Fluorinated Co-Solvents Enable Excellent Performances of Practical Cells Comprising LixSiO-Graphite Composite Anodes and LiNi0.89Co0.05Mn0.05Al0.01O2 (NCMA) Cathodes.

Li-ion batteries based on high specific capacity LixSiO-Graphite anodes and LiNi0.89Co0.05 Mn0.05Al0.01O2 (NCMA) cathodes may have numerous practical applications owing to high energy density without a necessary compromise on safety. SiO, which is an attractive Li insertion anode material, offers more cycling stability than Si and a higher capacity than graphite. Therefore, a new trend has emerged for developing composite C-Si anodes, possessing the excellent cyclability of graphite coupled with high capacity SiO. The composite structure described herein prevents the volume expansion of SiO and maintains the structural integrity during prolonged cycling. However, graphite electrodes suffer from exfoliation in propylene carbonate (PC) based electrolyte solutions, which avoids well known safety benefits related to a possible use of PC based electrolyte solutions in all kinds of Li batteries. Herein, it is reported that trifluoro propylene carbonate (TFPC) is compatible with graphite anodes. New electrolyte formulations are developed and tested containing fluorinated co-solvents and compared the performance of several electrolyte solutions, including conventional alkyl carbonates-based solutions in full Li-ion cells, which included LixSiO-Graphite anodes and LiNi0.89Co0.05Mn0.05Al0.01O2 (NCMA) cathodes. Cells with new electrolyte solutions developed herein demonstrated nearly twice capacity retention in prolonged cycling experiments compared to similar reference cells containing conventional electrolyte solutions.

Differential Substrate Sensing in Terpene Synthases from Plants and Microorganisms: Insight from Structural, Bioinformatic, and EnzyDock Analyses.

Terpene synthases (TPSs) catalyze the first step in the formation of terpenoids, which comprise the largest class of natural products in nature. TPSs employ a family of universal natural substrates, composed of isoprenoid units bound to a diphosphate moiety. The intricate structures generated by TPSs are the result of substrate binding and folding in the active site, enzyme-controlled carbocation reaction cascades, and final reaction quenching. A key unaddressed question in class I TPSs is the asymmetric nature of the diphosphate-(Mg2+)3 cluster, which forms a critical part of the active site. In this asymmetric ion cluster, two diphosphate oxygen atoms protrude into the active site pocket. The substrate hydrocarbon tail, which is eventually molded into terpenes, can bind to either of these oxygen atoms, yet to which is unknown. Herein, we employ structural, bioinformatics, and EnzyDock docking tools to address this enigma. We bring initial data suggesting that this difference is rooted in evolutionary differences between TPSs. We hypothesize that this alteration in binding, and subsequent chemistry, is due to TPSs originating from plants or microorganisms. We further suggest that this difference can cast light on the frequent observation that the chiral products or intermediates of plant and bacterial terpene synthases represent opposite enantiomers.

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene.

Terpene synthases are responsible for the biosynthesis of terpenes, the largest family of natural products. Hydropyrene synthase generates hydropyrene and hydropyrenol as its main products along with two byproducts, isoelisabethatrienes A and B. Fascinatingly, a single active site mutation (M75L) diverts the product distribution towards isoelisabethatrienes A and B. In the current work, we study the competing pathways leading to these products using quantum chemical calculations in the gas phase. We show that there is a great thermodynamic preference for hydropyrene and hydropyrenol formation, and hence most likely in the synthesis of the isoelisabethatriene products kinetic control is at play.

Can Anions Be Inserted into MXene?

Despite the continuous progress in the research and development of Ti3C2Tx (MXene) electrodes for high-power batteries and supercapacitor applications, the role of the anions in the electrochemical energy storage and their ability to intercalate between the MXene sheets upon application of positive voltage have not been clarified. A decade after the discovery of MXenes, the information about the possibility of anion insertion into the restacked MXene electrode is still being questioned. Since the positive potential stability range in diluted aqueous electrolytes is severely limited by anodic oxidation of the Ti, the possibility of anion insertion was evaluated in concentrated aqueous electrolyte solutions and aprotic electrolytes as well. To address this issue, we have conducted in situ gravimetric electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D) measurements in highly concentrated LiCl and LiBr electrolytes, which enable a significant extension of the operation range of the MXene electrodes toward positive potentials. Also, halogens are among the smallest anions and should be easier to intercalate between MXene layers, in comparison to multiatomic anions. On the basis of mass change variations in the positive voltage range and complementary density functional theory calculations, it was demonstrated that insertion of anionic species into MXene, within the range of potentials of interest for capacitive energy storage, is not likely to occur. This can be explained by the strong negative charge on Ti3C2Tx sheets terminated by functional groups.

Concentration-Dependent Self-Assembly of an Unusually Large Hexameric Hydrogen-Bonded Molecular Cage.

The sizes of available self-assembled hydrogen-bond-based supramolecular capsules and cages are rather limited. The largest systems have volumes of approximately 1400-2300 Å3 . Herein, we report a large, hexameric cage based on intermolecular amide-amide dimerization. The unusual structure with openings, reminiscent of covalently linked cages, is held together by 24 hydrogen bonds. With a diameter of 2.3 nm and a cavity volume of ∼2800 Å3 , the assembly is larger than any previously known capsule/cage structure relying exclusively on hydrogen bonds. The self-assembly process in chlorinated, organic solvents was found to be strongly concentration dependent, with the monomeric form prevailing at low concentrations. Additionally, the formation of host-guest complexes with fullerenes (C60 and C70 ) was observed.

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro.

The coronavirus SARS-CoV-2 main protease, Mpro, is conserved among coronaviruses with no human homolog and has therefore attracted significant attention as an enzyme drug target for COVID-19. The number of studies targeting Mpro for in silico screening has grown rapidly, and it would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. Clearly, current attempts at designing drugs targeting Mpro with the aid of computational docking would benefit from a priori knowledge of the ability of docking programs to predict correct binding modes and score these correctly. In the current work, we tested the ability of several leading docking programs, namely, Glide, DOCK, AutoDock, AutoDock Vina, FRED, and EnzyDock, to correctly identify and score the binding mode of Mpro ligands in 193 crystal structures. None of the codes were able to correctly identify the crystal structure binding mode (lowest energy pose with root-mean-square deviation < 2 Å) in more than 26% of the cases for noncovalently bound ligands (Glide: top performer), whereas for covalently bound ligands the top score was 45% (EnzyDock). These results suggest that one should perform in silico campaigns of Mpro with care and that more comprehensive strategies including ligand free energy perturbation might be necessary in conjunction with virtual screening and docking.

Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1ß-ol and Unnatural Derivatives via Supramolecular Catalysis.

Terpenes constitute one of the most structurally varied classes of natural products. A wide range of these structures are produced in nature by type I terpene cyclase enzymes from one single substrate. However, such reactivity has proven difficult to reproduce in solution with man-made systems. Herein we report the shortest synthesis of the tricyclic sesquiterpene presilphiperfolan-1ß-ol to date, utilizing the supramolecular resorcinarene capsule as catalyst for the key step. This synthetic approach also allows access to unnatural derivatives of the natural product, which would not be accessible through the biosynthetic machinery. Additionally, this study provides useful insight into the biosynthesis of the presilphiperfolanol natural products, including the first experimental evidence consistent with the proposed biosynthetic connection between caryophyllene and the presilphiperfolanols.

Understanding the role of active site residues in CotB2 catalysis using a cluster model.

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of a large number of terpenes. CotB2 is a diterpene cyclase from Streptomyces melanosporofaciens, which catalyzes the formation of cycloocta-9-en-7-ol, a precursor to the next-generation anti-inflammatory drug cyclooctatin. In this work, we present evidence for the significant role of the active site's residues in CotB2 on the reaction energetics using quantum mechanical calculations in an active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures.

Discovering Monoterpene Catalysis Inside Nanocapsules with Multiscale Modeling and Experiments.

Large-scale production of natural products, such as terpenes, presents a significant scientific and technological challenge. One promising approach to tackle this problem is chemical synthesis inside nanocapsules, although enzyme-like control of such chemistry has not yet been achieved. In order to better understand the complex chemistry inside nanocapsules, we design a multiscale nanoreactor simulation approach. The nanoreactor simulation protocol consists of hybrid quantum mechanics-molecular mechanics-based high temperature Langevin molecular dynamics simulations. Using this approach we model the tail-to-head formation of monoterpenes inside a resorcin[4]arene-based capsule (capsule I). We provide a rationale for the experimentally observed kinetics of monoterpene product formation and product distribution using capsule I, and we explain why additional stable monoterpenes, like camphene, are not observed. On the basis of the in-capsule I simulations, and mechanistic insights, we propose that feeding the capsule with pinene can yield camphene, and this proposal is verified experimentally. This suggests that the capsule may direct the dynamic reaction cascades by virtue of π-cation interactions.

A promising drug candidate for the treatment of glaucoma based on a P2Y6-receptor agonist.

Extracellular nucleotides can regulate the production/drainage of the aqueous humor via activation of P2 receptors, thus affecting the intraocular pressure (IOP). We evaluated 5-OMe-UDP(α-B), 1A, a potent P2Y6-receptor agonist, for reducing IOP and treating glaucoma. Cell viability in the presence of 1A was measured using [3-(4, 5-dimethyl-thiazol-2-yl) 2, 5-diphenyl-tetrazolium bromide] (MTT) assay in rabbit NPE ciliary non-pigmented and corneal epithelial cells, human retinoblastoma, and liver Huh7 cells. The effect of 1A on IOP was determined in acute glaucomatous rabbit hyaluronate model and phenol-induced chronic glaucomatous rabbit model. The origin of activity of 1A was investigated by generation of a homology model of hP2Y6-R and docking studies. 1A did not exert cytotoxic effects up to 100 mM vs. trusopt and timolol in MTT assay in ocular and liver cells. In normotensive rabbits, 100 µM 1A vs. xalatan, trusopt, and pilocarpine reduced IOP by 45 vs. 20-30%, respectively. In the phenol animal model, 1A (100 µM) showed reduction of IOP by 40 and 20%, following early and late administration, respectively. Docking results suggest that the high activity and selectivity of 1A is due to intramolecular interaction between Pα-BH3 and C5-OMe which positions 1A in a most favorable site inside the receptor. P2Y6-receptor agonist 1A effectively and safely reduces IOP in normotense, acute, and chronic glaucomatous rabbits, and hence may be suggested as a novel approach for the treatment of glaucoma.

Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.

Analysis of the Spectroscopic Aspects of Cationic Dye Basic Orange 21.

Spectroscopic properties of cationic dye basic orange 21 (BO21) in solutions, in solids, and within leukocytes were examined. Results obtained with solutions indicate that influence of variables such as pH, viscosity, salt composition, and various proteins on the absorption spectrum of BO21 is negligible. However, in the presence of heparin, a blue shift (484-465 nm) is observed, which is attributed to the aggregation of BO21 on the polyanion. Applying density functional theory demonstrates that in aqueous solutions (a) the formation of BO21 oligomers is thermodynamically favorable, they are oriented in an antiparallel dipolar arrangement, and their binding energies are lower than those of parallel dipolar arrangements, (b) association between BO21 aggregates and heparin is highly favorable, and (c) the blue shift is due to the mixing of π → π* transitions caused by BO21 molecule stacking. However, when embedded in basophils, the absorption spectra of intracellular BO21 is extremely red-shifted, with two peaks (at 505 and 550 nm) found to be attributed to BO21 and the BO21-heparin complex, respectively, which are intracellularly hosted in nonaqueous environments. Initial evidence of the ability to differentiate between leukocyte types by BO21 is presented.

Metallocorroles as Nonprecious-Metal Catalysts for Oxygen Reduction.

The future of affordable fuel cells strongly relies on the design of earth-abundant (non-platinum) catalysts for the electrochemical oxygen reduction reaction (ORR). However, the bottleneck in the overall process occurs therein. We have examined herein trivalent Mn, Fe, Co, Ni, and Cu complexes of ß-pyrrole-brominated corrole as ORR catalysts. The adsorption of these complexes on a high-surface-area carbon powder (BP2000) created a unique composite material, used for electrochemical measurements in acidic aqueous solutions. These experiments disclosed a clear dependence of the catalytic activity on the metal center of the complexes, in the order of Co>Fe>Ni>Mn>Cu. The best catalytic performance was obtained for the Co(III) corrole, whose onset potential was as positive as 0.81 V versus the reversible hydrogen electrode (RHE). Insight into the properties of these systems was gained by spectroscopic and computational characterization of the reduced and oxidized forms of the metallocorroles.

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer.

Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics-molecular mechanics approach with a recently developed semiempirical AM1-SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C-H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important.

Odd-even effect in molecular electronic transport via an aromatic ring.

A distinct odd-even effect on the electrical properties, induced by monolayers of alkyl-phenyl molecules directly bound to Si(111), is reported. Monomers of H2C═CH-(CH2)n-phenyl, with n = 2-5, were adsorbed onto Si-H and formed high-quality monolayers with a binding density of 50-60% Si(111) surface atoms. Molecular dynamics simulations suggest that the binding proximity is close enough to allow efficient π-π interactions and therefore distinctly different packing and ring orientations for monomers with odd or even numbers of methylenes in their alkyl spacers. The odd-even alternation in molecular tilt was experimentally confirmed by contact angle, ellipsometry, FT-IR, and XPS with a close quantitative match to the simulation results. The orientations of both the ring plane and the long axis of the alkyl spacer are more perpendicular to the substrate plane for molecules with an even number of methylenes than for those with an odd number of methylenes. Interestingly, those with an even number conduct better than the effectively thinner monolayers of the molecules with the odd number of methylenes. We attribute this to a change in the orientation of the electron density on the aromatic rings with respect to the shortest tunneling path, which increases the barrier for electron transport through the odd monolayers. The high sensitivity of molecular charge transport to the orientation of an aromatic moiety might be relevant to better control over the electronic properties of interfaces in organic electronics.

Mechanistic docking in terpene synthases using EnzyDock.

Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.

Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters.

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.

The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.

Structural analysis of electrolyte solutions for rechargeable Mg batteries by stereoscopic means and DFT calculations.

We present a rigorous analysis of unique, wide electrochemical window solutions for rechargeable magnesium batteries, based on aromatic ligands containing organometallic complexes. These solutions are comprised of the transmetalation reaction products of Ph(x)MgCl(2-x) and Ph(y)AlCl(3-y) in different proportions, in THF. In principle, these reactions involve the exchange of ligands between the magnesium and the aluminum based compounds, forming ionic species and neutral molecules, such as Mg(2)Cl(3)(+)·6THF, MgCl(2)·4THF, and Ph(y)AlCl(4-y)(-) (y = 0-4). The identification of the equilibrium species in the solutions is carried out by a combination of Raman spectroscopy, multinuclear NMR, and single-crystal XRD analyses. The association of the spectroscopic results with explicit identifiable species is supported by spectral analyses of specially synthesized reference compounds and DFT quantum-mechanical calculations. The correlation between the identified solution equilibrium species and the electrochemical anodic stability window is investigated. This study advances both development of new nonaqueous solution chemistry and possible development of high-energy density rechargeable Mg batteries.