Crystallographic and first-principles density functional theory study on the structure,noncovalent interactions,and chemical reactivity of 1,5-benzodiazepin-2-ones derivatives

The present work arose out of a desire to fundamentally understand the molecular geometry, weak interactions, electron density delocalization, and chemical reactivity features of 1,5-benzodiazepines-containing family. Herein, a complete X-ray crystallographic study, supported by trustworthy sets of computational approaches, has been reported for two organic crystals. Quantifying intramolecular and intermolecular interactions by Hirshfeld-Becke surfaces analysis conjointly with noncovalent interaction-reduced density gradient topological study revealed that supramolecular assemblies are stabilized by N-H ^… O (inter) and O-H ^… N (intra) hydrogen bonds, Cg ^… Cg (π ^… π) and C-H(O) ^… π intercontacts, as well as Van der Waals interactions and steric effects. The long-range-corrected functional wB97XD, which uses Grimme's D2 dispersion model, seems to be just right for our systems. The quantum theory of atoms in molecules analysis confirms that both significant O1-H1…N1 and N2-H2A…O2 H-bonds are weak and electrostatic in nature. Furthermore, global reactivity indices computed via the conceptual density functional theory framework allows these molecules to be classified as moderate electrophiles and marginal nucleophiles. The active sites favorable for nucleophilic/electrophilic attacks were also predicted based on local Parr functions. Finally, a comparative evaluation on the aromaticity character and π-π stacking ability has been done for different (pseudo) rings.     

Characterization, synthesis and self-aggregation of (-)-alternarlactam: a new fungal cytotoxin with cyclopentenone and isoquinolinone scaffolds

(-)-Alternarlactam [(-)-1], a new promising cytotoxin against two human cancer cell lines, was isolated from an endophyte culture and synthesized (along with (+)-1) from readily available starting materials. The absolute configuration, chirality-activity relevance and self-aggregation of (-)-1 were assigned by a combination of synthetic, spectroscopic and computational approaches. The full characterization of the new fungal cytotoxin may provide valuable information in the discovery of new antitumor agents.     

Exploration of pyrazole based aldo-x bifunctional building blocks for the synthesis of pyrazole annulated molecular architectures

Over the last decade, the synthetic chemist's community has attracted attention towards aldo-x precursors due to their versatility to afforded variety of heterocyclic frameworks. The aldo-x bifunctional building blocks (AXB3s) contain two or more reactive sites with different reactivity, which may offer new opportunities for the introduction of diversity in core skeleton, which may be of great biological and medicinal relevance. In this context, pyrazole based AXB3s such as 4-iodopyrazole-3/5-carbaldehyde may be explored for achieving pyrazole fused/linked heterocyclic skeletons by employing different organic transformations. Specifically, iodo substituted pyrazoles provide a new platform for the installation of desired pattern via transition-metal catalyzed approaches. Herein, we have assembled the strategies towards the development of pyrazole substituted and fused molecular architectures by using 4-iodopyrazole-3/5-carbaldehydes and pyrazole C-3)/C5- carbaldehydes. The photophysical data of some fluorescent pyrazole derivatives have also been discussed.     

‐Aminonitriles: From Sustainable Preparation to Applications in Natural Product Synthesis

Due to their numerous reactivity modes, α‐aminonitriles represent versatile and valuable building blocks in organic total synthesis. Since their discovery by Adolph Strecker in 1850, this compound class has seen a wide dissemination in synthetic applications from laboratory to million‐ton industrial scale and was extensively used in the syntheses of various classes of natural products. As these compounds provide a multitude of reactivity options, we feel that a broad overview of their multiple reaction modes may reveal less familiar opportunities for successful total synthesis planning. This personal account article will thus focus on α‐aminonitriles used as key intermediates in selected natural product synthesis sequences which have been reported in the two decades since Enders’ and Shilvock's seminal review. Natural α‐aminonitriles will also briefly be treated.     

Electrochemical studies of seven regioisomers of Tris

Seven of the possible 46 constitutional isomers of tris[di(ethoxycarbonyl)methano[60]fullerene have been isolated and their electrochemical properties studied in CH(2)Cl(2). A two-electron controlled potential electrolysis of each of these isomers results in competing retro-Bingel and isomerization reactions with preferential loss of one or two of the addends. PM3 and AM1 computational studies indicate that while the reactivity of neutral precursors is kinetically controlled, charging of the neutral species with two electrons results in an umpolung of reactivity and introduction of thermodynamic control. Lowering the electrolysis temperature increases the proportion of isomerization, and a new tris-isomer never obtained before via synthetic methods has been isolated.     

Benchmarking computational chemistry approaches on iminodiacetic acid

In the present study, theoretical harmonic vibrational frequencies (IR and Raman), carbon and proton NMR chemical shifts, geometric parameters, atomic charges (only for heteroatoms), reactivity indices (eLUMO, eHOMO, electronegativity, and hardness), and thermodynamical data (inner energy, enthalpy, Gibbs free energy, and entropy) of iminodiacetic acid (IDA) molecule have been investigated. We utilized ORCA software for B3LYP and HF (combined with Pople and Karlsruhe basis sets) calculations and MOPAC2016 software for semi-empirical calculations (AM1, PM3, and PM6). Theoretical vibrational frequencies and carbon and proton NMR chemical shifts have been compared with the corresponding experimental data. Although there was a strong correlation between the experimental and computational vibrational frequencies at low frequencies (<2200 cm^?1), the computational predictions of vibrational frequencies were unsuccessful at high frequencies (>2200 cm^?1). Distinctly, the studied computational approaches appeared to perform better in the prediction of carbon and proton NMR chemical shifts. Theoretical vibrational frequencies were also compared to each other to understand the impact of method choice (HF vs B3LYP D3 vs semi-empirical methods), dispersion correction (B3LYP D3 vs B3LYP), water solvation (SMD supplemented vs non-supplemented calculations), the family of basis set (Pople vs Karlsruhe basis sets), numbers of zeta (double vs triple zeta), polarization function (polarized vs nonpolarized basis sets), and diffusion function (diffusion supplemented vs non-supplemented basis sets). Moreover, geometric parameters, heteroatom charges, reactivity indices, and thermodynamical data produced by distinct computational approaches, as well, were compared to each other. Based on these comparisons, we detected critical factors (such as water solvation) acting on the computation of geometries, energies, and charges.     

Investigating the role of the strong field ligands in [FeFe] hydrogenase: spectroscopic and functional characterization of a semi-synthetic mono-cyanide active site

Artificial maturation of hydrogenases provides a path towards generating new semi-synthetic enzymes with novel catalytic properties. Here enzymes featuring a synthetic asymmetric mono-cyanide cofactor have been prepared using two different hydrogenase scaffolds. Their structure and reactivity was investigated in order to elucidate the design rationale behind the native di-cyanide cofactor, and by extension the second coordination sphere of the active-site pocket. Surprisingly, the choice of host enzyme was found to have a dramatic impact on reactivity. Moreover, the study shows that synthetic manipulations of the active-site can significantly increase inhibitor tolerance, as compared to native [FeFe] hydrogenase, while retaining the enzyme''s native capacity for reversible catalysis.

Cyanide to carbonyl exchange in semi-synthetic [FeFe] hydrogenases: exploring the role of the strong field ligands of the active site and their interaction with the protein matrix via spectroscopy and electrochemistry.     

NHC ligands versus cyclopentadienyls and phosphines as spectator ligands in organometallic catalysis

N-heterocyclic carbenes are compared with cyclopentadienyls and phosphines in terms of bonding and reactivity. Synthetic difficulties that currently prevent the general incorporation of NHCs into chelate, pincer and tripod ligand architectures are related to the inability of the NHC to reversibly decoordinate to correct binding ‘errors’ in the initial kinetic products of NHC complex formation. The strengths and weaknesses of current synthetic approaches, such as Lin’s Ag₂O transmetallation route, are discussed. Linker dependent reactivity patterns are related to azole ring orientation effects and some aspects of cyclometalation are considered.     

Computational and Synthetic Investigation of Cationic Rearrangement in the Putative Biosynthesis of Justicane Triterpenoids

A biomimetic cationic structural rearrangement of the oleanolic acid framework is reported for the gram‐scale synthesis and structural reassignment of justicioside E aglycone. The mechanism of the putative biosynthetic rearrangement is investigated with kinetic, computational, and synthetic approaches. The precursor to rearrangement was accessed through two strategic advancements: (1) synthesis of a 1,3‐diketone via oxidation of a β‐silyl enone, and (2) diastereoselective 1,3‐diketone reduction to form a syn‐1,3‐diol using SmI₂ with PhSH as a key additive.     

Azanone (HNO): generation,stabilization and detection

HNO (nitroxyl, azanone), joined the ‘biologically relevant reactive nitrogen species’ family in the 2000s. Azanone is impossible to store due to its high reactivity and inherent low stability. Consequently, its chemistry and effects are studied using donor compounds, which release this molecule in solution and in the gas phase upon stimulation. Researchers have also tried to stabilize this elusive species and its conjugate base by coordination to metal centers using several ligands, like metalloporphyrins and pincer ligands. Given HNO''s high reactivity and short lifetime, several different strategies have been proposed for its detection in chemical and biological systems, such as colorimetric methods, EPR, HPLC, mass spectrometry, fluorescent probes, and electrochemical analysis. These approaches are described and critically compared. Finally, in the last ten years, several advances regarding the possibility of endogenous HNO generation were made; some of them are also revised in the present work.

HNO (nitroxyl, azanone), joined the ‘biologically relevant reactive nitrogen species’ family in the 2000s.     

Photocatalysis as an Effective Tool for Upcycling Polymers into Value-Added Molecules

Shaping a sustainable future is closely tied to the development of advanced plastic recycling technologies. As global recycling rates remain low, the lion's share of post-consumer plastics is either incinerated or disposed of in landfills. This unbalanced plastic waste management not only poses severe environmental risks, but also entails an irrevocable loss of chemical resources that are embedded in synthetic polymers. To give plastic waste a new life, a series of photocatalytic methods has recently been reported that convert polymers directly into value-added organic molecules. These approaches operate at ambient temperature, show high reactivity/selectivity, and provide alternative reaction pathways as compared to thermal depolymerizations. This Minireview highlights the scientific breakthroughs in upcycling polymers through state-of-the-art photocatalysis under environmentally benign conditions.     

Computational investigation of the suitability of heterocyclic aromatic compounds with two heteroatoms in the 1 and 3 ring positions as dienes for the diels alder reaction

Semiempirical and density functional theory computational studies were carried out with the target determining the reactivity of five membered heterocycles with heteroatoms in the 1 and 3 positions as dienes for Diels-Alder reactions. The relative reactivity was evaluated in their reaction with acetylene, ethylene, and cyclopropene as dienophiles for cycloaddition. Qualitative criteria such as uniformity of heterocycle bond orders, change of bond orders and frontier molecular orbital energies in transformation of reactants into transition state structures were used to determine the relative reactivity in comparison with furan. These results are compared with the computed activation barriers as well as with experimental findings, where available. If cycloaddition is feasible with these heterocycles, a new synthetic transformation of simple organic compounds to valuable prostaglandin derivatives can be accomplished.     

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Until recently, the field of diversity and library design has more or less ignored natural products as a compound source. This is probably due to at least two reasons. First, combinatorial and reaction-based approaches have been major focal points in the early days of computational library design. In addition, a widespread view is that natural products are often highly complex and not amenable to medicinal chemistry efforts. This contribution introduces recent computational approaches to systematically analyze natural molecules and bridge the gap between natural products and synthetic chemistry programs. Large scale comparisons of natural and synthetic molecules are discussed as well as studies designed to identify `synthetic mimics' of natural products with specific activity. In addition, a concept for the design of natural/synthetic hybrid libraries is introduced. Although research in this area is still in its early stages, an important lesson to be learned from computational analyses is that there is no need to a priori `shy away' from natural products as a source for molecular design.     

Data enhanced Hammett-equation: reaction barriers in chemical space

It is intriguing how the Hammett equation enables control of chemical reactivity throughout chemical space by separating the effect of substituents from chemical process variables, such as reaction mechanism, solvent, or temperature. We generalize Hammett''s original approach to predict potential energies of activation in non aromatic molecular scaffolds with multiple substituents. We use global regression to optimize Hammett parameters ρ and σ in two experimental datasets (rate constants for benzylbromides reacting with thiols and ammonium salt decomposition), as well as in a synthetic dataset consisting of computational activation energies of ∼2400 S_N2 reactions, with various nucleophiles and leaving groups (–H, –F, –Cl, –Br) and functional groups (–H, –NO₂, –CN, –NH₃, –CH₃). Individual substituents contribute additively to molecular σ with a unique regression term, which quantifies the inductive effect. The position dependence of substituents can be modeled by a distance decaying factor for S_N2. Use of the Hammett equation as a base-line model for Δ-machine learning models of the activation energy in chemical space results in substantially improved learning curves reaching low prediction errors for small training sets.

We generalize Hammett''s original approach to predict potential energies of activation in non aromatic molecular scaffolds with multiple substituents.     

Hexakis‐Adducts of [60]Fullerene with Different Addition Patterns: Templated Synthesis,Physical Properties,and Chemical Reactivity

Representatives of two classes of hexakis‐adducts of C₆₀ were prepared by templated synthesis strategies. Compound 8 with a dipyridylmethano addend in a pseudo‐octahedral addition pattern was obtained by DMA‐templated addition (DMA=9,10‐dimethylanthracene; Scheme 1) and served as the starting material for the first supramolecular fullerene dimer 2 . Hexakis‐adduct 12 also possesses a pseudo‐octahedral addition pattern and was obtained by a sequence of tether‐directed remote functionalization, tether removal, and regioselective bis‐functionalization (Scheme 2). With its two diethynylmethano addends in trans‐1 position, it is a precursor for fascinating new oligomers and polymers that feature C₆₀ moieties as part of the polymeric backbone (Fig. 1). With the residual fullerene π‐electron chromophore reduced to a `cubic cyclophane'‐type sub‐structure (Fig. 4), and for steric reasons, 8 and 12 no longer display electrophilic reactivity. As a representative of the second class of hexakis‐adducts, (±)‐ 1 , which features six addends in a distinct helical array along an equatorial belt, was prepared by a route that involved two sequential tether‐directed remote functionalization steps (Schemes 3 and 5). In compound (±)‐ 1 , π‐electron conjugation between the two unsubstituted poles of the carbon sphere is maintained via two (E)‐stilbene‐like bridges (Fig. 4). As a result, (±)‐ 1 features very different chemical reactivity and physical properties when compared to hexakis‐adducts with a pseudo‐octahedral addition pattern. Its reduction under cyclic voltammetric conditions is greatly facilitated (by 570 mV), and it readily undergoes additional, electronically favored Bingel additions at the two sterically well‐accessible central polar 6‐6 bonds under formation of heptakis‐ and octakis‐adducts, (±)‐ 30 and (±)‐ 31 , respectively (Scheme 6). The different extent of the residual π‐electron delocalization in the fullerene sphere is also reflected in the optical properties of the two types of hexakis‐adducts. Whereas 8 and 12 are bright‐yellow (end‐absorption around 450 nm), compound (±)‐ 1 is shiny‐red, with an end‐absorption around 600 nm. This study once more demonstrates the power of templated functionalization strategies in fullerene chemistry, providing addition patterns that are not accessible by stepwise synthetic approaches.     

Confidence limits,error bars and method comparison in molecular modeling. Part 2: comparing methods

The calculation of error bars for quantities of interest in computational chemistry comes in two forms: (1) Determining the confidence of a prediction, for instance of the property of a molecule; (2) Assessing uncertainty in measuring the difference between properties, for instance between performance metrics of two or more computational approaches. While a former paper in this series concentrated on the first of these, this second paper focuses on comparison, i.e. how do we calculate differences in methods in an accurate and statistically valid manner. Described within are classical statistical approaches for comparing widely used metrics such as enrichment, area under the curve and Pearson’s product-moment coefficient, as well as generic measures. These are considered of over single and multiple sets of data and for two or more methods that evince either independent or correlated behavior. General issues concerning significance testing and confidence limits from a Bayesian perspective are discussed, along with size-of-effect aspects of evaluation.     

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

Metabolism of xenobiotics remains a central challenge for the discovery and development of drugs, cosmetics, nutritional supplements, and agrochemicals. Metabolic transformations are frequently related to the incidence of toxic effects that may result from the emergence of reactive species, the systemic accumulation of metabolites, or by induction of metabolic pathways. Experimental investigation of the metabolism of small organic molecules is particularly resource demanding; hence, computational methods are of considerable interest to complement experimental approaches. This review provides a broad overview of structure- and ligand-based computational methods for the prediction of xenobiotic metabolism. Current computational approaches to address xenobiotic metabolism are discussed from three major perspectives: (i) prediction of sites of metabolism (SOMs), (ii) elucidation of potential metabolites and their chemical structures, and (iii) prediction of direct and indirect effects of xenobiotics on metabolizing enzymes, where the focus is on the cytochrome P450 (CYP) superfamily of enzymes, the cardinal xenobiotics metabolizing enzymes. For each of these domains, a variety of approaches and their applications are systematically reviewed, including expert systems, data mining approaches, quantitative structure-activity relationships (QSARs), and machine learning-based methods, pharmacophore-based algorithms, shape-focused techniques, molecular interaction fields (MIFs), reactivity-focused techniques, protein-ligand docking, molecular dynamics (MD) simulations, and combinations of methods. Predictive metabolism is a developing area, and there is still enormous potential for improvement. However, it is clear that the combination of rapidly increasing amounts of available ligand- and structure-related experimental data (in particular, quantitative data) with novel and diverse simulation and modeling approaches is accelerating the development of effective tools for prediction of in vivo metabolism, which is reflected by the diverse and comprehensive data sources and methods for metabolism prediction reviewed here. This review attempts to survey the range and scope of computational methods applied to metabolism prediction and also to compare and contrast their applicability and performance.     

Machine learning modelling of chemical reaction characteristics: yesterday,today, tomorrow

The synthesis of the desired chemical compound is the main task of synthetic organic chemistry. The predictions of reaction conditions and some important quantitative characteristics of chemical reactions as yield and reaction rate can substantially help in the development of optimal synthetic routes and assessment of synthesis cost. Theoretical assessment of these parameters can be performed with the help of modern machine-learning approaches, which use available experimental data to develop predictive models called quantitative or qualitative structure–reactivity relationship (QSRR) modelling. In the article, we review the state-of-the-art in the QSRR area and give our opinion on emerging trends in this field.