For decades, one of the overarching objectives of self-assembly science has been to define the rules necessary to build functional, artificial materials with rich and adaptive phase behavior from the bottom-up. To this end, the computational and experimental efforts of chemists, physicists, materials scientists, and biologists alike have built a body of knowledge that spans both disciplines and length scales. Indeed, today control of self-assembly is extending even to supramolecular and molecular levels, where crystal engineering and design of porous materials are becoming exciting areas of exploration. Nevertheless, at least at the nanoscale, there are many stones yet to be turned. While recent breakthroughs in nanoparticle (NP) synthesis have amassed a vast library of nanoscale building blocks, NP–NP interactions in situ remain poorly quantified, in large part due to technical and theoretical impediments. While increasingly many applications for self-assembled architectures are being demonstrated, it remains difficult to predict-and therefore engineer-the pathways by which these structures form. Here, we describe how investigations using liquid-phase transmission electron microscopy (TEM) have begun to play a role in pursuing some of these long-standing questions of fundamental and far-reaching interest.

Liquid-phase TEM is unique in its ability to resolve the motions and trajectories of single NPs in solution, making it a powerful tool for studying the dynamics of NP self-assembly. Since 2012, liquid-phase TEM has been used to investigate the self-assembly behavior of a variety of simple, metallic NPs. In this Account, however, we focus on our work with anisotropic NPs, which we show to have very different self-assembly behavior, and especially on how analysis methods we and others in the field are developing can be used to convert their motions and trajectories revealed by liquid-phase TEM into quantitative understanding of underlying interactions and dynamics.

In general, liquid-phase TEM studies may help bridge enduring gaps in the understanding and control of self-assembly at the nanoscale. For one, quantification of NP–NP interactions and self-assembly dynamics will inform both computational and statistical mechanical models used to describe nanoscale phenomena. Such understanding will also lay the groundwork for establishing new and generalizable thermodynamic and kinetic design rules for NP self-assembly. Synergies with NP synthesis will enable investigations of building blocks with novel, perhaps even evolving or active behavior. Moreover, in the long run, we foresee the possibility of applying the guidelines and models of fundamental nanoscale interactions which are uncovered under liquid-phase TEM to biological and biomimetic systems at similar dimensions.

Carbon geosequestration (CGS) has been identified as a key technology to reduce anthropogenic greenhouse gas emissions and thus significantly mitigate climate change. In CGS, CO₂ is captured from large point-source emitters (e.g., coal fired power stations), purified, and injected deep underground into geological formations for disposal. However, the CO₂ has a lower density than the resident formation brine and thus migrates upward due to buoyancy forces. To prevent the CO₂ from leaking back to the surface, four trapping mechanisms are used: (1) structural trapping (where a tight caprock acts as a seal barrier through which the CO₂ cannot percolate), (2) residual trapping (where the CO₂ plume is split into many micrometer-sized bubbles, which are immobilized by capillary forces in the pore network of the rock), (3) dissolution trapping (where CO₂ dissolves in the formation brine and sinks deep into the reservoir due to a slight increase in brine density), and (4) mineral trapping (where the CO₂ introduced into the subsurface chemically reacts with the formation brine or reservoir rock or both to form solid precipitates).

The efficiency of these trapping mechanisms and the movement of CO₂ through the rock are strongly influenced by the CO₂–brine–rock wettability (mainly due to the small capillary-like pores in the rock which form a complex network), and it is thus of key importance to rigorously understand CO₂-wettability. In this context, a substantial number of experiments have been conducted from which several conclusions can be drawn: of prime importance is the rock surface chemistry, and hydrophilic surfaces are water-wet while hydrophobic surfaces are CO₂-wet. Note that CO₂-wet surfaces dramatically reduce CO₂ storage capacities. Furthermore, increasing pressure, salinity, or dissolved ion valency increases CO₂-wettability, while the effect of temperature is not well understood.

Indeed theoretical understanding of CO₂-wettability and the ability to quantitatively predict it are currently limited although recent advances have been made. Moreover, data for real storage rock and real injection gas (which contains impurities) is scarce and it is an open question how realistic subsurface conditions can be reproduced in laboratory experiments. In conclusion, however, it is clear that in principal CO₂-wettability can vary drastically from completely water-wet to almost completely CO₂-wet, and this possible variation introduces a large uncertainty into trapping capacity and containment security predictions.

Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20–30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs.

In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA.

The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64–179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.

Until recently, the chemistry of boronyl (BO), a diatomic radical isolectronic with the cyano (CN) species, has remained unknown. The boronyl group is characterized by a boron–oxygen multiple bond, and because of the inherent electron deficiency of the boron atom, boronyls (RBO) are highly reactive and typically only exist in their cyclotrimeric form (RBO)₃. Due to their invaluable role as reactants, the isolation of the monomers in gas phase experiments has been extensively sought after by the organic synthesis and physical organic chemistry communities but never achieved. Besides the interests from a physical organic and synthetic point of view, boronyls also play a role as reaction intermediates in boron-assisted rocket propulsion systems.

In this Account, we review recent experimental work in which gas phase organo boronyl monomers (RBO) are formed via bimolecular reactions of the boronyl radical (BO) with C2–C6 unsaturated hydrocarbons. The investigated hydrocarbons are widely exploited as fuels, and their reactions with boronyl radicals under single collision conditions lead to the formation of organo boronyls. Our studies also elucidate the mechanisms of their formation reactions thus furnishing a comprehension at the molecular level of this reaction class. The variety of the employed hydrocarbon substrates has allowed us to systematically classify the chemical behavior of the boronyl radicals. With the exception of the case of the dimethylacetylene reaction, the boron monoxide radical versus atomic hydrogen exchange mechanisms were always open leading to the formation of highly unsaturated organo boronyl monomers (RBO), which could be easily identified because they cannot trimerize under single collision conditions.

Besides the hydrogen displacement pathway, methylacetylene, dimethylacetylene, and propylene, carrying one or two methyl groups, were also found to eliminate a methyl group. In all systems, the reactions were barrierless, indirect, and initiated by addition of the boron monoxide radical to the π electron density of the hydrocarbon molecule, with the radical center located at the boron atom of the BO radical, thus leading to doublet radical intermediates. These intermediates either decompose via hydrogen or methyl loss or isomerize prior to their decomposition via atomic hydrogen or migration of the BO moiety. A consistent trend suggests that all exit transition states are rather tight with those involved in the hydrogen atom loss depicting exit barriers of typically 25 to 35 kJ mol^–1, whereas the methyl loss pathways are associated with tighter exit transition states located about 30–50 kJ mol^–1 above the separated products. Further, the overall energetics suggest that those bimolecular reactions are exoergic by 40–90 kJ mol^–1. These findings confirm that this reaction class leads to the formation of highly unsaturated organo boronyl molecules.

The modification of heterogeneous catalysts through the chemisorption of chiral molecules is a method to create catalytic sites for enantioselective surface reactions. The chiral molecule is called a chiral modifier by analogy to the terms chiral auxiliary or chiral ligand used in homogeneous asymmetric catalysis. While there has been progress in understanding how chirality transfer occurs, the intrinsic difficulties in determining enantioselective reaction mechanisms are compounded by the multisite nature of heterogeneous catalysts and by the challenges facing stereospecific surface analysis. However, molecular descriptions have now emerged that are sufficiently detailed to herald rapid advances in the area. The driving force for the development of heterogeneous enantioselective catalysts stems, at the minimum, from the practical advantages they might offer over their homogeneous counterparts in terms of process scalability and catalyst reusability. The broader rewards from their study lie in the insights gained on factors controlling selectivity in heterogeneous catalysis. Reactions on surfaces to produce a desired enantiomer in high excess are particularly challenging since at room temperature, barrier differences as low as ∼2 kcal/mol between pathways to R and S products are sufficient to yield an enantiomeric ratio (er) of 90:10. Such small energy differences are comparable to weak interadsorbate interaction energies and are much smaller than chemisorption or even most physisorption energies.

In this Account, we describe combined experimental and theoretical surface studies of individual diastereomeric complexes formed between chiral modifiers and prochiral reactants on the Pt(111) surface. Our work is inspired by the catalysis literature on the enantioselective hydrogenation of activated ketones on cinchona-modified Pt catalysts. Using scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations, we probe the structures and relative abundances of non-covalently bonded complexes formed between three representative prochiral molecules and (R)-(+)-1-(1-naphthyl)ethylamine ((R)-NEA). All three prochiral molecules, 2,2,2-trifluoroacetophenone (TFAP), ketopantolactone (KPL), and methyl 3,3,3-trifluoropyruvate (MTFP), are found to form multiple complexation configurations around the ethylamine group of chemisorbed (R)-NEA. The principal intermolecular interaction is NH···O H-bonding. In each case, submolecularly resolved STM images permit the determination of the prochiral ratio (pr), pro-R to pro-S, proper to specific locations around the ethylamine group. The overall pr observed in experiments on large ensembles of KPL–(R)-NEA complexes is close to the er reported in the literature for the hydrogenation of KPL to pantolactone on (R)-NEA-modified Pt catalysts at 1 bar H₂. The results of independent DFT and STM studies are merged to determine the geometries of the most abundant complexation configurations. The structures reveal the hierarchy of chemisorption and sometimes multiple H-bonding interactions operating in complexes. In particular, privileged complexes formed by KPL and MTFP reveal the participation of secondary CH···O interactions in stereocontrol. State-specific STM measurements on individual TFAP–(R)-NEA complexes show that complexation states interconvert through processes including prochiral inversion. The state-specific information on structure, prochirality, dynamics, and energy barriers delivered by the combination of DFT and STM provides insight on how to design better chiral modifiers.

Inverting glycosyltransferases enforce in the active site an intramolecular, acid–base catalyzed glycosidation that, due to proximity of the donor anomeric carbon and the acceptor hydroxyl group, follows an S_N2-type reaction. Spacers, tethering donor and acceptor via nonreacting functional groups, led in intramolecular glycosidations to excellent yields and, independent of the donor anomeric configuration, to either the α- or the β-anomer. The requirement of a demanding protecting group pattern confines the application of this efficient method. Only the method where the 2-hydroxyl group of a mannopyranosyl donor is tethered via an acetal spacer to the reacting acceptor functional group is used for β-mannopyranoside synthesis. The most elegant method, tethering donor and acceptor covalently to the spacer via the leaving group and the reacting functional group, was so far not as efficient as hoped. This method is very efficient when donor and acceptor are temporarily assembled through a hydrogen-bond facilitating a stretched hexagon-like transition state. This follows from the stereoselective O-glucopyranosyl trichloroacetimidate transformation into O-glucopyranosyl phosphate with dibenzyl phosphoric acid as acceptor that can be regarded as A═B–C–H acceptor type. Generalizing this concept to the use of alcohols as acceptors requires reversible generation of an A–B–C–H adduct where A–H represents the acceptor (RO–H) and B═C a catalyst that has to fulfill several criteria. Among these criteria are low affinity to nitrogen, avoiding glycosyl donor activation in the absence of acceptor, and high affinity to oxygen in order to generate the A–B–C–H adduct with increased proton acidity. Thus, hydrogen-bond mediated self-assembly of donor and acceptor and concomitant donor activation via a transition state is available, which enforces an acid–base catalyzed S_N2-type reaction. It could be shown that PhBF₂, Ph₂BF, and PhSiF₃ are such catalysts that fulfill the desired four functions: reversible adduct formation with the acceptor, hydrogen-bond mediated tethering of this adduct with the donor, and acid- and base-catalysis of the glycosidation. Also Lewis acidic metal salts, particularly the dimeric gold(III) chloride, turned out to exhibit excellent B═C type catalyst properties. Worth mentioning in this context is the ability of gold(III) chloride to regioselectively activate diols.

As thioureas have high affinity to anions and also to neutral compounds through strong hydrogen bonds, their binding to alcohols and concomitant activation of O-glycosyl trichloroacetimidates was of interest. Yet, even the acidic N,N′-bis[3,5-bis(trifluoromethyl)phenyl]-thiourea was unable to catalyze glycosidations. However, as a cocatalyst to acids, thiourea exerts a strong effect that, based on NMR studies, leads first to a hydrogen-bond mediated catalyst–cocatalyst–acceptor complex. This complex activates the donor in an intramolecular, acid–base catalyzed reaction that is again closely related to the action of inverting glycosyltransferases. Thus, from O-(α-glycosyl) trichloroacetimidates, good yields of the inversion products, that is, the β-glycosides, are obtained. This novel conceptual approach to glycosidation revealed that for retention of configuration in addition a catalytic nucleophile is required that enables formation of the α-glucoside from the α-trichloroacetimidate. Preliminary studies with a catalyst possessing this 5-fold function, that is, adduct formation with the acceptor, hydrogen-bonding between the reactants, acid and base catalysis, and a catalytic nucleophile as part of a chiral framework supporting facial selection, exhibited good chances for final success in this endeavor.

The cell envelope is an integral and essential component of Gram-negative bacteria. As the front line during host–pathogen interactions, it is directly challenged by host immune responses as well as other harsh extracellular stimuli. The high permeability of the outer-membrane and the lack of ATP energy system render it difficult to maintain important biological activities within the periplasmic space under stress conditions. The HdeA/B chaperone machinery is the only known acid resistant system found in bacterial periplasm, enabling enteric pathogens to survive through the highly acidic human stomach and establish infections in the intestine. These two homologous chaperones belong to a fast growing family of conditionally disordered chaperones that conditionally lose their well-defined three-dimensional structures to exert biological activities. Upon losing ordered structures, these proteins commit promiscuous binding of diverse clients in response to environmental stimulation. For example, HdeA and HdeB are well-folded inactive dimers at neutral pH but become partially unfolded to protect a wide array of acid-denatured proteins upon acid stress. Whether these conditionally disordered chaperones possess client specificities remains unclear. This is in part due to the lack of efficient tools to investigate such versatile and heterogeneous protein–protein interactions under living conditions.

Genetically encoded protein photo-cross-linkers have offered a powerful strategy to capture protein–protein interactions, showing great potential in profiling protein interaction networks, mapping binding interfaces, and probing dynamic changes in both physiological and pathological settings. Despite great success, photo-cross-linkers that can simultaneously capture the promiscuous binding partners and directly identify the interaction interfaces remain technically challenging. Furthermore, methods for side-by-side profiling and comparing the condition-dependent client pools from two homologous chaperones are lacking.

Herein, we introduce our recent efforts in developing a panel of versatile genetically encoded photo-cross-linkers to study the disorder-mediated chaperone–client interactions in living cells. In particular, we have developed a series of proteomic-based strategies relying on these new photo-cross-linkers to systematically compare the client profiles of HdeA and HdeB, as well as to map their interaction interfaces. These studies revealed the mode-of-action, particularly the client specificity, of these two conditionally disordered chaperones. In the end, some recent elegant work from other groups that applied the genetically encoded photo-cross-linking strategy to illuminate important protein–protein interactions within bacterial cell envelope is also discussed.

Protein kinases are enzymes that catalyze the covalent transfer of the γ-phosphate of an adenosine triphosphate (ATP) molecule onto a tyrosine, serine, threonine, or histidine residue in the substrate and thus send a chemical signal to networks of downstream proteins. They are important cellular signaling enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Unregulated protein kinase activity is often associated with a wide range of diseases, therefore making protein kinases major therapeutic targets. A prototypical system of central interest to understand the regulation of kinase activity is provided by tyrosine kinase c-Src, which belongs to the family of Src-related non-receptor tyrosine kinases (SFKs). Although the broad picture of autoinhibition via the regulatory domains and via the phosphorylation of the C-terminal tail is well characterized from a structural point of view, a detailed mechanistic understanding at the atomic-level is lacking. Advanced computational methods based on all-atom molecular dynamics (MD) simulations are employed to advance our understanding of tyrosine kinase activation.

The computational studies suggest that the isolated kinase domain (KD) is energetically most favorable in the inactive conformation when the activation loop (A-loop) of the KD is not phosphorylated. The KD makes transient visits to a catalytically competent active-like conformation. The process of bimolecular trans-autophosphorylation of the A-loop eventually locks the KD in the active state. Activating point mutations may act by slightly increasing the population of the active-like conformation, enhancing the availability of the A-loop to be phosphorylated. The Src-homology 2 (SH2) and Src-homology 3 (SH3) regulatory domains, depending upon their configuration, either promote the inactive or the active state of the kinase domain. In addition to the roles played by the SH3, SH2, and KD, the Src-homology 4-Unique domain (SH4-U) region also serves as a key moderator of substrate specificity and kinase function. Thus, a fundamental understanding of the conformational propensity of the SH4-U region and how this affects the association to the membrane surface are likely to lead to the discovery of new intermediate states and alternate strategies for inhibition of kinase activity for drug discovery. The existence of a multitude of KD conformations poses a great challenge aimed at the design of specific inhibitors. One promising computational strategy to explore the conformational flexibility of the KD is to construct Markov state models from aggregated MD data.

Lost or damaged cells in tissues and organs can be replaced by transplanting therapeutically competent cells. This approach requires methods that effectively manipulate cellular identities and properties to generate sufficient numbers of desired cell types for transplantation. These cells can be generated by reprogramming readily available somatic cells, such as fibroblasts, into induced pluripotent stem cells (iPSCs), which can replicate indefinitely and give rise to any somatic cell type. This reprogramming can be achieved with genetic methods, such as forced expression of pluripotency-inducing transcription factors (TFs), which can be further improved, or even avoided, with pharmacological agents. We screened chemical libraries for such agents and identified small molecules that enhance TF-mediated pluripotency induction in somatic cells. We also developed cocktails of small molecules that can functionally replace combinations of TFs required to induce pluripotency in mouse and human somatic cells. Importantly, we devised and established a general strategy to develop effective pharmacological cocktails for specific cellular reprogramming processes. In the search for useful small molecules, we also discovered and characterized previously unknown mechanisms pertinent to cellular reprogramming.

A more direct method to access scarce cells for cell transplantation is transdifferentiation, which uses combinations of cell-type specific TFs to reprogram fibroblasts into the target somatic cell types across lineage boundaries. We created an alternative strategy for cellular transdifferentiation that epigenetically activates somatic cells by pairing temporal treatment with reprogramming molecules and tissue-specific signaling molecules to generate cells of multiple lineages. Using this cell-activation and signaling-directed (CASD) transdifferentiation paradigm, we converted fibroblasts into a variety of somatic cells found in major organs, such as the heart, brain, pancreas, and liver. Specifically, we induced, isolated, and expanded (long-term) lineage-specific progenitor cells that can give rise to a defined range of cell types relevant to specific tissues or organs. Transplanting these progenitor cells or their progeny was therapeutically beneficial in animal models of diseases and organ damage. Importantly, we developed chemically defined conditions, without any genetic factors, that convert fibroblasts into cells of the cardiac and neural lineages, further extending the realm of pharmacological reprogramming of cells.

Continuously advancing technologies in pharmacological reprogramming of cells may benefit and advance regenerative medicine. The established pharmacological tools have already been applied to enhance the processes of cellular reprogramming and improve the quality of cells for their clinical applications. The rapidly increasing number of readily available bioactive chemical tools will fuel our efforts to reprogram cells for transplantation therapies.

Biomacromolecules, such as nucleic acids, proteins, and virus particles, are persistent molecular entities with dimensions that exceed the range of their intermolecular forces hence undergoing degradation by thermally induced bond-scission upon heating. Consequently, for this type of molecule, the absence of a liquid phase can be regarded as a general phenomenon. However, certain advantageous properties usually associated with the liquid state of matter, such as processability, flowability, or molecular mobility, are highly sought-after features for biomacromolecules in a solvent-free environment. Here, we provide an overview over the design principles and synthetic pathways to obtain solvent-free liquids of biomacromolecular architectures approaching the topic from our own perspective of research. We will highlight the milestones in synthesis, including a recently developed general surfactant complexation method applicable to a large variety of biomacromolecules as well as other synthetic principles granting access to electrostatically complexed proteins and DNA.

These synthetic pathways retain the function and structure of the biomacromolecules even under extreme, nonphysiological conditions at high temperatures in water-free melts challenging the existing paradigm on the role of hydration in structural biology. Under these conditions, the resulting complexes reveal their true potential for previously unthinkable applications. Moreover, these protocols open a pathway toward the assembly of anisotropic architectures, enabling the formation of solvent-free biomacromolecular thermotropic liquid crystals. These ordered biomaterials exhibit vastly different mechanical properties when compared to the individual building blocks. Beyond the preparative aspects, we will shine light on the unique potential applications and technologies resulting from solvent-free biomacromolecular fluids: From charge transport in dehydrated liquids to DNA electrochromism to biocatalysis in the absence of a protein hydration shell. Moreover, solvent-free biological liquids containing viruses can be used as novel storage and process media serving as a formulation technology for the delivery of highly concentrated bioactive compounds. We are confident that this new class of hybrid biomaterials will fuel further studies and applications of biomacromolecules beyond water and other solvents and in a much broader context than just the traditional physiological conditions.

Adaptable crystalline frameworks are important in modern solid-state chemistry as they are able to accommodate a wide range of elements, oxidation states, and stoichiometries. Owing to this ability, such adaptable framework structures are emerging as the prototypes for technologically important advanced functional materials. In this Account, the idea of cosubstitution is explored as a useful “pairing” concept that can potentially lead to the creation of many new members of one particular framework structure. Cosubstitution as practiced is the simultaneous replacement of two or more cations, anions, complex anions, other fundamental building units, or vacancies. Although the overall sum of the oxidation states is constant, each component is not necessarily isovalent. This methodology is typically inspired by either mineral-type structural prototypes found in nature or those discovered in the laboratory. Either path leads to the appearance of new phases and the discovery of new materials. In addition, the chemical cosubstitution approach can be successfully adopted to improve physical properties associated with structures.

This Account is structured as follows: first, we illustrate the significance and background of chemical cosubstitution by reviewing mineral-inspired structures, such as perovskite and lyonsite, and the structural unit discovered in some selected solid state compounds. With time, the number of lyonsite related phases should rival or even surpass the perovskite family. Several members of the lyonsite-type have been identified as Li-ion conductors and photocatalysts. There is also a noncentrosymmetric structure-type, and therefore the other properties associated with the loss of inversion symmetry should be anticipated. Next, we illustrate recent advances in the synthesis of the new cosubstituted solid state materials from our two groups including (1) nonlinear optical materials, (2) luminescent materials, (3) transparent conducting oxides, and (4) photocatalyst and photovoltaic materials. We emphasize that a concerted and rigorous theoretical and experimental approach will be required to define thermodynamic stability of the complex cosubstitution chemistries, structures, and properties that are yet unknown. We conclude by summarizing the topic and suggesting other possible adaptable framework structures where cosubstitution can be expected.

Molecular compounds, organic and inorganic, crystallize in diverse and complex structures. They continue to inspire synthetic efforts and “crystal engineering”, with implications ranging from fundamental questions to pharmaceutical research. The structural complexity of molecular solids is linked with diverse intermolecular interactions: hydrogen bonding with all its facets, halogen bonding, and other secondary bonding mechanisms of recent interest (and debate). Today, high-resolution diffraction experiments allow unprecedented insight into the structures of molecular crystals. Despite their usefulness, however, these experiments also face problems: hydrogen atoms are challenging to locate, and thermal effects may complicate matters. Moreover, even if the structure of a crystal is precisely known, this does not yet reveal the nature and strength of the intermolecular forces that hold it together.

In this Account, we show that periodic plane-wave-based density functional theory (DFT) can be a useful, and sometimes unexpected, complement to molecular crystallography. Initially developed in the solid-state physics communities to treat inorganic solids, periodic DFT can be applied to molecular crystals just as well: theoretical structural optimizations “help out” by accurately localizing the elusive hydrogen atoms, reaching neutron-diffraction quality with much less expensive measurement equipment. In addition, phonon computations, again developed by physicists, can quantify the thermal motion of atoms and thus predict anisotropic displacement parameters and ORTEP ellipsoids “from scratch”.

But the synergy between experiment and theory goes much further than that. Once a structure has been accurately determined, computations give new and detailed insights into the aforementioned intermolecular interactions. For example, it has been debated whether short hydrogen bonds in solids have covalent character, and we have added a new twist to this discussion using an orbital-based theory that once more had been developed for inorganic solids. However, there is more to a crystal structure than a handful of short contacts between neighboring residues. We hence have used dimensionally resolved analyses to dissect crystalline networks in a systematic fashion, one spatial direction at a time. Initially applied to hydrogen bonding, these techniques can be seamlessly extended to halogen, chalcogen, and pnictogen bonding, quantifying bond strength and cooperativity in truly infinite networks. Finally, these methods promise to be useful for (bio)polymers, as we have recently exemplified for α-chitin. At the interface of increasingly accurate and popular DFT methods, ever-improving crystallographic expertise, and new challenging, chemical questions, we believe that combined experimental and theoretical studies of molecular crystals are just beginning to pick up speed.

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted–Polanyi–Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics.

In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO₂(110), while the kinetics of the OER over RuO₂(110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G_rds^#, defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G_max(RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG_loss, as a descriptor for the kinetics.

The controlled and reproducible formation of colloidal semiconductor nanocrystals (or quantum dots) is of central importance in nanoscale science and technology. The tunable size- and shape-dependent properties of such materials make them ideal candidates for the development of efficient and low-cost displays, solar cells, light-emitting devices, and catalysts. The formidable difficulties associated with the macroscale preparation of semiconductor nanocrystals (possessing bespoke optical and chemical properties) result from the fact that underlying reaction mechanisms are complex and that the reactive environment is difficult to control. Automated microfluidic reactors coupled with monitoring systems and optimization algorithms aim to elucidate complex reaction mechanisms that govern both nucleation and growth of nanocrystals. Such platforms are ideally suited for the efficient optimization of reaction parameters, assuring the reproducible synthesis of nanocrystals with user-defined properties.

This Account aims to inform the nanomaterials community about how microfluidic technologies can supplement flask experimentation for the ensemble investigation of formation mechanisms and design of semiconductor nanocrystals. We present selected studies outlining the preparation of quantum dots using microfluidic systems with integrated analytics. Such microfluidic reaction systems leverage the ability to extract real-time information regarding optical, structural, and compositional characteristics of quantum dots during nucleation and growth stages.

The Account further highlights our recent research activities focused on the development and application of droplet-based microfluidics with integrated optical detection systems for the efficient and rapid screening of reaction conditions and a better understanding of the mechanisms of quantum dot synthesis. We describe the features and operation of fully automated microfluidic reactors and their subsequent application to high-throughput parametric screening of metal chalcogenides (CdSe, PbS, PbSe, CdSeTe), ternary and core/shell heavy metal-free quantum dots (CuInS₂, CuInS₂/ZnS), and all-inorganic perovskite nanocrystals (CsPbX₃, X = Cl, Br, I) syntheses. Critically, concurrent absorption and photoluminescence measurements on millisecond to second time scales allow the extraction of basic parameters governing nanocrystal formation. Moreover, experimental data obtained from such microfluidic platforms can be directly supported by theoretical models of nucleation and growth. To this end, we also describe the use of metamodeling algorithms able to accurately predict optimized conditions of CdSe synthesis using a minimal number of sample parameters.

Importantly, we discuss future challenges that must be addressed before microfluidic technologies are in a position to be widely adopted for the on-demand formation of nanocrystals. From a technology perspective, these challenges include the development of novel engineering platforms for the formation of complex architectures, the integration of monitoring systems able to harvest photophysical and structural information, the incorporation of continuous purification systems, and the application of optimization algorithms to multicomponent quantum dot systems.

Cooperative catalysis has attracted tremendous attention in recent years, emerging as a key strategy for the development of novel atom-economic and environmentally more benign catalytic processes. In particular, Noyori-type complexes with metal–nitrogen bonds have been extensively studied and evolved as privileged catalysts in hydrogenation chemistry. In contrast, catalysts containing metal–sulfur bonds as the reactive site are out of the ordinary, despite their abundance in living systems, where they are assumed to play a key role in biologically relevant processes. For instance, the heterolysis of dihydrogen catalyzed by [NiFe] hydrogenase is likely to proceed through cooperative H–H bond splitting at a polar nickel–sulfur bond.

This Account provides an overview of reported metal–sulfur complexes that allow for cooperative E–H bond (E = H, Si, and B) activation and highlights the potential of this motif in catalytic applications. In recent years, our contributions to this research field have led to the development of a broad spectrum of synthetically useful transformations catalyzed by cationic ruthenium(II) thiolate complexes of type [(DmpS)Ru(PR₃)]⁺BAr^F₄^– (DmpS = 2,6-dimesitylphenyl thiolate, Ar^F = 3,5-bis(trifluoromethyl)phenyl). The tethered coordination mode of the bulky 2,6-dimesitylphenyl thiolate ligand is crucial, stabilizing the coordinatively unsaturated ruthenium atom and also preventing formation of binuclear sulfur-bridged complexes. The ruthenium–sulfur bond of these complexes combines Lewis acidity at the metal center and Lewis basicity at the adjacent sulfur atom. This structural motif allows for reversible heterolytic splitting of E–H bonds (E = H, Si, and B) across the polar ruthenium–sulfur bond, generating a metal hydride and a sulfur-stabilized E⁺ cation. Hence, this activation mode provides a new strategy to catalytically generate silicon and boron electrophiles.

After transfer of the electrophile to a Lewis-basic substrate, the resulting neutral ruthenium(II) hydride can either act as a hydride donor (reductant) or as a proton acceptor (Brønsted base); the latter scenario is followed by dihydrogen release. On the basis of this concept, the tethered ruthenium(II) thiolate complexes emerged as widely applicable catalysts for various transformations, which can be categorized into (i) dehydrogenative couplings [Si–C(sp²), Si–O, Si–N, and B–C(sp²)], (ii) chemoselective reductions (hydrogenation and hydrosilylation), and (iii) hydrodefluorination reactions. All reactions are promoted by a single catalyst motif through synergistic metal–sulfur interplay. The most prominent examples of these transformations are the first catalytic protocols for the regioselective C–H silylation and borylation of electron-rich heterocycles following a Friedel–Crafts mechanism.

Since 2004, when the first synthetic glycoconjugate vaccine against the pneumonia and meningitis causing bacterium Haemophilus influenza type b (Hib) approved for human use in Cuba was reported, 34 million doses of the synthetic vaccine have been already distributed in several countries under the commercial name of Quimi-Hib. However, despite the success of this product, no other synthetic glycoconjugate vaccine has been licensed in the following 13 years. As well as avoiding the need to handle pathogens, synthetic glycoconjugates offer clear advantages in terms of product characterization and the possibility to understand the parameters influencing immunogenicity. Nevertheless, large scale application of synthetic sugars has been perceived as challenging because of manufacturing costs and process complexity compared to natural polysaccharides.

Chemoenzymatic approaches, one-pot protocols, and automated solid-phase synthesis are rendering carbohydrate production considerably more attractive for industrialization. Here we identify three areas where chemical approaches can advance this progress: (i) chemical or enzymatic methods enabling the delivery of the minimal polysaccharide portion responsible for an effective immune response; (ii) site-selective chemical or enzymatic conjugation strategies for the exploration of the conjugation point in immune responses against carbohydrate-based vaccines, and the consistent preparation of more homogeneous products; (iii) multicomponent constructs targeting receptors responsible for immune response modulation in order to control its quality and magnitude.

We discuss how synthesis of bacterial oligosaccharides is useful toward understanding the polysaccharide portion responsible for immunogenicity, and for developing robust and consistent alternatives to natural heterogeneous polysaccharides. The synthesis of sugar analogues can lead to the identification of hydrolytically more stable versions of oligosaccharide antigens. The study of bacterial polysaccharide biosynthesis aids the development of in vitro hazard-free oligosaccharide production.

Novel site-selective conjugation methods contribute toward deciphering the role of conjugation sites in the immunogenicity of glycoconjugates and prove to be particularly useful when glycans are conjugated to protein serving as carrier and antigen.

The orthogonal incorporation of two different carbohydrate haptens enables the reduction of vaccine components. Finally, coordinated conjugation of glycans and small molecule immunopotentiators supports simplification of vaccine formulation and localization of adjuvant.

Synergistic advancement of these areas, combined with competitive manufacturing processes, will contribute to a better understanding of the features guiding the immunological activity of glycoconjugates and, ultimately, to the design of improved, safer vaccines.