10 simple rules to create a serious game, illustrated with examples from structural biology

Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games, games that allow people to produce and/or analyze scientific data. Interestingly, it is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience ( Phylo , DocMolecules , HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games

Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system

The porous MIL-47 material shows a selective adsorption behavior for para-, ortho-, and meta-isomers of xylenes, making the material a serious candidate for separation applications. The origin of the selectivity lies in the differences in interactions (energetic) and confining (entropic). This paper investigates the xylene-framework interactions and the xylene-xylene interactions with quantum mechanical calculations, using a dispersion-corrected density functional and periodic boundary conditions to describe the crystal. First, the strength and geometrical characteristics of the optimal xylene-xylene interactions are quantified by studying the pure and mixed pairs in gas phase. An extended set of initial structures is created and optimized to sample as many relative orientations and distances as possible. Next, the pairs are brought in the pores of MIL-47. The interaction with the terephthalic linkers and other xylenes increases the stacking energy in gas phase (-31.7 kJ/mol per pair) by roughly a factor four in the fully loaded state (-58.3 kJ/mol per xylene). Our decomposition of the adsorption energy shows various trends in the contributing xylene-xylene interactions. The absence of a significant difference in energetics between the isomers indicates that entropic effects must be mainly responsible for the separation behavior

Advances in ab-initio theory of Multiferroics. Materials and mechanisms: modelling and understanding

Within the broad class of multiferroics (compounds showing a coexistence of magnetism and ferroelectricity), we focus on the subclass of "improper electronic ferroelectrics", i.e. correlated materials where electronic degrees of freedom (such as spin, charge or orbital) drive ferroelectricity. In particular, in spin-induced ferroelectrics, there is not only a {\em coexistence} of the two intriguing magnetic and dipolar orders; rather, there is such an intimate link that one drives the other, suggesting a giant magnetoelectric coupling. Via first-principles approaches based on density functional theory, we review the microscopic mechanisms at the basis of multiferroicity in several compounds, ranging from transition metal oxides to organic multiferroics (MFs) to organic-inorganic hybrids (i.e. metal-organic frameworks, MOFs)Comment: 22 pages, 9 figure

Geometry analysis and systematic synthesis of highly porous isoreticular frameworks with a unique topology

Porous coordination polymers are well known for their easily tailored framework structures and corresponding properties. Although systematic modulations of pore sizes of binary prototypes have gained great success, simultaneous adjustment of both pore size and shape of ternary prototypes remains unexplored, owing to the difficulty in controlling the self-assembly of multiple molecular building blocks. Here we show that simple geometry analysis can be used to estimate the influence of the linker lengths and length ratios on the synthesis/construction difficulties and framework stabilities of a highly symmetric, ternary prototype composed of a typical trinuclear metal cluster and two types of bridging carboxylate ligands. As predicted, systematic syntheses with 5×5 ligand combinations produced 13 highly porous isoreticular frameworks, which show not only systematic adjustment of pore volumes (0.49–2.04 cm3 g−1) and sizes (7.8–13.0 Å; 5.2–12.0 Å; 7.4–17.4 Å), but also anisotropic modulation of the pore shapes

Three-dimensional lanthanide-organic frameworks based on di-, tetra-, and hexameric clusters

Three-dimensional lanthanide-organic frameworks formulated as (CH3)2NH2[Ln(pydc)2] · 1/2H2O [Ln3+ ) Eu3+ (1a) or Er3+ (1b); pydc2- corresponds to the diprotonated residue of 2,5-pyridinedicarboxylic acid (H2pydc)], [Er4(OH)4(pydc)4(H2O)3] ·H2O (2), and [PrIII 2PrIV 1.25O(OH)3(pydc)3] (3) have been isolated from typical solvothermal (1a and 1b in N,N-dimethylformamide - DMF) and hydrothermal (2 and 3) syntheses. Materials were characterized in the solid state using single-crystal X-ray diffraction, thermogravimetric analysis, vibrational spectroscopy (FT-IR and FT-Raman), electron microscopy, and CHN elemental analysis. While synthesis in DMF promotes the formation of centrosymmetric dimeric units, which act as building blocks in the construction of anionic ∞ 3{[Ln(pydc)2]-} frameworks having the channels filled by the charge-balancing (CH3)2NH2 + cations generated in situ by the solvolysis of DMF, the use of water as the solvent medium promotes clustering of the lanthanide centers: structures of 2 and 3 contain instead tetrameric [Er4(μ3-OH)4]8+ and hexameric |Pr6(μ3-O)2(μ3-OH)6| clusters which act as the building blocks of the networks, and are bridged by the H2-xpydcx- residues. It is demonstrated that this modular approach is reflected in the topological nature of the materials inducing 4-, 8-, and 14-connected uninodal networks (the nodes being the centers of gravity of the clusters) with topologies identical to those of diamond (family 1), and framework types bct (for 2) and bcu-x (for 3), respectively. The thermogravimetric studies of compound 3 further reveal a significant weight increase between ambient temperature and 450 °C with this being correlated with the uptake of oxygen from the surrounding environment by the praseodymium oxide inorganic core

Highly Water-Stable Zirconium Metal-Organic Framework UiO-66 Membranes Supported on Alumina Hollow Fibers for Desalination

In this study, continuous zirconium(IV)-based metal-organic framework (Zr-MOF) membranes were prepared. The pure-phase Zr-MOF (i.e., UiO-66) polycrystalline membranes were fabricated on alumina hollow fibers using an in situ solvothermal synthesis method. Single-gas permeation and ion rejection tests were carried out to confirm membrane integrity and functionality. The membrane exhibited excellent multivalent ion rejection (e.g., 86.3% for Ca2+, 98.0% for Mg2+, and 99.3% for Al3+) on the basis of size exclusion with moderate permeance (0.14 L m-2 h-1 bar-1) and good permeability (0.28 L m-2 h-1 bar-1 μm). Benefiting from the exceptional chemical stability of the UiO-66 material, no degradation of membrane performance was observed for various tests up to 170 h toward a wide range of saline solutions. The high separation performance combined with its outstanding water stability suggests the developed UiO-66 membrane as a promising candidate for water desalination

Reticular synthesis and the design of new materials

The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62718/1/nature01650.pd

Reticular synthesis of porous molecular 1D nanotubes and 3D networks

Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal–organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of ‘reticular synthesis’, in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the ‘node and strut’ principles of reticular synthesis to molecular crystals