Energy Decomposition Techniques Research Articles

Simultaneous desulfurization and dearomatization of simulated straight-run diesel with novel green DBN-based ionic liquids

Given the surplus of diesel fuel in China and the extensive utilization of renewable energy sources, there is a growing inclination to eliminate organic sulphur and aromatic hydrocarbons from diesel fuel for its application as high-quality ethylene cracking feedstock. In this study, a series of 1,5-diazabicyclo[4.3.0]non-5-ene (DBN)-based ionic liquids with [DBNH]+ as the cation and imidazole as the anion were designed and synthesized for the simultaneous desulfurization and dearomatization of straight-run diesel fuel. Considering factors such as extractant stability, residue content in oil, and separation performance, [DBNH][Tr], exhibiting excellent performance characteristics, was screened as the optimal extractant. Following three-stage cross-flow extraction with an extractant/oil ratio of 3:1 at 30 °C, complete removals of sulfides (benzothiophene) and polycyclic aromatic hydrocarbons (1-methylnaphthalene) were achieved while saturated alkanes reached up to 95.8 wt%, making it suitable for ethylene cracking applications. The interaction mechanisms between ionic liquids and oil components were revealed by atoms in molecules (AIM) topology analysis, independent gradient model based on Hirshfeld partition (IGMH) analysis, and symmetric adaptive perturbation theory energy decomposition techniques, revealing that dispersion-dominated van der Waals (VDW) forces primarily govern interactions due to π-π stacking.

Mechanistic Insights into the Origins of Selectivity in a Cu-Catalyzed C-H Amidation Reaction.

The catalytic transformation of C-H to C-N bonds offers rapid access to fine chemicals and high-performance materials, but achieving high selectivity from undirected aminations of unactivated C(sp3)-H bonds remains an outstanding challenge. We report the origins of the reactivity and selectivity of a Cu-catalyzed C-H amidation of simple alkanes. Using a combination of experimental and computational mechanistic studies and energy decomposition techniques, we uncover a switch in mechanism from inner-sphere to outer-sphere coupling between alkyl radicals and the active Cu(II) catalyst with increasing substitution of the alkyl radical. The combination of computational predictions and detailed experimental validation shows that simultaneous minimization of both Cu-C covalency and alkyl radical size increases the rate of reductive elimination and that both strongly electron-donating and electron-withdrawing substituents on the catalyst accelerate the selectivity-determining C-N bond formation process as a result of a change in mechanism. These findings offer design principles for the development of improved catalyst scaffolds for radical C-H functionalization reactions.

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease.

The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, Mpro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, Mpro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C70 as an innovative scaffold for the inhibition of SARS-CoV-2 Mpro. At odds with masitinib, both C60 and C70 interact more strongly with SARS-CoV-2 Mpro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to Mpro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding.

Variational Energy Decomposition Analysis of Charge-Transfer Interactions between Metals and Ligands in Carbonyl Complexes.

Variational energy decomposition analyses have been presented to quantify the σ-dative, ligand-to-metal forward charge transfer (CT) and the π-conjugative, metal-to-ligand backward charge delocalization on a series of isolelectronic transition-metal carbonyl complexes M(CO)6, including M = Ti2-, V-, Cr, Mn+, and Fe2+. Although the qualitative features of these energy terms are understood, well-defined quantitative studies have been scarce. Consistent with early findings, electrostatic and Pauli exchange effects play a key role in σ-donation, resulting in blue shifts in ligand vibrational frequency in the complex geometries. Excluding chemical bonding interactions between the CO ligand and the metal fragments in the energy decomposition analysis, we found that loosely bound electrostatic complexes can be formed at a longer metal-to-ligand distance due to the exponential decay of Pauli exchange. In all complexes, the overall binding stabilization can be attributed to CT effects, with opposing trends between σ-donation and π-back bonding that follows an order of Ti2- (4.4) > V1- (2.6) > Cr (1.5) > Mn1+ (1.1) > Fe2+ (0.5) in π-to-σ CT ratio. These electronic and energetic features are mirrored in the vibrational frequency shifts induced by different factors. The present investigation may help stimulate the use of energy decomposition techniques to understand the structure and activity of metallocatalysts using density functional theory.

An Improved PIII/PV═O-Catalyzed Reductive C-N Coupling of Nitroaromatics and Boronic Acids by Mechanistic Differentiation of Rate- and Product-Determining Steps.

Experimental, spectroscopic, and computational studies are reported that provide an evidence-based mechanistic description of an intermolecular reductive C–N coupling of nitroarenes and arylboronic acids catalyzed by a redox-active main-group catalyst (1,2,2,3,4,4-hexamethylphosphetane P-oxide, i.e., 1·[O]). The central observations include the following: (1) catalytic reduction of 1·[O] to PIII phosphetane 1 is kinetically fast under conditions of catalysis; (2) phosphetane 1 represents the catalytic resting state as observed by 31P NMR spectroscopy; (3) there are no long-lived nitroarene partial-reduction intermediates observable by 15N NMR spectroscopy; (4) the reaction is sensitive to solvent dielectric, performing best in moderately polar solvents (viz. cyclopentylmethyl ether); and (5) the reaction is largely insensitive with respect to common hydrosilane reductants. On the basis of the foregoing studies, new modified catalytic conditions are described that expand the reaction scope and provide for mild temperatures (T ≥ 60 °C), low catalyst loadings (≥2 mol%), and innocuous terminal reductants (polymethylhydrosiloxane). DFT calculations define a two-stage deoxygenation sequence for the reductive C–N coupling. The initial deoxygenation involves a rate-determining step that consists of a (3+1) cheletropic addition between the nitroarene substrate and phosphetane 1; energy decomposition techniques highlight the biphilic character of the phosphetane in this step. Although kinetically invisible, the second deoxygenation stage is implicated as the critical C–N product-forming event, in which a postulated oxazaphosphirane intermediate is diverted from arylnitrene dissociation toward heterolytic ring opening with the arylboronic acid; the resulting dipolar intermediate evolves by antiperiplanar 1,2-migration of the organoboron residue to nitrogen, resulting in displacement of 1·[O] and formation of the target C–N coupling product upon in situ hydrolysis. The method thus described constitutes a mechanistically well-defined and operationally robust main-group complement to the current workhorse transition-metal-based methods for catalytic intermolecular C–N coupling.

Hydrogen transfer reaction: Bond formation and bond cleavage through the eyes of interacting quantum atoms

Hydrogen transfer from hydroquinone to the methoxy radical was studied using the density functional theory. The energy decomposition technique, interacting quantum atoms, was employed for a detailed investigation of the changes that the bonds of interest go through along the minimum energy path in the vicinity of the transition state. The whole system was divided either into two or three fragments. The two-fragment analysis enabled investigation of the bond that is formed or the one that is cleaved by defining the fragments as reactants and as products, respectively. The three-fragment analysis (the fragments being semiquinone, hydrogen atom and methoxy radical) was used for the simultaneous analysis of the two phenomena, bond cleavage and bond formation. Additionally, it enabled the interaction between the particle that donates the hydrogen atom and the one that accepts it to be investigated. This interaction is characterized by attractive non-classical and repulsive classical interactions. It was demonstrated that the transferring hydrogen atom undergoes the most pronounced energy changes and gives the largest contribution to the deformation energy.

Theory and practice of modeling van der Waals interactions in electronic-structure calculations.

The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.

On approximation of Ginzburg–Landau minimizers by [formula omitted]-valued maps in domains with vanishingly small holes

We consider a two-dimensional Ginzburg–Landau problem on an arbitrary domain with a finite number of vanishingly small circular holes. A special choice of scaling relation between the material and geometric parameters (Ginzburg–Landau parameter vs. hole radius) is motivated by a recently discovered phenomenon of vortex phase separation in superconducting composites. We show that, for each hole, the degrees of minimizers of the Ginzburg–Landau problems in the classes of S1-valued and C-valued maps, respectively, are the same. The presence of two parameters that are widely separated on a logarithmic scale constitutes the principal difficulty of the analysis that is based on energy decomposition techniques.

Synthesis, structure and DFT study of asymmetrical NHC complexes of cymantrene derivatives and their application in the dehydrogenative dimerization reaction of thiols

Asymmetrical NHC complexes of cymantrene and methylcymantrene have been synthesised through the photochemical substitution of carbonyl ligands in the presence of the imidazol-2-ylidene salts. The carbene substituents have been varied between compact (L1) and bulky (L2 and L3) substituents to produce an array of differently sized carbene ligands. The solid state crystal structures of three of the complexes confirmed the bonding pattern of the ligand towards available metal centres and an in-depth DFT study provided insight into electronic and steric aspects. Application of the Extended Transition State coupled with Natural Orbitals for Chemical Valence (ETS-NOCV) energy decomposition technique indicated various NOCV channels for each Mn–L bond (L = 3-ethyl-1-methylimidazolylidene carbene, triphenylphosphine or acetonitrile), describing the density and energy changes of specific (σ and π) attributes of each bond. N-heterocyclic carbenes of cymantrene derivatives and their triphenylphosphine-substituted analogue are equivalent σ-donors, with 53% and 56%, respectively, of the total binding energy originating from σ-donation. However, NHC complexes show considerably less π character in the metal-carbene bond. Hydrogen interactions in the NHC complexes were also identified in the ETS-NOCV calculations and provided quantification of the hydrogen interactions witnessed in the solid state structures. Calculated Wiberg bond indices, bond dissociation enthalpies, percentage buried volumes and percentage sigma and pi-bonding characteristics quantified the bonding and electronic aspects of the ligand-metal interactions within the complex.

Rational Approaches for the Design of Effective Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitors

The binding of several classes of nonnucleoside reverse transcriptase inhibitors (NNRTIs) to wild-type (wtRT) and K103N mutant (mRT) human immunodeficiency virus type 1 (HIV-1) reverse transcriptase is studied by molecular dynamics and energy decomposition techniques. The imidoylthiourea (ITU), diaryltriazine (DATA), and diarylpyrimidine (DAPY) NNRTIs studied maintain the hydrogen bond with Lys101 during the 3 ns molecular dynamics trajectories. When bound to mRT, all the DAPYs studied establish hydrogen bonds with Glu138; among these, those of the potent inhibitors TMC120 and TMC125 are water-mediated. The molecular interactions of the NNRTIs in the binding pocket are correlated to the drugs' potency. Quantitative free energy analyses show a linear relationship between the van der Waals energetic component and the potency against wtRT. The molecular basis of the interaction between NNRTIs and RT presented here provide quantitative approaches for the design of novel effective anti-HIV drugs.

Revisiting Hydrophobic Mismatch with Free Energy Calculations of Transmembrane Helix Tilting

Membrane proteins are involved in various cellular processes via interactions between their helices and the surrounding lipid environments. It is energetically favorable for transmembrane (TM) domain to match the hydrophobic thickness of the lipid bilayer. We have utilized a helix tilt restraint potential and the free energy decomposition technique to characterize the microscopic forces governing tilting of various TM peptides in different conditions. To investigate the influence of hydrophobic length of TM helix on its tilting, we used a model peptide called WALP (acetyl-GW2(LA)nLW2A-NH2) by varying systematically the length of the peptide (WALP16, WALP19, WALP23, and WALP27). Also, to study the influence of membrane hydrophobic thickness on TM helix tilting, we used two kind of lipid bilayer (DMPC and POPC). Finally, we used arginine, lysine, and alanine as a flanking residue instead of tryptophan (acetyl-GX2(LA)8LX2A-NH2: X = R, K, and A) to examine the influence of various anchoring residues on TM helix tilting. The detail structural features and energetic contribution from hydrophobic (mis)match between lipid and peptides are presented and discussed.

Results for the C5G7 3-D Extension benchmark using the discrete ordinates code PANDA

We present solutions of the 3-D Extension C5G7 benchmark using the discrete ordinates S N code PANDA. The problem is a 3-D heterogeneous LWR core calculation with different levels of control rod insertion. It was devised by the OECD/NEA Expert Group on 3-D Radiation Transport Benchmarks. In the present paper we describe the numerical methods used in these calculations. Considering parallelization, the first submitted results were obtained using an energy decomposition technique, since then, more accurate new results have been obtained using a 3-D spatial decomposition parallel method. For geometry and material modeling on a regular 3-D orthogonal mesh, a volume fraction method is employed for mixed material cells treatment. Numerous calculations were performed in order to study the eigenvalue and pin wise fission rates convergence as a function of spatial and angular mesh refinements. Accurate 3-D solutions of the heterogeneous reactor benchmark require a high level of spatial and angular discretization leading to huge calculations in terms of CPU time and memory requirements.

Theoretical study of aqueous uranyl carbonate (UO 2CO 3) and its hydrated complexes: UO 2CO 3· nH 2O ( n=1–3)

Extensive ab initio calculations have been carried out to study the structure and bonding of hydrated UO 2CO 3 complexes using state-of-the-art techniques. The structures of aqueous UO 2CO 3 and its hydrated complexes have been further studied by considering the solvent as a polarizable continuum dielectric. The calculations have been carried out using polarization continuum, self-consistent isodensity polarizable continuum model, and conductor like screen models. The calculated uranyl frequencies of the hydrated UO 2CO 3 have been compared with the available vibrational frequencies and the nature of water binding has been analyzed using energy decomposition techniques.