The Many Roles of Quantum Chemical Predictions in Synthetic Organic Chemistry

This account discusses representative case studies for various applications of quantum chemical calculations in synthetic organic chemistry. These include confirmation of target structures, methodology development, and catalyst design. These examples demonstrate how predictions from quantum chemical calculations can be utilized to streamline synthetic efforts.     

The road to non-enzymatic molecular networks

This Minireview gives an overview of recent progress in the design and analysis of chemical systems that utilize template-directed autocatalytic and cross-catalytic processes as a means of wiring dynamically interacting molecules. Synthetic networks comprising two to nine replicating species are discussed. It is shown that for larger systems, more catalytic pathways must be manipulated to control the entire network topology and specific functionality of the individual species or subnetworks. Cellular biochemistry is an example of a natural functional molecular network; synthetic self-organized networks can provide additional models of complex systems.     

trans‐Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions

The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3‐proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two‐dimensional dynamic systems with a high degree of complexity evolution. The transamination–transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate‐limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity‐generating element.     

Nucleotide-Selective Templated Self-Assembly of Nanoreactors under Dissipative Conditions

Nature adopts complex chemical networks to finely tune biochemical processes. Indeed, small biomolecules play a key role in regulating the flux of metabolic pathways. Chemistry, which was traditionally focused on reactions in simple mixtures, is dedicating increasing attention to the network reactivity of highly complex synthetic systems, able to display new kinetic phenomena. Herein, we show that the addition of monophosphate nucleosides to a mixture of amphiphiles and reagents leads to the selective templated formation of self-assembled structures, which can accelerate a reaction between two hydrophobic reactants. The correct matching between nucleotide and the amphiphile head group is fundamental for the selective formation of the assemblies and for the consequent up-regulation of the chemical reaction. Transient stability of the nanoreactors is obtained under dissipative conditions, driven by enzymatic dephosphorylation of the templating nucleotides. These results show that small molecules can play a key role in modulating network reactivity, by selectively templating self-assembled structures that are able to up-regulate chemical reaction pathways.     

Catalytic,Mild, and Selective Oxyfunctionalization of Linear Alkanes: Current Challenges

Selective catalysts for sustainable oxidation of alkanes are highly demanded because of the abundance of these molecules in the environment, the possibility to transform them into higher‐value compounds, such as chemicals or synthetic fuels, and the fact that, kinetically speaking, this is a difficult reaction. Numerous chemical and biological catalysts have been developed in the lasts decades for this purpose, rendering the overview over this field of chemistry difficult. After giving a definition of the ideal catalyst for alkane oxyfunctionalization, this review aims to present the catalysts available today that are closest to ideal.     

Fuel‐Selective Transient Activation of Nanosystems for Signal Generation

The transient activation of function using chemical fuels is common in nature, but much less in synthetic systems. Progress towards the development of systems with a complexity similar to that of natural ones requires chemical fuel selectivity. Here, we show that a self‐assembled nanosystem, composed of monolayer‐protected gold nanoparticles and a fluorogenic peptide, is activated for transient signal generation only in case the chemical fuel matches the recognition site present at the nanoparticle surface. A modification of the recognition site in the nanosystem completely changes the chemical fuel selectivity. When two nanosystems are simultaneously present, the selectivity expressed by the system depends on the concentration of nucleotide added.     

Application of a Supramolecular‐Ligand Library for the Automated Search for Catalysts for the Asymmetric Hydrogenation of Industrially Relevant Substrates

A procedure is described for the automated screening and lead optimization of a supramolecular‐ligand library for the rhodium‐catalyzed asymmetric hydrogenation of five challenging substrates relevant to industry. Each catalyst is (self‐) assembled from two urea‐functionalized ligands and a transition‐metal center through hydrogen‐bonding interactions. The modular ligand structure consists of three distinctive fragments: the urea binding motif, the spacer, and the ligand backbone, which carries the phosphorus donor atom. The building blocks for the ligand synthesis are widely available on a commercial basis, thus enabling access to a large number of ligands of high structural diversity. The simple synthetic steps enabled the scale‐up of the ligand synthesis to multigram quantities. For the catalyst screening, a library of twelve new chiral ligands was prepared that comprised substantial variation in electronic and steric properties. The automated procedures employed ensured the fast catalyst assembly, screening, and direct acquisition of samples for analysis. It appeared that the most selective catalyst was different for every substrate investigated and that small variations in the building blocks had a major impact on the catalyst performance. For two substrates, a catalyst was found that provided the product with outstanding enantioselectivity. The subsequent automated optimization of these two leads showed that an increase of catalyst loading, dihydrogen pressure, and temperature had a positive effect on the catalyst activity without affecting the catalyst selectivity.     

Recognition of Anions by Synthetic Receptors in Aqueous Solution

Natural anion binding systems achieve high substrate affinity and selectivity most often by arranging converging binding sites inside a cavity or cleft that is well shielded from surrounding solvent molecules by the folded peptide chain. Types of interactions employed for anion recognition are electrostatic interactions, hydrogen-bonding, and coordination to a Lewis-acidic metal center. In this review, successful strategies aimed at the development of synthetic receptors active in water or aqueous solvent mixtures are described. It is shown that considerable progress has been made during recent years in the development of potent anion receptors and that for every type of interaction used in nature for anion binding, corresponding synthetic models exist today. Representative examples of these systems are presented with a special emphasis on synthetic receptors whose characterization involved a detailed thermodynamic analysis of complex formation to demonstrate the important interplay between enthalpy and entropy for anion recognition in water.This revised version was published online in July 2005 with a corrected issue number.     

Micro/Nanomotors for Water Purification

Self-propelled micro/nanomotors are synthetic machines that can convert different sources of energy into motion; at the same time, they are able to serve innovative environmental applications, for example, water purification. The self-propelled micro and nanomachines can rapidly zoom through the solution, carrying catalytic surface or chemical to remove or degrade pollutants in a much faster fashion than that of static systems, which depend on diffusion and fluxes. This review highlights the recent progress of micro/nanomotors in water pollutant detection and pollutant removal applications.     

Rapid Conventional and Microwave-Assisted Decarboxylation of L-Histidine and Other Amino Acids via Organocatalysis with R-Carvone Under Superheated Conditions

This article reports a new methodology taking advantage of superheated chemistry via either microwave or conventional heating for the facile decarboxylation of alpha amino acids using the recoverable organocatalyst, R-carvone. The decarboxylation of amino acids is an important synthetic route to biologically active amines, and traditional methods of amino acid decarboxylation are time consuming (taking up to several days in the case of L-histidine), are narrow in scope, and make use of toxic catalysts. Decarboxylations of amino acids including L-histidine occur in just minutes while replacing toxic catalysts with green catalyst, spearmint oil. Yields are comparable to or exceed previous methods and purification of product ammonium chloride salts is aided by an isomerization reaction of residual catalyst to phenolic carvacrol. The method has been shown to be effective for the decarboxylations of a range of natural, synthetic, and protected amino acids.     

Asymmetric Phase‐Transfer‐Catalyzed Intramolecular N‐Alkylation of Indoles and Pyrroles: A Combined Experimental and Theoretical Investigation

Asymmetric phase‐transfer catalysis (PTC) has risen to prominence over the last decade as a straightforward synthetic methodology for the preparation of pharmacologically active compounds in enantiomerically pure form. However, the complex interplay of weak nonbonded interactions (between catalyst and substrate) that could account for the stereoselection in these processes is still unclear, with tentative pictorial mechanistic representations usually proposed. Here we present a full account dealing with the enantioselective phase‐transfer‐catalyzed intramolecular aza‐Michael reaction (IMAMR) of indolyl esters, as a valuable synthetic tool to obtain added‐value compounds, such as dihydro‐pyrazinoindolinones. A combined computational and experimental investigation has been carried out to elucidate the key mechanistic aspects of this process.     

Spatial and Directional Control over Self‐Assembly Using Catalytic Micropatterned Surfaces

Catalyst‐assisted self‐assembly is widespread in nature to achieve spatial control over structure formation. Reported herein is the formation of hydrogel micropatterns on catalytic surfaces. Gelator precursors react on catalytic sites to form building blocks which can self‐assemble into nanofibers. The resulting structures preferentially grow where the catalyst is present. Not only is a first level of organization, allowing the construction of hydrogel micropatterns, achieved but a second level of organization is observed among fibers. Indeed, fibers grow with their main axis perpendicular to the substrate. This feature is directly linked to a unique mechanism of fiber formation for a synthetic system. Building blocks are added to fibers in a confined space at the solid–liquid interface.     

Activity-stability parameterization of homogeneous green oxidation catalysts

Small-molecule synthetic homogeneous-oxidation catalysts are normally poorly protected from self-destruction under operating conditions. Achieving design control over both activity and half-life is important not only in advancing the utility of oxidation catalysts, but also in minimizing hazards associated with their use and disposal. Iron(III)-TAML (tetraamido-macrocyclic ligand) oxidant catalysts rapidly activate H(2)O(2) for numerous significant processes, exhibiting high and differing activity and varying half-lives depending upon the TAML design. A general approach is presented that allows for the simultaneous determination of the second-order rate constant for the oxidation of a targeted substrate by the active catalyst (k(II)) and the rate constant for the intramolecular self-inactivation of the active catalyst (k(i)). The approach is valid if the formation of the active catalyst from its resting state and the primary oxidizing agent, measured by the second-order rate constant k(I), is fast and the catalyst concentration is very low, such that bimolecular inactivation pathways can be neglected. If the oxidation process is monitored spectrophotometrically and is set up to be incomplete, the kinetic trace can be analyzed by using the equation ln(lnA(t))/A(infnity)=ln(k(II)/k(i)[Fe(III)](tot)-k(i)t, from which k(II) and k(i) can be determined. Here, A(t) and A(infinity) are absorbances at time t and at the end of reaction (t=infinity), respectively, and [Fe(III)](tot) is the total catalyst concentration. Several tools were applied to examine the validity of the approach by using a variety of different Fe(III)-TAML catalysts, H(2)O(2) and tBuOOH as oxidizing agents, and the dyes safranine O and orange II as target substrates. Learning how catalyst activities (k(II)) and catalyst half-lives (k(i)) can be controlled by ligand design is an important step in creating green catalysts that will not persist in the environment after they have achieved their purpose.     

Stereoselective Arene‐Forming Aldol Condensation: Synthesis of Configurationally Stable Oligo‐1,2‐naphthylenes

Structurally well‐defined oligomers are fundamental for the functionality of natural molecular systems and key for the design of synthetic counterparts. Herein, we describe a strategy for the efficient synthesis of individual stereoisomers of 1,2‐naphthylene oligomers by iterative building block additions and consecutive stereoselective arene‐forming aldol condensation reactions. The catalyst‐controlled atropoenantioselective and the substrate‐controlled atropodiastereoselective aldol condensation reaction provide structurally distinct ter‐ and quaternaphthalene stereoisomers, which represent configurationally stable analogues of otherwise stereodynamic, helically shaped ortho‐phenylenes.     

Refining of plant oils to chemicals by olefin metathesis

Plant oils are attractive substrates for the chemical industry. Their scope for the production of chemicals can be expanded by sophisticated catalytic conversions. Olefin metathesis is an example, which also illustrates generic issues of "biorefining" to chemicals. Utilization on a large scale requires high catalyst activities, which influences the choice of the metathesis reaction. The mixture of different fatty acids composing a technical-grade plant oil substrate gives rise to a range of products. This decisively determines possible process schemes, and potentially provides novel chemicals and intermediates not employed to date.     

Novel and efficient copper-catalysed synthesis of nitrogen-linked medium-ring biaryls

Herein, a new copper-catalysed strategy for the synthesis of rare nitrogen-linked seven-, eight- and nine-membered biaryl ring systems is described. It is proposed that the reaction proceeds through a highly activated intramolecularly co-ordinated copper catalyst. The process is technically simple, proceeds under relatively mild conditions, displays a broad substrate scope and forms biologically valuable products that are difficult to synthesise by other methods. We envisage that this methodology will prove useful in a wide synthetic context, with possible applications in both target-oriented and diversity-oriented synthesis.     

Fe-catalyzed Selective N-Formylation Protocol for Amines Using Glycolic Acid as C1 Bio-Building Block

Due to current global issues involving climate change and energy crises, it requires several complete overhauls in process developments sectors of energy and chemical manufacturing industries towards more sustainable and readily applicable protocols. As a contribution to this goal with an example of iron-based catalysis, this work presents a synthetic protocol for synthesis of N-formamides with glycolic acid as a C1 bio-building block, which is catalyzed through earth abundant and magnetically active Fe powder as catalyst. The protocol was applied to a wide variety of substrates affording yields in the range of 68–94 % and also performed well at 1 gram and 5 gram scale with yields of up to 86 % and 83 %, respectively. The catalyst was shown to be reusable up to 4 runs and the spent catalyst has been studied using PXRD and XPS analyses to determine catalyst deactivation and its remediation. Plausible reaction pathway has been suggested based on control experiments and GC-MS results for the process.     

Overriding Intrinsic Reactivity in Aliphatic C−H Oxidation: Preferential C3/C4 Oxidation of Aliphatic Ammonium Substrates

The site‐selective C?H oxidation of unactivated positions in aliphatic ammonium chains poses a tremendous synthetic challenge, for which a solution has not yet been found. Here, we report the preferential oxidation of the strongly deactivated C3/C4 positions of aliphatic ammonium substrates by employing a novel supramolecular catalyst. This chimeric catalyst was synthesized by linking the well‐explored catalytic moiety Fe(pdp) to an alkyl ammonium binding molecular tweezer. The results highlight the vast potential of overriding the intrinsic reactivity in chemical reactions by guiding catalysis using supramolecular host structures that enable a precise orientation of the substrates.     

Urea-Functionalized Fe4L6 Cages for Supramolecular Gold Catalyst Encapsulation to Control Substrate Activation Modes

The excellent catalytic performances of enzymes in terms of activity and selectivity are an inspiration for synthetic chemists and this has resulted in the development of synthetic containers for supramolecular catalysis. In such containers the local environment and pre-organization of catalysts and substrates leads to control of the activity and selectivity of the catalyst. Herein we report a supramolecular strategy to encapsulate single catalysts in a urea-functionalized Fe₄L₆ cage, which can co-encapsulate a functionalized urea substrate through hydrogen bonding. Distinguished selectivity is obtained, imposed by the cage as site isolation only allows catalysis through π activation of the substrate and as a result the selectivity is independent of catalyst concentration. The encapsulated catalyst is more active than the free analogue, an effect that can be ascribed to transitionstate stabilization rather than substrate pre-organization, as revealed by the MM kinetic data. The simple strategy reported here is expected to be of general use in many reactions, for which the catalyst can be functionalized with a sulfonate group required for encapsulation.     

Density Functional Theory Study of Reaction Equilibria in Signal Amplification by Reversible Exchange

An in-depth theoretical analysis of key chemical equilibria in Signal Amplification by Reversible Exchange (SABRE) is provided, employing density functional theory calculations to characterize the likely reaction network. For all reactions in the network, the potential energy surface is probed to identify minimum energy pathways. Energy barriers and transition states are calculated, and harmonic transition state theory is applied to calculate exchange rates that approximate experimental values. The reaction network energy surface can be modulated by chemical potentials that account for the dependence on concentration, temperature, and partial pressure of molecular constituents (hydrogen, methanol, pyridine) supplied to the experiment under equilibrium conditions. We show that, under typical experimental conditions, the Gibbs free energies of the two key states involved in pyridine-hydrogen exchange at the common Ir-IMes catalyst system in methanol are essentially the same, i. e., nearly optimal for SABRE. We also show that a methanol-containing intermediate is plausible as a transient species in the process.