Molecular Design Learned from the Natural Product Porphyra-334: Molecular Generation via Chemical Variational Autoencoder versus Database Mining via Similarity Search, A Comparative Study.

A comparative study is presented. The method via chemical variational autoencoder (VAE) and the method via similarity search are compared, focusing on their generation ability for new functional molecular design. Focusing on the natural porphyra-334 as a model molecule, we generated three groups: molecules of mycosporine-like amino acids (MAAs) as seeds ( ), molecules generated via chemical VAE ( ) and molecules gathered via similarity search ( ).

Spontaneous Combustion of 2-Bromo-3-Methoxythiophene: A Study on Reaction Pathways and Energetics by Quantum Chemical Calculations.

Reaction pathways and energetics for the dimerization and trimerization reactions of 2-bromo-3-methoxythiophene (2Br-3Met) molecules are investigated using hybrid density functional theory (DFT) calculations to obtain insight into the oligomerization reaction observed in the spontaneous combustion of pure liquid 2Br-3Met. The calculations show that the carbon-bromine bond in a 2Br-3Met molecule elongates easily, and the trans addition of this C-Br bond to a double bond in the neighboring 2Br-3Met molecule occurs easily at room temperature, reflecting the evaluated activation energy of Δ = 12.46 kcal/mol (enthalpy) or Δ = 35.

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene.

Diarylethenes are well-known photochromic compounds, which undergo cyclization and cycloreversion reactions between open- and closed-ring isomers. Recently, diarylethene derivatives with photoswitchable fluorescent properties were prepared. They are applicable for fluorescence imaging including bio-imaging.

Unique Structural Relaxations and Molecular Conformations of Porphyra-334 at the Excited State.

Quantum chemistry based simulations were used to examine the excited state of porphyra-334, one of the fundamental mycosporine-like amino acids present in a wide variety of aqueous organisms. Our calculations reveal three characteristic aspects of porphyra-334 related to either its ground or excited state. Specifically, (i) the ground state (S) structure consists of a planar geometry in which three units can be identified, the central cyclohexene ring, the glycine branch, and the threonine branch, reflecting the π conjugation of the system; (ii) the first singlet excited state (S) shows a large oscillator strength and a typical ππ* excitation character; and (iii) upon relaxation at S, the originally ground state planar structure undergoes a relaxation to a nonplanar one, S, especially at the carbon-nitrogen (CN) groups linking the cyclohexene ring to the glycine or threonine arm.

Pharmacological evidence for the relationship between the NMDA receptor and nitric oxide pathway and the antidepressant-like effects of glucagon-like peptide-2 in the mouse forced-swim test.

We previously demonstrated that glucagon-like peptide-2 (GLP-2) exerted antidepressant-like effects in mice. The aim of the present study was to investigate the relationship between N-methyl--aspartate (NMDA) receptor-nitric oxide-cyclic guanosine monophosphate (NO-cGMP) pathway and the antidepressant-like effects of GLP-2 in the forced-swim test (FST) in mice. Intracerebroventricularly administered GLP-2 (3 μg/mouse) decreased the immobility time in the FST.

Hydrogen storage mechanism and diffusion in metal-organic frameworks.

Diffusion and storage of hydrogen molecules in metal-organic frameworks are crucial for the development of next-generation energy storage devices. By resorting to the first principles modeling, we compute the diffusion coefficient of molecular hydrogen in these systems in a range of temperatures where MOF-based devices are expected to operate. The explicit inclusion of the electronic structure shows that diffusivities are one order of magnitude smaller than those reported by classical simulations, evidencing the insufficiency of the empirical force fields used so far.

Intelligent Image-Activated Cell Sorting.

A fundamental challenge of biology is to understand the vast heterogeneity of cells, particularly how cellular composition, structure, and morphology are linked to cellular physiology. Unfortunately, conventional technologies are limited in uncovering these relations. We present a machine-intelligence technology based on a radically different architecture that realizes real-time image-based intelligent cell sorting at an unprecedented rate.

A detailed insight into the catalytic reduction of NO operated by Cr-Cu nanostructures embedded in a CeO surface.

Replacing rare and expensive elements, such as Pt, Pd, and Rh, commonly used in catalytic devices with more abundant and less expensive ones is mandatory to realize efficient, sustainable and economically appealing three-way catalysts. In this context, the surface of a Cr-Cu/CeO2 system represents a versatile catalyst for the conversion of toxic NO into harmless N2. Yet, a clear picture of the underlying mechanism is still missing.

How seaweeds release the excess energy from sunlight to surrounding sea water.

We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function, providing evidence for a remarkable dynamic change in the number of hydrogen bonds among water molecules and between the porphyra-334 and its surrounding hydrating water. Hydrogen bonds between the porphyra-334 and close by water molecules can act directly and rather easily to promote an efficient transfer of the excess kinetic energies of the porphyra-334 to the surrounding solvating water molecules via an activation of the collective modes identified as hydrogen-bond stretching modes in liquid water which eventually results in a disruption of the hydrogen bond network.

An atomic-level insight into the basic mechanism responsible for the enhancement of the catalytic oxidation of carbon monoxide on a Cu/CeO surface.

The reaction mechanisms of CO molecules interacting with a Cu/CeO surface and related morphological modifications occurring upon removal of O atoms to generate CO are investigated by first-principles dynamical simulations complemented by a free-energy sampling technique. We show that the reactivity of oxygen atoms located in the first layer in the vicinity of the Cu site is remarkably high because of a reduction of the O coordination number. Moreover, we evidence that the doped Cu atoms are responsible for an enhancement of the exposure of other surrounding O atoms, even below the first surface layer, which can then easily react with CO and are gradually removed from the system in the oxidation process.

Simple but Efficient Method for Inhibiting Sintering and Aggregation of Catalytic Pt Nanoclusters on Metal-Oxide Supports.

A simple and efficient method to inhibit aggregation of Pt clusters supported on metal oxide was developed, preserving the accessible clusters surface where catalytically active sites are located even at relatively high temperatures up to 700 K. The key idea was the inclusion of transition metal atoms such as Ni into the Pt clusters, thus anchoring the clusters through formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, first-principles molecular dynamics enhanced with free-energy sampling methods were used.

The absence of a gap state and enhancement of the Mars-van Krevelen reaction on oxygen defective Cu/CeO2 surfaces.

We report a detailed first-principles analysis of the electronic structures of oxygen defective CeO2 and Cu/CeO2 surfaces aimed at elucidating the disappearance of the gap state of defective CeO2 when a Cu atom is added at the surface. The top of the valence band of Cu/CeO2 originates from the O 2p states around this Cu atom. We show that this redistribution of electronic states at the defective Cu/CeO2 surface enhances the reactivity of the surface O atoms.

Reducing the Cost and Preserving the Reactivity in Noble-Metal-Based Catalysts: Oxidation of CO by Pt and Al-Pt Alloy Clusters Supported on Graphene.

The oxidation mechanisms of CO to CO2 on graphene-supported Pt and Pt-Al alloy clusters are elucidated by reactive dynamical simulations. The general mechanism evidenced is a Langmuir-Hinshelwood (LH) pathway in which O2 is adsorbed on the cluster prior to the CO oxidation. The adsorbed O2 dissociates into two atomic oxygen atoms thus promoting the CO oxidation.

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene.

We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.

Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase: the origin of stronger antiferromagnetic couplings than other purple acid phosphatases.

The electronic structure and magnetic interactions of the active site of sweet potato purple acid phosphatase (PAP) were investigated by using UHF, pure DFT (UBLYP), and hybrid DFT methods (UB3LYP and UB2LYP). PAP catalyzes the hydrolysis of a phosphate ester under acidic conditions and contains a binuclear metal center. Sweet potato PAP provides stronger antiferromagnetic coupling than other PAPs.

Enhancement and stabilization of desulfurization activity of Rhodococcus erythropolis KA2-5-1 by feeding ethanol and sulfur components.

We developed a fed-batch culture system fed with ethanol and restricted amounts of sulfur compounds to enhance and stabilize the desulfurizing activity in bacterial cells. In this system using dibenzothiophene (DBT) as the sole sulfur source, a desulfurizing bacterium Rhodococcus erythropolis KA2-5-1 cultivated with small amounts of sulfur showed stable desulfurizing activity and a low rate of growth. However, the cells cultured with excess amounts of sulfur showed unstable activity and a high growth rate.

Oxygen affinity of hemoglobin regulates O2 consumption, metabolism, and physical activity.

The oxygen affinity of hemoglobin is critical for gas exchange in the lung and O(2) delivery in peripheral tissues. In the present study, we generated model mice that carry low affinity hemoglobin with the Titusville mutation in the alpha-globin gene or Presbyterian mutation in the beta-globin gene. The mutant mice showed increased O(2) consumption and CO(2) production in tissue metabolism, suggesting enhanced O(2) delivery by mutant Hbs.

Impaired cell cycle control of neuronal precursor cells in the neocortical primordium of presenilin-1-deficient mice.

Recent studies have implicated presenilin-1 (PS-1) in the processing of the amyloid precursor protein and Notch-1. We show that PS-1 has biological effects on differentiation and cell cycle control of neuronal precursor cells in vivo using PS-1-deficient mice. The expression of Class III beta-tubulin was upregulated throughout the neocortical primordia of PS-1-deficient E14 embryos, especially on the ventricular surface.

A novel enzyme, 2'-hydroxybiphenyl-2-sulfinate desulfinase (DszB), from a dibenzothiophene-desulfurizing bacterium Rhodococcus erythropolis KA2-5-1: gene overexpression and enzyme characterization.

Dibenzothiophene (DBT), a model of organic sulfur compound in petroleum, is microbially desulfurized to 2-hydroxybiphenyl (2-HBP), and the gene operon dszABC was required for DBT desulfurization. The final step in the microbial DBT desulfurization is the conversion of 2'-hydroxybiphenyl-2-sulfinate (HBPSi) to 2-HBP catalyzed by DszB. In this study, DszB of a DBT-desulfurizing bacterium Rhodococcus erythropolis KA2-5-1 was overproduced in Escherichia coli by coexpression with chaperonin genes, groEL/groES, at 25 degrees C.