When will RNA get its AlphaFold moment?

The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches. We believe that there are challenges preventing the successful development of deep learning-based methods like AlphaFold for RNA in the short term. Broadly speaking, the challenges are the limited number of structures and alignments making data-hungry deep learning methods unlikely to succeed. Additionally, there are several issues with the existing structure and sequence data, as they are often of insufficient quality, highly biased and missing key information. Here, we discuss these challenges in detail and suggest some steps to remedy the situation. We believe that it is possible to create an accurate RNA structure prediction method, but it will require solving several data quality and volume issues, usage of data beyond simple sequence alignments, or the development of new less data-hungry machine learning methods.

New Section Editor of Acta Crystallographica, Section B.

Introducing the new Section Editor of Acta Crystallographica Section B.

Copepod life history evolution under high- and low-food regimes.

Copepods play a critical role in the carbon cycle of the planet - they mediate the sequestration of carbon into the deep ocean and are the trophic link between phytoplankton and marine food webs. Global change stressors that decrease copepod productivity create the potential for catastrophic positive feedback loops. Accordingly, a growing list of studies examine the evolutionary capacity of copepods to adapt to the two primary stressors associated with global change: warmer temperatures and lower pH. But the evolutionary capacity of copepods to adapt to changing food regimes, the third major stressor associated with global change, remains unknown. We used experimental evolution to explore how a 10-fold difference in food availability affects life history evolution in the copepod, Tisbe sp. over 2 years, and spanning 30+ generations. Different food regimes evoked evolutionary responses across the entire copepod life history: we observed evolution in body size, size-fecundity relationships and offspring investment strategies. Our results suggest that changes to food regimes reshape life histories and that cryptic evolution in traits such as body size is likely. We demonstrate that evolution in response to changes in ocean productivity will alter consumer life histories and may distort trophic links in marine foodchains. Evolution in response to changing phytoplankton productivity may alter the efficacy of the global carbon pump in ways that have not been anticipated until now.

Coordination chemistry of nitrile-functionalized mixed thia-aza macrocycles [9]aneN2S and [9]aneNS2 towards silver(I).

The coordination chemistry towards silver(I) of the small-ring macrocycles [9]aneN2S (1-thia-4,7-diazacyclononane) and [9]aneNS2 (1,4-dithia-7-azacyclononane) incorporating nitrile-functionalized pendant arms is considered both in the presence and the absence of exogenous bridging ligands. The aim is to understand the influence of the number and length of the pendant arms on the nuclearity and dimensionality of the resulting complexes. The X-ray crystal structures of the complexes bis[4,7-bis(cyanomethyl)-1-thia-4,7-diazacyclononane-κ3N,N',S]silver(I) tetrafluoridoborate, [Ag(C10H16N4S)2]BF4 or [Ag(L1)2]BF4, [4,7-bis(2-cyanoethyl)-1-thia-4,7-diazacyclononane-κ3N,N',S](thiocyanato-κS)silver(I), [Ag(C12H20N4S)(NCS)] or [Ag(L2)(SCN)], and µ-thiocyanato-κ2S:S-bis{[7-(2-cyanoethyl)-1,4-dithia-7-azacyclononane-κ3N,S,S']silver(I)} tetrafluoridoborate, [Ag2(C9H16N2S2)2(SCN)]BF4 or [Ag2(L3)2(µ-SCN)]BF4, are discussed in relation to analogous compounds in the literature.

Exceptional Packing Density of Ammonia in a Dual-Functionalized Metal-Organic Framework.

We report the reversible adsorption of ammonia (NH3) up to 9.9 mmol g-1 in a robust Al-based metal-organic framework, MFM-303(Al), which is functionalized with free carboxylic acid and hydroxyl groups. The unique pore environment decorated with these acidic sites results in an exceptional packing density of NH3 at 293 K (0.801 g cm-3) comparable to that of solid NH3 at 193 K (0.817 g cm-3). In situ synchrotron X-ray diffraction and inelastic neutron scattering reveal the critical role of free -COOH and -OH groups in immobilizing NH3 molecules. Breakthrough experiments confirm the excellent performance of MFM-303(Al) for the capture of NH3 at low concentrations under both dry and wet conditions.

Can Serendipity Still Hold Any Surprises in the Coordination Chemistry of Mixed-Donor Macrocyclic Ligands? The Case Study of Pyridine-Containing 12-Membered Macrocycles and Platinum Group Metal Ions PdII, PtII, and RhIII.

This study investigates the coordination chemistry of the tetradentate pyridine-containing 12-membered macrocycles L1-L3 towards Platinum Group metal ions PdII, PtII, and RhIII. The reactions between the chloride salts of these metal ions and the three ligands in MeCN/H2O or MeOH/H2O (1:1 v/v) are shown, and the isolated solid compounds are characterized, where possible, by mass spectroscopy and 1H- and 13C-NMR spectroscopic measurements. Structural characterization of the 1:1 metal-to-ligand complexes [Pd(L1)Cl]2[Pd2Cl6], [Pt(L1)Cl](BF4), [Rh(L1)Cl2](PF6), and [Rh(L3)Cl2](BF4)·MeCN shows the coordinated macrocyclic ligands adopting a folded conformation, and occupying four coordination sites of a distorted square-based pyramidal and octahedral coordination environment for the PdII/PtII, and RhIII complexes, respectively. The remaining coordination site(s) are occupied by chlorido ligands. The reaction of L3 with PtCl2 in MeCN/H2O gave by serendipity the complex [Pt(L3)(m-1,3-MeCONH)PtCl(MeCN)](BF4)2·H2O, in which two metal centers are bridged by an amidate ligand at a Pt1-Pt2 distance of 2.5798(3) Å and feature one square-planar and one octahedral coordination environment. Density Functional Theory (DFT) calculations, which utilize the broken symmetry approach (DFT-BS), indicate a singlet d8-d8 PtII-PtII ground-state nature for this compound, rather than the alleged d9-d7 PtI-PtIII mixed-valence character reported for related dinuclear Pt-complexes.

Selective Gas Uptake and Rotational Dynamics in a (3,24)-Connected Metal-Organic Framework Material.

The desolvated (3,24)-connected metal-organic framework (MOF) material, MFM-160a, [Cu3(L)(H2O)3] [H6L = 1,3,5-triazine-2,4,6-tris(aminophenyl-4-isophthalic acid)], exhibits excellent high-pressure uptake of CO2 (110 wt% at 20 bar, 298 K) and highly selective separation of C2 hydrocarbons from CH4 at 1 bar pressure. Henry's law selectivities of 79:1 for C2H2:CH4 and 70:1 for C2H4:CH4 at 298 K are observed, consistent with ideal adsorption solution theory (IAST) predictions. Significantly, MFM-160a shows a selectivity of 16:1 for C2H2:CO2. Solid-state 2H NMR spectroscopic studies on partially deuterated MFM-160-d12 confirm an ultra-low barrier (∼2 kJ mol-1) to rotation of the phenyl group in the activated MOF and a rotation rate 5 orders of magnitude slower than usually observed for solid-state materials (1.4 × 106 Hz cf. 1011-1013 Hz). Upon introduction of CO2 or C2H2 into desolvated MFM-160a, this rate of rotation was found to increase with increasing gas pressure, a phenomenon attributed to the weakening of an intramolecular hydrogen bond in the triazine-containing linker upon gas binding. DFT calculations of binding energies and interactions of CO2 and C2H2 around the triazine core are entirely consistent with the 2H NMR spectroscopic observations.

Guest-Controlled Incommensurate Modulation in a Meta-Rigid Metal-Organic Framework Material.

Structural transitions of host systems in response to guest binding dominate many chemical processes. We report an unprecedented type of structural flexibility within a meta-rigid material, MFM-520, which exhibits a reversible periodic-to-aperiodic structural transition resulting from a drastic distortion of a [ZnO4N] node controlled by the specific host-guest interactions. The aperiodic crystal structure of MFM-520 has no three-dimensional (3D) lattice periodicity but shows translational symmetry in higher-dimensional (3 + 2)D space. We have directly visualized the aperiodic state which is induced by incommensurate modulation of the periodic framework of MFM-520·H2O upon dehydration to give MFM-520. Filling MFM-520 with CO2 and SO2 reveals that, while CO2 has a minimal structural influence, SO2 can further modulate the structure incommensurately. MFM-520 shows exceptional selectivity for SO2 under flue-gas desulfurization conditions, and the facile release of captured SO2 from MFM-520 enabled the conversion to valuable sulfonamide products. MFM-520 can thus be used as a highly efficient capture and delivery system for SO2.

Porous Metal-Organic Polyhedra: Morphology, Porosity, and Guest Binding.

Designing porous materials which can selectively adsorb CO2 or CH4 is an important environmental and industrial goal which requires an understanding of the host-guest interactions involved at the atomic scale. Metal-organic polyhedra (MOPs) showing permanent porosity upon desolvation are rarely observed. We report a family of MOPs (Cu-1a, Cu-1b, Cu-2), which derive their permanent porosity from cavities between packed cages rather than from within the polyhedra. Thus, for Cu-1a, the void fraction outside the cages totals 56% with only 2% within. The relative stabilities of these MOP structures are rationalized by considering their weak nondirectional packing interactions using Hirshfeld surface analyses. The exceptional stability of Cu-1a enables a detailed structural investigation into the adsorption of CO2 and CH4 using in situ X-ray and neutron diffraction, coupled with DFT calculations. The primary binding sites for adsorbed CO2 and CH4 in Cu-1a are found to be the open metal sites and pockets defined by the faces of phenyl rings. More importantly, the structural analysis of a hydrated sample of Cu-1a reveals a strong hydrogen bond between the adsorbed CO2 molecule and the Cu(II)-bound water molecule, shedding light on previous empirical and theoretical observations that partial hydration of metal-organic framework (MOF) materials containing open metal sites increases their uptake of CO2. The results of the crystallographic study on MOP-gas binding have been rationalized using DFT calculations, yielding individual binding energies for the various pore environments of Cu-1a.

Aza- and Mixed Thia/Aza-Macrocyclic Receptors with Quinoline-Bearing Pendant Arms for Optical Discrimination of Zinc(II) or Cadmium(II) Ions.

The synthesis and coordination properties of two fluorescent chemosensors, featuring [9]aneN3 (1,4,7-triazacyclononane; L1) and [12]aneNS3 (1-aza-4,7,10-trithiacyclododecane; L2) as receptor units, and a quinoline pendant arm with an amide group as a functional group spacer are described. The optical responses of L1 and L2 in the presence of several metal ions were analysed in MeCN/H2 O (1 : 4 v/v) solutions. A selective chelation enhancement of fluorescence (CHEF) effect was observed in the presence of Zn2+ in the case of L1, and in the presence of Cd2+ in the case of L2, following the formation of a 1 : 1 and a 1 : 2 metal/ligand complex, respectively, which was also confirmed by potentiometric measurements. 1 H and 13 C NMR measurements in CD3 CN/CDCl3 in combination with molecular mechanics calculations show that for both complexes of L1 and L2 with Zn2+ and Cd2+ , respectively, the coordination of the carbonyl group from the pendant arm could be the origin of the observed optical selectivity.

A transition metal-gallium cluster formed via insertion of "GaI".

The reaction between a two-coordinate Co(ii) diaryl complex and "GaI" affords 2,6-Pmp2C6H3CoGa3I5, in a new geometry for a heavier group 13-transition metal cluster. Experimental and computational investigations show that this compound is best described as a nido metalla-group 13 cluster.

Innovative Molecular Design Strategies in Materials Science Following the Aurophilicity Concept.

The past decade has seen a diverse range of breakthrough inventions that are derived from gold complexes, including the application of aurophilic interactions in the preparation of stimuli-responsive materials. Examples of these gold-based materials include aurophilicity-induced metallogelators, mechanochromic, thermochromic, vapochromic, and solvatochromic luminescent compounds, as well as sensory materials for the detection of metal ions. Sophisticated properties of gold complexes with Au···Au contacts have been explored at the edge of several disciplines including chemistry, crystallography, molecular engineering and advanced materials. As science paves its way to innovation, cross-disciplinary research moves from being a luxury to becoming a necessity. Development of the concept of aurophilicity and its use in designing novel materials is a true example of innovation on a multidisciplinary platform. As miniaturization continues to influence the next generation of technological advancement, using the properties of molecules as chemical tools to enable such developments becomes extremely important. In this Review, recent examples of gold complexes which exhibit a response to external stimuli have been collected and some of their potential applications discussed for selected cases.

Electron crystallography.

A Special Issue on the topic of Electron Crystallography, now available in the August 2019 issue of Acta Crystallographica, Section B, contains contributions which we hope will interest readers of IUCrJ.

A Highly Active Bidentate Magnesium Catalyst for Amine-Borane Dehydrocoupling: Kinetic and Mechanistic Studies.

A magnesium complex (1) featuring a bidentate aminopyridinato ligand is a remarkably selective catalyst for the dehydrocoupling of amine-boranes. This reaction proceeds to completion with low catalyst loadings (1 mol %) under mild conditions (60 °C), exceeding previously reported s-block systems in terms of selectivity, rate, and turnover number (TON). Mechanistic studies by in situ NMR analysis reveals the reaction to be first order in both catalyst and substrate. A reaction mechanism is proposed to account for these findings, with the high TON of the catalyst attributed to the bidentate nature of the ligand, which allows for reversible deprotonation of the substrate and regeneration of 1 as a stable resting state.

[9]aneN3-based fluorescent receptors for metal ion sensing, featuring urea and amide functional groups.

We describe here the synthesis and coordination properties of three new derivatives of [9]aneN3 containing phenyl/quinoline pendant arm derivatives (L1, L2 and L3, respectively) also featuring urea (L1-L2) or amide (L3) functions as "non-innocent" spacers. At first, L1, L2 and L3 were studied considering the interaction with a series of anions (AcO-, BzO-, H2PO4-, F-, and Cl-) by means of 1H NMR measurements. Subsequently, the optical responses of L2 and L3 in the presence of several metal ions Cd2+, Co2+, Cu2+, Fe3+, Hg2+, K+, Mg2+, Mn2+, Ni2+, Zn2+ and Pb2 were analysed in MeCN/H2O (4 : 1 v/v). As observed by spectrophotometric and spectrofluorimetric titrations, there were significant changes in the absorbance and fluorescent emission of L2 upon addition of increasing amounts of Cd2+, Zn2+, Pb2+ and Cu2+ in MeCN/H2O (4 : 1 v/v). In particular, titrations of L2 with Cd2+, Zn2+ or Pb2+ showed an almost comparable CHEF effect up to an M2+/L2 molar ratio of 1. Overall, no significant optical selectivity was observed in the case of L2. Conversely, L3 revealed an OFF-ON selective response only in the presence of the Zn2+ ion in MeCN/H2O (4 : 1 v/v), which can be attributed to the formation of both 1 : 1 and 1 : 2 metal-to-ligand complexes, as also confirmed by potentiometric measurements. Finally, crystals of [ZnL1(Ac)](Ac) (1), [CuL1(Cl)](Cl)·H2O (2) and [CuL3](NO3) (3) were grown and analysed by X-ray diffraction. 1 and 3 feature the metal center in a pseudo-octahedral coordination geometry coordinated also by the carbonyl group from one pendant arm, while in the case of 2, one of the six coordination sites in the final distorted octahedral geometry is occupied by the nitrogen donor from the urea group of one pendant arm.

Host-guest selectivity in a series of isoreticular metal-organic frameworks: observation of acetylene-to-alkyne and carbon dioxide-to-amide interactions.

In order to develop new porous materials for applications in gas separations such as natural gas upgrading, landfill gas processing and acetylene purification it is vital to gain understanding of host-substrate interactions at a molecular level. Herein we report a series of six isoreticular metal-organic frameworks (MOFs) for selective gas adsorption. These materials do not incorporate open metal sites and thus provide an excellent platform to investigate the effect of the incorporation of ligand functionality via amide and alkyne groups on substrate binding. By reducing the length of the linker in our previously reported MFM-136, we report much improved CO2/CH4 (50 : 50) and CO2/N2 (15 : 85) selectivity values of 20.2 and 65.4, respectively (1 bar and 273 K), in the new amide-decorated MOF, MFM-126. The CO2 separation performance of MFM-126 has been confirmed by dynamic breakthrough experiments. In situ inelastic neutron scattering and synchrotron FT-IR microspectroscopy were employed to elucidate dynamic interactions of adsorbed CO2 molecules within MFM-126. Upon changing the functionality to an alkyne group in MFM-127, the CO2 uptake decreases but the C2H2 uptake increases by 68%, leading to excellent C2H2/CO2 and C2H2/CH4 selectivities of 3.7 and 21.2, respectively. Neutron powder diffraction enabled the direct observation of the preferred binding domains in MFM-126 and MFM-127, and, to the best of our knowledge, we report the first example of acetylene binding to an alkyne moiety in a porous material, with over 50% of the acetylene observed within MFM-127 displaying interactions (<4 Å) with the alkyne functionality of the framework.

Unequivocal Experimental Evidence of the Relationship between Emission Energies and Aurophilic Interactions.

In this paper, we describe experimental evidence of a change in the emission energy as a function of the Au-Au distance. We have employed a luminescent complex exhibiting an aurophilic interaction, which is weak enough to allow its length to be modified by external pressure but rigid enough to confer structural stability on the complex. By determining the crystal structures and emission characteristics over a range of pressures, we have identified an exponential relationship between the energy of the emitted light and the metal-metal distances under pressure. This result can be indirectly related to the repulsive branch of the fitted function representing the energy of the system in the ground state at different Au-Au distances. The relativistic nature of gold appears to play an important role in the behavior of this complex.

High Volumetric Hydrogen Adsorption in a Porous Anthracene-Decorated Metal-Organic Framework.

We report an unprecedented ligand-based binding domain for D2 within a porous metal-organic framework (MOF) material as confirmed by neutron powder diffraction studies of D2-loaded MFM-132a. A tight pocket of 6 Å diameter is formed by the close packing of three anthracene panels, and it is here rather than the open metal sites where D2 binds preferentially. As a result, MFM-132a shows exceptional volumetric hydrogen adsorption (52 g L-1 at 60 bar and 77 K) and the highest density of adsorbed H2 within its pores among all the porous materials reported to date under the same conditions. This work points to a new direction for H2 storage in porous materials using polyaromatic ligand-based sites.

Selective reduction and homologation of carbon monoxide by organometallic iron complexes.

Carbon monoxide is a key C1 feedstock for the industrial production of hydrocarbons, where it is used to make millions of tonnes of chemicals, fuels, and solvents per annum. Many transition metal complexes can coordinate CO, but the formation of new C-C bonds in well-defined compounds from the scission and subsequent coupling of two or more CO moieties at a transition metal centre remains a challenge. Herein, we report the use of low-coordinate iron(II) complexes for the selective scission and homologation of CO affording unusual squaraines and iron carboxylates at ambient temperature and pressure. A modification of the ligand framework allows for the isolation and structural characterisation of a proposed metallacyclic Fe(II) carbene intermediate. These results indicate that, with the appropriate choice of supporting ligands, it is possible to cleave and homologate carbon monoxide under mild conditions using an abundant and environmentally benign low-coordinate, first row transition metal.