Synthesis, X-ray diffraction analysis and nonlinear optical properties of hexacoordinated organotin compounds derived from Schiff bases

Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism

Predicting RNA solvent accessibility using only primary sequence data can be regarded as sequence-based prediction work. Currently, the established studies for sequence-based RNA solvent accessibility prediction are limited due to the available number of datasets and black box prediction. To improve these issues, we first expanded the available RNA structures and then developed a sequence-based model using modified attention layers with different receptive fields to conform to the stem-loop structure of RNA chains. We measured the improvement with an extended dataset and further explored the model's interpretability by analysing the model structures, attention values and hyperparameters. Finally, we found that the developed model regarded the pieces of a sequence as templates during the training process. This work will be helpful for researchers who would like to build RNA attribute prediction models using deep learning in the future.

Predicting RNA solvent accessibility from multi-scale context feature via multi-shot neural network

Knowledge of RNA solvent accessibility has recently become attractive due to the increasing awareness of its importance for key biological process. Accurately predicting the solvent accessibility of RNA is crucial for understanding its 3D structure and biological function. In this study, we develop a novel computational method, termed M²pred, for accurately predicting the solvent accessibility of RNA from sequence-based multi-scale context feature. In M²pred, three single-view features, i.e., base-pairing probabilities, position-specific frequency matrix, and a binary one-hot encoding, are first generated as three feature sources, and immediately concatenated to engender a super feature. Secondly, for the super feature, the matrix-format features of each nucleotide are extracted using an initialized sliding window technique, and regularly stacked into a cube-format feature. Then, using multi-scale context feature extraction strategy, a pyramid feature constructed of contextual feature of four scales related to target nucleotides is extracted from the cube-format feature. Finally, a customized multi-shot neural network framework, which is equipped with four different scales of receptive fields mainly integrating several residual attention blocks, is designed to dig discrimination information from the contextual pyramid feature. Experimental results demonstrate that the proposed M²pred achieve a high prediction performance and outperforms existing state-of-the-art prediction methods of RNA solvent accessibility.

Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network

MOTIVATION

RNA solvent accessibility, similar to protein solvent accessibility, reflects the structural regions that are accessible to solvents or other functional biomolecules, and plays an important role for structural and functional characterization. Unlike protein solvent accessibility, only a few tools are available for predicting RNA solvent accessibility despite the fact that millions of RNA transcripts have unknown structures and functions. Also, these tools have limited accuracy. Here, we have developed RNAsnap2 that uses a dilated convolutional neural network with a new feature, based on predicted base-pairing probabilities from LinearPartition.

RESULTS

Using the same training set from the recent predictor RNAsol, RNAsnap2 provides an 11% improvement in median Pearson Correlation Coefficient (PCC) and 9% improvement in mean absolute errors for the same test set of 45 RNA chains. A larger improvement (22% in median PCC) is observed for 31 newly deposited RNA chains that are non-redundant and independent from the training and the test sets. A single-sequence version of RNAsnap2 (i.e. without using sequence profiles generated from homology search by Infernal) has achieved comparable performance to the profile-based RNAsol. In addition, RNAsnap2 has achieved comparable performance for protein-bound and protein-free RNAs. Both RNAsnap2 and RNAsnap2 (SingleSeq) are expected to be useful for searching structural signatures and locating functional regions of non-coding RNAs.

AVAILABILITY AND IMPLEMENTATION

Standalone-versions of RNAsnap2 and RNAsnap2 (SingleSeq) are available at https://github.com/jaswindersingh2/RNAsnap2. Direct prediction can also be made at https://sparks-lab.org/server/rnasnap2. The datasets used in this research can also be downloaded from the GITHUB and the webserver mentioned above.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Sn6 and Na4 Oxo Clusters Based Non-centrosymmetric Framework for Solution Iodine Absorption and Second Harmonic Generation Response

A three-dimensional non-centrosymmetric cluster organic framework has successfully been built from the {Sn₆} and {Na₄} cluster units via the oxalate ligand, which belongs to the first 3D framework containing different cluster units in the field of tin-oxo clusters. Besides the interesting structural characteristics, the obtained 3D framework not only can efficiently adsorb the iodine molecules but also displays the second harmonic generation response under the 1064 nm Q-switch laser.

State of the Art of Boron and Tin Complexes in Second- and Third-Order Nonlinear Optics §

Boron and tin complexes have been a versatile and very interesting scaffold for the design of nonlinear optical (NLO) chromophores. In this paper we present a wide range of reports since the 1990s to date, which include second-order (e.g., second harmonic generation) and third-order (e.g., two-photon absorption) NLO properties. After a short introduction on the origin of the NLO response in molecules, the different features associated with the introduction of these inorganic motifs in the organic-based NLO materials are discussed: Their effect on the accepting/donating capabilities of the substituents, on the efficiency of the π-conjugated linkage, and on the topology of the chromophores which can be tuned from the first generation of “push-pull” chromophores to more sophisticated two- or three-dimensional architectures.

Crystal structure, Hirshfeld surface analysis and anti-oxidant capacity of 2,2'-{(1E,1'E)-[1,2-phenyl-enebis(aza-nylyl-idene)]bis-(methanylyl-idene)}bis-(5-benz-yloxy)phenol

The whole mol-ecule of the title Schiff base compound, C34H28N2O4, is generated by mirror symmetry, with the mirror bis-ecting the central benzene ring. It was synthesized via the condensation reaction of 1,2-di-amine-benzene with 4-benz-yloxy-2-hy-droxy-benzaldehyde. The mol-ecule is V-shaped and there are two intra-molecular O-H⋯N hydrogen bonds present forming S(6) ring motifs. The configuration about the C=N imine bonds is E. The central benzene ring makes dihedral angles of 41.9 (2) and 43.6 (2)° with the phenol ring and the outer benz-yloxy ring, respectively. The latter two rings are inclined to each other by 84.4 (2)°. In the crystal, mol-ecules are linked by C-H⋯π inter-actions, forming layers lying parallel to the ab plane. The Hirshfeld surface analysis and the two-dimensional fingerprint plots confirm the predominance of these inter-actions in the crystal structure. The anti-oxidant capacity of the compound was determined by the cupric reducing anti-oxidant capacity (CUPRAC) process.

A sulfonated Schiff base dimethyltin(iv) coordination polymer: synthesis, characterization and application as a catalyst for ultrasound- or microwave-assisted Baeyer–Villiger oxidation under solvent-free conditions

The sulfonated Schiff base dimethyltin(iv) coordination polymer is an efficient heterogeneous catalyst for the peroxidative Baeyer–Villiger oxidation of ketones, under ultrasound or microwave irradiation and solvent- and additive-free conditions.

Four-coordinate nickel(ii) and copper(ii) complex based ONO tridentate Schiff base ligands: synthesis, molecular structure, electrochemical, linear and nonlinear properties, and computational study

The properties of NLO active ternary Ni(ii)- and Cu(ii)-unsymmetrical Schiff base complexes were explored in concert with DFT calculations.