Ab Initio Quantum Chemical Calculations Research Articles

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.

Visualization of the Interfacial Electrostatic Complementarity: A Method for Analysis of Protein-Protein Interaction Based on Ab Initio Quantum Chemical Calculations.

In this study, we report a method for analyzing the protein-protein interaction based on ab initio quantum chemical calculations, which we refer to as "Visualization of the interfacial electrostatic complementarity (VIINEC)." This method visually provides the electrostatic complementarity at the protein-protein interface; in addition, the ratio of the attractive interaction is calculated. Illustrative calculations revealed that VIINEC could successfully quantify the electronic induced fit owing complex formation, which was responsible for 5%-10% of the total electrostatic complementarity. Furthermore, the contribution of each amino acid to the electrostatic complementarity was evaluated, providing useful information for various applications, including rational antibody designs. Interestingly, a part of the mechanism causing the specificity of the protein-protein bindings was also demonstrated using VIINEC. This is an important achievement of this study because the specificity of the biomolecular interactions is essential for biological functions.

Isotope Shifts of Radium Monofluoride Molecules.

Isotope shifts of ^{223-226,228}Ra^{19}F were measured for different vibrational levels in the electronic transition A^{2}Π_{1/2}←X^{2}Σ^{+}. The observed isotope shifts demonstrate the particularly high sensitivity of radium monofluoride to nuclear size effects, offering a stringent test of models describing the electronic density within the radium nucleus. Abinitio quantum chemical calculations are in excellent agreement with experimental observations. These results highlight some of the unique opportunities that short-lived molecules could offer in nuclear structure and in fundamental symmetry studies.

A hybrid molecular sensitizer for triplet fusion upconversion

Triplet fusion upconversion is useful for a broad spectrum of applications ranging from solar cells, photoredox catalysis, to biophotonics applications, especially in the near-infrared (NIR, >700 nm) range. This upconverting system typically demands efficient conversion of spin-singlet harvested energy through intersystem crossing to spin-triplet states, accessible only in rare metallic-coordinating macrocycle compounds or heavy-metal-containing semiconductor quantum dots for triplet sensitization. Herein, we describe an organic–inorganic system for NIR-to-visible triplet fusion upconversion, interfacing commonly-seen, non-metallic, infrared dyes (IR806, IR780, indyocynine green, and CarCl) and lanthanide nanocrystal (sodium ytterbium fluoride) as a hybrid molecular sensitizer, which extracts molecular spin-singlet energy to nanocrystal-enriched ytterbium dopants at ~48% efficiency (IR806, photoexciation at 808 nm). Moreover, ytterbium sub-lattice energy migration increases the interaction possibility between the nanocrystal and the freely-diffusing rubrenes in solution, resulting in 24-fold (IR806) to 1740-fold (indocyanine green) upconversion (600 nm) increase, depending on the IR dye type, as compared to the one without ytterbium nanotransducers. Ab initio quantum chemistry calculations identify enhanced spin-orbital coupling in the ytterbium-IR806 complex and high energy transfer rate in the ytterbium-rubrene interaction (1010 s−1). Employing inorganic lanthanide nanocrystals as nanotransducers unleashes the potential use of non-metallic infrared organic dyes for triplet fusion upconversion.

Isomerization Dynamics in the Symmetric and Asymmetric Fragmentation of Ethane Dications.

Hydrogen- or proton-migration-induced isomerization has recently been of concern for its critical role in the dissociation of organic molecules of astrophysical or biological relevance. Herein we present a combined experimental and theoretical study of the two-body C-C bond breakdown dissociation of ethane dication. For the asymmetric fragmentation channel CH2+ + CH4+, the kinetic energy release measurements and ab initio quantum chemical calculations demonstrate that the reaction pathway involving hydrogen-migration-induced isomerization of [CH3-CH3]2+ to [CH2-CH4]2+ can be accessed via the lowest triplet state rather than the ground singlet state of ethane dication. Interestingly, it is found that a considerable proportion of the yield of symmetric fragmentation CH3+ + CH3+, which is usually considered from a direct Coulomb explosion and seemingly independent of isomerization, could come from the dissociation of ethane dication in the ground singlet state with the involvement of [CH3-CH3]2+ isomerization to intermediate [H2C(H2)CH2]2+ of the diborane-like double-bridged structure.

Rate Constants for Abstraction of H from the Fluoromethanes by H, O, F, and OH

In this work, we compiled and critically evaluated rate constants from the literature for abstraction of H from the homologous series consisting of the fluoromethanes (CH3F, CH2F2, and CHF3) and methane (CH4) by the radicals H atom, O atom, OH, and F atom. These reactions have the form RH + X → R + HX. Rate expressions for these reactions are provided over a wide range of temperatures (300–1800 K). Expanded uncertainty factors f (2σ) are provided at both low and high temperatures. We attempted to provide rate constants that were self-consistent within the series—evaluating the system, not just individual reactions. For many of the reactions, the rate constants in the literature are available only over a limited temperature range (or there are no reliable measurements). In these cases, we predicted the rate constants in a self-consistent manner employing relative rates for other reactions in the homologous series using empirical structure–activity relationships, used empirical correlations between rate constants at room temperature and activation energies at high temperatures, and used relative rates derived from ab initio quantum chemical calculations to assist in rate constant predictions.

Ultrafast Resonant Interatomic Coulombic Decay Induced by Quantum Fluid Dynamics

When weakly-bound complexes are multiply excited by intense electromagnetic radiation, energy can be exchanged between neighboring atoms through a type of resonant interatomic Coulombic decay (ICD). This decay mechanism due to multiple excitations has been predicted to be relatively slow, typically lasting tens to hundreds of picoseconds. Here, we directly measure the ICD timescale in resonantly excited helium droplets using a high resolution, tunable, extreme ultraviolet free electron laser. Over an extensive range of droplet sizes and laser intensities, we discover the decay to be surprisingly fast, with decay times as fast as 400 femtoseconds, and to only present a weak dependence on the density of the excited states. Using a combination of time dependent density functional theory and ab initio quantum chemistry calculations, we elucidate the mechanisms of this ultrafast decay process where pairs of excited helium atoms in one droplet strongly attract each other and form merging void bubbles which drastically accelerates ICD.

Expanded Inverse-Sandwich Complexes of Lanthanum Borides: La2B10- and La2B11.

Inverse-sandwich structures have been observed recently for dilanthanide boride clusters, in which two Ln atoms sandwich a monocyclic Bx ring for x = 7-9. An interesting question is if larger Bx rings are possible to form such inverse-sandwich clusters. Here we address this question by investigating La2B10- and La2B11- using photoelectron spectroscopy and ab initio quantum chemical calculations. Photoelectron spectra of La2B10- and La2B11- show complicated, but well-resolved, spectral features that are used to compare with theoretical calculations. We have found that global minimum structures of the two clusters are based on the octa-boron ring. The global minimum of La2B10- consists of two chiral enantiomers with C1 symmetry, which can be viewed as adding a B2 unit off-plane to the B8 ring, whereas that of La2B11- can be viewed as adding a B3 unit in-plane to the B8 ring in a second coordination shell. Chemical bonding analyses reveal localized B-B bonds on the edge of the clusters and delocalized bonds in the expanded boron frameworks. The interactions between the La atoms and the boron frameworks include the unique (d-p)δ bonding, which was found to be the key for inverse-sandwich complexes with monocyclic boron rings. The current study confirms that the largest monocyclic boron ring to form the inverse-sandwich structures is B9 and provide insights into the structural evolutions of larger lanthanide boride clusters.