A review on the structural characterization of nanomaterials for nano-QSAR models.

Quantitative structure-activity relationship (QSAR) models are routinely used to predict the properties and biological activity of chemicals to direct synthetic advances, perform massive screenings, and even to register new substances according to international regulations. Currently, nanoscale QSAR (nano-QSAR) models, adapting this methodology to predict the intrinsic features of nanomaterials (NMs) and quantitatively assess their risks, are blooming. One of the challenges is the characterization of the NMs. This cannot be done with a simple SMILES representation, as for organic molecules, because their chemical structure is complex, including several layers and many inorganic materials, and their size and geometry are key features. In this review, we survey the literature for existing predictive models for NMs and discuss the variety of calculated and experimental features used to define and describe NMs. In the light of this research, we propose a classification of the descriptors including those that directly describe a component of the nanoform (core, surface, or structure) and also experimental features (related to the nanomaterial's behavior, preparation, or test conditions) that indirectly reflect its structure.

MicotoXilico: An Interactive Database to Predict Mutagenicity, Genotoxicity, and Carcinogenicity of Mycotoxins.

Mycotoxins are secondary metabolites produced by certain filamentous fungi. They are common contaminants found in a wide variety of food matrices, thus representing a threat to public health, as they can be carcinogenic, mutagenic, or teratogenic, among other toxic effects. Several hundreds of mycotoxins have been reported, but only a few of them are regulated, due to the lack of data regarding their toxicity and mechanisms of action. Thus, a more comprehensive evaluation of the toxicity of mycotoxins found in foodstuffs is required. In silico toxicology approaches, such as Quantitative Structure-Activity Relationship (QSAR) models, can be used to rapidly assess chemical hazards by predicting different toxicological endpoints. In this work, for the first time, a comprehensive database containing 4360 mycotoxins classified in 170 categories was constructed. Then, specific robust QSAR models for the prediction of mutagenicity, genotoxicity, and carcinogenicity were generated, showing good accuracy, precision, sensitivity, and specificity. It must be highlighted that the developed QSAR models are compliant with the OECD regulatory criteria, and they can be used for regulatory purposes. Finally, all data were integrated into a web server that allows the exploration of the mycotoxin database and toxicity prediction. In conclusion, the developed tool is a valuable resource for scientists, industry, and regulatory agencies to screen the mutagenicity, genotoxicity, and carcinogenicity of non-regulated mycotoxins.

Improving a Methane C-H Activation Complex by Metal and Ligand Alterations from Computational Results.

We present results for a series of complexes derived from a titanium complex capable of activating C-H bonds under mild conditions (PNP)Ti═CHtBu(CH2tBu), where PNP = N[2-PiPr2-4-methylphenyl]2-. In addition to the initial activation of methane, a tautomerization reaction to a terminal methylidene is also explored due to methylidene's potential use as a synthetic starting point. Analogous complexes with other low-cost 3d transition metals were studied, such as scandium, titanium, vanadium, and chromium as both isoelectronic and isocharged complexes. Our results predict that V(IV) and V(V) complexes are promising for methane C-H bond activation. The V(V) complex has a low rate-determining barrier for methane activation, specifically 16.6 kcal/mol, which is approximately 12 kcal/mol less than that for the Ti complex, as well as having a moderate tautomerization barrier of 29.8 kcal/mol, while the V(IV) complex has a methane activation barrier of 19.0 kcal/mol and a tautomerization barrier of 31.1 kcal/mol. Scandium and chromium complexes are much poorer for C-H bond activation; scandium has very high barriers, while chromium strongly overstabilizes the alkylidene intermediate, potentially stopping the further reaction. In addition to the original PNP ligand, some of the most promising ligands from a previous work were tested, although (as shown previously) modification of the ligand does not typically have large effects on the activity of the system. Our best ligand modification improves the performance of the V(V) complex via the substitution of the nitrogen in PNP by phosphorus, which reduces the tautomerization barrier by 5 to 24.4 kcal/mol.

Structural-Functional Properties of Asymmetric Fluoro-Alkoxy Substituted Benzothiadiazole Homopolymers with Flanked Chalcogen-Based Heterocycles.

The synthesis and characterization of asymmetric alkoxy- are reported, fluoro-benzothiadiazole (BT) acceptor core derivatized with a series of six different heterocycles (selenophene, thiophene, furan, 5-thiazole, 2-thiazole and 2-oxazole). The effect of the flanked-heterocycles containing different chalcogen atoms of the six homopolymers (HPX) is studied using optical, thermal, electrochemical, and computational analysis. Computational calculations indicate a strong relationship between the most stable conformation for each homopolymer and their bearing heterocycle, thus homopolymers HPSe', HPTp', HPFu', and HPTzC5, adopted the syn-syn and syn-anti conformations due to their noncovalent interactions with shorter distances, while HPTzC2' and HPOx' demonstrate preference for the anti-anti conformation. Optical property studies of the homopolymers reveal a strong red-shift in solution and film upon exchanging the chalcogen atom from Oxygen < Sulfur < Selenium in HPFu, HPTp, and HPSe, respectively. In addition, deeper highest occupied molecular orbital (HOMO) energy levels are observed when the donor-acceptor moieties (HPSe, HPTp, and HPFu) are substituted for the acceptor-acceptor systems such as HPTzC5, HPTzC2, and HPOx. Improved packing and morphology are exhibited for the donor-acceptor homopolymers. Thus, having a flanked heterocycle containing different chalcogen-atoms in polymeric systems is one way of tuning the physicochemical properties of conjugated materials for optoelectronic applications.

Transition-Metal-Free Homopolymerization of Pyrrolo[2,3-d:5,4-d']bisthiazoles via Nucleophilic Aromatic Substitution.

Novel methods to synthesize electron-deficient π-conjugated polymers utilizing transition-metal-free coupling reactions for the use of nonfunctionalized monomers are attractive due to their improved atom economy and environmental prospective. Herein we describe the use of iPrMgCl·LiCl complex to afford thiazole-based conjugated polymers in the absence of any transition metal catalyst, that enables access to well-defined polymers with good molecular weights. The mechanistically distinct polymerizations proceeded via nucleophilic aromatic substitution (SNAr) reaction supported by density functional theory (DFT) calculations. This work demonstrates the first example of fully conjugated thiazole-based aromatic homopolymers without the need of any transition metal catalyst.

Delayed Linker Addition (DLA) Synthesis for Hybrid SOD ZIFs with Unsubstituted Imidazolate Linkers for Propylene/Propane and n-Butane/i-Butane Separations.

We present a novel synthesis strategy termed delayed linker addition (DLA) to synthesize hybrid zeolitic-imidazolate frameworks containing unsubstituted imidazolate linkers (Im) with SOD topology (hereafter termed Im/ZIF-8). Im linker incorporation can create larger voids and apertures, which are important properties for gas storage and separation. To date, there have been only a handful of reports of Im linkers incorporated into ZIF-8 frameworks, typically requiring arduous and complicated post synthesis approaches. DLA, as reported here, is a simple one-step synthesis strategy allowing high incorporation of Im linker into the ZIF-8 framework while still retaining its SOD topology. We fabricated mixed-matrix membranes (MMMs) with 6FDA-DAM polymer and Im/ZIF-8 obtained via DLA as a filler. The Im/ZIF-8-containing MMMs showed excellent performance for both propylene/propane and n-butane/i-butane separation, displaying permeability and ideal selectivity well above the polymer upper bound. Moreover, highly detailed molecular simulations shed light to the aperture size and flexibility response of Im/ZIF-8 and its improved diffusivity as compared to ZIF-8.

The Chemistry of Short-Lived α-Fluorocarbocations.

The present study of the chemistry of short-lived α-fluorocarbocations reveals that even inactive methyl carbons can serve as nucleophiles, attacking a cationic center. This, in turn, facilitates the synthesis of a cyclopropane ring in certain triterpene backbones. We report the synthesis of compounds similar to 2, containing a bridgehead cyclopropane, and compounds of type 3 with an 11 membered bicyclic ring consisting of two bridgehead double bonds (anti-Bredt) within a triterpene skeleton. The synthesis involves three unconventional chemical processes: (a) a methyl group serving as a nucleophile; (b) the unexpected and unprecedented synthesis of a strained system in the absence of an external neighboring trigger; and (c) the formation of an 11-membered bicyclic diene ring within a triterpenoid skeleton. An α-fluorocarbocation mechanism is proposed and supported by density functional theory calculations.

Computational investigation of cobalt and copper bis (oxothiolene) complexes as an alternative for olefin purification.

Considering that olefins present a large volume feedstock, it is reasonable to expect that their purification is industrially critical. After the discovery of the nickel bis (dithiolene) complex Ni(S2C2(CF3)2)2 that exhibits electro-catalytic activity with olefins but tends to decompose by a competitive reaction route, related complexes have been explored experimentally and theoretically. In this paper, a computational examination is performed on differently charged cobalt and copper bis (oxothiolene) complexes [M (OSC2(CN)2)2] to test their potential applicability as the catalysts for olefin purification, using the simplest olefin, ethylene. Possible reaction pathways for ethylene addition on these complexes were explored, to determine whether some of these candidates can avoid the reaction route that leads to decomposition, which is distinctive from the nickel complex, and to form stable adducts that can subsequently release ethylene by reduction. Our calculations suggest that the neutral cobalt complex might be an alternative catalyst, because all its forms can bind ethylene to produce stable interligand adducts with moderate to low activation barriers, rather than to form intraligand adducts that lead to decomposition. The calculations also predict that these interligand adducts are capable of releasing ethylene upon reduction. In addition, it can produce the desired interligand adducts following two different reaction pathways, assigned as the direct and the indirect, with no need for anion species as co-catalysts, which is crucial for the nickel complex. Thus, the olefin purification process could be much simpler by using this catalyst.

Defining New Limits in Gas Separations Using Modified ZIF Systems.

Zeolitic-imidazolate frameworks (ZIFs) are candidate materials for the next generation of membranes for cheaper, "greener" separations. More than a decade after ZIF introduction, the high propylene/propane selectivity of ZIF-8 and ZIF-67 is the only example of ZIF membranes with remarkable selectivity efficiency despite their numerous advantages over other families of materials. Herein, we demonstrate the effectiveness of molecular-scale modification in the design of new ZIF materials useful for the separation of important and highly challenging mixtures such as He/CH4, H2/CH4, O2/N2, CO2/CH4, and CO2/N2. Via computational methods, metal and linker substitutions are employed to produce new ZIF-8 variants with a finely discretized range of aperture sizes, as these govern the kinetic-based selectivity of the material. The permeability and selectivity through the ZIF-8 variants of the gases under study are estimated, and their performance is compared with an extensive number of polymeric, metal-organic framework, covalent-organic framework, and mixed-matrix membranes. The comparison shows that some of the ZIF-8 analogues can be used as membranes of unprecedented high separation performance. The scope of this work is to highlight the effectiveness of the molecular level design as means of membrane development to address the global need for cheaper separation methods and CO2 emission reduction.

Green Light-Responsive CO-Releasing Polymeric Materials Derived from Ring-Opening Metathesis Polymerization.

Carbon monoxide (CO) is an important biological gasotransmitter in living cells. Precise spatial and temporal control over release of CO is a major requirement for clinical application. To date, the most reported carbon monoxide releasing materials use expensive fabrication methods and require harmful and poorly designed tissue-penetrating UV irradiation to initiate the CO release precisely at infected sites. Herein, we report the first example of utilizing a green light-responsive CO-releasing polymer P synthesized via ring-opening metathesis polymerization. Both monomer M and polymer P were very stable under dark conditions and CO release was effectively triggered using minimal power and low energy wavelength irradiation (550 nm, ≤28 mW). Time-dependent density functional theory (TD-DFT) calculations were carried out to simulate the electronic transition and insight into the nature of the excitations for both L and M. TD-DFT calculations indicate that the absorption peak of M is mainly due to the excitation of the seventh singlet excited state, S7. Furthermore, stretchable materials using polytetrafluoroethylene (PTFE) strips based on P were fabricated to afford P-PTFE, which can be used as a simple, inexpensive, and portable CO storage bandage. Insignificant cytotoxicity as well as cell permeability was found for M and P against human embryonic kidney cells.

Tunable model promoters in DFT simulations of catalysts.

Promoter atoms can tune a catalyst's activity and selectivity by transferring charge to and from the active site. Rational design of promoted catalysts, using density functional theory calculations, is today limited by the need to simulate many catalyst and promoter configurations. We present a simple approximation that rapidly captures some trends in promoter effects, at a cost of complexity comparable with simulating unpromoted catalysts. Negative (positive) noninteger point charges introduced into the catalyst simulate how electropositive (electronegative) promoters might affect each predicted intermediate. Calculations return Sabatier plots, relating promoters' predicted efficacy to readily measured properties such as catalyst work functions. We illustrate our approach for two reactions associated with the Fischer-Tropsch process, hydrogen-deuterium scrambling, and carbon monoxide dissociation over ruthenium. Consistent with experiment, electropositive promoters are predicted to accelerate hydrogen scrambling and unassisted CO dissociation. Simulations also provide a new prediction: electronegative promoters accelerate hydrogen-assisted CO dissociation over hydrogen-precovered surfaces by stabilizing the initial CO adsorption. © 2019 Wiley Periodicals, Inc.

On the Efficient Separation of Gas Mixtures with the Mixed-Linker Zeolitic-Imidazolate Framework-7-8.

A recently reported modification of the zeolitic-imidazolate framework-8 (ZIF-8) with partial replacement of the 2-methylimidazolate (mIm) linker with benzimidazolate (bIm), namely ZIF-7-8, is investigated with molecular simulations using a first-time reported force field. The size of the ZIF-7-8 aperture, which governs the gas-separation efficiency of this material and which has not been estimated before for this modification, is smaller than that of the original ZIF-8. The diffusivities of CO2, N2, and CH4 estimated through transition state theory calculations result in remarkably high diffusion selectivities for CO2/CH4 and CO2/N2 mixtures. This performance enhancement is investigated in terms of structural flexibility in the form of the aperture motion through extensive estimation of the effective diameter, the total effective area, and the motion of the aperture linkers, of both ZIF-8 and ZIF-7-8. Both apertures exhibit an oscillation through the rotation of the linkers, which are adjusted according to the size of the penetrant molecules the moment they pass through it. Finally, a subsequent analysis reveals that there is strong dependency of the separation performance on the bIm-to-mIm ratio: below 33% bIm incorporation, the appearance of ZIF-8-alike wide apertures decreases dramatically the size-based selectivity of the mixtures in ZIF-7-8.

When Hartree-Fock exchange admixture lowers DFT-predicted barrier heights: Natural bond orbital analyses and implications for catalysis.

The conventional wisdom in density functional theory (DFT) is that standard approximations systematically underestimate chemical reaction barrier heights and that exact (Hartree-Fock-like, HF) exchange admixture improves this. This conventional wisdom is inconsistent with the good performance of functionals without HF exchange for many reactions on metal catalyst surfaces. We have studied several "anomalous" gas-phase reactions where this conventional wisdom is upended, and a HF exchange admixture decreases or does not affect the predicted barrier heights [Mahler et al., J. Chem. Phys. 146, 234103 (2017)]. Here we show how natural bond orbital analyses can help identify and explain some factors that produce anomalous barriers. Applications to pnictogen inversion, standard benchmark reaction barrier datasets, and a model Grubbs catalyst illustrate the utility of this approach. This approach is expected to aid DFT users in choosing appropriate functionals, and aid DFT developers in devising DFT approximations generally applicable to catalysis.

Tailoring the gas separation efficiency of metal organic framework ZIF-8 through metal substitution: a computational study.

The influence of a zeolitic imidazolate framework (ZIF)'s metal identity on its gas separation performance is studied extensively through molecular simulations for a variety of gases. ZIF-8 is used as the original framework for alterations of different metal substitutes of the Zn2+ metal. ZIF-8 consists of cages connected by narrow apertures that exhibit flexibility through "swelling", allowing for relatively large penetrants to diffuse. Replacing the central metal atom in the basic tetrahedral unit of ZIF-8 with Cd, Co or Be results in three different structures with increasing bonding stiffness with their neighboring atoms. The metal modification approach offers a way to control the flexibility and the size of the aperture, which constitutes the main energy barrier of the penetrant's hop-like diffusion between the framework's cages. Newly developed force fields are reported and utilized here; the new frameworks are compared to the original one, in terms of the diffusivity of various gas molecules as a function of their size (from He to n-butane). The correlation of the gas diffusivity with the aperture flexibility-molecular size relation is investigated. The results reveal that the aperture flexibility-molecular size relation governs the diffusivity, which shapes a common trend along all modifications. Furthermore, a new generalized method is employed for the screening of the various modifications for specific gas separations. This method is useful to detect optimum separation performance for the various modifications: CdIF-1 (Cd) for n-butane/iso-butane mixture; ZIF-67 (Co) for propylene/n-propane and ethylene/ethane mixtures; BeIF-1 (Be) for CO2/C2H6, CO2/CH4 and CO2/N2 mixtures.

What Happens Without Nickel? Cyclization Reactions of Ethylene with Ethanedithial and Related Molecules.

We present a computational study of the mechanism of the formation of 6-member heterocycles through the binding of ethylene to oxaldehyde, ethanedithial, and 2-thioxoacetaldehyde. This process is related to the olefin separation technology by metal dithiolenes and dioxolenes, being the formation of those heterocycles the main decomposition route. We also present a benchmark of 26 density functionals (spanning hybrid, double-hybrid, range-separated, semilocal, and local functionals) related to CCSD(T)/CBS reference values. Both the cyclization reaction and the isomerization of the cyclic product are included in the benchmark. The best functional among those tested for these reactions is ωB97XD, and the effect of the basis set is also investigated for it. © 2017 Wiley Periodicals, Inc.

Ancillary Ligand Effects upon the Photochemistry of Mn(bpy)(CO)3X Complexes (X = Br-, PhCC-).

The photochemistry of two Mn(bpy)(CO)3X complexes (X = PhCC-, Br-) has been studied in the coordinating solvents THF (terahydrofuran) and MeCN (acetonitrile) employing time-resolved infrared spectroscopy. The two complexes are found to exhibit strikingly different photoreactivities and solvent dependencies. In MeCN, photolysis of 1-(CO)(Br) [1 = Mn(bpy)(CO)2] affords the ionic complex [1-(MeCN)2]Br as a final product. In contrast, photolysis of 1-(CO)(CCPh) in MeCN results in facial to meridional isomerization of the parent complex. When THF is used as solvent, photolysis results in facial to meridional isomerization in both complexes, though the isomerization rate is larger for X = Br-. Pronounced differences are also observed in the photosubstitution chemistry of the two complexes where both the rate of MeCN exchange from 1-(MeCN)(X) by THFA (tetrahydrofurfurylamine) and the nature of the intermediates generated in the reaction are dependent upon X. DFT calculations are used to support analysis of some of the experiments.

Methane Activations by Titanium Neopentylidene Complexes: Electronic Resilience and Steric Control.

The titanium neopentylidene complex (PNP)Ti═CHtBu(CH2tBu) (PNP = N[2-PiPr2-4-methylphenyl]2-) is capable of activating both sp2 and sp3 C-H bonds under mild conditions. In addition to methane C-H activation, competition between the initial hydrogen abstraction reaction to form the methane activation product and the tautomerization reaction of this product to form a terminal methylidene was also explored. Several modifications of the PNP and CHtBu ligands were explored to determine the effect of these changes on C-H bond activation. In general, on the one hand, the modifications involving electronic effects have small and inconsistent influence on the stability of the intermediates and products and on the reaction barriers. On the other hand, the use of bulky groups in the ligands favors the methane activation process. By replacing the iPr groups in the PNP ligand with tBu groups, both methane activation and tautomerization reactions become more energetically favorable than in the unmodified complex. On the one hand, the largest acceleration of the methane C-H activation occurs when tBu groups in the phosphine are combined with an extra CH2 linker between the aromatic ring and the phosphine. On the other hand, replacing the nitrogen in the PNP ligand by phosphorus results in lower barriers for the tautomerization reaction and the stabilization of the product of the tautomerization although it remains slightly less stable than product of methane C-H activation. While several ligand modifications related to the electronic effects were examined, it is interesting that most of them did not make a significant change on the barriers for either reaction, indicating a significant resilience of this titanium complex, which could be used to enhance the practical aspects of the complex without a significant loss of its activity.

Why are GGAs so accurate for reaction kinetics on surfaces? Systematic comparison of hybrid vs. nonhybrid DFT for representative reactions.

"Jacob's Ladder" of approximate exchange-correlation (XC) functionals in Kohn-Sham density functional theory are widely accepted to have systematic errors in reaction barriers. The first-rung local spin-density approximation (LDA) typically predicts barriers below generalized gradient approximations, which in turn predict barriers below experiment and below fourth-rung hybrid functionals incorporating a fraction of exact exchange. We show that several reactions from previous literature reports, as well as new simulations of carbon-carbon coupling in the Fischer-Tropsch process, do not follow this conventional picture. We introduce the AB9 test set of nine abnormal reaction barriers, in which density gradient corrections and exact exchange admixture tend to lower rather than to raise predicted barriers. Comparisons of normal and abnormal reactions rationalize this phenomenon in terms of how density gradient and exact-exchange corrections stabilize transition states relative to reaction intermediates. Multireference diagnostics confirm that this behavior is not merely a consequence of multireference character. Benchmarks of the AB9 set, using the best available ab initio reference values, highlight the role of symmetry breaking and show surprisingly good performance from both the LDA and "Rung 3.5" functionals. This motivates benchmarks of the AB9 set in future XC functional development.

Nickel Bis(diselenolene) as a Catalyst for Olefin Purification.

Nickel bis(dithiolene) reversibly binds olefins via a known interligand binding mechanism, but the complex has limited practical use, due to a competitive intraligand addition which results in decomposition. The present work examines an alternative nickel-based complex that eliminates the decomposition route. Specifically, we have examined the olefin binding processes of nickel bis(diselenolene) complexes using modern density functional theory. Both the inter- and intraligand adducts of the nickel bis(diselenolenes) are thermodynamically more stable than their dithiolene analogues. We have predicted that nickel bis(diselenolene) complexes do not decompose after the intraligand addition, and that the overall activation energies for the kinetically accessible products are quite small. In short, our computational work predicts that nickel bis(diselenolene) complexes are better electrocatalysts for olefin purification than the previous candidates, superior to the previously studied nickel bis(dithiolene) complexes.

Computational Study of the Palladium-Catalyzed Carbonylative Synthesis of Aromatic Acid Chlorides: The Synergistic Effect of PtBu3 and CO on Reductive Elimination.

We describe herein computational studies on the unusual ability of Pd(PtBu3 )2 to catalyze formation of highly reactive acid chlorides from aryl halides and carbon monoxide. These show a synergistic role of carbon monoxide in concert with the large cone angle PtBu3 that dramatically lowers the barrier to reductive elimination. The tertiary structure of the phosphine is found to be critical in allowing CO association and the generation of a high energy, four coordinate (CO)(PR3 )Pd(COAr)Cl intermediate. The stability of this complex, and the barrier to elimination, is highly dependent upon phosphine structure, with the tertiary steric bulk of PtBu3 favoring product formation over other ligands. These data suggest that even difficult reductive eliminations can be rapid with CO association and ligand manipulation. This study also represents the first detailed exploration of all the steps involved in palladium-catalyzed carbonylation reactions with simple phosphine ligands, including the key rate-determining steps and palladium(0) catalyst resting state in carbonylations.