GPCRLigNet: rapid screening for GPCR active ligands using machine learning.

Molecules with bioactivity towards G protein-coupled receptors represent a subset of the vast space of small drug-like molecules. Here, we compare machine learning models, including dilated graph convolutional networks, that conduct binary classification to quickly identify molecules with activity towards G protein-coupled receptors. The models are trained and validated using a large set of over 600,000 active, inactive, and decoy compounds. The best performing machine learning model, dubbed GPCRLigNet, was a surprisingly simple feedforward dense neural network mapping from Morgan fingerprints to activity. Incorporation of GPCRLigNet into a high-throughput virtual screening workflow is demonstrated with molecular docking towards a particular G protein-coupled receptor, the pituitary adenylate cyclase-activating polypeptide receptor type 1. Through rigorous comparison of docking scores for molecules selected with and without using GPCRLigNet, we demonstrate an enrichment of potentially potent molecules using GPCRLigNet. This work provides a proof of principle that GPCRLigNet can effectively hone the chemical search space towards ligands with G protein-coupled receptor activity.

Helical Molecular Springs with Varying Spring Constants.

We report a general synthetic route toward helical ladder polymers with varying spring constants, built with chirality-assisted synthesis (CAS). Under tension and compression, these shape-persistent structures do not unfold, but rather stretch and compress akin classical Hookean springs. Our synthesis is adaptable to helices with different pitch and diameter, which allowed us to investigate how molecular flexibility in solution depends on the exact geometry of the ladder polymers. Specifically, we showed with molecular dynamic simulations and by measuring the longitudinal 1 H NMR relaxation times (T1 ) for our polymers at different Larmor frequencies, that increasing the helix diameter leads to increased flexibility. Our results present initial design rules for tuning the mechanical properties of intrinsically helical ladder polymers in solution, which will help inspire a new class of robust, spring-like molecular materials with varying mechanical properties.

Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein.

Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.

Selective Monofunctionalization Enabled by Reaction-History-Dependent Communication in Catalytic Rotaxanes.

Selective monofunctionalization of substrates with distant, yet equally reactive functional groups is difficult to achieve, as it requires the second functional group to selectively modulate its reactivity once the first functional group has reacted. We now show that mechanically interlocked catalytic rings can effectively regulate the reactivity of stoppering groups in rotaxanes over a distance of about 2 nm. Our mechanism of communication is enabled by a unique interlocked design, which effectively removes the catalytic rings from the substrates by fast dethreading as soon as the first reaction has taken place. Our method not only led to a rare example of selective monofunctionalization, but also to a "molecular if function". Overall, the study presents a way to get distant functional groups to communicate with each other in a reaction-history-dependent manner by creating linkers that can ultimately perform logical operations at the molecular level.

Enantioselective Electrophilic Aromatic Nitration: A Chiral Auxiliary Approach.

Enantioselective electrophilic aromatic nitration methodology is needed to advance chirality-assisted synthesis (CAS). Reported here is an enantioselective aromatic nitration strategy operating with chiral diester auxiliaries, and it provides an enantioselective synthesis of a C3v -symmetric tribenzotriquinacene (TBTQ). These axially-chiral structures are much sought-after building blocks for CAS, but they were not accessible prior to this work in enantioenriched form without resolution of enantiomers. This nitration strategy controls the stereochemistry of threefold nitration reactions from above the aromatic rings with chiral diester arms. Dicarbonyl-to-arenium chelation rigidifies the reaction systems, so that remote stereocenters position the ester-directing groups selectively over specific atoms of the TBTQ framework. Closely guided by computational design, a more selective through-space directing arm was first predicted with density functional theory (DFT), and then confirmed in the laboratory, to outperform the initial structural design. This enantio- and regioselective TBTQ synthesis opens a new pathway to access building blocks for CAS.

Effect of Large Electrolyte Anions on the Sequential Oxidations of Bis(fulvalene)diiron Attached to Glassy Carbon by an Ethynyl Linkage.

Two ethynyl-derivatized isomers of bis(fulvalene)diiron (BFD, 1,1'-biferrocenylene) were prepared and covalently attached to glassy carbon electrodes through their ethynyl group by three different electrode modification methods. Cyclic voltammetry and square wave (SW) voltammetry were used to characterize surface coverages of 1.4-5.5 × 10-10 mol cm-2, the higher of these corresponding to roughly a monolayer, based on computation of an idealized close-packing structure for ethynylbis(fulvalene)diiron (E-BFD) on a solid surface. In a dichloromethane solution containing a smaller electrolyte anion such as [PF6]- or [ClO4]-, the E-BFD-modified electrodes exhibited two quasi-Nernstian one-electron oxidations. In contrast, the current for the second oxidation process, [E-BFD]+/2+, was diminished in electrolytes containing one of the large fluoroaryl borate anions, [B(C6F5)4]- or [B(C6H3(CF3)2)4]-. The effect was enhanced for electrodes having higher surface coverages being probed at shorter voltammetric time scales. SW voltammetry showed that the diminished currents for [E-BFD]+/2+ in large-anion electrolytes are not caused by slow electron transfer. Rather, they are attributed to mixed diffusivity of the counter-anions at the electrode/solution interface, as [E-BFD]+ and the anion form the optimum (lowest-energy) configuration of a 1:1 ion pair. The interior transport of the anion required to reach this configuration may be sterically encumbered, accounting for the diminished charge transfer observed with electrolytes containing large anions.

Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-µs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

Crystal-Packing-Driven Enrichment of Atropoisomers.

Crystal-packing forces can have a significant impact on the relative stabilities of different molecules and their conformations. The magnitude of such effects is, however, not yet well understood. Herein we show, that crystal packing can completely overrule the relative stabilities of different stereoisomers in solution. Heating of atropoisomers (i.e. "frozen-out" conformational isomers) in solution leads to complex mixtures. In contrast, solid-state heating selectively amplifies minor (<25 mole %) components of these solution-phase mixtures. We show that this heating strategy is successful for compounds with up to four rotationally hindered σ bonds, for which a single stereoisomer out of seven can be amplified selectively. Our results demonstrate that common supramolecular interactions-for example, [methyl⋅⋅⋅π] coordination and [C-H⋅⋅⋅O] hydrogen bonding-can readily invert the relative thermodynamic stabilities of different molecular conformations. These findings open up potential new avenues to control the folding of macromolecules.

Cooperative Reactivity in an Extended-Viologen-Based Cyclophane.

A tetracationic pyridinium-based cyclophane with a box-like geometry, incorporating two juxtaposed alkyne functions, has been synthesized. The triple bonds are reactive through cycloadditions toward dienes and azides, promoted by the electron-withdrawing nature of the pyridinium rings, as well as by the strain inherent in the cyclophane. The cycloadditions proceeded in high yields, with the cyclophane reacting faster than its acyclic analogue. While the cyclophane contains two reactive triple bonds, there is no evidence for a stable monofunctional intermediate-only starting material and the difunctional product have been detected by (1)H NMR spectroscopy. Molecular modeling of the energy landscape reveals a lower barrier for the kinetically favored second cycloaddition compared with the first one. This situation results in tandem cascading reactions within rigid cyclophanes, where reactions at a first triple bond induce increased reactivity at a distal second alkyne.

Anodic Methods for Covalent Attachment of Ethynylferrocenes to Electrode Surfaces: Comparison of Ethynyl Activation Processes.

The electrochemical oxidation of ferrocenes having an H- or Li-terminated ethynyl group has been studied, especially as it relates to their covalent anchoring to carbon surfaces. The anodic oxidation of lithioethynylferrocene (1-Li) results in rapid loss of Li(+) and formation of the ethynyl-based radical FeCp(η(5)-C5H4)(C≡C), (1, Cp = η(5)-C5H5), which reacts with the electrode. Chemically modified electrodes (CMEs) were thereby produced containing strongly bonded, ethynyl-linked monolayers and electrochemically controlled multilayers. Strong attachments of ethynylferrocenes to gold and platinum surfaces were also possible. The lithiation/anodic oxidation process is a mirror analogue of the diazonium/cathodic reduction process for preparation of aryl-modified CMEs. A second method produced an ethynylferrocene-modified electrode by direct anodic oxidation of the H-terminated ethynylferrocene (1-H) at a considerably more positive potential. Both processes produced robust modified electrodes with well-defined ferrocene-based surface cyclic voltammetry waves that remained unchanged for as many as 10(4) scans. Ferrocene derivatives in which the ethynyl moiety was separated from the cyclopentadienyl ring by an ether group showed very similar behavior. DFT calculations were performed on the relevant redox states of 1-H, 1-Li, and 1, with emphasis on the ferrocenyl vs ethynyl character of their high valence orbitals. Whereas the HOMOs of both 1-H and 1-Li have some ethynyl character, the SOMOs of the corresponding monocations are strictly ferrocenium in makeup. Predominant ethynyl character returns to the highest valence orbitals after loss of Li(+) from [1-Li](+) or loss of H(+) from [1-H](2+). These anodic processes hold promise for the controlled chemical modification of carbon and other electrode surfaces by a variety of ethynyl or alkynyl-linked organic and metal-containing systems.

Ultrafast Photoinduced Symmetry-Breaking Charge Separation and Electron Sharing in Perylenediimide Molecular Triangles.

We report on a visible-light-absorbing chiral molecular triangle composed of three covalently linked 1,6,7,12-tetra(phenoxy)perylene-3,4:9,10-bis(dicarboximide) (PDI) units. The rigid triangular architecture reduces the electronic coupling between the PDIs, so ultrafast symmetry-breaking charge separation is kinetically favored over intramolecular excimer formation, as revealed by femtosecond transient absorption spectroscopy. Photoexcitation of the PDI triangle dissolved in CH2Cl2 gives PDI(+•)-PDI(-•) in τCS = 12.0 ± 0.2 ps. Fast subsequent intramolecular electron/hole hopping can equilibrate the six possible energetically degenerate ion-pair states, as suggested by electron paramagnetic resonance/electron-nuclear double resonance spectroscopy, which shows that one-electron reduction of the PDI triangle results in complete electron sharing among the three PDIs. Charge recombination of PDI(+•)-PDI(-•) to the ground state occurs in τCR = 1.12 ± 0.01 ns with no evidence of triplet excited state formation.

Functionalizing pillar[n]arenes.

Macrocyclic chemistry has relied on the dominance of some key cavitands, including cyclodextrins, calixarenes, cyclophanes, and cucurbiturils, to advance the field of host-guest science. Very few of the many other cavitands introduced by chemists during these past few decades have been developed to near the extent of these four key players. A relatively new family of macrocycles that are becoming increasingly dominant in the field of macrocyclic chemistry are the pillar[n]arenes composed of n hydroquinone rings connected in their 2- and 5-positions by methylene bridges. This substitution pattern creates a cylindrical or pillar-like structure that has identical upper and lower rims. The preparation of pillar[n]arenes is facile, with pillar[5]- through pillar[7]arene being readily accessible and the larger macrocycles (n = 8-14) being accessible in diminishing yields. The rigid pillar[n]arene cavities are highly π-electron-rich on account of the n activated aromatic faces pointing toward their centers, allowing the cavities to interact strongly with a range of π-electron-deficient guests including pyridiniums, alkylammoniums, and imidazoliums. The substitution pattern of pillar[n]arenes bestows chirality onto the macrocycle in the form of n chiral planes. The absolute configuration of the chiral planes in pillar[n]arenes can be either fixed or rapidly undergoing inversion. The future of pillar[n]arenes is going to be dependent on their ability to fulfill specific applications. Chemical modification of the parent pillar[n]arenes lets us create functionalized hosts with anticipated chemical or physical properties. The featured potential applications of pillar[n]arenes to date are far reaching and include novel hosts with relevance to nanotechnology, materials science, and medicine. Pillar[n]arenes have an overwhelming advantage over other hosts since the number of ways available to incorporate handles into their structures are diverse and easy to implement. In this Account, we describe the routes to chemically modified pillar[n]arenes by discussing the chemistry of their functionalization: monofunctionalization, difunctionalization, rim differentiation, perfunctionalization, and phenylene substitution. We assess the synthetic complications of employing these functionalization procedures and survey the potential applications and novel properties that arise with these functionalized pillar[n]arenes. We also highlight the challenges and the synthetic approaches that have yet to be fully explored for the selective chemical modification of these hosts. Finally, we examine a related class of macrocycles and consider their future applications. We trust that this Account will stimulate the development of new methods for functionalizing these novel hosts to realize pillar[n]arene-containing compounds capable of finding applications.

Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis.

Chirality-assisted synthesis (CAS) is a general approach to control the shapes of large molecular strips. CAS is based on enantiomerically pure building blocks that are designed to strictly couple in a single geometric orientation. Fully shape-persistent structures can thus be created, even in the form of linear chains. With CAS, selective recognition between large host and guest molecules can reliably be designed de novo. To demonstrate this concept, three C-shaped strips that can embrace a pillar[5]arene macrocycle were synthesized. The pillar[5]arene bound to the strips was a better host for electron-deficient guests than the free macrocycle. Experimental and computational evidence is provided for these unique cooperative interactions to illustrate how CAS could open the door towards the precise positioning of functional groups for regulated supramolecular recognition and catalysis.

Redox switchable daisy chain rotaxanes driven by radical-radical interactions.

We report the one-pot synthesis and electrochemical switching mechanism of a family of electrochemically bistable 'daisy chain' rotaxane switches based on a derivative of the so-called 'blue box' (BB(4+)) tetracationic cyclophane cyclobis(paraquat-p-phenylene). These mechanically interlocked molecules are prepared by stoppering kinetically the solution-state assemblies of a self-complementary monomer comprising a BB(4+) ring appended with viologen (V(2+)) and 1,5-dioxynaphthalene (DNP) recognition units using click chemistry. Six daisy chains are isolated from a single reaction: two monomers (which are not formally 'chains'), two dimers, and two trimers, each pair of which contains a cyclic and an acyclic isomer. The products have been characterized in detail by high-field (1)H NMR spectroscopy in CD3CN-made possible in large part by the high symmetry of the novel BB(4+) functionality-and the energies associated with certain aspects of their dynamics in solution are quantified. Cyclic voltammetry and spectroelectrochemistry have been used to elucidate the electrochemical switching mechanism of the major cyclic daisy chain products, which relies on spin-pairing interactions between V(•+) and BB(2(•+)) radical cations under reductive conditions. These daisy chains are of particular interest as electrochemically addressable molecular switches because, in contrast with more conventional bistable catenanes and rotaxanes, the mechanical movement of the ring between recognition units is accompanied by significant changes in molecular dimensions. Whereas the self-complexed cyclic monomer-known as a [c1]daisy chain or molecular 'ouroboros'-conveys sphincter-like constriction and dilation of its ultramacrocyclic cavity, the cyclic dimer ([c2]daisy chain) expresses muscle-like contraction and expansion along its molecular length.

Assembly of supramolecular nanotubes from molecular triangles and 1,2-dihalohydrocarbons.

Precise control of molecular assembly is a challenging goal facing supramolecular chemists. Herein, we report the highly specific assembly of a range of supramolecular nanotubes from the enantiomeric triangular naphthalenediimide-based macrocycles (RRRRRR)- and (SSSSSS)-NDI-Δ and a class of similar solvents, namely, the 1,2-dihalo-ethanes and -ethenes (DXEs). Three kinds of supramolecular nanotubes are formed from the columnar stacking of NDI-Δ units with a 60° mutual rotation angle as a result of cooperative [C-H···O] interactions, directing interactions of the [X···X]-bonded DXE chains inside the nanotubes and lateral [X···π] or [π···π] interactions. They include (i) semiflexible infinite nanotubes formed in the gel state from NDI-Δ and (E)-1,2-dichloroethene, (ii) rigid infinite nonhelical nanotubes produced in the solid state from NDI-Δ and BrCH2CH2Br, ClCH2CH2Br, and ClCH2CH2I, and (iii) a pair of rigid tetrameric, enantiomeric single-handed (P)- and (M)-helical nanotubes formed in the solid state from the corresponding (RRRRRR)- and (SSSSSS)-NDI-Δ with ClCH2CH2Cl. In case (i), only the electron-rich C═C double bond of (E)-1,2-dichloroethene facilitates the gelation of NDI-Δ. In cases (ii) and (iii), the lengths of anti-DXEs determine the translation of the chirality of NDI-Δ into the helicity of nanotubes. Only ClCH2CH2Cl induces single-handed helicity into the nanotubes. The subtle interplay of noncovalent bonding interactions, resulting from the tiny structural variations involving the DXE guests, is responsible for the diverse and highly specific assembly of NDI-Δ. This research highlights the critical role that guests play in constructing assembled superstructures of hosts and offers a novel approach to creating supramolecular nanotubes.

Amino-functionalized pillar[5]arene.

The recently introduced pillar[n]arenes have provided chemists with receptors that, when incorporated into materials, confer unique properties upon them. The symmetrical rims and cylindrical shape of pillar[5]arene begs the question--can these pillar-like receptors be linked covalently end-to-end in order to create tubular structures by a growth-from-template approach? In our efforts to produce these one-dimensional extended structures, we have developed a new method of functionalizing pillar[5]arene in which one of the five hydroquinone units is converted into a diaminobenzoquinone analogue. The resulting diaminopillar[5]arene derivative, which undergoes a stereochemical inversion process that is slow on the (1)H NMR timescale, can be chemically modified yet further in a direction that is orthogonal to the plane of its methylene bridging carbons through the formation of oxazole heterocycles. This strategy has been employed to create rigid oligomers that resemble one-dimensional tubular arrays. As a proof-of-principle, a rigid pillar[5]arene dimer has been isolated and characterized in the solution state as a 1:1 complex with an extended viologen for which it acts as a receptor.

Synthesis and structural data of tetrabenzo[8]circulene.

In 1976, the first attempted synthesis of the saddle-shaped molecule [8]circulene was reported. The next 37 years produced no advancement towards the construction of this complicated molecule. But remarkably, over the last six months, a flurry of progress has been made with two groups reporting independent and strikingly different strategies for the synthesis of [8]circulene derivatives. Herein, we present a third synthetic method, in which we target tetrabenzo[8]circulene. Our approach employs a Diels-Alder reaction and a palladium-catalyzed arylation reaction as the key steps. Despite calculations describing the instability of [8]circulene, coupled with the reported instability of synthesized derivatives of the parent molecule, the addition of four fused benzenoid rings around the periphery of the molecule provides a highly stable structure. This increased stability over the parent [8]circulene was predicted by using Clar's theory of aromatic sextets and is a result of the compound becoming fully benzenoid upon incorporation of these additional rings. The synthesized compound exhibits remarkable stability under ambient conditions-even at elevated temperatures-with no signs of decomposition over several months. The solid-state structure of this compound is significantly twisted compared to the calculated structure primarily as a result of crystal-packing forces in the solid state. Despite this contortion from the lowest-energy structure, a range of structural data is presented confirming the presence of localized aromaticity in this large polycyclic aromatic hydrocarbon.

Second-sphere coordination revisited.

Since the concept of second-sphere coordination of transition metal complexes was introduced by Alfred Werner in 1913, the investigation of the phenomenon has emerged as a major thrust area - a significant part of which is based on the use of transition metal complexes as first coordination spheres as well as macrocycles as second-sphere ligands in promoting the assembly and dictating the main structural features of the second-sphere adducts. In this review, we first of all summarize the work carried out in our laboratory on the second-sphere coordination chemistry of transition metal complexes in the past three decades. Significant advances of relevance to the second-sphere coordination chemistry of square-planar gold complex anions with cyclodextrins are presented as the second part of this review.

Electron delocalization in a rigid cofacial naphthalene-1,8:4,5-bis(dicarboximide) dimer.

Investigating through-space electronic communication between discrete cofacially oriented aromatic π-systems is fundamental to understanding assemblies as diverse as double-stranded DNA, organic photovoltaics and thin-film transistors. A detailed understanding of the electronic interactions involved rests on making the appropriate molecular compounds with rigid covalent scaffolds and π-π distances in the range of ca. 3.5 Å. Reported herein is an enantiomeric pair of doubly-bridged naphthalene-1,8:4,5-bis(dicarboximide) (NDI) cyclophanes and the characterization of four of their electronic states, namely 1) the ground state, 2) the exciton coupled singlet excited state, 3) the radical anion with strong through-space interactions between the redox-active NDI molecules, and 4) the diamagnetic diradical dianion using UV/Vis/NIR, EPR and ENDOR spectroscopies in addition to X-ray crystallography. Despite the unfavorable Coulombic repulsion, the singlet diradical dianion dimer of NDI shows a more pronounced intramolecular π-π stacking interaction when compared with its neutral analog.

A square-planar tetracoordinate oxygen-containing Ti4O17 cluster stabilized by two 1,1'-ferrocenedicarboxylato ligands.

By introducing steric constraints into molecular compounds, it is possible to achieve atypical coordination geometries for the elements. Herein, we demonstrate that a titanium-oxo cluster [{Ti4(µ4-O)(µ2-O)2}(OPr(i))6(fdc)2], which possesses a unique edge-sharing Ti4O17 octahedron tetramer core, is stabilized by the constraints produced by two orthogonal 1,1'-ferrocenedicarboxylato (fdc) ligands. As a result, a square-planar tetracoordinate oxygen (ptO) can be generated. The bonding pattern of this unusual anti-van't Hoff/Le Bel oxygen, which has been probed by theoretical calculations, can be described by two horizontally σ-bonded 2p(x) and 2p(y) orbitals along with one perpendicular nonbonded 2p(z) orbital. While the two ferrocene units are separated spatially by the ptO with an Fe⋅⋅⋅Fe separation of 10.4 Å, electronic communication between them still takes place as revealed by the cluster's two distinct one-electron electrochemical oxidation processes.