High-level Ab Initio Research Articles

High level ab initio binding energy distribution of molecules on interstellar ices: Hydrogen fluoride

The knowledge of the binding energy of molecules on astrophysically relevant ices can help to obtain an estimate of the desorption rate, i.e. the molecules residence time on the surface. This represents an important parameter for astrochemical models, and it is crucial to determine the chemical fate of interstellar complex organic molecules formed on the surface of dust grains and observed in the densest regions of the interstellar medium through rich rotational lines. In this work, we propose a new robust procedure to study the interaction of atoms and molecules with interstellar ices, based on ab initio molecular dynamics and density functional theory, validated by high-level ab initio methods at a CCSD(T)/CBS level. We have applied this procedure to a simple but astronomically relevant molecule, hydrogen fluoride (HF), a promising tracer of the molecular content of galaxies. In total we found 13 unique equilibrium structures of HF binding to small water clusters of up to 4 molecules, with binding energies ranging from 1208 K to 7162 K (2.40 to 14.23 kcal mol−1). We computed a 22-molecules model of amorphous solid water (ASW) surface using ab initio molecular dynamics simulations and carried out a systematic analysis of the binding sites of HF, in terms of binding modes and binding energies. Considering 10 different water clusters configurations, we found a binding energy distribution with an average value of 5313±74 K, and a dispersion of 921±115 K (10.56±0.15 kcal mol−1), and a dispersion of 921±115 K (1.83±0.23 kcal mol−1). Finally, the effect of the electrostatic field of the 22 water molecules on the binding energies was investigated incrementally by symmetry adapted perturbation theory, in order to gauge the effect of the water environment on the binding energies. The results indicate that the extent of the electrostatic interaction of HF with ASW depends strongly on the properties of the binding site on the water cluster. We expect that this work will provide a solid foundation for a systematic development of a binding energy distribution database of small molecules on astrophysically relevant surfaces.

Proceeding on the riddles of ketene pyrolysis by applying ab initio quantum chemical computational methods in a detailed kinetic modeling study

As ketene is a crucial intermediate for the high-temperature combustion of oxygenated hydrocarbons in general, an in-depth understanding of its chemistry is a fundamental requirement for the kinetic modeling of bio-based fuels. To gain a profound insight into the decomposition of ketene and subsequent reaction pathways high level ab initio methods were used. DSD-PBEP86/cc-pVTZ level of theory was applied for the geometries and frequencies, while single-point energies were determined at the CCSDT-1a level of theory extrapolated to the basis set limit. The reaction rate parameters for 38 reactions involved in the ketene chemistry including C1 to C4 species like acetylene, ethylene, propyne and allene were computed. For a total of 16 species, the thermochemistry were updated. The calculated rate parameters and the two new species cyclopropenone and 1,4-dioxo-1,3-butadiene were used to update the AramcoMech 3.0 base mechanism, which was then validated against speciation measurements during ketene pyrolysis. A reaction pathway analysis was performed to find the most prominent reactions at the investigated conditions and to discuss the simulation results. A significant improvement in the model’s prediction capability was found when applying the newly calculated reaction rate parameter and thermochemical data.

10.4314/bcse.v31i1.11

Analytical measurement of materials requires exact knowledge of their acid dissociation constant (p K a ) values. In recent years, quantum mechanical calculations have been extensively used to study of acidities in the aqueous solutions and the results were compared with the experimental values. In this study, a theoretical study was carried out on xylenol orange (in water solution) by ab initio method. We calculated the p K a values of xylenol orange in water, using high-level ab initio (PM3), DFT (HF, B3LYP/6-31+G(d)) and SCRF methods. The experimental determination of these values (p K a ,s) is a challenge because xylenol orange has a low solubility in water. We considered several ionization reactions and equilibriums in water that constitute the indispensable theoretical basis to calculate the p K a values of xylenol orange. The results show that the calculated p K a values have a comparable agreement with the experimentally determined p K a values. Therefore, this method can be used to predict such properties for indicators, drugs and other important molecules. KEY WORDS : Ab initio, DFT method, Ionization constant, Xylenol orange, Atomic charge Bull. Chem. Soc. Ethiop. 2017 , 31(1), 127-136. DOI: http://dx.doi.org/10.4314/bcse.v31i1.11

Theoretical Investigations on the Oxidation of Heptafluoro-iso-butyronitrile by Atomic Oxygen in Dielectric Breakdown.

Heptafluoro-iso-butyronitrile [(CF3)2CFCN, in abbr., C4] with CO2 gas mixture is a promising dielectric candidate to replace sulfur hexafluoride (SF6) for the sake of environmental concern. Detailed mechanisms for the reactions of C4 with atomic oxygen in both triplet and singlet due to dissociation of CO2 were proposed using high-level ab initio methods including density functional theory, quadratic complete basis set, multireference Rayleigh-Schrodinger perturbation theory, and state-averaged multiconfiguration self-consistent field. The reaction of C4 with O(3P) proceeds via the stepwise C-O and N-O addition/elimination and direct displacement mechanisms. The reaction paths are bifurated into cis and trans conformations. The predominant product channel is the C-O association with the barriers 6.1-6.8 kcal/mol to form the C3F7C(O)N intermediates and followed by the C-C bond cleavage to produce C3F7 and NCO radicals. On the singlet surface, the three-center intramolecular conversion to form the C3F7OCN isomer becomes competitive. The singlet-triplet intersystem crossing is favorable due to the significant spin-orbital coupling. Master equation calculations were carried out to obtain the temperature- and pressure-dependent rate coefficients and yields of the O(3P) + C4 reaction and were compared with the analogous reactions of nitriles. It was found that only the NCO + C3F7 product channel is significant. The overall rate coefficients are pressure-independent in the range 1-10 atm and can be expressed by k∞(T/K)=(6.41 ± 0.22) × 10-13(T/298)1.30±0.01e-(3241.5±24.5)/T cm3 molecule-1 s-1. The present theoretical work provides useful insights into the breakdown diagnostic of the C4/CO2 insulation gas.

Evaluation of Single-Reference DFT-Based Approaches for the Calculation of Spectroscopic Signatures of Excited States Involved in Singlet Fission

Singlet fission (SF) has the potential to dramatically increase solar cell efficiency by converting one singlet exciton to two free triplet excitons via a correlated triplet pair intermediate. Identification and characterization of excited states involved in SF are of great importance for understanding the fundamentals of SF. Despite their importance, it is still non-trivial to distinguish various species in transient absorption spectra due to their spectral overlaps and ultra-short lifetimes. Theoretical modeling of SF and its electronically excited state absorption (ESA) is generally challenging due to the multi-exciton nature of the correlated triplet pair, which usually requires description by expensive high-level ab initio methods. In this work, taking TIPS-pentacene monomer and its covalently linked dimer as representative examples, we demonstrate the use of single-reference DFT-based approaches to simulate the ESA spectra during SF. In particular, the singlet and triplet ESA are evaluated by TDDFT, QR-TDDFT, SLR-TDDFT, SF-TDDFT, and UTDDFT, in combination with ten different exchange-correlation functionals. The correlated triplet pair and its ESA are characterized by broken-symmetry DFT and TDDFT, and the role of orbital relaxation is highlighted. With a rational choice of exchange-correlation functionals, we found the resulting spectra to show good agreement with transient absorption experiments and certain improvements over high-order CI methods.

Combustion of silane-nitrous oxide-argon mixtures: Analysis of laminar flame propagation and condensed products

The laminar burning rate, the explosion peak pressure, and the pressure rise coefficient have been measured for the first time for silane-nitrous oxide-argon mixtures using the spherically expanding flame technique in a constant volume combustion chamber. For these three parameters, the values obtained were higher than for hydrogen-nitrous oxide-argon and typical hydrocarbon-based mixtures. A maximum burning rate of 1800 g/m2 s was measured at 101 kPa, whereas under similar conditions, a maximum burning rate around 950 g/m2 s has been reported for hydrogen-nitrous oxide-argon mixtures. To better understand the chemical dynamics of flames propagating in SiH4–N2O–Ar mixtures, a detailed reaction model from the literature was improved using collision limit violation analysis and updated thermodynamic properties calculated with a high-level ab initio approach. The reaction model predicts the burning rate within 14% on average but demonstrates error close to 50% for the richest mixtures. The chemistry of the H–O–N system is important under all the conditions presently studied. The chemistry of the Si–H–O–N system demonstrates an increasing importance under rich conditions. In particular, the reactions (i) forming SiOx(s); (ii) describing the interaction of Si-species with N2O; and (iii) involving silicon hydrides, have an important role for the heat release dynamics. The condensed combustion products formed in the silane-nitrous oxide-argon flames were sampled and characterized using electron micrograph, electronic diffraction, energy-dispersive spectroscopy, and X-ray powder diffraction. For all equivalence ratios, silica spherical particles with a mean diameter in the range 200–300 nm were observed. In addition, for mixtures with Φ ≥ 2.2, silicon nanowires were formed. X-ray diffraction experiments showed that the silicon nanowires are composed of metal silicon characterized by a cubic structure (lattice parameter: a=5.425Å) with the Fm-3m space group.

Absence of Triplets in Single-Photon Double Ionization of Methanol.

Despite the abundance of data concerning single-photon double ionization of methanol, the spin state of the emitted electron pair has never been determined. Here we present the first evidence that identifies the emitted electron pair spin as overwhelmingly singlet when the dication forms in low-energy configurations. The experimental data show that while the yield of the CH2O+ + H3+ Coulomb explosion channel is abundant, the metastable methanol dication is largely absent. According to high-level ab initio simulations, these facts indicate that photoionization promptly forms singlet dication states, where they quickly decompose through various channels, with significant H3+ yields on the low-lying states. In contrast, if we assume that the initial dication is formed in one of the low-lying triplet states, the ab initio simulations exhibit a metastable dication, contradicting the experimental findings. Comparing the average simulated branching ratios with the experimental data suggests a >3 order of magnitude enhancement of the singlet:triplet ratio compared with their respective 1:3 multiplicities.

A case study of density functional theory and domain-based local pair natural orbital coupled cluster for vibrational effects on EPR hyperfine coupling constants: vibrational perturbation theory versus ab initio molecular dynamics

Local approximations of high-level ab initio methods make superior accuracy in the computation of molecular properties accessible by drastically decreasing computational times. As a consequence, these methods become applicable not only for large systems but also in schemes for which large numbers of calculations are necessary. In this work, we apply a recently developed open-shell implementation of the domain-based pair natural orbital coupled cluster singles doubles (DLPNO-CCSD) approach for the computation of vibrational corrections to the isotropic values of electron paramagnetic resonance (EPR) hyperfine coupling constants. We assess density functional theory (DFT) and DLPNO-CCSD approaches using two common but very different schemes: (1) vibrational perturbation theory based on equilibrium geometries, and (2) explicit canonical ensemble averages using configuration snapshots sampled from revPBE0-D3(0) ab initio molecular dynamics simulations. Both approaches are found to yield very similar results for the spin probe 2,2,3,4,5,5-hexamethylperhydroimidazol-1-oxyl (HMI) and are both feasible for systems of around 30 atoms. However, the numerical stability required for higher derivatives can become a limitation for local correlation methods in the case of vibrational perturbation theory.

Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach.

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2 ) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.

Reliable reduction potentials of diaryliodonium cations and aryl radicals in acetonitrile from high-level ab initio computations

The experimental values of the standard reduction potentials of diaryliodonium cations (Ar2I+) and aryl radicals (Ar•) are generally not deemed reliable owing to the irreversibility of electrode processes, often aggravated by blocking the electrode by the grafted layer. They are, however, required for the prediction of suitability of photoinitiators and the course of arylation reactions or aryl radical surface modifications. Here, we present accurate E° values of reduction of symmetrical and unsymmetrical Ar2I+, and of Ar• in MeCN, obtained from calculations based on the gas-phase redox energetics from the high-level explicitly correlated coupled-cluster method (CCSD(T)-F12) combined with the SMD solvation free energies. Plausible paths of C–I bond cleavage in unsymmetrical Ar2I+ cations were also predicted from reference values of the C–I bond dissociation energies (BDEs) in Ar2I+. The computed reduction potentials were compared with available experimental data and with results from other quantum chemical methods including other implicit solvation models. A perfect linear correlation with Hammett σ constants was found for the computed potentials of Ar2I+ reduction. This correlation equation may be used for rapid estimation of reduction potentials of other Ar2I+ cations, but also for the prediction of the fate of other processes, in which diaryliodonium cations take part, like aryl exchange reactions or the ability to initiate photopolymerisation.

(Invited) Multiscale Modeling of Formation and Properties of Solid-Electrolyte Interphases in Li-Ion Batteries

In this talk we will discuss recent efforts on multiscale modeling of solid-electrolyte interphase (SEI) and cathode-electrolyte interphases(CEI). The complexity and multiscale phenomena operating at electrode/electrolyte interfaces do not allow to access all necessary length and time scales using a single modeling approach. Combining information from high-level ab initio and DFT calculations, polarizable atomistic molecular dynamics simulations, coarse-grained implicit solvent simulations and continuum level modeling, we focus on understanding the mechanisms of formation of SEI/CEI layers, mechanisms of Li-ion transport, and mechanical and failure properties of SEI during charging/discharging processes.

Theoretical study of the low-lying electronic states, including the spin-orbit interactions, of the sulfur monochloride cation.

High-level ab initio computations have been performed on the experimentally unknown species SCl+. The low-lying Λ-S electronic states correlated to the first and the second dissociation channels as well as their corresponding Ω states have been investigated by the icMRCI+Q methodology employing basis sets up to quintuple-ζ quality. Information about potential energy curves, electron configurations, spectroscopic constants, dipole moments and transition properties are derived and discussed. The results for SCl+ represent an improvement over our previous theoretical descriptions for the ground state. In addition, several low-lying excited states that have not been accessed experimentally and theoretically are also been well characterized in this work. The accuracy of our predictions for SCl+ are verified by comparisons of spectroscopic constants and vibrational levels between our accompany SCl computations and those reported in literatures for the neutral species. The feasibility of performing laser cooling of SCl+ has also been discussed and the photoelectron spectrum of SCl+(X3Σ-)+e←SCl(X2Π) is simulated.

Long-Range N-N Bonding by Rydberg Electrons.

By using high-level ab initio methods, we examine the nature of bonding between Rydberg electrons hosted by two four-coordinate nitrogen centers embedded in a hydrocarbon scaffold. The electronic structure of these species resembles that of diradicals, yet the diffuse nature of the orbitals hosting the unpaired electrons results in unusual features. The unpaired Rydberg electrons exhibit long-range bonding interactions, leading to stabilization of the singlet state (relative to the triplet) and a reduced number of effectively unpaired electrons. However, thermochemical gains due to through-space bonding are offset by strong Coulomb repulsion between positively charged nitrogen cores. The kinetic stability of these Rydberg diradicals may be controlled by a judicious choice of the molecular scaffold, suggesting possible strategies for their experimental characterization.

The high-temperature rotation-vibration spectrum and rotational clustering of silylene (SiH2)

A rotation-vibration line list for the electronic ground state (X˜1A1) of SiH2 is presented. The line list, named CATS, is suitable for temperatures up to 2000 K and covers the wavenumber range 0–10 000 cm−1 (wavelengths > 1.0 µm) for states with rotational excitation up to J=52. Over 310 million transitions between 593 804 energy levels have been computed variationally with a new empirically refined potential energy surface, determined by refining to 75 empirical term values with J ≤ 5 and a newly computed high-level ab initio dipole moment surface. This is the first, comprehensive high-temperature line list to be reported for SiH2 and it is expected to aid the study of silylene in plasma physics, industrial processes and possible astronomical detection. Furthermore, we investigate the phenomenon of rotational energy level clustering in the spectrum of SiH2. The CATS line list is available from the ExoMol database (www.exomol.com) and the CDS database.

Biological control of S-nitrosothiol reactivity: potential role of sigma-hole interactions.

S-Nitrosothiols (RSNOs) are ubiquitous biomolecules whose chemistry is tightly controlled in vivo, although the specific molecular mechanisms behind this biological control remain unknown. In this work, we demonstrate, using high-level ab initio and DFT calculations, the ability of RSNOs to participate in intermolecular interactions with electron pair donors/Lewis bases (LBs) via a σ-hole, a region of positive electrostatic potential on the molecular surface at the extension of the N-S bond. Importantly, σ-hole binding is able to modulate the properties of RSNOs by changing the balance between two chemically opposite (antagonistic) resonance components, R-S+[double bond, length as m-dash]N-O- (D) and R-S-/NO+ (I), which are, in addition to the main resonance structure R-S-N[double bond, length as m-dash]O, necessary to describe the unusual electronic structure of RSNOs. σ-Hole binding at the sulfur atom of RSNO promotes the resonance structure D and reduces the resonance structure I, thereby stabilizing the weak N-S bond and making the sulfur atom more electrophilic. On the other hand, increasing the D-character of RSNO by other means (e.g. via N- or O-coordination of a Lewis acid) in turn enhances the σ-hole bonding. Our calculations suggest that in the protein environment a combination of σ-hole bonding of a negatively charged amino acid sidechain at the sulfur atom and N- or O-coordination of a positively charged amino acid sidechain is expected to have a profound effect on the RSNO electronic structure and reactivity.

How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface.

Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level ab initio calculations at the CCSD(T)/CBS level predicted a possibility for energetically low-cost (±1 kcal mol-1) changes of the bond angle and bond lengths in a wide range, from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.

The atmospheric importance of methylamine additions to Criegee intermediates.

Criegee intermediates are important targets for study in atmospheric chemistry because of their capacity to oxidize airborne species. Among these species, ammonia has received critical attention for its presence in polluted agricultural or industrial areas and its role in forming particulate matter and condensation nuclei. Although methylamine has been given less attention than ammonia, both theoretical and experimental studies have demonstrated that the additional methyl substitution on the ammonia derivatives increases the rate constants for some systems. This suggests that the methylamine addition to Criegee intermediates could be more significant to atmospheric processes. In this work, geometries are optimized at the DF-CCSD(T)/ANO1 level for the methylamine addition reactions to the simplest Criegee intermediate and the anti- and syn-methylated Criegee intermediates. Energies for each stationary point were computed at the CCSD(T)/CBS level with corrections from the CCSDT(Q) method. Rate constants are obtained for each reaction using canonical transition state theory. Although methylamine addition proved to be a more favorable reaction relative to ammonia addition, the significantly lower concentration of atmospheric methylamine limits the prevalence of these reactions, even in the most optimal conditions. It is unlikely that the methylamine addition to Criegee intermediates will contribute significantly to the consumption of Criegee intermediates in the atmosphere.

Short-Range Disorder in TeO2 Melt and Glass.

High-resolution X-ray pair distribution functions for molten and glassy TeO2 reveal coordination numbers nTeO ≈ 4. However, distinct from the known α-, β-, and γ-TeO2 polymorphs, there is considerable short-range disorder such that no clear cutoff distance between bonded and nonbonded interactions exists. We suggest that this is similar to disorder in δ-TeO2 and arises from a broad distribution of asymmetric Te-O-Te bridges, something that we observe becomes increasingly asymmetric with increasing liquid temperature. Such behavior is qualitatively consistent with existing interpretations of Raman scattering spectra, and equivalent to temperature-induced coordination number reduction, for sufficiently large cutoff radii. Therefore, TeO2 contains a distribution of local environments that are, furthermore, temperature dependent, making it distinct from the canonical single-oxide glass formers. Our results are in good agreement with high-level ab initio cluster calculations.

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Theoretical and experimental studies of bonding in the main group homonuclear diatomic molecules have been pursued for many years, and they possess serious challenges for scientists. Most of the early experimental work have been carried out by Herzberg.1,2 We take a relook at the bonding motifs of Period 2 homonuclear diatomic molecules (from Li2 to Ne2) using varieties of quantum chemical tools, commonly used for intermolecular bonding/interactions now. The methods employed include Atoms in Molecules (AIM), Non-covalent Index plot (NCI), Electrostatic potential (ESP), and Potential Acting on one Electron in a Molecule (PAEM). The spectroscopic constants i.e., equilibrium bond distances (re), harmonic frequencies (ω), bond dissociation energies (De) have all been evaluated using high-level ab initio methods and critically compared with the experimental results. Multi-reference calculations (CASSCF) on B2 and C2 have been carried out as they have a large number of low lying electronic states. Bonding within these homonuclear diatomic molecules show all the diversities that are encountered in inter/intra-molecular bonding in chemistry. Based on the AIM analysis, these 8 homonuclear diatomic molecules could be divided into three different groups, based on the correlation between binding energy and the electron density at the bond critical point. However, PAEM/ESP analysis allows us to analyse all eight of them as one group having a good correlation between binding energy and the PAEM/ESP at the critical point between the two atoms. Our results highlight the arbitrariness in relying on some computational tools to characterize a bond as covalent (shared) or ionic/electrostatic (closed). In contrast, they also show the usefulness of the various methods in exploring similarities and differences in bonding. We propose that from Li2 to Ne2, all homonuclear diatomic molecules are bound by ‘chemical bonds’. The Period 2 homo-nuclear diatomic ‘molecules’ from the ‘covalent Li2’ to the ‘van der Waals Ne2’ show a rich diversity of 'bonds' that one can see in all inter- and intra-molecular interactions encountered in physics, chemistry and biology. Here, we show that these display a continuum in ‘chemical bonds!’

Characterization of the low-lying electronic states of tin monohydride cation including the spin-orbit coupling effect: A theoretical perspective.

High-level ab initio computations have been performed on SnH+. The potential energy curves and spectroscopic constants of the low-lying Λ-S electronic states, as well as their associated Ω states, are derived at the icMRCI+Q level employing basis sets of quintuple-ζ quality. The transition dipole moments, Einstein coefficients, radiative lifetimes and Franck-Condon factors of three spin-forbidden transition bands ( [Formula: see text] , [Formula: see text] and [Formula: see text] ) are determined. Comparisons between our predictions and available experimental results indicate reasonable agreement. The spin-orbit coupling effect has been proved to affect these low-lying electronic states significantly.