3D Motifs Research Articles

Perovskites for Laser and Detector Applications

Perovskite materials have triggered a renewed interest in photovoltaic research in the recent years. They display crystal forms with 0D, 1D and 2D, 3D motifs, and several chemical forms, namely inorganic (titanates, rubidiates, nobiates, tantalates etc.), organic/inorganic metal halides with single to multiple cations, and even organic polymer or quantum dot‐infused hybrids. Each crystal type and chemical form are endowed with specific physicochemical, optical, electronic, and morphological properties. These unique properties render them suitable for targeted applications, namely photovoltaics, LEDs, photocatalysis/electrolysis/solar fuels/solar and Li‐ion batteries, gas‐sensors, ferroelectrics, capacitors, transistors and memristors, photodetectors, and lasers, for advanced quantum cryptography and outer space applications. At first, the crystal and material types, and physicochemical, morphological, and optoelectronic properties of perovskite materials are discussed. Particularly, we focus on those properties which cumulatively contribute to their application in the abovementioned fields. Simultaneously, a comprehensive discussion about the advances in each field is presented. Structure/property/application relationships with key advances demonstrate the versatility of perovskites in modern optoelectronic technologies.

RCPred: RNA complex prediction as a constrained maximum weight clique problem

BackgroundRNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an original approach that takes advantage of the high number of RNA secondary structure and RNA-RNA interaction prediction tools. We formulate the problem of RNA complex prediction as the determination of the best combination (according to the free energy) of predicted RNA secondary structures and RNA-RNA interactions.ResultsWe model those predicted structures and interactions as a graph in order to have a combinatorial optimization problem that is a constrained maximum weight clique problem. We propose an heuristic based on Breakout Local Search to solve this problem and a tool, called RCPred, that returns several solutions, including motifs like internal and external pseudoknots. On a large number of complexes, RCPred gives competitive results compared to the methods of the state of the art.ConclusionsWe propose in this paper a method called RCPred for the prediction of several secondary structures of RNA complexes, including internal and external pseudoknots. As further works we will propose an improved computation of the global energy and the insertion of 3D motifs in the RNA complexes.

Five new cobalt(II) complexes based on indazole derivatives: synthesis, DNA binding and molecular docking study

Five cobalt(II) complexes based on 1H-indazole-3-carboxylic acid (H2L), [Co(phen)(HL)2]·2H2O (1), [Co(5,5′-dimethyl-2,2′-bipy)(HL)2] (2), [Co(2,2′-bipy)2(HL)2]·5H2O (3), [Co2(2,9-dimethyl-1,10-phen)2(L)2] (4) and [Co2(6,6′-dimethyl-2,2′-bipy)2(L)2]·H2O (5) (2,2'-bipy = 2,2′-bipyridine, phen = 1,10-phenanthroline), have been synthesized and structurally characterized by elemental analyses, IR and UV-vis spectroscopies and single-crystal X-ray crystallography. The results indicate that 1–3 possess mononuclear Co(II) structures, while 4 and 5 exhibit binuclear structure. 1D water tape which is linked by the multiple hydrogen bonds was embedded in the 3D motif of complex 3. Complexes 4 and 5 show two orthogonal planes of motif that was constituted by phen/2,2′-bipy and indazole acid, respectively. The intermolecular interactions including hydrogen bonding and π-π stacking interactions are stabilizing these complexes. The interactions of the synthesized complexes with calf-thymus DNA (CT-DNA) have been investigated by UV-vis absorption titration, ethidium bromide displacement assay and viscosity measurements. The results reveal that the complexes could interact with CT-DNA via a groove binding mode. Their behavior rationalization was further theoretically studied by molecular docking.

Geometric Determinants of In-Situ Direct Laser Writing

Direct laser writing (DLW) is a three-dimensional (3D) manufacturing technology that offers significant geometric versatility at submicron length scales. Although these characteristics hold promise for fields including organ modeling and microfluidic processing, difficulties associated with facilitating the macro-to-micro interfaces required for fluid delivery have limited the utility of DLW for such applications. To overcome this issue, here we report an in-situ DLW (isDLW) strategy for creating 3D nanostructured features directly inside of—and notably, fully sealed to—sol-gel-coated elastomeric microchannels. In particular, we investigate the role of microchannel geometry (e.g., cross-sectional shape and size) in the sealing performance of isDLW-printed structures. Experiments revealed that increasing the outward tapering of microchannel sidewalls improved fluidic sealing integrity for channel heights ranging from 10 μm to 100 μm, which suggests that conventional microchannel fabrication approaches are poorly suited for isDLW. As a demonstrative example, we employed isDLW to 3D print a microfluidic helical coil spring diode and observed improved flow rectification performance at higher pressures—an indication of effective structure-to-channel sealing. We envision that the ability to readily integrate 3D nanostructured fluidic motifs with the entire luminal surface of elastomeric channels will open new avenues for emerging applications in areas such as soft microrobotics and biofluidic microsystems.

Metal ion induced single-crystal-to-single-crystal transformation and luminescent sensing properties of resorcin[4]arene-based metal–organic frameworks

In this work, two new resorcin[4]arene-based metal–organic frameworks (MOFs), namely, [(CH3)2NH2][Zn3(HL)(L)(DMF)(H2O)2]·2H2O (1-Zn) and [(CH3)2NH2]2[Cd3(L)2(H2O)4]·2DMF·2H2O (2-Cd), have been synthesized under solvothermal conditions (H4L represents the resorcin[4]arene-based ligand). 1-Zn exhibits a layer structure, while 2-Cd shows a 3D motif. Remarkably, by immersing 1-Zn in an aqueous solution of Cu2+ ions, a new Cu(II)-MOF [Cu2(H2L)2(H2O)2]·3.5H2O (1-Cu) was achieved via a metal ion induced single-crystal-to-single-crystal (SCSC) transformation manner, involving generation of new metal-O bond and change of metal ion coordination geometry. Moreover, luminescent detection properties for Fe3+ ions and Cr2O72− ions were also investigated with 1-Zn and 2-Cd as luminescent sensors.

An adaptive geometric search algorithm for macromolecular scaffold selection.

A wide variety of protein and peptidomimetic design tasks require matching functional 3D motifs to potential oligomeric scaffolds. For example, during enzyme design, one aims to graft active-site patterns—typically consisting of 3–15 residues—onto new protein surfaces. Identifying protein scaffolds suitable for such active-site engraftment requires costly searches for protein folds that provide the correct side chain positioning to host the desired active site. Other examples of biodesign tasks that require similar fast exact geometric searches of potential side chain positioning include mimicking binding hotspots, design of metal binding clusters and the design of modular hydrogen binding networks for specificity. In these applications, the speed and scaling of geometric searches limits the scope of downstream design to small patterns. Here, we present an adaptive algorithm capable of searching for side chain take-off angles, which is compatible with an arbitrarily specified functional pattern and which enjoys substantive performance improvements over previous methods. We demonstrate this method in both genetically encoded (protein) and synthetic (peptidomimetic) design scenarios. Examples of using this method with the Rosetta framework for protein design are provided. Our implementation is compatible with multiple protein design frameworks and is freely available as a set of python scripts (https://github.com/JiangTian/adaptive-geometric-search-for-protein-design).

Synthesis of Structurally Diverse N-Substituted Quaternary-Carbon-Containing Small Molecules from α,α-Disubstituted Propargyl Amino Esters.

N‐containing quaternary stereocenters represent important motifs in medicinal chemistry. However, due to their inherently sterically hindered nature, they remain underrepresented in small molecule screening collections. As such, the development of synthetic routes to generate small molecules that incorporate this particular feature are highly desirable. Herein, we describe the diversity‐oriented synthesis (DOS) of a diverse collection of structurally distinct small molecules featuring this three‐dimensional (3D) motif. The subsequent derivatisation and the stereoselective synthesis exemplified the versatility of this strategy for drug discovery and library enrichment. Chemoinformatic analysis revealed the enhanced sp3 character of the target library and demonstrated that it represents an attractive collection of biologically diverse small molecules with high scaffold diversity.

The Striatum Organizes 3D Behavior via Moment-to-Moment Action Selection

Many naturalistic behaviors are built from modular components that are expressed sequentially. Although striatal circuits have been implicated in action selection and implementation, the neural mechanisms that compose behavior in unrestrained animals are not well understood. Here, we record bulk and cellular neural activity in the direct and indirect pathways of dorsolateral striatum (DLS) as mice spontaneously express action sequences. These experiments reveal that DLS neurons systematically encode information about the identity and ordering of sub-second 3D behavioral motifs; this encoding is facilitated by fast-timescale decorrelations between the direct and indirect pathways. Furthermore, lesioning the DLS prevents appropriate sequence assembly during exploratory or odor-evoked behaviors. By characterizing naturalistic behavior at neural timescales, these experiments identify a code for elemental 3D pose dynamics built from complementary pathway dynamics, support a role for DLS in constructing meaningful behavioral sequences, and suggest models for how actions are sculpted over time.

Diversity and motif conservation in protein 3D structural landscape: exploration by a new multivariate simulation method.

In this paper, diversity and conservation in the 'landscape' of random variation of protein tertiary structures are explored for quantitative feature-vector models of major types of functionally important 3D structural motifs. For this, I have deployed a recently developed nonparametric regression (NPR)-based multidimensional copula method of simulation. Apart from improved accuracy of multidimensional random sample generation, the simulation provides additional insight into diversity in the protein structural landscape in terms of random variation in the feature-vector. It shows the relative importance of several features, with biological implications, in conservation of motifs. Mapping of this landscape in distance-preserving 2D eigenspace also shows consistency in demarcation of different motif classes and preservation of their characteristic patterns in this 2D space.

RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution.

Viroids are circular noncoding RNAs infecting plants [1, 2]. During infection, viroids, like RNA viruses, generate swarms of sequence variants called quasispecies [3, 4]. Viroids in Avsunviroidae family replicate in chloroplasts and display the highest mutation rates among all living entities [5]. Viroids in Pospiviroidae family replicate in the nucleus with a relatively lower mutation rate resembling some RNA viruses [6]. Those sequence variants generated during replication are described by the concept of sequence space, which harnesses a geometric representation to illustrate genetic similarities via physical distances. Given the high mutation rate and fast propagation, viroid RNAs have a potentially large sequence space for the evolution of new variants. However, in reality, they use only a small fraction of this space. Constraints of viral sequence space may include genome size, replication fidelity, error thresholds, host or tissue tropism, etc. These factors have been nicely reviewed elsewhere [3, 7, 8] and are not the focus of this Pearl. In addition, RNA secondary structures have been considered, though not adequately, as a constraint factor [8]. Viroids, in contrast to viruses, entirely rely on their RNA structural motifs for function due to their noncoding nature, which offers insights into their capacity to explore regions of sequence space influenced by RNA structures. Here, we describe that 3-dimensional (3D) structural motifs formed by non–Watson-Crick (non-WC) base pairs in viroid RNAs act as a critical constraint for the sequence space of viroid genome evolution. This constraint operates because RNA 3D motifs can play crucial roles by mediating (1) RNA–RNA interactions for the folding of a part or a whole of RNA into a distinct tertiary conformation and (2) RNA–protein interactions. Therefore, mutations in a 3D motif that do not disrupt the structure and function will be retained in the population, whereas mutations that disrupt the 3D structures of motifs, and consequently the function, will be lost.

Theoretical study on the charge transport in single crystals of TCNQ, F2-TCNQ and F4-TCNQ.

2,5-Difluoro-7,7,8,8-tetracyanoquinodimethane (F2-TCNQ) was recently reported to display excellent electron transport properties in single crystal field-effect transistors (FETs). Its carrier mobility can reach 25 cm2 V-1 s-1 in devices. However, its counterparts TCNQ and F4-TCNQ (tetrafluoro-7,7,8,8-tetracyanoquinodimethane) do not exhibit the same highly efficient behavior. To better understand this significant difference in charge carrier mobility, a multiscale approach combining semiclassical Marcus hopping theory, a quantum nuclear enabled hopping model and molecular dynamics simulations was performed to assess the electron mobilities of the Fn-TCNQ (n = 0, 2, 4) systems in this work. The results indicated that the outstanding electron transport behavior of F2-TCNQ arises from its effective 3D charge carrier percolation network due to its special packing motif and the nuclear tunneling effect. Moreover, the poor transport properties of TCNQ and F4-TCNQ stem from their invalid packing and strong thermal disorder. It was found that Marcus theory underestimated the mobilities for all the systems, while the quantum model with the nuclear tunneling effect provided reasonable results compared to experiments. Moreover, the band-like transport behavior of F2-TCNQ was well described by the quantum nuclear enabled hopping model. In addition, quantum theory of atoms in molecules (QTAIM) analysis and symmetry-adapted perturbation theory (SAPT) were used to characterize the intermolecular interactions in TCNQ, F2-TCNQ and F4-TCNQ crystals. A primary understanding of various noncovalent interaction responses for crystal formation is crucial to understand the structure-property relationships in organic molecular materials.

Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures.

An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel, found to be involved in protein-protein interactions and substrate recognition. We compare functional top face diagrams of the integrin-type β-propeller domain and two non-integrin type β-propeller domains of virginiamycin B lyase and WD Repeat-Containing Protein 5.

Corrigendum: RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.

Corrigendum: RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.

Metrological Aspects of Surface Topographies Produced by Different Machining Operations Regarding Their Potential Functionality

AbstractThis paper presents a comprehensive methodology for measuring and characterizing the surface topographies on machined steel parts produced by precision machining operations. The performed case studies concern a wide spectrum of topographic features of surfaces with different geometrical structures but the same values of the arithmetic mean height Sa. The tested machining operations included hard turning operations performed with CBN tools, grinding operations with Al2O3ceramic and CBN wheels and superfinish using ceramic stones. As a result, several characteristic surface textures with the Sa roughness parameter value of about 0.2 μm were thoroughly characterized and compared regarding their potential functional capabilities. Apart from the standard 2D and 3D roughness parameters, the fractal, motif and frequency parameters were taken in the consideration.

Pb@Pb8 Basket-like-Cluster-Based Lead Tellurate-Nitrate Kleinman-Forbidden Nonlinear-Optical Crystal: Pb9Te2O13(OH)(NO3)3.

The first lead tellurate-nitrate nonlinear-optical (NLO) crystal, Pb9Te2O13(OH)(NO3)3, featuring a 3D anionic diamondlike toplogical structural motif formulated as [Pb9O13]8- constructed by unique nonanuclear basket-shaped Pb@Pb8O14 clusters has been hydrothermally achieved, in which the Pb@Pb8O14 cluster shows a core-shell structure with one PbO10 polyhedron enclosed by eight PbOx (x = 3 and 4) polyhedera via edge and face sharing. The hexavalent Te in TeO5(OH) octahedra is linked to a [Pb9O13]8- cluster to form a rare [Pb9Te2O13(OH)]3+ cationic framework. The compound demonstrates a powder second-harmonic-generation (SHG) response of about 1.2 times that of KH2PO4 (KDP) as well as a wide transparency range. Calculations on the local dipole moment and SHG coefficient reveal that the net polarization is zero because of a Kleinman-forbidden point group. Further analysis shows that the SHG response results from structure-induced variations by thermal vibrations of the lattice rather than the intrinsic dipole moment, which offers another insight on the design of new NLO materials.

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.

RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local three-dimensional (3D) motifs shaping the full 3D architecture of the molecule. Recent contributions have identified and organized recurrent local 3D motifs, but applications of this knowledge for predictive purposes is still in its infancy. We recently developed a computational framework, named RNA-MoIP, to reconcile RNA secondary structure and local 3D motif information available in databases. In this paper, we introduce a web service using our software for predicting RNA hybrid 2D–3D structures from sequence data only. Optionally, it can be used for (i) local 3D motif prediction or (ii) the refinement of user-defined secondary structures. Importantly, our web server automatically generates a script for the MC-Sym software, which can be immediately used to quickly predict all-atom RNA 3D models. The web server is available at http://rnamoip.cs.mcgill.ca.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5′-Bistetrazole-1,1′-diolate (TKX-50)

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5′-bistetrazole-1,1′-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ∼10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ∼3 GPa. The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel ani...

Structural Motifs in Class I and Class II Plant Defensins for Phospholipid Interactions:Intriguing Role of Ligand Binding and Modes of Action

Structural Motifs in Class I and Class II Plant Defensins for Phospholipid Interactions:Intriguing Role of Ligand Binding and Modes of Action Defensins are cationic antimicrobial peptides widespread in nature. Plants, as sessile organisms exposed to fungi and other pathogens have developed mechanisms to deal with infection. Plant defensins are considered infection responsive molecules, nevertheless, several abiotic factors are elicitors and a set of modes of action are reported. Phospholipid binding profiles are characteristic of both, class I and class II defensins. Comparing the amino acid composition of class I, MtDEF4 and class II, NaD1, structural differences or motifs of primary structure for phospholipid ligand are analyzed, as a result a Gly residue of the γ–core loop is proposed as feature of class I phospholipid binding defensins in this review. Because the two groups of defensins are present in Solanaceae plants, the synergy or overlaping function is a possibility. The N-ter and the γ–core loop define the 3D ligand binding site of phosphoinositide phosphatidylinositol 4,5-bisphosphate (PIP2) in NaD1 class II defensin, while the basic residues in the γ–core loop of the class I representative defensin MtDEF4; are essential for cell entry. Defensins of Capsicum highlight structural constrains for distinctive lipid binding profiles of class I and class II defensins. Primary and 3D structural motifs, particularly residues in positions 4 and 42 and the widely studied γ−core are involved in the interaction site for protein-PIP2/PA binding, while the hydrophobic surfaces must interact with additional components of membrane or cell wall constituents. The 3D binding pocket for phospholipid binding shows that class II members target head-group-phosphates of the PIP2 in the inositol ring, as demonstrated for NaD1, thus charged residues are involved in phosphate ligand coordination also in MtDEF4. Phylogenetic relationships with Medicago truncatula defensins denote the conserved class I peptide motifs in Solanaceae and Leguminoseae. This review summarizes the state of the art related to modes of action of sphigolipid vs. phospholipid binding plant defensin and unveil particular motifs of mature peptide class I and class II defensins in Solanaceae that have shown distinctive binding to phosphoinositides and phosphatidic acid.

Structure, solution assembly, and electroconductivity of nanosized argento-organic-cluster/framework templated by chromate.

In view of elucidating potential structures and assembly mechanism of silver clusters and silver cluster-based metal-organic frameworks, we prepared four argento-organic-clusters/frameworks where the structures were directed by chromate in the presence of different thiolates. All four structures with tBuC6H4S-, SiBu-, and SiPr- consist of three core-shells, an inner CrO42-, an intermediate Ag-S aggregate and finally the protective organic moieties. {(HNEt3)3[Ag(CrO4)4@Ag46(SC6H4tBu)24(CF3COO)18(DMF)4]} (1) is a supertetrahedron with an inner Ag(CrO4)4 tetrahedron shelled by four fused Ag11.5S6 lobes. [(CrO4)5@Ag40(SiBu)27(CF3COO)3]n (2) is an undulated snake-like tube housing the infinite CrO42- tetrahedra. [(CrO4)2@Ag41(SiBu)30(NO3)3(CN)4]n (3) forms an uncommon 7-connected kwh network incorporating hexagonal layers of Ag19(SiBu)15 balls with a single inner CrO42- connected by another Ag atom. Both enantiomeric chiral qtz frameworks of [CrO4@Ag20(SiPr)10(Cr2O7)2(COOCF3)4(DMF)4]n (4) were structurally characterized. In 4, Cr2O72- connects the Ag20(SiPr)10 clusters with a trapped CrO42- into a 3D quartz (qtz) structure, where the spherical cluster acts like oxygen and Cr2O72- takes the place of Si in SiO2. Electrospray ionization mass spectrometry (ESI-MS) analysis of the reaction solutions of 1-4 clearly indicated that (i) the Ag(CrO4)4@Ag46 core of 1 can retain its molecular structure in the solution and (ii) the chromate-templated polynuclear silver-thiolate species in solution are important building blocks to construct the 1D or 3D motif for 2-4. The electrochemistry in sulfuric acid and enhancement of the electrical conductivity upon I2 doping have also been reported.

Synthesis of a biological active β-hairpin peptide by addition of two structural motifs

The idea of privileged scaffolds – that there seem to be more bioactive compounds found around some structures than others – is well established for small drug molecules, but has little significance for standalone peptide secondary structures whose adaptable shapes escape the definition of a 3D motif in the absence of a protein scaffold. Here, we joined two independent biological functions in a single highly restricted peptide to support the hypothesis that the β-hairpin shape is the common basis of two otherwise unrelated biological recognition processes. To achieve this, the hydrophobic cluster HWX4LV from the decapeptide cyclic hairpin model peptide C1-C10cyclo-CHWEGNKLVC was included in the bicyclic peptide 2. The designed β-hairpin peptide C4-C17, C8-C13bicyclo-KHQCHWECTZGRCRLVCGRSGS (2, Z=citrulline), serves, on the one hand, as a specific epitope for rheumatoid autoantibodies and, on the other hand, shows a not negligible antibiotic effect against the bacterial strain E. coli AS19.