Article
Chemistry, Physical
Yao-Yao Huang, Zheng-Hua He, Guang-Fu Ji
Summary: The thermolysis of beta-HMX under different thermodynamics states has been investigated using quantum-based molecular dynamics method. The reaction is mainly initiated by molecular ring breaking and alkyl dehydrogenation. The cleavage of N-N and C-N bonds is hindered under high pressure, while the cleavage of C-H bond is significantly enhanced. NO3 is more favorably produced under low pressure, promoting hydrogen transfer to form H2O or OH. The reaction kinetics constants reflect that the initial endothermic reaction is slower under high pressure, but the subsequent exothermic reaction is significantly accelerated with a larger reaction heat of 368.05 cal.g(-1).
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Ioulia K. Mati, William Edwards, Domenico Marson, Edward J. Howe, Scott Stinson, Paola Posocco, Euan R. Kay
Summary: This study investigates the reaction kinetics for nanoparticle-bound hydrazones, revealing that surface-confined reactions are influenced by multiscale effects and proceed more slowly compared to their solution-phase counterparts. Molecular dynamics simulations uncover distinct supramolecular architectures and unexpected dynamic features of surface-bound molecules that explain experimentally observed trends in reactivity.
Article
Chemistry, Multidisciplinary
Luis Ruiz Pestana, Teresa Head-Gordon
Summary: The evaporation mechanism of nanodroplets is different from that of macroscopic water droplets. Regardless of hydrophobicity, the evaporation rate of nanodroplets does not follow the traditional mode and their evaporation behavior is characterized by non-equilibrium wetting. The vapor concentration on the surface of nanodroplets does not reach a steady state. The evaporative lifetime of nanodroplets is directly related to the hydrophobicity of the substrate.
Article
Thermodynamics
Huanhuan Wang, Bingzhi Liu, Cheng Xie, Yanbo Li, Jintao Cui, Lili Xing, Zhandong Wang
Summary: This study investigates the thermal decomposition reaction pathways of isopentanol through theoretical calculations, showing that water elimination and C-C bond dissociation play significant roles in its unimolecular decomposition.
COMBUSTION AND FLAME
(2022)
Article
Chemistry, Physical
Gianmarco Vanuzzo, Adriana Caracciolo, Timothy K. Minton, Nadia Balucani, Piergiorgio Casavecchia, Carlo de Falco, Alberto Baggioli, Carlo Cavallotti
Summary: The article presents investigations on the products, branching fractions, and rate constants of the phenoxylation reaction through experimental and theoretical studies to enhance the accuracy and reliability of combustion models.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Multidisciplinary
Lei-Min Zhao, Li-Shuo Zheng, Xiaoping Wang, Wei Jiang
Summary: This study reports a molecular shuttle based on a rotaxane, which is influenced by an acid-responsive asymmetric macrocycle. Upon protonation induced by trifluoroacetic acid (TFA), the macrocycle translocates and the shuttling kinetics are hindered by steric hindrance. The shuttling kinetics depend on the concentration of TFA and a kinetic intermediate can be captured.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Placido Arenas-Fernandez, Fernando Aguilar-Galindo, Inmaculada Suarez, Baudilio Coto
Summary: Naphthenic acids (NAs) are toxic compounds naturally present in petroleum sources and can cause severe corrosion and catalyst deactivation. Two ionic liquids (ILs), [EMIm][OAc] and [P14,6,6,6][CCN2], were studied for their extraction capacity. Molecular dynamics simulations and quantum mechanical calculations were used to analyze the extraction mechanisms, showing that [EMIm][OAc] undergoes a neutralization reaction while [P14,6,6,6][CCN2] undergoes physical extraction.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Engineering, Chemical
Yishu Yan, Junbo Xu, Shenglan Liu, Min Wang, Chao Yang
Summary: Using ReaxFF molecular dynamics, the thermostability of cross-linked and non-cross-linked phenolic was compared to study the effect of cross-linked and branched structures on the pyrolysis mechanism. The results indicate that phenolic tends to break into low-boiling molecules with less than 4 carbon atoms and polymerizes into macromolecules with more than 1500 carbon atoms during pyrolysis. The findings suggest that phenolic resin with high degree of crosslinking and branching has better thermostability and preserves its carbon skeleton more effectively.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Miloslav Pekar
Summary: Autocatalytic reactions, in contrast to traditional mass-action kinetics, can be verified and generalized using modern non-equilibrium thermodynamics, ensuring consistency with the entropic inequality.
Article
Chemistry, Applied
Zhiguo Yan, Dan Chen, Ling Huang, Jieqing Liu, Heqing Fu, Yang Xiao, Shaoping Li
Summary: This study investigates the diffusion behavior of key components in the alkylation reaction of benzene and methanol catalyzed by H-ZSM-5 zeolite. The presence of CH3O- intermediates in CH3-ZSM-5 zeolite enhances the diffusion of p-xylene.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Article
Engineering, Environmental
Ruize Sun, Mingyu Yu, Guangqian Luo, Xian Li, Hong Tian, Hong Yao
Summary: This research investigates the reaction mechanism between sulfur and Hg-0 through quantum chemical calculations and electronic wavefunction analysis. It shows that branched S-n isomers react with Hg-0 spontaneously with heat release, and have higher reaction rate constants than cyclic S-n molecules. Furthermore, electronic wavefunction analysis characterizes the breaking and formation of Hg-S and S-S bonds during the reaction process.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Engineering, Environmental
Kejiang Li, Rita Khanna, Hang Zhang, Alberto Conejo, Shufang Ma, Zeng Liang, Guangyue Li, Mansoor Barati, Jianliang Zhang
Summary: The atomic scale understanding of gasification interactions between graphene and CO2 is limited. Reactive force field molecular dynamics simulation studies showed non-linear gasification kinetics with abnormal thermal behavior in the intermediate temperature range. The three-stage reaction process involved defect formation, carbon chain breaking, and adsorption of CO2 on active carbon sites to enhance gasification. The presence of a monovacancy promoted reaction kinetics only at relatively low temperatures.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Thermodynamics
Nicholas Tsolas, Karan Bopaiah, Tanner Middleton
Summary: In this study, the effects of non-equilibrium low-temperature plasmas on the pyrolysis and oxidation kinetics of iso-octane were examined using a plasma-coupled flow reactor facility. The results showed that the plasma enhanced the chemical reactivity and lowered the hot-ignition temperature below 900 K. A 0D plasma-coupled kinetic model was used to obtain detailed kinetic insight, and it displayed good agreement with the experimental data for fuel consumption and intermediate formation during pyrolysis conditions. The model also had satisfactory agreement with the experiments for oxidation conditions, except for discrepancies observed at lower temperatures.
COMBUSTION AND FLAME
(2023)
Article
Thermodynamics
Irina A. Graur, Marina A. Batueva, Moritz Wolf, Elizaveta Ya. Gatapova
Summary: This article conducts numerical simulations of monatomic vapor condensation on its liquid phase using three different methods. The results show good agreement among these methods for monatomic gases. The Moment Method is found to have great potential for efficient estimation of condensation fluxes while respecting the conservation of mass, momentum, and energy. The study also discusses the presence and effects of an inverted temperature gradient during the condensation process, and proposes a methodology for extracting the condensation coefficient based on the Moment Method results.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Chemistry, Multidisciplinary
Pedro Recio, Silvia Alessandrini, Gianmarco Vanuzzo, Giacomo Pannacci, Alberto Baggioli, Demian Marchione, Adriana Caracciolo, Vanessa J. Murray, Piergiorgio Casavecchia, Nadia Balucani, Carlo Cavallotti, Cristina Puzzarini, Vincenzo Barone
Summary: This study reveals that intersystem crossing between the pre-reactive complex and the reaction barrier can control the rate of bimolecular reactions for weakly coupled potential energy surfaces, even in the absence of heavy atoms. By conducting crossed-beam experiments and computational simulations, it is found that for the O(P-3) plus pyridine reaction, the main products are pyrrole and CO, obtained through a spin-forbidden ring-contraction mechanism. The reaction rates at low to moderate temperatures are mainly dominated by intersystem crossing.
Article
Chemistry, Physical
Carlos Martin-Fernandez, Jeremy N. Harvey
Summary: The study discusses the relationship between errors in density functional theory and errors in self-consistent densities obtained from different density functional approximations, as well as how to measure and evaluate density sensitivity. Two widely applicable metrics for any density functional approximation are reported, along with how they can be used to classify chemical systems based on their sensitivity to small variations in density.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Applied
Akinobu Matsuzawa, Jeremy N. Harvey, Fahmi Himo
Summary: This review highlights the importance of computational studies in realizing that bimetallic complexes are the active catalytic species in some reactions, rather than monometallic complexes as previously assumed. The combination of experimental observations and computation of metal precursor speciation is a powerful tool in predicting the presence of bimetallic intermediates or transition states.
TOPICS IN CATALYSIS
(2022)
Article
Chemistry, Medicinal
Francesc Sabanes Zariquiey, Edgar Jacoby, Ann Vos, Herman W. T. van Vlijmen, Gary Tresadern, Jeremy Harvey
Summary: The combination of mixed-solvent molecular dynamics (MD) and time-structure independent component analysis (TICA) was applied to four retrospective case studies, and the results were compared with previous experimental and computational findings. It was found that the successful identification of cryptic pockets depends on the system and the cosolvent probes. The conformational state of the targets plays a critical role in docking studies with the parent ligands, which has implications for virtual screening applications.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Organic
Xianjun Xu, Huangdi Feng, Xiaoyong Zhang, Liangliang Song, Luc Van Meervelt, Johan Van der Eycken, Jeremy N. Harvey, Erik V. Van der Eycken
Summary: A palladium-catalyzed reaction for the synthesis of fused polycyclic indolizines has been developed. Experimental and theoretical studies suggest that the reaction involves C-C and C-O bond cleavage, providing a new approach for heterocycle synthesis.
Article
Chemistry, Physical
Xiaoyong Zhang, Pierre-Louis Lefebvre, Jeremy N. Harvey
Summary: The solvent environment has minimal influence on transition state passage dynamics of the Diels-Alder reaction in aprotic solvents, with the notable effect occurring far from the transition state region where reactants are caged within the reactant well.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Julien Escudero, Pieter Mampuys, Carl Mensch, Charles B. Bheeter, Robby Vroemans, Romano V. A. Orru, Jeremy Harvey, Bert U. W. Maes
Summary: o-Phenylene N-substituted iminocarbonates can be obtained through aerobic Ni-catalyzed reaction of readily available catechols and isocyanides. The choice of oxidant and absence of base are crucial to avoid unwanted catechol oxidation. This method is generally applicable to other oxidation-sensitive aromatic 1,2-bisnucleophiles, providing a new approach to important bicyclic heterocycles.
Article
Chemistry, Multidisciplinary
Stefan Lulf, Luxuan Guo, Tobias Parchomyk, Jeremy N. Harvey, Konrad Koszinowski
Summary: This study investigates the oxidative addition of organyl halides to phenylferrate anions in the gas phase, revealing the impact of different iron complexes on reactivity and reaction pathways. DFT calculations provide insights into the high reactivity of Ph2Fe(I)(-) complex.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Ahmed M. Rozza, Marcell Papp, Neil R. McFarlane, Jeremy N. Harvey, Julianna Olah
Summary: This study used a combination of theoretical tools to investigate various aspects of NO binding and reaction intermediates. The results suggest that NO binding leads to conformational changes in the protein.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Pablo Ramos-Sanchez, Jeremy N. Harvey, Jose A. Gamez
Summary: A novel algorithm is proposed to explore the chemical space by generating reaction networks using heuristics based on chemical theory. The algorithm improves performance by considering only transformations that break two chemical bonds and form two new ones. It estimates energy barriers using quantum chemical calculations and can also identify missed species during the previous step to further define the reaction network. The algorithm has successfully identified the most important reaction pathways in five different chemical reactions.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Andrea Daru, Carlos Martin-Fernandez, Jeremy N. Harvey
Summary: This article presents a mechanistic investigation of the iron-catalyzed Kumada reaction involving clusters as active species. It suggests that 11- and 13-coordinated clusters are fundamental for initiating the reaction, and proposes a classic initiation step.
Article
Chemistry, Physical
Tamara Rinkovec, Demian Kalebic, Mark Van der Auweraer, Wim Dehaen, Jeremy N. Harvey, Steven De Feyter
Summary: In this study, the effect of concentration on the self-assembled molecular network formation process was investigated using scanning tunneling microscopy. Isophthalic acids were chosen as a model system, and the adsorption behavior was evaluated at the nanoscale. The results showed the existence of a critical concentration for self-assembly, with the molecular structure having a significant impact on this threshold value. Furthermore, highly cooperative behavior was observed at the liquid/solid interface, providing a rare example of quantitative measurement of cooperative phenomena.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Biochemistry & Molecular Biology
Anastasia V. Lilina, Simon Leekens, Hani M. Hashim, Pieter-Jan Vermeire, Jeremy N. Harvey, Sergei V. Strelkov
Summary: Intermediate filaments (IFs) are essential components of the metazoan cytoskeleton, but their molecular architecture and assembly process are not fully understood. This study investigated the structure and stability of human vimentin, a model IF protein, and found that different regions of the protein have varying stability. These findings contribute to a better understanding of the molecular mechanisms driving IF assembly.
Article
Chemistry, Physical
Tolga Yaman, Jeremy N. N. Harvey
Summary: Novel density functional theory (DFT) calculations were performed to investigate the mechanism of a base-free Suzuki-Miyaura cross-coupling reaction with phosphine ligands. The results are consistent with experimental findings and suggest a mechanism involving recycling of the arylboronic acid moiety. Our calculations focus on the transmetalation and reductive elimination steps.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Physical
Maarten Konings, Jeremy N. Harvey, Jeïrome Loreau
Summary: In this work, Gaussian process regression machine learning representations of the three lowest coupled 2A' adiabatic electronic potential energy surfaces of the ArH2+ reactive system are presented. The nonadiabatic coupling matrix elements are also calculated. Accurate ab initio electronic structure calculations, taking into account the spin-orbit coupling, serve as input for the machine learning training process. The fitted potential energy surfaces show high accuracies, meeting the requirements for chemical dynamics at low temperature.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Tamara Rinkovec, Demian Kalebic, Mark Van der Auweraer, Wim Dehaen, Jeremy N. Harvey, Steven De Feyter
Summary: This study investigates the effect of concentration on the self-assembly process of molecular networks using scanning tunneling microscopy. The research aims to improve the understanding of 2D supramolecular chemistry by obtaining quantitative data. The results show highly cooperative behavior and the significant impact of molecular structure on the critical concentration.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
