Ligand design by targeting a binding site water

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A_2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A_2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.     

Facilitated inversion complicates the stereodynamics of an SN2 reaction at nitrogen center

Bimolecular nucleophilic substitution (S_N2) reactions at carbon center are well known to proceed with the stereospecific Walden-inversion mechanism. Reaction dynamics simulations on a newly developed high-level ab initio analytical potential energy surface for the F⁻ + NH₂Cl nitrogen-centered S_N2 and proton-transfer reactions reveal a hydrogen-bond-formation-induced multiple-inversion mechanism undermining the stereospecificity of the N-centered S_N2 channel. Unlike the analogous F⁻ + CH₃Cl S_N2 reaction, F⁻ + NH₂Cl → Cl⁻ + NH₂F is indirect, producing a significant amount of NH₂F with retention, as well as inverted NH₂Cl during the timescale within the unperturbed NH₂Cl molecule gets inverted with only low probability, showing the important role of facilitated inversions via an FH…NHCl⁻-like transition state. Proton transfer leading to HF + NHCl⁻ is more direct and becomes the dominant product channel at higher collision energies.

Multiple-inversion, the analogue of the double-inversion pathway recently revealed for S_N2@C, is the key mechanism in S_N2 at N center undermining stereospecificity.     

Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABABR1a

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA_BR1a) and modulate its synaptic transmission. The work provided an important structural foundation for the modulation of GABA_BR1a; however, the detailed molecular interaction mechanism, crucial for future drug design, remains elusive. Here, we further investigated the dynamical interactions between sAPP peptides and the natively unstructured sushi 1 domain using all-atom molecular dynamics simulations, for both the 17-residue sAPP peptide (APP 17-mer) and its minimally active 9 residue segment (APP 9-mer). We then explored mutations of the APP 9-mer with rigorous free energy perturbation (FEP) calculations. Our in silico mutagenesis studies revealed key residues (D4, W6, and W7) responsible for the binding with the sushi 1 domain. More importantly, one double mutation based on different vertebrate APP sequences from evolution exhibited a stronger binding (ΔΔG = −1.91 ± 0.66 kcal mol⁻¹), indicating a potentially enhanced GABA_BR1a modulator. These large-scale simulations may provide new insights into the binding mechanism between sAPP and the sushi 1 domain, which could open new avenues in the development of future GABA_BR1a-specific therapeutics.

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA_BR1a) and modulate its synaptic transmission.     

Engineering of TMDC–OSC hybrid interfaces: the thermodynamics of unitary and mixed acene monolayers on MoS2

Hybrid systems of two-dimensional (2D) materials such as transition metal dichalcogenides (TMDCs) and organic semiconductors (OSCs) have become subject of great interest for future device architectures. Although OSC–TMDC hybrid systems have been used in first device demonstrations, the precise preparation of ultra-thin OSC films on TMDCs has not been addressed. Due to the weak van der Waals interaction between TMDCs and OSCs, this requires precise knowledge of the thermodynamics at hand. Here, we use temperature-programmed desorption (TPD) and Monte Carlo (MC) simulations of TPD traces to characterize the desorption kinetics of pentacene (PEN) and perfluoropentacene (PFP) on MoS₂ as a model system for OSCs on TMDCs. We show that the monolayers of PEN and PFP are thermally stabilized compared to their multilayers, which allows preparation of nominal monolayers by selective desorption of multilayers. This stabilization is, however, caused by entropy due to a high molecular mobility rather than an enhanced molecule–substrate bond. Consequently, the nominal monolayers are not densely packed films. Molecular mobility can be suppressed in mixed monolayers of PEN and PFP that, due to intermolecular attraction, form highly ordered films as shown by scanning tunneling microscopy. Although this reduces the entropic stabilization, the intermolecular attraction further stabilizes mixed films.

Entropic stabilization enables the fabrication of (perfluoro-)pentacene monolayers on MoS₂ by selective multilayer desorption but reduces order and packing density. Intermolecular attraction allows to create ordered close-packed molecular monolayers.     

Selective modification of two-dimensional MoS2 nanosheets by polymer grafting

We reported on the direct creation of polymer brushes on two-dimensional molybdenum disulfide via the formation of C-S bond by UV-induced photopolymerization. The functionalization can be manipulated in forming polymer grafts on one side or both sides of the nanosheets.     

A reconstructed porous copper surface promotes selectivity and efficiency toward C2 products by electrocatalytic CO2 reduction

Electrocatalytic synthesis of multicarbon (C₂₊) products from CO₂ reduction suffers from poor selectivity and low energy efficiency. Herein, a facile oxidation–reduction cycling method is adopted to reconstruct the Cu electrode surface with the help of halide anions. The surface composed of entangled Cu nanowires with hierarchical pores is synthesized in the presence of I⁻, exhibiting a C₂ faradaic efficiency (FE) of 80% at −1.09 V vs. RHE. A partial current density of 21 mA cm⁻² is achieved with a C₂ half-cell power conversion efficiency (PCE) of 39% on this electrode. Such high selective C₂ production is found to mainly originate from CO intermediate enrichment inside hierarchical pores rather than the surface lattice effect of the Cu electrode.

The Cu electrode surface is reconstructed by a halide anion assisted method for promoting CO₂ reduction.     

Structure and redox tuning of gas adsorption properties in calixarene-supported Fe(ii)-based porous cages

We describe the synthesis of Fe(ii)-based octahedral coordination cages supported by calixarene capping ligands. The most porous of these molecular cages has an argon accessible BET surface area of 898 m² g⁻¹ (1497 m² g⁻¹ Langmuir). The modular synthesis of molecular cages allows for straightforward substitution of both the bridging carboxylic acid ligands and the calixarene caps to tune material properties. In this context, the adsorption enthalpies of C₂/C₃ hydrocarbons ranged from −24 to −46 kJ mol⁻¹ at low coverage, where facile structural modifications substantially influence hydrocarbon uptakes. These materials exhibit remarkable stability toward oxidation or decomposition in the presence of air and moisture, but application of a suitable chemical oxidant generates oxidized cages over a controlled range of redox states. This provides an additional handle for tuning the porosity and stability of the Fe cages.

We describe the synthesis of Fe(ii)-based coordination cages whose stability and gas adsorption properties can be tuned through structural modifications and redox reactivity.     

Highly efficient visible-light photocatalytic ethane oxidation into ethyl hydroperoxide as a radical reservoir

Photocatalytic ethane conversion into value-added chemicals is a great challenge especially under visible light irradiation. The production of ethyl hydroperoxide (CH₃CH₂OOH), which is a promising radical reservoir for regulating the oxidative stress in cells, is even more challenging due to its facile decomposition. Here, we demonstrated a design of a highly efficient visible-light-responsive photocatalyst, Au/WO₃, for ethane oxidation into CH₃CH₂OOH, achieving an impressive yield of 1887 μmol g_cat⁻¹ in two hours under visible light irradiation at room temperature for the first time. Furthermore, thermal energy was introduced into the photocatalytic system to increase the driving force for ethane oxidation, enhancing CH₃CH₂OOH production by six times to 11 233 μmol g_cat⁻¹ at 100 °C and achieving a significant apparent quantum efficiency of 17.9% at 450 nm. In addition, trapping active species and isotope-labeling reactants revealed the reaction pathway. These findings pave the way for scalable ethane conversion into CH₃CH₂OOH as a potential anticancer drug.

Highly efficient visible-light driven photocatalytic oxidation of ethane into ethyl hydroperoxide was realized for the first time over Au/WO₃.     

Transition-metal-mediated reduction and reversible double-cyclization of cyanuric triazide to an asymmetric bitetrazolate involving cleavage of the six-membered aromatic ring

Cyanuric triazide reacts with several transition metal precursors, extruding one equivalent of N₂ and reducing the putative diazidotriazeneylnitrene species by two electrons, which rearranges to N-(1′H-[1,5′-bitetrazol]-5-yl)methanediiminate (biTzI²⁻) dianionic ligand, which ligates the metal and dimerizes, and is isolated from pyridine as [M(biTzI)]₂Py₆ (M = Mn, Fe, Zn, Cu, Ni). Reagent scope, product analysis, and quantum chemical calculations were combined to elucidate the mechanism of formation as a two-electron reduction preceding ligand rearrangement.

Cyanuric triazide reacts with transition metal precursors, extruding N₂ and reducing the ligand by two electrons, which breaks an aromatic ring and rearranges to a bitetrazolylmethanediiminate (biTzI²⁻) ligand, forming two new aromatic rings.     

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design. However, their broad uptake and impact is held back by the notoriously complex setup of the calculations. Only a few tools other than the free energy perturbation approach by Schrödinger Inc. (referred to as FEP+) currently enable end-to-end application. Here, we present for the first time an approach based on the open-source software pmx that allows to easily set up and run alchemical calculations for diverse sets of small molecules using the GROMACS MD engine. The method relies on theoretically rigorous non-equilibrium thermodynamic integration (TI) foundations, and its flexibility allows calculations with multiple force fields. In this study, results from the Amber and Charmm force fields were combined to yield a consensus outcome performing on par with the commercial FEP+ approach. A large dataset of 482 perturbations from 13 different protein–ligand datasets led to an average unsigned error (AUE) of 3.64 ± 0.14 kJ mol⁻¹, equivalent to Schrödinger''s FEP+ AUE of 3.66 ± 0.14 kJ mol⁻¹. For the first time, a setup is presented for overall high precision and high accuracy relative protein–ligand alchemical free energy calculations based on open-source software.

Relative ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design.     

Enantioselective total synthesis of (−)-myrifabral A and B

A catalytic enantioselective approach to the Myrioneuron alkaloids (−)-myrifabral A and (−)-myrifabral B is described. The synthesis was enabled by a palladium-catalyzed enantioselective allylic alkylation, that generates the C(10) all-carbon quaternary center. A key N-acyl iminium ion cyclization forged the cyclohexane fused tricyclic core, while vinyl boronate cross metathesis and oxidation afforded the lactol ring of (−)-myrifabral A. Adaptation of previously reported conditions allowed for the conversion of (−)-myrifabral A to (−)-myrifabral B.

A catalytic enantioselective approach to the Myrioneuron alkaloids (−)-myrifabral A and (−)-myrifabral B is described.     

Fluorescent probe for the imaging of superoxide and peroxynitrite during drug-induced liver injury

Drug-induced liver injury (DILI) is an important cause of potentially fatal liver disease. Herein, we report the development of a molecular probe (LW-OTf) for the detection and imaging of two biomarkers involved in DILI. Initially, primary reactive oxygen species (ROS) superoxide (O₂˙⁻) selectively activates a near-infrared fluorescence (NIRF) output by generating fluorophore LW-OH. The C C linker of this hemicyanine fluorophore is subsequently oxidized by reactive nitrogen species (RNS) peroxynitrite (ONOO⁻), resulting in cleavage to release xanthene derivative LW-XTD, detected using two-photon excitation fluorescence (TPEF). An alternative fluorescence pathway can occur through cleavage of LW-OTf by ONOO⁻ to non-fluorescent LW-XTD-OTf, which can react further with the second analyte O₂˙⁻ to produce the same LW-XTD fluorescent species. By combining NIRF and TPEF, LW-OTf is capable of differential and simultaneous detection of ROS and RNS in DILI using two optically orthogonal channels. Probe LW-OTf could be used to detect O₂˙⁻ or O₂˙⁻ and ONOO⁻ in lysosomes stimulated by 2-methoxyestradiol (2-ME) or 2-ME and SIN-1 respectively. In addition, we were able to monitor the chemoprotective effects of tert-butylhydroxyanisole (BHA) against acetaminophen (APAP) toxicity in living HL-7702 cells. More importantly, TPEF and NIRF imaging confirmed an increase in levels of both O₂˙⁻ and ONOO⁻ in mouse livers during APAP-induced DILI (confirmed by hematoxylin and eosin (H&E) staining).

Drug-induced liver injury (DILI) is an important cause of potentially fatal liver disease.     

Light- and temperature-assisted spin state annealing: accessing the hidden multistability

Among responsive multistable materials, spin crossover (SCO) systems are of particular interest for stabilizing multiple spin states with various stimulus inputs and physical outputs. Here, in a 2D Hofmann-type coordination polymer, [Fe(isoq)₂{Au(CN)₂}₂] (isoq = isoquinoline), a medium-temperature annealing process is introduced after light/temperature stimulation, which accesses the hidden multistability of the spin state. With the combined effort of magnetic, crystallographic and Mössbauer spectral investigation, these distinct spin states are identified and the light- and temperature-assisted transition pathways are clarified. Such excitation-relaxation and trapping-relaxation joint mechanisms, as ingenious interplays between the kinetic and thermodynamic effects, uncover hidden possibilities for the discovery of multistable materials and the development of multistate intelligent devices.

Two new two-stage manipulation protocols, namely light- and temperature-assisted spin state annealing (LASSA/TASSA), are applied to a spin crossover coordination polymer, [Fe(isoq)₂{Au(CN)₂}₂], revealing the hidden multistability of spin states.     

Observations of tetrel bonding between sp3-carbon and THF

We report the direct observation of tetrel bonding interactions between sp³-carbons of the supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas and crystalline phase. The intermolecular contact is established via σ-holes and is driven mainly by electrostatic forces. The complex manifests distinct binding geometries when captured in the crystalline phase and in the gas phase. We elucidate these binding trends using complementary gas phase quantum chemical calculations and find a total binding energy of −11.2 kcal mol⁻¹ for the adduct. Our observations pave the way for novel strategies to engineer sp³-C centred non-covalent bonding schemes for supramolecular chemistry.

sp³-C⋯THF tetrel bonding was observed in the crystalline state and in the gas phase. Density functional calculations revealed interaction energies up to −11.2 kcal mol⁻¹ and showed that these adducts are held together mainly by electrostatics.     

An earth-abundant bimetallic catalyst coated metallic nanowire grown electrode with platinum-like pH-universal hydrogen evolution activity at high current density

A self-supported and flexible current collector solely made of earth-abundant elements, NiCo layered double hydroxide (LDH) wrapped around Cu nanowires (Cu-Ws) grown on top of commercially available Cu mesh (Cu-m), outperforms the benchmark 40 wt% Pt/C in catalyzing the electrochemical hydrogen evolution reaction (HER). The Cu-m/Cu-W/NiCo-LDH cathode operates both in acidic and alkaline media exhibiting high turnover frequencies (TOF) at 30 mV (0.3 H₂ s⁻¹ in 1 M KOH and 0.32 H₂ s⁻¹ in 0.5 M H₂SO₄, respectively) and minimal overpotentials of 15 ± 6 mV in 1 M KOH and 27 ± 2 mV in 0.5 M H₂SO₄ at −10 mA cm⁻². Cu-m/Cu-W/NiCo-LDH outperforms the activity of 40 wt% Pt/C that needs overpotentials of 22 and 18 mV in 1 M KOH and 0.5 M H₂SO₄, respectively. With a tremendous advantage over Pt/C in triggering proton reduction with fast kinetics, similar mass activity and pH-universality, the current collector demonstrates outstanding operational durability even at above −1 A cm⁻². The high density of electronic states near the Fermi energy level of Cu-Ws is found to be a pivotal factor for efficient electron transfer to the NiCo-LDH catalyst. This class of self-supported electrodes is expected to trigger rapid progress in developing high performance energy conversion and storage devices.

A flexible self-supported electrode made of earth-abundant elements, NiCo layered double hydroxide wrapped around Cu nanowires grown on Cu mesh, outperforms the benchmark 40 wt% Pt/C in catalyzing electrochemical hydrogen evolution reaction.     

Anion mediated,tunable isoguanosine self-assemblies: decoding the conformation influence and solvent effects

Systematic investigations were performed with various substituted groups at C8 purine and ribose. A series of isoG analogs, C8-phenyl substituted isoG were synthesized and applied for Cs⁺ coordination. The structural proximity between purine and ribose limited pentaplex formation for C8-phenyl substituted isoG derivatives. Based on this observation, deoxy isoG derivative with modification on ribose (tert-butyldimethylsilyl ether) was applied to assemble with the Cs⁺ cation. Critical solvent (CDCl₃ and CD₃CN) and anion (BPh₄⁻, BARF⁻, and PF₆⁻) effects were revealed, leading to the controllable formation of various stable isoG pentaplexes, including singly charged decamer, doubly charged decamer, and 15-mer, etc. Finally, the X-ray crystal structure of [isoG₂₀Cs₃]³⁺(BARF⁻)₃ was successfully obtained, which is the first example of multiple-layer deoxy isoG binding with the Cs⁺ cation, providing solid evidence of this new isoG ionophore beyond two-layer sandwich self-assembly.

The first example of multiple-layer deoxy isoG self-assembly was characterized by X-ray crystal structure. Critical solvent and anion effects were revealed, leading to the controllable formation of various stable isoG assemblies.     

Vertically Grown Few-Layer MoS2 Nanosheets on Hierarchical Carbon Nanocages for Pseudocapacitive Lithium Storage with Ultrahigh-Rate Capability and Long-Term Recyclability

Molybdenum disulfide (MoS₂) is an intensively studied anode material for lithium-ion batteries (LIBs) owing to its high theoretical capacity, but it is still confronted by severe challenges of unsatisfactory rate capability and cycle life. Herein, few-layer MoS₂ nanosheets, vertically grown on hierarchical carbon nanocages (hCNC) by a facile hydrothermal method, introduce pseudocapacitive lithium storage owing to the highly exposed MoS₂ basal planes, enhanced conductivity, and facilitated electrolyte access arising from good hybridization with hCNC. Thus, the optimized MoS₂/hCNC exhibits reversible capacities of 1670 mAh g⁻¹ at 0.1 A g⁻¹ after 50 cycles, 621 mAh g⁻¹ at 5.0 A g⁻¹ after 500 cycles, and 196 mAh g⁻¹ at 50 A g⁻¹ after 2500 cycles, which are among the best for MoS₂-based anode materials. The specific power and specific energy, which can reach 16.1 kW and 252.8 Wh after 3000 cycles, respectively, indicate great potential in high-power and long-life LIBs. These findings suggest a promising strategy for exploring advanced anode materials with high reversible capacity, high-rate capability, and long-term recyclability.     

Uncovering an oxide ion substitution for the OH− + CH3F reaction

Theoretical investigations on chemical reactions allow us to understand the dynamics of the possible pathways and identify new unexpected routes. Here, we develop a global analytical potential energy surface (PES) for the OH⁻ + CH₃F reaction in order to perform high-level dynamics simulations. Besides bimolecular nucleophilic substitution (S_N2) and proton abstraction, our quasi-classical trajectory computations reveal a novel oxide ion substitution leading to the HF + CH₃O⁻ products. This exothermic reaction pathway occurs via the CH₃OH⋯F⁻ deep potential well of the S_N2 product channel as a result of a proton abstraction from the hydroxyl group by the fluoride ion. The present detailed dynamics study of the OH⁻ + CH₃F reaction focusing on the surprising oxide ion substitution demonstrates how incomplete our knowledge is of fundamental chemical reactions.

Reaction dynamics simulations on a high-level ab initio analytical potential energy surface reveal a novel oxide ion substitution channel for the OH⁻ + CH₃F reaction.     

Single-molecule junctions of multinuclear organometallic wires: long-range carrier transport brought about by metal–metal interaction

Here, we report multinuclear organometallic molecular wires having (2,5-diethynylthiophene)diyl-Ru(dppe)₂ repeating units. Despite the molecular dimensions of 2–4 nm the multinuclear wires show high conductance (up to 10⁻² to 10⁻³G₀) at the single-molecule level with small attenuation factors (β) as revealed by STM-break junction measurements. The high performance can be attributed to the efficient energy alignment between the Fermi level of the metal electrodes and the HOMO levels of the multinuclear molecular wires as revealed by DFT–NEGF calculations. Electrochemical and DFT studies reveal that the strong Ru–Ru interaction through the bridging ligands raises the HOMO levels to access the Fermi level, leading to high conductance and small β values.

Multinuclear organometallic molecular wires having (diethynylthiophene)diyl-Ru(dppe)₂ repeating units show high conductance with small attenuation factors. The strong Ru–Ru interaction is the key for the long-range carrier transport.