Article
Chemistry, Physical
Saikat Mukherjee, Mario Barbatti
Summary: The problem of zero-point energy leakage in classical trajectory calculations can be prevented by using the LP-ZPE method, which pumps back leaked energy into corresponding vibrational modes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Sascha Gehrke, Promit Ray, Timo Stettner, Andrea Balducci, Barbara Kirchner
Summary: The study found that at very low concentrations, water is well dispersed and best characterized as shared solvent molecules; at higher concentrations, water forms larger aggregates and increasingly approaches a bulk-like state; the rotational and librational dynamics of water molecules become faster with increasing concentration, while translational dynamics become slower, and all dynamics are faster with higher temperature.
Article
Chemistry, Physical
Paula Gomez-Alvarez, Eva G. Noya, Enrique Lomba
Summary: The study aims to obtain a molecular understanding of water and alcohol adsorption in pure-silica zeolites using molecular simulation techniques. The research found differences in adsorption behavior between MFI and MEL zeolites, despite their structural similarities, which are attributed to the underlying molecular interactions.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Claudia Brocks, Chandan K. Das, Jifu Duan, Shanika Yadav, Ulf-Peter Apfel, Subhasri Ghosh, Eckhard Hofmann, Martin Winkler, Vera Engelbrecht, Lars V. Schaefer, Thomas Happe
Summary: This study proposes a new strategy to improve the O-2 stability of [FeFe]-hydrogenases by blocking the O-2 diffusion pathway and protecting the catalytic cofactor.
Article
Materials Science, Multidisciplinary
Qiang Feng, Menglu Shen, Jiaming Zhu, Jiang Li, Jie Zhang, Shaoyun Guo
Summary: A novel PU/EP IPN damping material with a broad high-damping temperature range was successfully prepared by using 21-hydroxyl β-cyclodextrins as chain extenders, which showed superior damping effects at different temperatures compared to traditional materials.
MATERIALS & DESIGN
(2021)
Article
Microbiology
Ryan W. Penhallurick, Maya D. Durnal, Alliyah Harold, Toshiko Ichiye
Summary: Enzymes from extremophilic microbes are generally adapted to function in extreme conditions, but adaptations for high temperatures and pressures can be challenging to understand. Studies suggest that some microbial enzymes may have specific adaptations for high pressure, such as Tyr103 in MyDHFR possibly playing a role in adaptation to high pressures.
Article
Chemistry, Physical
Aswin V. Muthachikavil, Baoliang Peng, Georgios M. Kontogeorgis, Xiaodong Liang
Summary: The hydrogen-bonded structures in liquid water play a crucial role in its unique properties. The formation of locally favored tetrahedral structures (LFTS) is attributed to water's ability to form hydrogen bonds. Molecular dynamics simulations are commonly used to determine hydrogen bonding based on certain geometric or energetic criteria. In this study, the statistical information of hydrogen-bonded structures in liquid water is analyzed using the iAMOEBA water model. The results show that the tetrahedral environments in liquid water consist mainly of molecules that donate and accept two hydrogens, but not exclusively.
Article
Chemistry, Physical
I. K. Bakulin, I. V. Kopanichuk, N. D. Kondratyuk
Summary: The structure of aqueous 1,4-dioxane solution was investigated using molecular dynamics approach. The overestimation of enthalpy of mixing is related to the lower numbers of water-water and higher numbers of dioxane-water hydrogen bonds. The study provides the total number of hydrogen bonds per oxygen atom and specific numbers for water-water and dioxane-water pairs in the solution.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Zhouyueyang Cheng, Yimin Zhu
Summary: Froth properties are crucial for the mineral processing industry. This study investigated the froth stabilities of two collectors, DOPA and TOPA, and developed a new collector to adjust the flotation performance. Surface tension measurements and molecular dynamics simulations were used to predict the hydrophobicity and froth properties. The experiment results showed that DOPA and TOPA were more robust collectors and could improve the froth stability. The study provided a new case for adjusting flotation performance by developing a collector and predicting its froth stability.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Chemistry, Physical
J. R. C. Santos, P. E. Abreu, J. M. C. Marques
Summary: This study employed molecular dynamics simulations to calculate diffusion coefficients of various pesticides, with comparisons to experimental data revealing some errors, which were rationalized in terms of solute-solvent interactions.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Multidisciplinary
Masaki Donoshita, Yukihiro Yoshida, Mikihiro Hayashi, Ryuichi Ikeda, Susumu Tanaka, Yasuhisa Yamamura, Kazuya Saito, Shogo Kawaguchi, Kunihisa Sugimoto, Hiroshi Kitagawa
Summary: This study demonstrates control over the stacking patterns in 2D molecular assemblies through chemical modification, focusing on a hydrogen-bonded cocrystal system. Experimental results show that the stability order of overlapping patterns may be influenced by the entropic effect of molecular motion, as detected using nuclear quadrupole resonance spectroscopy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Materials Science, Characterization & Testing
Wanying Li, Jiahao Ma, Shinan Wu, Junying Zhang, Jue Cheng
Summary: This study utilized molecular dynamics simulations to investigate the impact of hydrogen bonds on epoxy networks. The results showed that H-bonds significantly affected the Young's modulus, whereas their influence on T-g was limited compared to factors like molecular weight and steric hindrance. This study provides valuable insights into the behavior of H-bonds in furan rings and may guide the design of epoxy resins effectively.
Article
Biochemistry & Molecular Biology
Emil I. Fatullaev, Oleg V. Shavykin, Igor M. Neelov
Summary: The molecular dynamics method was used to investigate the structure and properties of dendrigrafts in methanol-water mixtures with varying methanol fractions. At low methanol fractions, the properties of the dendrigrafts resemble those in pure water. With decreasing dielectric constant and increasing methanol fraction, the dendrigrafts experience collapse, resulting in reduced size, increased internal density, and increased intramolecular hydrogen bonds. The secondary structure changes from an elongated polyproline II helix to a beta-sheet structure at intermediate methanol fractions, and eventually transitions to compact alpha-helix conformations at high methanol fractions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Kevin C. Robben, Christopher M. Cheatum
Summary: This study introduces a novel least-squares fitting metric for fitting multidimensional spectra to generalized Kubo line-shape models, and shows the advantages of this method over the centerline-slope (CLS) method. Experimental results suggest that model fitting is a more robust method of measuring spectral diffusion compared to the CLS method.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Wenqi Hu, Hexu Zhang, Peng Cheng, Lan Chen, Zhi Chen, Svetlana Klyatskaya, Mario Ruben, Johannes V. Barth, Kehui Wu, Yi-Qi Zhang
Summary: By combining surface-confined reactions with supramolecular self-assembly, simple molecular precursors can be transformed into higher-level tectons to generate complex tessellations with unique properties. Using low-temperature scanning tunneling microscopy, efficient chemical reactions converting EP precursors into BPE-Ag complexes were confirmed, leading to the formation of three distinct types of nanoporous supramolecular architectures with BPE-Ag dimers as the basic units.
