Half-Pancake Bonding in Asphaltenes

Aggregation of asphaltenes in petroleum crude oil is a well-known and ongoing problem for petroleum production. Asphaltenes aggregate even in situations where polycyclic aromatic hydrocarbon (PAH) model compounds do not, which implies that there is more to the phenomenon than just π-stacking. Half-pancake bonds involving stable radical PAH have been hypothesized to contribute to asphaltene aggregation (Zhang, Y.;Energy Fuels 2020, 34 (8), 9094−9107). We report density functional theory calculations on half-pancake bonding in asphaltene model compounds. Pancake and half-pancake bonds can be viewed as multi-center generalizations of (common) two-electron covalent bonds and (rare) odd-electron bonds, respectively. In the absence of other effects, we find negligible half-pancake bonding between radical PAH and neutral nonradical PAH. Introducing heteroatoms can produce modestly strong donor-acceptor half-pancake-type interactions. Our results suggest that half-pancake bonding alone is too weak and too rare to drive asphaltene aggregation. However, interactions between stable organic radicals, heteroatoms, and polar groups may contribute to aggregation

Enhanced Enthalpies of Formation from Density Functional Theory through Molecular Reference States

Accurate prediction of enthalpy of formation is an important goal for theoretical methods. As such, the ability of a density functional to accurately predict enthalpies of formation for a wide variety of compounds is often used as a critical test of its efficacy. These enthalpies are typically calculated by modeling formation reactions from the isolated atoms that make up the molecule. However, the enthalpy of formation can be calculated from any valid reference state, e.g., as in isodesmic reactions, and using different reference states can alter the accuracy of prediction. We have had excellent results using a single molecular reference state per element, namely C60 for carbon and the diatomic standard reference states for hydrogen, nitrogen, oxygen, and fluorine. This molecular reference scheme can be viewed as a better measure of the upper limit of accuracy of a density functional/basis set pair, as it leads to generally more accurate predictions than are possible using atomic energies. For example, LSDA’s unsigned average error drops from 158.8 to 11.6 kcal/mol, and PBE’s error improves to 5.1 kcal/mol from 35.8 kcal/mol with the 6-311G(2df,2p) basis set. This scheme also makes small basis sets far more accurate, indicates that a revision of the relative thermochemical accuracy of functionals may be required, and can remove qualitative failures for some functional/basis set pairs

Parametrization of Atomic Energies to Improve Small Basis Set Density Functional Thermochemistry

Enthalpies of formation predicted with density functional theory and small basis sets can be greatly improved by treating the atomic energies as empirical parameters. When a variety of functionals and small basis sets are used, the root-mean-square error in enthalpies of formation is reduced by a factor of approximately two for the least improved functional/basis set pair, with significantly larger reductions for other functionals, especially LSDA. When the 3-21G* and 3-21+G* basis sets are used with nonempirical functionals, it is possible to achieve accuracy greater than that of PM3, which was primarily designed to reproduce enthalpies of formation. In addition to decreasing statistical errors, our procedure can also remove qualitative errors in density functional/basis set pairs that fail for the prediction of enthalpies of formation

Performance of Density Functionals with Small Split Valence Basis Sets^†

Though there have been many studies of density functional theory and various density functionals for large basis sets, there have been extremely limited studies of DFT with smaller basis sets. This paper discusses the ability of a series of density functionals to reproduce experimental heats of formation at the 3-21G*, 3-21+G*, and MIDI! basis sets. Also included are G3, G3MP2, MNDO, and PM3 calculations for comparison purposes. Good results for 3-21G* were obtained using mPW exchange with gradient-corrected correlation functionals LYP, PBEc, and PW91c, and 3-21+G* performed well with PBEx and PW91x exchange functionals when coupled with these same gradient-corrected correlation functionals. Unexpectedly good results were also obtained with G96P86/3-21G*, given each individual functionals performance in other functional pairings. MIDI! was outperformed, in general, by both 3-21G* and 3-21+G*

Virtual Experiments on Real Asphaltenes: Predicting Properties Using Quantum Chemical Simulations of Structures from Non-contact Atomic Force Microscopy

Molecular characterization of structure–property relationships in the asphaltene fraction of heavy-oil-based complex mixtures is an enormous challenge. Non-contact atomic force microscopy (nc-AFM) can now provide molecular structures of individual asphaltene molecules. However, it remains difficult to relate those structures to properties. This work uses quantum chemistry simulations to address this challenge. We report “virtual experiments” on databases of 28 steam-cracked tar asphaltene molecules and 10 petroleum asphaltene molecules identified in nc-AFM images (Schuler, B.; Fatayer, S.; Meyer, G.; Rogel, E.; Moir, M.; Zhang, Y.; Harper, M. R.; Pomerantz, A. E.; Bake, K. D.; Witt, M.; Peña, D.; Kushnerick, J. D.; Mullins, O. C.; Ovalles, C.; van den Berg, F. G. A.; Gross, L. Heavy Oil Based Mixtures of Different Origins and Treatments Studied by Atomic Force Microscopy. Energy Fuels 2017, 31, 6856−6861, DOI: 10.1021/acs.energyfuels.7b00805). Our simulations provide three primary conclusions. First, computed ensemble proton nuclear magnetic resonance (NMR) spectra of steam-cracked tar asphaltenes validate the hypothesis that ∼3% of fluorene protons seen in nc-AFM images are below the NMR detection limit as a result of inhomogeneous broadening. Second, computed toluene-to-heptane solvent transfer free energies of steam-cracked tar and petroleum asphaltenes are consistent with the observation that more alkane-soluble subfractions will be dominated by smaller molecules (Groenzin, H.; Mullins, O. C.; Eser, S.; Mathews, J.; Yang, M.-G.; Jones, D. Molecular Size of Asphaltene Solubility Fractions. Energy Fuels 2003, 17, 498−503, DOI: 10.1021/ef010239g). Computed electrostatic potential maps suggest that the steric environments of asphaltene heteroatoms will be important for their role in intermolecular interactions. Third, computed radical reaction energies of steam-cracked tar asphaltenes are consistent with the observation that asphaltenes at elevated temperatures can donate hydrogen atoms to anthracene and accept hydrogen atoms from dihydroanthracene (Naghizada, N.; Prado, G. H. C.; de Klerk, A. Uncatalyzed Hydrogen Transfer during 100–250 °C Conversion of Asphaltenes. Energy Fuels 2017, 31, 6800−6811, DOI: 10.1021/acs.energyfuels.7b00661). Moreover, many asphaltene molecules possess “dual” reactivity, being both good hydrogen atom acceptors and good hydrogen atom donors. These results motivate application of quantum chemistry to interpreting and contextualizing nc-AFM experiments

A Benchmark Study of H₂ Activation by Au₃ and Ag₃ Clusters

We present a high-level computational study of the activation and disassociation of H₂ on triatomic gold and silver clusters as well as benchmarks of various density functional theory (DFT) approximations. The reaction was modeled using complete basis set (CBS) extrapolated CCSD­(T) energies at MP2/def2-QZVPP geometries. Our calculations considered several isomers of dissociated H₂ on the metal trimer as well as transition states between them. High-level results were then used to benchmark 30 different semilocal, hybrid, double hybrid, and Rung 3.5 DFT functionals as well as Hartree–Fock and MP2 theory. The effect of optimizing the geometries using DFT was also studied with a smaller set of functionals. The results indicate that double-hybrid functionals, especially mPW2PLYP, accurately model this class of reactions, albeit at computational cost higher than standard DFT. The range-separated (screened) hybrids HSE06 and HISSb are also successful and provide a reasonable balance of computational cost and accuracy. These methods are particularly promising for treatments of coinage metal clusters and surfaces

Insights into the Structure and Dynamics of the Dinuclear Zinc β-Lactamase Site from <i>Bacteroides fragilis</i>^†

Herein, we report quantum chemical calculations and molecular dynamics (MD) simulations of the dinuclear form of the Bacteroides fragilis zinc β-lactamase. We studied four different configurations which differ in the protonation state of the Asp103 residue and in the presence or absence of a Zn1−OH−Zn2 bridge. The flexibility of the Zn1−OH−Zn2 bridge was studied by means of quantum mechanical (QM) calculations on cluster models while the relative stabilities of the different configurations were estimated from QM linear scaling calculations on the enzyme. Contacts between important residues (Cys104, Asp69, Lys185, etc.), the solvation of the zinc ions, and the conformation of the active site β-hairpin loop were characterized by the MD analyses. The influence of the buried sodium ion close to the Zn2 position was investigated by carrying out a secondary simulation where the sodium ion was replaced with an internal water molecule. The comparative structural analyses among the different MD trajectories augmented with energetic calculations have demonstrated that the B. fragilis protein efficiently binds the internal Na+ ion observed crystallographically. Moreover, we found that when Asp103 is unprotonated, a rigid Zn1−OH−Zn2 bridge results, while for neutral Asp103, a fluctuating Zn1−Zn2 distance was possible via the breaking and formation of the Zn1−OH−Zn2 bridge. The mechanistic implications of these observations are discussed in detail

The Distinctive Electronic Structures of Rhenium Tris(thiolate) Complexes, an Unexpected Contrast to the Valence Isoelectronic Ruthenium Tris(thiolate) Complexes

The noninnocent 2-diphenylphosphino-benzenethiolate (DPPBT) ligand containing both phosphorus and sulfur donors delocalizes the electron density in a manner reminiscent of dithiolenes. The electronic structure of the <b>[ReL</b>_<b>3</b><b>]</b>^{<b><i>n</i></b>} (L = DPPBT, <i>n</i> = 0, 1+, 2+) complexes was probed with density-functional theory (DFT) and high-level ab initio methods including complete active space self-consistent field (CASSCF and CASPT2) and coupled cluster (CCSD and CCSD­(T)). DFT predicts a slight preference for a closed-shell (CS) singlet ground state for the neutral <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b> and stronger preferences for low-spin ground states for the oxidized <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b>. High-level ab initio methods confirm a CS singlet with a Re­(III) (d⁴, <i>S</i> = 0) center as the ground state of <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b>. Thus, this neutral Re species has considerably less thiyl radical character than the valence isoelectronic <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>, which is mainly a Ru­(III) (d⁵, <i>S</i> = 1/2) anti-ferromagnetically (AF) coupled to a thiyl radical (<i>S</i> = 1/2). However, the oxidized derivatives <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> show significant metal-stabilized thiyl radical character like <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>. Both <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b> and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> have major contributions from Re­(III) (d⁴, <i>S</i> = 1) centers AF coupled to thiyl and dithiyl DPPBT ligands. These findings are consistent with the experimental chemistry as <b>[RuL</b>_<b>3</b><b>]</b>^<b>+</b>, <b>[ReL</b>_<b>3</b><b>]</b>^<b>+</b>, and <b>[ReL</b>_<b>3</b><b>]</b>^<b>2+</b> can add ethylene to form the new C–S bonds, but <b>[ReL</b>_<b>3</b><b>]</b>^<b>0</b> cannot. The thiyl radicals on the S2 position (the S trans to a P donor) serve as the intrinsic electron acceptors in the actual ethylene addition reactions with Ru and Re tris­(thiolate) complexes

Computational Exploration of Alternative Catalysts for Olefin Purification: Cobalt and Copper Analogues Inspired by Nickel Bis(dithiolene) Electrocatalysis

Olefin purification is an important process in petrochemistry. The behavior of the nickel bis­(dithiolene) complex Ni­(S₂C₂(CF₃)₂)₂ (<b>1</b>_{<b>_Ni</b>}) as an electrocatalyst for this process was thoroughly explored experimentally and computationally. Here, computational investigations with the ωB97X-D functional were conducted to explore alternative candidates [M­(S₂C₂(CF₃)₂)₂]^<i>n</i> (M = Co with <i>n</i> = 0, −1, −2, −3 and Cu with <i>n</i> = +1, 0, −1, −2) for olefin purification by using ethylene as a model. The reaction mechanism for these alternative catalysts was calculated to determine if any of these alternatives could block the decomposition route that exists for the Ni catalyst, bind ethylene efficiently to form the adducts, and release ethylene upon reduction. Calculations predict that the neutral cobalt complex <b>1</b>_{<b>_Co</b>} binds and releases olefin upon reduction with low activation barriers. Furthermore, <b>1</b>_{<b>_Co</b>}, unlike <b>1</b>_{<b>_Ni</b>}, catalyzes the desired reaction without the need of the anion as a cocatalyst. The Co atom directly coordinates with ethylene more favorably than Ni, facilitating the indirect pathway that is found to lead to the formation of the desired interligand adduct. The reduction and oxidation processes involved in the reaction are computed to occur under reasonable experiment conditions. Among the copper complexes, the calculations predict that the anionic copper complex <b>1</b>_{<b>_Cu</b>}^<b>–</b> also may be an alternative catalyst, whose performance is somewhat worse than <b>1</b>_{<b>_Ni</b>}. The reaction of <b>1</b>_{<b>_Cu</b>}^<b>–</b> with ethylene is predicted to be thermodynamically neutral. New catalysts that need no electrochemical regenerations may be possible by designing appropriate dithiolene ligands for <b>1</b>_{<b>_Cu</b>}^<b>–</b>

Mechanism of Ethylene Addition to Nickel Bis(oxothiolene) and Nickel Bis(dioxolene) Complexes

The electrochemically reversible binding of olefins by nickel bis­(dithiolene) has been extensively studied, both theoretically and computationally. To optimize a catalyst for this process, we have investigated all possible reaction pathways of ethylene addition onto the related complex nickel bis­(dioxolene), and the two isomers (<i>cis</i> and <i>trans</i>) of nickel bis­(oxothiolene). Modern DFT calculations predict that the nickel bis­(dioxolene) complex has limited practical use due to high barriers to binding. However, each of the two isomers of the nickel bis­(oxothiolene) complexes display enhanced properties versus the original nickel bis­(dithiolene) complex. Specifically, in nickel bis­(dithiolene), the intraligand binding of olefins leads to decomposition, whereas interligand binding is required for reversibility; the two nickel bis­(oxothiolene) complexes have greater selectivity toward the formation of the desired interligand adducts. For the full reaction pathways, the new complexes’ binding mechanisms are contrasted with the mechanism of the original catalyst