Polydopamine is the first adhesive polymer that can functionalize surfaces made of virtually all material chemistries. The material‐independent surface modification properties of polydopamine allow the functionalization of various types of medical and energy devices. However, the mechanism of dopamine polymerization has not yet been clearly demonstrated. Covalent oxidative polymerization via 5,6‐dihydroxyindole (DHI), which is similar to the mechanism for synthetic melanin synthesis, has been the clue. Here, it is reported that a physical, self‐assembled trimer of (dopamine)2/DHI exists in polydopamine, which has been known to be formed only by covalent polymerization. It is also found that the trimeric complex is tightly entrapped within polydopamine and barely escapes from the polydopamine complex. The result explains the previously reported in vitro and in vivo biocompatibility. The study reveals a different perspective of polydopamine formation, where it forms in part by the self‐assembly of dopamine and DHI, providing a new clue toward understanding the structures of catecholamines such as melanin.

Graphene has emerged as a versatile material with outstanding electronic properties that could prove useful in many device applications. Recently, the demonstration of spin injection into graphene and the observation of long spin relaxation times and lengths have suggested that graphene could play a role in 'spintronic' devices that manipulate electron spin rather than charge. In particular it has been found that zigzag graphene nanoribbons have magnetic (or spin) states at their edges, and that these states can be either antiparallel or parallel. Here we report the results of first-principles simulations that predict that spin-valve devices based on graphene nanoribbons will exhibit magnetoresistance values that are thousands of times higher than previously reported experimental values. These remarkable values can be linked to the unique symmetry of the band structure in the nanoribbons. We also show that it is possible to manipulate the band structure of the nanoribbons to generate highly spin-polarized currents.

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand complex. We also apply a distance-aware graph attention algorithm with gate augmentation to increase the performance of our model. As a result, our model shows better performance than docking and other deep learning methods for both virtual screening and pose prediction. In addition, our model can reproduce the natural population distribution of active molecules and inactive molecules.

Devices in which a single strand of DNA is threaded through a nanopore could be used to efficiently sequence DNA. However, various issues will have to be resolved to make this approach practical, including controlling the DNA translocation rate, suppressing stochastic nucleobase motions, and resolving the signal overlap between different nucleobases. Here, we demonstrate theoretically the feasibility of DNA sequencing using a fluidic nanochannel functionalized with a graphene nanoribbon. This approach involves deciphering the changes that occur in the conductance of the nanoribbon as a result of its interactions with the nucleobases via π-π stacking. We show that as a DNA strand passes through the nanochannel, the distinct conductance characteristics of the nanoribbon (calculated using a method based on density functional theory coupled to non-equilibrium Green function theory) allow the different nucleobases to be distinguished using a data-mining technique and a two-dimensional transient autocorrelation analysis. This fast and reliable DNA sequencing device should be experimentally feasible in the near future.

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We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules with five target properties. We were also able to adjust a single property without changing the others and to manipulate it beyond the range of the dataset.Electronic supplementary materialThe online version of this article (10.1186/s13321-018-0286-7) contains supplementary material, which is available to authorized users.

A minimal subnetwork is extracted from a very complex full network upon exploring the reaction pathways connecting reactants and products with minimum dissociation and formation of chemical bonds. Such a process reduces computational cost and correctly predicts the pathway for two representative reactions.

Spintronic devices are very important for futuristic information technology. Suitable materials for such devices should have half-metallic properties so that only one spin passes through the device. In particular, organic half metals have the advantage that they may be used for flexible devices and have a long spin-coherence length. We predict that the one-dimensional infinite chromium porphyrin array, which we call Cr-PA(∞), shows half-metallic behavior when the spins on the chromium atoms are in a parallel alignment. Since the chromium atoms are separated by a large distance (>8 Å), the coupling between spins is small and thus their directions can be readily controlled by an external magnetic field. In the ferromagnetic state, the band gap for major spin electrons is 0.30 eV, while there is no band gap for the minor spin electrons, thus reflecting the half-metallic property. This unique property originates from the high spin state of Cr which results in the spin asymmetry of the conduction band in Cr-PA(∞). Electron transport of Cr-PA(1,2,3) is calculated with the nonequilibrium Green function technique in the presence of Au electrodes. It turned out that the spin-filtering ability appears from the dimeric Cr-PA(2). Thus, a new organometallic framework for designing a spin filter is proposed. Though many others have designed novel spintronic devices, none of them are realized due to the lack of a practical fabrication method at present. However, the porphyrin-based spintronic device provides a synthesizable framework.