Comprehensive Analysis of Deuterium Isotope Effects on Ionic HOπ Interactions Using Multi-Component Quantum Mechanics Methods.

Deuterium isotope effects on interaction energies and geometrical parameters in several HO(DO)ene and HO+(DO)yne complexes, which involve O-H(D)π interactions, have been analyzed using the MP2 level of the multi-component molecular orbital method (MC_MP2), which can incorporate the nuclear quantum effects of light nuclei, such as protons and deuterons. The MC_MP2 calculations revealed that DO replacement reduced the interaction energies of the complexes and induced changes in geometrical parameters. In addition, natural energy decomposition analysis (NEDA) revealed a strong correlation between the H/D isotope effects on the H/Dπ distances and on each energy component.

A theoretical study on muoniated N-heterocyclic carbenes using path integral molecular dynamics.

Several N-heterocyclic carbenes (NHCs) are experimentally observed upon the addition of muonium (Mu), and the hyperfine coupling constants (HFCCs) of muon are measured. Theoretical investigation of Mu has been challenging due to significant quantum effects. Herein, we performed an ab initio path integral molecular dynamics (PIMD) simulation, which accurately considers multi-dimensional quantum effects, to theoretically investigate muoniated 1,3-dihydro-2H-imidazole-2-ylidene (Mu-IY).

Efficient quantum mechanical minimum free energy path calculation by combining path integral hybrid Monte Carlo and climbing image nudged elastic band methods, and its application to the addition reaction of hydrogen isocyanide to formaldehyde.

We propose an efficient algorithm for a minimum free energy path calculation based on the path integral hybrid Monte Carlo (PIHMC) method by combining the climbing image-nudged elastic band (CI-NEB) and the thermodynamic integration (TI) methods. Here, the CI-NEB and the TI methods are used to find a transition state along the reaction path and evaluate the free energy path, respectively. Our algorithm is applied to the Walden inversion reaction of the hydronium ions (H3O+).

The TrkC-PTPσ complex governs synapse maturation and anxiogenic avoidance via synaptic protein phosphorylation.

The precise organization of pre- and postsynaptic terminals is crucial for normal synaptic function in the brain. In addition to its canonical role as a neurotrophin-3 receptor tyrosine kinase, postsynaptic TrkC promotes excitatory synapse organization through interaction with presynaptic receptor-type tyrosine phosphatase PTPσ. To isolate the synaptic organizer function of TrkC from its role as a neurotrophin-3 receptor, we generated mice carrying TrkC point mutations that selectively abolish PTPσ binding.

Characteristics of membrane transport, metabolism, and target protein binding of cyclic depsipeptide destruxin E in HeLa cells.

Cyclic peptides have attracted attention as new modalities for drug development owing to their unique pharmacokinetic and pharmacodynamic properties. Destruxin E, a 19-membered cyclodepsipeptide, is a promising candidate drug for cancer therapy. The purpose of the present study was to clarify the molecular mechanisms underlying membrane transport, metabolism, and the binding for target molecules of destruxin E in human cervical carcinoma HeLa cells used as a model of cancer cells.

Nuclear quantum effects on the intramolecular hydrogen bonds in biuret and biguanide.

We focus on the unique aspects of biuret and biguanide, which form six-membered ring structures intramolecular hydrogen bonds. The proton donor and acceptor atoms differ between biuret and biguanide, leading to varying energy barrier heights for proton transfer. We performed path integral molecular dynamics (PIMD) simulations for biuret and biguanide to investigate the correlation between proton transfer and the degree of the delocalization of π-electrons in the six-membered ring framework structure.

Ultrafine Spatial Modulation of Diazapyrene-Based Two-Dimensional Conjugated Covalent Organic Frameworks.

Tailormade bottom-up synthesis of covalent organic frameworks (COFs) from various functional building blocks offer not only tunable topology and pore size but also multidimensional properties. High crystallinity is one of the prerequisites for their structures and associated physicochemical properties. Among different π-conjugated motifs for constructing COFs, pyrene-based tetragonal structures are effective in achieving highly ordered and crystalline states.

Nuclear quantum and H/D isotope effects on aromaticity: path integral molecular dynamics study.

Aromaticity is an important concept in organic chemistry, and thus, many theoretical and experimental studies have been conducted so far. However, the majority of theoretical studies have concentrated on the aromaticity of the stationary point structures. Herein, the influence of nuclear quantum fluctuation (nuclear quantum effects: NQEs) and thermal fluctuation on the aromaticity of benzene have been analyzed by path integral molecular dynamics (PIMD) simulation.

Theoretical study of short-range exchange interaction based on semiconductor dielectric function model toward time-dependent dielectric density functional theory.

This study explores various models of semiconductor dielectric functions, with a specific emphasis on the large wavenumber spectrum and the derivation of the screened exchange interaction. Particularly, we discuss the short-range effect of the screened exchange potential. Our investigation reveals that the short-range effect originating from the high wavenumber spectrum is contingent upon the dielectric constant of the targeted system.

Nuclear quantum effects in phase transition between Ice VII and Ice X.

The theoretical modeling of high-pressure ice remains challenging owing to the complexity in accurately reflecting its properties attributable to nuclear quantum effects. To explore the nuclear quantum effects of the phase transition between Ice VII and Ice X, we introduce an approach based on ab initio path-integral molecular dynamics. The results indicate that quantum effects facilitate the phase transition, with the observed isotope effects consistent with the experimental outcomes.

Hypoxia suppresses glucose-induced increases in collective cell migration in vascular endothelial cell monolayers.

Blood glucose levels fluctuate during daily life, and the oxygen concentration is low compared to the atmosphere. Vascular endothelial cells (ECs) maintain vascular homeostasis by sensing changes in glucose and oxygen concentrations, resulting in collective migration. However, the behaviors of ECs in response to high-glucose and hypoxic environments and the underlying mechanisms remain unclear.

Location of the Shared Proton in Proton-Bound Dimer Compound of Hydrogen Sulfate and Formate: Path Integral Molecular Dynamics Study.

The structure of the proton-bound dimer compound of hydrogen sulfate and formate has been studied by considering nuclear quantum effects (NQEs) using the path integral molecular dynamics method. This study unveiled the location of the shared proton and answered the following question: "Is the shared proton localized on either an anion or located around the center of two anions?" We have elucidated that the shared proton is distributed in the region beyond the transition state due to the NQEs, even though the shared proton did not completely overcome the transition state for the proton shuttle.

Molecular Mechanism of SLC6A8 Dysfunction with c.1699T > C (p.S567P) Mutation in Cerebral Creatine Deficiency Syndromes.

Cerebral creatine deficiency syndromes (CCDS) are neurodevelopmental disorders caused by a decrease in creatine levels in the central nervous system (CNS) due to functional mutations in creatine synthetic enzymes or creatine transporter (CRT/SLC6A8). Although SLC6A8 mutations have been reported to be the most frequent cause of CCDS, sufficient treatment for patients with CCDS harboring SLC6A8 mutations has not yet been achieved. This study aimed to elucidate the molecular mechanism of SLC6A8 dysfunction caused by the c.

A path integral molecular dynamics study on the muoniated xanthene-thione molecule.

A positive Mu is a useful tool for investigating the spin density of radical species. The theoretical estimation of its behavior in a molecule requires the inclusion of a quantum effect due to the small mass of muonium. Herein, we performed ab initio a path integral molecular dynamics (PIMD) simulation, which accurately included a multi-dimensional quantum effect, for muoniated 9H-xanthene-9-thione (μXT).

Theoretical Study of the Molecular Passivation Effect of Lewis Base/Acid on Lead-Free Tin Perovskite Surface Defects.

Extensive research has been recently conducted to improve the power conversion efficiency (PCE) of perovskite solar cells. However, the charge carriers are easily trapped by the defect sites located at the interface between the perovskite layer and the electrode, which decreases the PCE. To reduce such defect sites, the passivation technique is frequently employed to coat small molecules on the perovskite surface during the manufacturing process.

Nuclear quantum and H/D isotope effects on intramolecular hydrogen bond in curcumin.

Curcumin and its derivatives possess intramolecular low-barrier hydrogen bonds for intramolecular proton transfer. The π-delocalization in the OCCCO framework of the hydrogen bond in these compounds is reorganized concomitantly with the proton transfer. To characterize the hydrogen bond and π-delocalization, we performed path integral molecular dynamics simulations, revealing that although the proton migration and reorganization of the π-delocalized structure showed a positive correlation, the correlation was weak.

Stability and bonding nature of positronic lithium molecular dianion.

We studied the stability of a system consisting of a positron (e+) and two lithium anions, [Li-; e+; Li-], using first-principles quantum Monte Carlo calculations combined with the multi-component molecular orbital method. While diatomic lithium molecular dianions Li22- are unstable, we found that its positronic complex can form a bound state with respect to the lowest energy decay into the dissociation channel Li2- and a positronium (Ps). The [Li-; e+; Li-] system has the minimum energy at the internuclear distance of ∼3 Å, which is close to the equilibrium internuclear distance of Li2-.

Improved activity for the oxygen evolution reaction using a tiara-like thiolate-protected nickel nanocluster.

Practical electrochemical water splitting and carbon-dioxide reduction are desirable for a sustainable energy society. In particular, facilitating the oxygen evolution reaction (OER, the reaction at the anode) will increase the efficiency of these reactions. Nickel (Ni) compounds are excellent OER catalysts under basic conditions, and atomically precise Ni clusters have been actively studied to understand their complex reaction mechanisms.

Direct Elucidation of the Vibrationally Averaged Structure of Benzene: A Path Integral Molecular Dynamics Study.

Path integral molecular dynamics (PIMD) simulations for CH, CD, and CT have been carried out to directly estimate the distribution of projected C-H(D,T) bond lengths onto the principal axis plane. The average values of raw C-H(D,T) bond lengths obtained from PIMD simulations are in the order of ⟨⟩ > ⟨⟩ > ⟨⟩ due to the anharmonicity of the potential energy curve. However, the projected C-H(D,T) bond lengths are almost the same as those reported by Hirano et al.

Quantitative Targeted Absolute Proteomics for Better Characterization of an In Vitro Human Blood-Brain Barrier Model Derived from Hematopoietic Stem Cells.

We previously developed an in vitro model of the human blood-brain barrier (BBB) based on the use of endothelial cells derived from CD34-hematopoietic stem cells and cultured with brain pericytes. The purpose of the present study was to provide information on the protein expression levels of the transporters, receptors, tight junction/adherence junction molecules, and transporter-associated molecules of human brain-like endothelial cells (hBLECs). The absolute protein expression levels were determined by liquid chromatography-mass spectrometry-based quantitative targeted absolute proteomics and compared with those from human brain microvessels (hBMVs).

Decomposition analysis on the excitation behaviors of thiazolothiazole (TTz)-based dyes the time-dependent dielectric density functional theory approach.

Thiazolothiazole (TTz)-based materials have been attracting much attention because of their widespread applications. In this paper, we discuss the excited electronic behaviors of asymmetric TTz dyes in solvents based on the time-dependent dielectric density functional theory method. Based on dipole moment and charge distribution (population) analyses, we discuss large intramolecular electron transfers, which are triggered by photon excitations, toward the acceptor part of dyes.

Molecular Dynamics Study on the Structure-Property Relationship of Self-Assembled Gear-Shaped Amphiphile Molecules with/without Methyl Groups.

Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (, , and ) of GSAs (, , and , respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The , , and monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively.

A comprehensive theoretical study of positron binding and annihilation properties of hydrogen bonded binary molecular clusters.

We studied the positron binding and annihilation of hydrogen bonded binary molecular clusters containing small inorganic molecules such as water, hydrogen fluoride, ammonia, hydrogen sulfide, hydrogen chloride, and phosphine, using first-principles calculation. While unimolecular systems of these species mostly exhibit no or very small positron binding energies (positron affinities), we found that all of their hydrogen bonding clusters have greater positive positron affinities. The permanent dipole moment enhanced by the formation of the intermolecular hydrogen bond acts as a dominant parameter to bind a positron for a given proton donor, whereas it is insufficient for reproducing the dependence of the positron affinity on substitutions of the proton donor.