Article
Plant Sciences
Gwi Ja Hwang, Mina Jang, Sangkeun Son, Byeongsan Lee, Jun-Pil Jang, Jung-Sook Lee, Sung-Kyun Ko, Young-Soo Hong, Jong Seog Ahn, Jae-Hyuk Jang
Summary: Three new trichostatin analogues, ulleunganilines A-C, and seven known trichostatins were isolated from Streptomyces sp. 13F051 cultures. The structures and activities of these compounds were determined through experiments, with compounds 1 and 3 displaying moderate histone deacetylase inhibitory activity. This suggests that the hydroxamate group and the N,N-dimethyl group are both essential for inhibitory activity.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Chemistry, Physical
Andrea M. Lucero Manzano, Esteban D. Cantero, Esteban A. Sanchez, Oscar Grizzi
Summary: This study investigates the deposition of antimony on TiO2(1 0 0), ranging from sub-monolayer to over 20 equivalent monolayers. Various characterization techniques were used to analyze the growth kinetics, reaction path, and temperature dependence. The results suggest that the antimony remains on the surface without significant incorporation into the bulk, forming flat islands.
APPLIED SURFACE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Tamas Tarjanyi, Ferenc Bogar, Janos Minarovits, Mario Gajdacs, Zsolt Toth
Summary: The adhesion of biomolecules to dental and orthopedic implants is crucial for the process of osseointegration. Molecular dynamics simulations were performed to compare the adhesion properties of 6 peptides on different titanium dioxide surfaces. The residence time, pulling force, and binding energy of each peptide were calculated, and the adhesion strengths of the peptides were ranked based on the simulation results.
Article
Chemistry, Multidisciplinary
Valeria Butera, Arianna Massaro, Ana B. Munoz-Garcia, Michele Pavone, Hermann Detz
Summary: Titanium dioxide (TiO2) has been extensively studied for its applications in catalysis and sensing. This study combines two first-principles methods to investigate the molecular recognition event and electronic structure effects on nanoparticles. A comparison of the methodologies helps in selecting an efficient, finite-size structural model for future research on biosensor electrocatalytic processes and biomass conversion catalysis.
FRONTIERS IN CHEMISTRY
(2021)
Article
Metallurgy & Metallurgical Engineering
Fan Yang, Liang-ying Wen, Qin Peng, Yan Zhao, Jian Xu, Mei-long Hu, Sheng-fu Zhang, Zhong-qing Yang
Summary: Based on density functional theory calculations, co-adsorption models of C or CO with Cl-2 on rutile TiO2 (100) surface were established. It was found that C was more favorable for the adsorption process than CO. The adsorption of Cl-2 on TiO2(100) surface was determined to be physisorption, while co-adsorption of C or CO with Cl-2 on TiO2(100) surface was chemisorptions.
JOURNAL OF CENTRAL SOUTH UNIVERSITY
(2021)
Article
Chemistry, Multidisciplinary
Francisco Gamarra, Jesus Medina, Wilson Lanchipa, Rocio Tamayo, Elisban Sacari
Summary: Pure and Fe-doped TiO2 nanoparticles were synthesized using the sol-gel method and characterized by various techniques. The results showed a correlation between crystallite size and dopant amount, as well as a decrease in band gap. The synthesized samples exhibited promising arsenic removal capacity and were not significantly affected by other ions.
Article
Engineering, Chemical
Haibiao Yu, Yan Pan, Yingying Zhang, Lifeng Gong, Zhenning Lou, Weijun Shan, Ying Xiong
Summary: In this study, TiO2 nanoparticles were functionalized with organic acids containing different numbers of hydroxyl groups. The adjustment of surface functional groups significantly affected the Ge(IV) adsorption capacity. The tartaric acid-functionalized TiO2 nanoparticles showed higher hydroxyl content and adsorption capacity than previously reported adsorbents, and also exhibited remarkable affinity for Ge(IV) in a metallurgical simulated solution.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2023)
Article
Chemistry, Physical
Zhongtian Mao, John R. Rumptz, Charles T. Campbell
Summary: The study revealed that silver grows as nanoparticles on rutile TiO2(100) films, with the differential heat of adsorption increasing with Ag coverage and remaining lower at 100 K compared to 300 K. The adhesion energy of Ag to rutile TiO2(100) was found to be large.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biochemistry & Molecular Biology
Nian-Zhi Li, Chen-Hsu Yu, Jhuan-Yu Wu, Shing-Jong Huang, Shou-Ling Huang, Richard P. Cheng
Summary: Cross-strand interactions between glutamate and arginine analogs with varying side-chain lengths were studied in beta-hairpin peptides using nuclear magnetic resonance methods. The fraction folded population trends could be explained by the strand propensity of the constituting residues, but this was not the case for peptides with lysine analogs. The diagonal ion-pairing interaction energetics were derived using double-mutant cycle analysis.
Article
Biochemistry & Molecular Biology
Lennart Nicke, Philip Horx, Ronny Mueller, Sylvia Els-Heindl, Armin Geyer
Summary: A generalized synthetic strategy is proposed for asymmetric beta-indoylated amino acids by 8-aminoquinoline (8AQ)-directed C(sp(3))-H functionalization. The peptides with (indol-3-yl)-3-phenylalanine at position 2 have shown a wide range of activities as ghrelin receptor inverse agonists, demonstrating the potential for systematic variation of indole group position in bioactive peptides.
Article
Multidisciplinary Sciences
Hongxia Zhao, Yong Yang, Xin Shu, Tao Wang, Qianping Ran
Summary: The study using MD simulations with INTERFACE-PCFF forcefield reveals that the adsorption conformations of PCEs on C3A and ettringite surfaces differ, with PCEs with fewer side chains being more favorable for adsorption due to stronger electrostatic interaction.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tamas Tarjanyi, Ferenc Bogar, Janos Minarovits, Mario Gajdacs, Zsolt Toth
Summary: Titanium (Ti) is commonly used in medical and dental implants due to its tensile strength and biocompatibility. Functionalization with the tetrapeptide KRSR has been shown to promote osteoblast adhesion to implant surfaces, potentially improving bone-to implant contact and stability during healing. Computational simulations suggest that the N-terminal lysine residue in KRSR plays a crucial role in its adhesion to the TiO2 surface, influencing osseointegration of dental implants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Bo Wen, Annabella Selloni
Summary: The study investigates the structure of carboxylic acid-modified TiO2 surfaces in contact with water, using density functional theory and ab initio molecular dynamics. It was found that isolated formic acid molecules adsorbed on the TiO2 surface remained stable, with protons transferred to form surface bridging hydroxyls. Adsorbed monolayers of formic acid molecules in water resulted in a negatively charged surface with solvated H3O+ ions nearby.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Luca Schio, Gregor Bavdek, Cesare Grazioli, Carolina Gutierrez Bolanos, Andrea Goldoni, Andrea Vittadini, Massimo Tormen, Luca Floreano
Summary: The efficiency of interfacial charge transfer for metal-tetraphenylporphyrins (M-TPPs) on rutile TiO2(110) depends on the molecular adsorption site and configuration. M(II)-TPPs with M = Co, Ni, Cu, Zn adsorb on the O-br rows with the same molecular conformation and form a commensurate phase with the same symmetry. The tendency to axial coordination determines the molecular adsorption energy and the preference for adsorption atop one O-br atom or on a bridge between two O-br atoms.
APPLIED SURFACE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Jing-Yuan Chang, Yen-Jin Pan, Pei-Yu Huang, Yi-Ting Sun, Chen-Hsu Yu, Zhi-Jun Ning, Shou-Ling Huang, Shing-Jong Huang, Richard P. Cheng
Summary: The beta-sheet is a common protein secondary structure and its aberrant aggregation is associated with neurodegenerative diseases. This study systematically investigates the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction in a beta-hairpin. Results show that the fraction folded population for peptides with diagonal ion pairs is generally lower compared to those with lateral ion pairs.
Article
Chemistry, Physical
Marzieh Saeedimasine, Erik G. Brandt, Alexander P. Lyubartsev
Summary: The study investigates the adsorption behavior of small biomolecules on different carbon-based nanomaterial surfaces using enhanced sampling molecular dynamics, finding that surface functionalization can significantly affect adsorption properties, enabling the design of nanosurfaces with highly selective adsorption properties beneficial for human health and environmental safety.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Crystallography
Paulo H. B. Brant Carvalho, Amber Mace, Inna Martha Nangoi, Alexandre A. Leitao, Chris A. Tulk, Jamie J. Molaison, Ove Andersson, Alexander P. Lyubartsev, Ulrich Haeussermann
Summary: The high pressure structural behavior of H-2 and Ne clathrate hydrates was investigated, and the transitions of H-2 and Ne hydrates under different pressure and temperature conditions were observed.
Article
Chemistry, Physical
Tiedong Sun, Vishal Minhas, Alexander Mirzoev, Nikolay Korolev, Alexander P. Lyubartsev, Lars Nordenskiold
Summary: Researchers have developed a coarse-grained model of the nucleosome core particle (NCP) using a systematic bottom-up approach. The model accurately reproduces the known structural features of the NCP and provides a realistic description of nucleosome-nucleosome attraction in the presence of multivalent cations. This model opens up possibilities for rigorous modeling of chromatin fibers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Xiaofeng Zhou, Bo Shen, Alexander Lyubartsev, Jiwei Zhai, Niklas Hedin
Summary: This article reviews the application of piezoelectric semiconductors in mechanoredox systems and photoredox catalysis, focusing on the advantages of piezoelectric heterostructures in converting mechanical energy into chemical energy and enhancing catalytic reactivity. The fundamental concepts of piezoelectricity and piezoelectric potential are discussed, and the mechanisms of various piezoelectric heterostructures in piezoand piezophotocatalysis are examined. The article also provides a summary of dynamic investigations into piezoand piezophotocatalytic processes and the development of piezotronic and piezophototronic effects. Design principles and future research directions in the field of piezoand piezophotocatalysis employing semiconductive heterostructures are derived.
Article
Chemistry, Multidisciplinary
Xiaofeng Zhou, Fei Yan, Alexander Lyubartsev, Bo Shen, Jiwei Zhai, Jose C. Conesa, Niklas Hedin
Summary: Piezoelectric semiconductors have been developed as redox catalysts, and a new methodology for synthesizing H2O2 using visible light and mechanical energy has been demonstrated. Carbon quantum dots are used as sensitizers to enhance the piezocatalytic activity, and the modulation of the material's piezoelectricity affects the piezophotocatalytic activity.
Article
Biochemistry & Molecular Biology
Delphine Menard, Leonard Blaschek, Konstantin Kriechbaum, Cheng Choo Lee, Henrik Serk, Chuantao Zhu, Alexander Lyubartsev, Nuoendagula, Zoltan Bacsik, Lennart Bergstrom, Aji Mathew, Shinya Kajita, Edouard Pesquet
Summary: Different vascular cell types control their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.
Article
Chemistry, Physical
Marzieh Saeedimasine, Fredrik Grote, Alexander P. Lyubartsev
Summary: In this study, ab initio molecular dynamics simulations were used to investigate the structural details of ZnO surfaces in water and develop a classical force field for hydrated ZnO surfaces. The simulations showed that water dissociates near unmodified ZnO surfaces, forming hydroxyl groups and protonating surface oxygen atoms. The developed force field was validated and can be used for modeling ZnO in various fluid environments and in interaction with biomolecules.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Mikhail Ivanov, Maksim Posysoev, Alexander P. Lyubartsev
Summary: This study proposes a bottom-up coarse-graining method using artificial neural networks to determine interactions within a coarse-grained model. The method is demonstrated on modeling methanol-water solutions and shows promising results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Roja Rahmani, Alexander P. Lyubartsev
Summary: The understanding of how nanomaterials interact with biological molecules is crucial for their biomedical applications and evaluation of toxicity. Molecular dynamics simulations were conducted to study the adsorption properties of 30 small molecules on ZnS surfaces in aqueous media. It was found that only a few anionic molecules showed significant binding to the pristine ZnS surface, while spherical ZnS nanoparticles exhibited stronger binding due to their surface facets. The presence of a poly-methylmethacrylate (PMMA) coating changed the binding preferences, with some molecules showing high affinity due to binding with the coating.
Article
Chemistry, Physical
Fredrik Grote, Alexander Lyubartsev, Sergey V. Dvinskikh, Vibhu Rinwa, Jan Holmbaeck
Summary: Binary mixtures of ethanol and phospholipids DOPC and DOPE were investigated for topical drug delivery applications using computer simulation and experimental approach. Molecular dynamics simulations and experimental measurements were used to compute and validate properties such as diffusion coefficients, relaxation times, and viscosity. The simulations revealed that the structure of ethanol-DOPC mixtures remains unchanged while ethanol-DOPE mixtures undergo structural rearrangements, indicating the stronger aggregation tendency of DOPE. These findings provide valuable insights into the development of advanced drug delivery formulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Fredrik Grote, Alexander P. Lyubartsev
Summary: In this study, the structure, dynamics, and reactivity of water on the surface of TiO2 nanoparticles fully immersed in water were investigated using ab initio molecular dynamics simulation. The results reveal that water dissociation can occur through a mechanism involving proton transfer across multiple water molecules, and the structural and dynamical properties of water near the nanoparticle surface differ from those on flat defect-free surfaces.
Article
Chemistry, Physical
Ian Rouse, David Power, Erik G. Brandt, Matthew Schneemilch, Konstantinos Kotsis, Nick Quirke, Alexander P. Lyubartsev, Vladimir Lobaskin
Summary: Nanomaterials have wide potential applications due to their unique properties and high activity, but interactions with living organisms can bring both advantages and risks. Predicting biological impacts and developing nanotechnology require overcoming the challenge of scaling from material-specific atomic descriptors to typical biomolecule length scales.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Paulo H. B. Brant Carvalho, Amber Mace, Ove Andersson, Chris A. Tulk, Jamie Molaison, Alexander P. Lyubartsev, Inna M. Nangoi, Alexandre A. Leitao, Ulrich Haeussermann
Summary: The high-pressure structural behavior of noble gas clathrate hydrates Ar•6.5H2O and Xe•7.2H2O was investigated by neutron powder diffraction at 95K, revealing pressure-induced amorphization at different pressures. Molecular dynamics simulations provided insight into the role of guest species in stabilizing or destabilizing the clathrate structures under pressure.