We present a method based on kinetic molecular theory that identifies reactions of various molecularities in molecular dynamics (MD) simulations of bulk gases. The method allows characterization of the thermodynamic conditions at which higher than bimolecular reactions are a factor in the mechanisms of complex gas-phase chemistry. Starting with Bodenstein's definition of termolecular collisions we derive analytical expressions for the frequency of higher molecularity collisions. We have developed a relationship for the ratio of the frequencies of termolecular to bimolecular collisions in terms of the temperature, density, and collision times. To demonstrate the method, we used ReaxFF in LAMMPS to carry out MD simulations for NVT ensembles of mixtures of H-O over the density range 120.2-332.7 kg m and temperature range 3000-5000 K. The simulations yield ReaxFF-based predictions of the relative importance of termolecular collisions O···H···O and bimolecular collisions O···H in the early chemistry of hydrogen combustion.
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http://dx.doi.org/10.1021/acs.jpca.8b11686 | DOI Listing |
J Chem Phys
June 2024
ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt, or they can be defined by a set of elementary reaction steps that form a chemical reaction network.
View Article and Find Full Text PDFStud Hist Philos Sci
April 2024
Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. Electronic address:
The term "molecularization" has been used by historians and sociologists of science to describe the transition from an anatomic view of the body to a submicroscopic one, where health and illness, indeed life itself, are increasingly defined in terms of an individual's "genetic landscape." Here we introduce the notion of the infra-molecular as a way of extending and nuancing the molecularization trope as it applies to the domain of (post)genomic oncology. In particular we look at how infra-molecularity is enacted in practice as part of the so-called "histology-agnostic" turn in clinical cancer research and care.
View Article and Find Full Text PDFMolecules
December 2023
Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations.
View Article and Find Full Text PDFInt J Biol Macromol
October 2023
Faculty of Chemical Engineering, Urmia University of Technology, Urmia, Iran.
The primary function of the drug delivery system is to transfer various drugs to certain parts of the body. The drug is transferred reliably in the molecularity imprinted system, based on adjusting the drug release mechanism to control the drug amount and treatment duration. Molecular Imprinting Technology can provide an efficient polymer system to detect bioactive molecules and has high adsorption capacity as drug delivery carriers.
View Article and Find Full Text PDFAcc Chem Res
June 2022
State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road, West Fuzhou 350002, P.R. China.
ConspectusFor the last two decades, materials scientists have contributed to a growing library of porous crystalline materials. These synthetic materials are typically extended networks, including metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), or discrete materials like metal-organic cages (MOCs) and porous organic cages (POCs). Advanced porous materials have shown promise for various applications due to their modular nature and structural tunability.
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