of FNgM3–kHk (Ng = Ar, Kr, Xe, and Rn; M = Cu, Ag and Au; k = 0–2) molecules

Recent finding on the unprecedented enhancement of noble gas-noble metal bonding strength on hydrogen doping in van der Waals type cationic complexes motivates us to explore the possibility of occurrence of noble gas (Ng) inserted neutral compounds involving prototype noble metal trimeric ions. MP2 and DFT based methods have been employed to investigate the structures, stabilities, energetics, harmonic vibrational frequencies, and charge distribution of the predicted neutral FNgM3, FNgM2H, and FNgMH2 (Ng = Ar, Kr, Xe, Rn; M = Cu, Ag, Au). All the predicted molecules are thermodynamically stable with respect to all plausible 2-body and 3-body dissociation channels, except the global minima products. However, sufficient large barrier heights provide enough kinetic stability to the predicted metastable molecules, which in turn can prevent them to dissociate into their respective global minima products. All the results clearly indicate that Ng–M bond has partial covalent character while an ionic interaction is found between F and Ng atoms in FNgM3−kHk (k = 0−2). Furthermore, the charge distribution and AIM analyses suggest that the predicted metastable FNgM3−kHk molecules should essentially exist in the form of [F]δ−[NgM3−kHk]δ+. All the results emphasise that it might be possible to prepare and characterise these predicted molecules by suitable experimental technique(s). Exploration of noble gas-noble metal bonding strength on neutralisation of prototype NgM3−kHk + (Ng = Ar, Kr, Xe, and Rn; M = Cu, Ag, and Au; k = 0−2) ions by fluoride anions through ab initio quantum chemical calculations.

Existence of noble gas-inserted phosphorus fluorides: FNgPF2 and FNgPF4 with Ng-P covalent bond (Ng = Ar, Kr, Xe and Rn).

The scarce literature on noble gas (Ng)-phosphorous chemical bonding and our recent theoretical prediction of the FNgP molecule motivate us to explore a unique novel class of neutral noble gas-inserted phosphorus trifluoride and pentafluoride molecules, i.e., FNgPF2 and FNgPF4 (Ng = Ar, Kr, Xe, and Rn). The predicted molecules have been designed by inserting an Ng atom between the F and P atoms in the PF3 and PF5 molecules. The minima and saddle point geometries of all the FNgPFn (n = 2 and 4) molecules have been optimized using density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). The coupled cluster theory (CCSD(T)) method is also used to optimize the FNgPF2 molecules to test the performance of the above-mentioned methods. The predicted FNgPF2 and FNgPF4 molecules are found to be energetically stable with respect to all the probable 2-body and 3-body dissociation channels, except for the one leading to the global minimum products (Ng + PF3 and Ng + PF5). The existence of large barrier heights corresponding to the saddle point geometries is responsible for the kinetic stability of the metastable FNgPFn (n = 2 and 4) molecules, which prevents them from dissociating into their global minima products. The optimized structural parameters, energetics and harmonic vibrational frequency analysis suggest that the Ng-P bond is covalent in nature, while the F-Ng bond is mostly ionic in nature with some degree of covalency in the predicted molecules. In fact, the Ng-P bond length in the experimentally observed Ng-PF3 van der Waals complex is reduced significantly in the isomeric FNgPF2 molecule, almost leading to a conventional covalent Ng-P bond (cf. 4.152 vs. 2.413 Å for the Kr-P bond). Furthermore, the charge distribution and the AIM analysis also confirm the above-mentioned conclusion and indicate that the predicted FNgPF2 and FNgPF4 molecules can be represented as [F]δ-[NgPF2]δ+ and [F]δ-[NgPF4]δ+, respectively. All the computational results strongly reinforce the possible existence of these predicted FNgPFn (n = 2 and 4) molecules and clearly indicate that it may be possible to synthesize and characterize these molecules under suitable experimental technique(s).

The Jahn-Teller and pseudo-Jahn-Teller effects in the propyne radical cation.

The Jahn-Teller (JT) and pseudo-Jahn-Teller (PJT) effects in the X̃2E, Ã2E and B̃2A1 electronic states of the propyne radical cation are investigated with the aid of ab initio quantum chemistry calculations and first principles quantum dynamics simulations. For the latter, both time-independent and time-dependent quantum mechanical methods are employed. Standard vibronic coupling theory is used to construct a symmetry consistent vibronic Hamiltonian in a diabatic electronic basis. Taylor series expansion of the elements of the diabatic electronic Hamiltonian is carried out and the parameters that appear in the expansion are derived from the ab initio calculated adiabatic electronic energies. It is found that the JT effect is weak in the X̃2E state as compared to that in the Ã2E state. Because of large energy separation, the PJT coupling among the JT-split components of the X̃2E state with the neighboring states is also very weak. However, the PJT coupling of the B̃2A1 state with the JT split components of the Ã2E state has some impact on the dynamics in the coupled Ã2E-B̃2A1 electronic states. The vibronic spectrum of each of these states is calculated and compared with the experimental results. The nonradiative internal conversion dynamics of excited cationic states is examined. Interesting comparison is made with the JT and PJT coupling effects in the nuclear dynamics of the X̃2E-Ã2E-B̃2B2 electronic states of the isomeric allene radical cation.

Enhancement of superexchange due to synergetic breathing and hopping in corner-sharing cuprates

Cuprates with corner-sharing CuO4 plaquettes have received much attention owing to the discoveries of high-temperature superconductivity and exotic states where spin and charge or spin and orbital degrees of freedom are separated. In these systems spins are strongly coupled antiferromagnetically via superexchange mechanisms, with high nearest-neighbour coupling varying among different compounds. The electronic properties of cuprates are also known to be highly sensitive to the presence, distance and displacement of apical oxygens perpendicular to the CuO2 planes. Here we present ab initio quantum chemistry calculations of the nearest-neighbour superexchange antiferromagnetic (AF) coupling J of two cuprates, Sr2CuO3 and La2CuO4. The former lacks apical oxygens, whilst the latter contain two apical oxygens per CuO2 unit completing a distorted octahedral environment around each Cu atom. Good agreement is obtained with experimental estimates for both systems. Analysis of the correlated wavefunctions together with extended superexchange models shows that there is an important synergetic effect of the Coulomb interaction and the O–Cu hopping, namely a correlated breathing-enhanced hopping mechanism. This is a new ingredient in superexchange models. Suppression of this mechanism leads to drastic reduction in the AF coupling, indicating that it is of primary importance in generating the strong interactions. We also find that J increases substantially as the distance between Cu and apical O is increased.

Designing Red-Shifted Molecular Emitters Based on the Annulated Locked GFP Chromophore Derivatives.

Bioimaging techniques require development of a wide variety of fluorescent probes that absorb and emit red light. One way to shift absorption and emission of a chromophore to longer wavelengths is to modify its chemical structure by adding polycyclic aromatic hydrocarbon (PAH) fragments, thus increasing the conjugation length of a molecule while maintaining its rigidity. Here, we consider four novel classes of conformationally locked Green Fluorescent Protein (GFP) chromophore derivatives obtained by extending their aromatic systems in different directions. Using high-level ab initio quantum chemistry calculations, we show that the alteration of their electronic structure upon annulation may unexpectedly result in a drastic change of their fluorescent properties. A flip of optically bright and dark electronic states is most prominent in the symmetric fluorene-based derivative. The presence of a completely dark lowest-lying excited state is supported by the experimentally measured extremely low fluorescence quantum yield of the newly synthesized compound. Importantly, one of the asymmetric modes of annulation provides a very promising strategy for developing red-shifted molecular emitters with an absorption wavelength of ∼600 nm, having no significant impact on the character of the bright S-S1 transition.

Optical Spectra of Oligofurans: A Theoretical Approach to the Transition Energies, Reorganization Energies, and the Vibronic Activity.

There is experimental evidence of high vibronic activity that accompanies the allowed transition between the ground state and the lowest electronic singlet excited state of oligofurans that contain two, three, and four furan rings. The absorption and emission spectra of the three lowest oligofurans measured at liquid nitrogen temperature show distinct fine structures that are reproduced using the projection-based model of vibronic coupling (with Dushinsky rotation included) parameterized utilizing either Density Functional Theory (DFT, with several different exchange-correlation functionals) or ab initio (CC2) quantum chemistry calculations. Using as a reference the experimental data concerning the electronic absorption and fluorescence for the eight lowest oligofurans, we first analyzed the performance of the exchange-correlation functionals for the electronic transition energies and the reorganization energies. Subsequently, we used the best functionals alongside with the CC2 method to explore how the reorganization energies are distributed among the totally symmetric vibrations, identify the normal modes that dominate in the fine structures present in the absorption and emission bands, and trace their evolution with the increasing number of rings in the oligofuran series. Confrontation of the simulated spectra with the experiment allows for the verification of the performance of the selected DFT functionals and the CC2 method.

Theoretical and Experimental Studies of Charge Ordering in CaFeO3 and SrFeO3 Crystals

A comparative study of the isoelectronic and perovskites has been performed by means of ab initio quantum chemical calculations and X‐ray absorption spectroscopy at the Fe K‐edge. EXAFS and XANES measurements are performed and discussed for the first time. The results of simulations are in good agreement with previous findings, supporting a cubic perovskite structure of and transition from the room‐temperature orthorhombic (space group ) charge‐delocalized state in to the low‐temperature monoclinic (space group ) charge‐disproportionated state. The local atomic and magnetic structures, as well as electronic properties, are discussed in detail.

Elaborated thermochemical treatment of HF, CO, N2, and H2O: Insight into HEAT and its extensions.

Empirical, highly accurate non-relativistic electronic total atomization energies (eTAEs) are established by combining experimental or computationally converged treatments of the nuclear motion and relativistic contributions with the total atomization energies of HF, CO, N2, and H2O obtained from the Active Thermochemical Tables. These eTAEs, which have estimated (2σ) uncertainties of less than 10 cm-1 (0.12 kJ mol-1), form the basis for an analysis of high-level ab initio quantum chemical calculations that aim at reproducing these eTAEs for the title molecules. The results are then employed to analyze the performance of the high-accuracy extrapolated ab initio thermochemistry, or High-Accuracy Extrapolated Ab Initio Thermochemistry (HEAT), family of theoretical methods. The method known as HEAT-345(Q), in particular, is found to benefit from fortuitous error cancellation between its treatment of the zero-pointenergy, extrapolation errors in the Hartree-Fock and coupled cluster contributions, neglect of post-(T) core-correlation, and the basis-set error involved in higher-level correlation corrections. In addition to shedding light on a longstanding curiosity of the HEAT protocol-where the cheapest HEAT-345(Q) performs comparably to the theoretically more complete HEAT-456QP procedure-this study lays the foundation for extended HEAT variants that offer substantial improvements in accuracy relative to the established approaches.

An investigation of inter-ligand coordination and flexibility: IRMPD spectroscopic and theoretical evaluation of calcium and nickel histidine dimers

Metallated gas-phase structures consisting of an intact and deprotonated histidine (His) ligand, M(His-H)(His)+, where M = Ca and Ni, were examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, ab initio quantum-chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using the 6-311+G(d,p) basis set. Single-point energies were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. For Ca(His-H)(His)+, the dominant structure has the metal center coordinating with the π nitrogen of the imidazole ring (Nπ) and both oxygen atoms of the carboxylate group of the deprotonated His ligand while coordinating with the backbone amine (Nα), Nπ, and the carbonyl oxygen of the carboxylic acid of the intact His ligand. The Ni(His-H)(His)+ species coordinates the metal ion through Nα, Nπ, and the carbonyl oxygen for both the deprotonated and intact His ligands, but also shows evidence for a minor secondary structure where the deprotonated His coordinates the metal at Nα, Nπ, and the deprotonated carbonyl oxygen and the intact His ligand is zwitterionic, coordinating the metal with both carboxylate oxygens. Different levels of theory predict different ground structures, highlighting the need for utilizing multiple levels of theory to help identify the gas-phase structure actually observed experimentally.