Article
Chemistry, Multidisciplinary
Qiyuan Zhao, Dylan M. Anstine, Olexandr Isayev, Brett M. Savoie
Summary: The emergence of & UDelta;-learning models provides a versatile route to accelerate high-level energy evaluations. However, these models are unable to predict reaction properties that require both high-level geometry and energy evaluation. This study introduces a & UDelta;(2)-learning model that predicts high-level activation energies based on low-level critical-point geometries. The model demonstrates excellent performance on unseen reactions and shows near chemical accuracy, making it an efficient strategy for accelerating chemical reaction characterization.
Article
Chemistry, Medicinal
Ziad Fakhoury, Gabriele C. Sosso, Scott Habershon
Summary: Recent advances in machine learning methods have made progress in protein structure prediction, but accurately generating and characterizing protein-folding pathways is still challenging. In this study, a directed walk strategy using the residue-level contact-map space was employed to generate protein folding trajectories. The strategy considers protein folding as transitions between connected minima on the potential energy surface. The generated folding paths were validated against direct molecular dynamics simulations, demonstrating the potential of this approach for studying protein folding.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Qiyuan Zhao, Hsuan-Hao Hsu, Brett M. Savoie
Summary: In this study, a classifier was trained to learn the features of reaction conformers that lead to successful transition state searches, enabling the down-selection of optimal conformers before incurring the cost of a high-level transition state search. The results showed that neglecting conformer contributions can lead to qualitatively incorrect activation energy estimations, while machine learning classifiers reliably down-select low-barrier reaction conformers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Fei Shuang, Penghao Xiao, Liming Xiong, Wei Gao
Summary: In this study, a computational investigation was conducted on the solid-solid phase transition of a model two-dimensional system from a hexagonal phase to a square phase under pressure. The atomistic mechanism and propagation method of the phase transition were determined using solid-state Dimer and nudged elastic band (NEB) methods. It was found that the phase nucleation was triggered by localized shear deformation caused by the relative shift between two adjacent atomic layers. Additionally, a defect-assisted low barrier propagation path was identified in the hexagonal to square phase transition. This study highlights the significance of using the Dimer method to explore unknown transition paths and provides insights into phase transition mechanisms of other solid-state and colloidal systems.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Materials Science, Multidisciplinary
Sweta Kumari, Amlan Dutta
Summary: This study investigates the nucleation of twinning dislocation loops in metals with fcc crystal structure using a combination of atomistic computations and continuum modeling. It explores both the conventional layer-by-layer model and the newly proposed alternate-shear mechanism for twin nucleation, finding differences in nucleation stress between the two mechanisms. The research also highlights the non-uniform variations in critical loop size and fractional Burgers vector with applied shear load.
MECHANICS OF MATERIALS
(2021)
Article
Chemistry, Physical
Yanhui Zhang, Stefano Sanvito
Summary: Understanding surface reactivity is crucial in various fields, and the surface reactions of ZrB2 exposed to harsh aerospace environments were studied using density functional theory and nudged elastic band methods. It was found that dissociative adsorption of O-2 dominates the reactivity of ZrB2 surfaces, while the reactions of H2O and CO are less active on Zr-surfaces and even less on B-terminated ones. Additionally, the reaction of O-2 and CO was shown to induce strong surface reconstruction at B-surfaces.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Michel Sassi, Kevin M. Rosso
Summary: Phase transformations between iron (oxyhydr)oxide minerals can occur through self-diffusion of ions in the solid state. However, it is unclear how important solid-state transformation pathways are under ambient conditions, especially for nanoparticles. In this study, density functional theory was used to evaluate the possibility of solid-state transformation from ferrihydrite (Fh) to goethite (Gt). The results show that solid-state transformation pathways to Gt are unlikely to be accessible for Fh nanoparticles under ambient conditions, suggesting the importance of other pathways.
ACS EARTH AND SPACE CHEMISTRY
(2022)
Review
Multidisciplinary Sciences
Weiyu Wang, Jun Xu, Feng Deng
Summary: This review examines the recent progress in the study of zeolites and relevant catalytic reactions using solid-state NMR methods to explore framework structures, catalytically active sites, and intermolecular interactions. It also discusses the application of solid-state NMR technique in understanding the mechanistic aspects of zeolite-catalyzed reactions, such as methanol and ethanol conversions.
NATIONAL SCIENCE REVIEW
(2022)
Article
Engineering, Mechanical
Li Li, Lijun Liu, Yoji Shibutani
Summary: The interactions between edge dislocations and <112>-axis symmetric tilt grain boundaries in copper were investigated through atomistic simulations. The results showed that the leading partial dislocation was absorbed into the grain boundary upon impact, while the trailing partial dislocation played a crucial role in determining the threshold reaction stress. The reaction energy barriers exhibited a linear relationship with the resolved shear stress or strain state, and the corresponding strain rate sensitivities obtained through activation volumes matched well with experimental data.
INTERNATIONAL JOURNAL OF PLASTICITY
(2022)
Article
Nanoscience & Nanotechnology
Jiao Wen, Jingyong Sun, Boxuan Du, Yu Chen, Xin Yan
Summary: The interfacial stability between the bond coating and single crystal superalloy substrate is crucial for their long-term performance. Through experiments and atomistic simulations, coatings with various phase structures were designed, and the intrinsic mechanism underlying recrystallization was investigated. Experimental results showed that recrystallization occurred in the specimen with coatings of medium Al content, while there was no secondary reaction zone in the specimen with coatings of the highest Al content. Simulation results demonstrated that a higher energy barrier was required for new grain nucleation in the substrate under beta-NiAl grains. These findings provide a fundamental understanding of interfacial stability and benefit the design of bond coatings for superalloys.
SCRIPTA MATERIALIA
(2023)
Article
Materials Science, Multidisciplinary
Yipin Si, Yin Zhang, Dengke Chen, Jonathan L. Wormald, Benjamin S. Anglin, David L. McDowell, Ting Zhu
Summary: This study calculates the Peierls barriers for screw and edge dislocation glide in a face-centered cubic (FCC) metal of Ni using the nudged elastic band (NEB) method. The results show a decreasing Peierls barrier with increasing shear stress, and the Peierls stress at which the barrier vanishes. The effects of boundary condition and system size on the barriers are also studied.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2023)
Article
Chemistry, Physical
Christopher Robertson, Ross Hyland, Andrew J. D. Lacey, Sebastian Havens, Scott Habershon
Summary: This article addresses the challenge of identifying multistep reaction mechanisms in complex chemical environments. By using a discrete optimization approach and screening autogenerated mechanisms, several barrierless reaction mechanisms for benzene formation in the interstellar medium are identified, which could supplement existing microkinetic models and operate in low temperature environments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Physics, Applied
Bo Zhou, Zhaoyu Zhou, Bo Li, Zilin Qu, Qi Song, Chunmei Zhang, Zhenyi Jiang, Yi Ding
Summary: The study investigates ion diffusion performance in 1T-delta-MnO2, obtaining potential energy surfaces of different ions within the density functional theory framework. The research not only quantitatively evaluates 1T-delta-MnO2 as an electrode material but also elucidates the impact of the cooperative Jahn-Teller effect on multivalent diffusion. The findings match reported results and provide practical guidelines for identifying MnO2-based fast-diffusion multivalent ion conductors.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Yuki Mitsuta, Toshio Asada
Summary: The nudged elastic band (NEB) method is widely used for reaction path (RP) finding, but some NEB calculations fail to converge to the minimum energy paths (MEPs) due to the occurrence of kinks caused by free bending of the bands. Therefore, we propose an extension of the NEB method called the nudged elastic stiffness band (NESB) method, which incorporates stiffness stress using a beam theory. The results from three examples demonstrate that the NESB method has three advantages: reducing the number of iterations, shortening the pathway length by reducing unnecessary fluctuations, and finding transition state (TS) structures by converging to paths close to the MEPs for systems with sharp curves on the MEPs.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
L. Dicks, D. J. Wales
Summary: The K-means algorithm, commonly used in scientific fields, generates clustering solutions that depend on the initial cluster coordinates. By employing the energy landscape approach, this study reveals that the solution landscapes for K-means cost function exhibit a funnelled structure, which is associated with efficient global optimization. The small barriers between clustering solutions contribute to the observed funnelled structure.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Agricultural Engineering
Oscar Oyola-Rivera, Jiayue He, George W. Huber, James A. Dumesic, Nelson Cardona-Martinez
Summary: This study investigated the catalytic conversion of cellulose to levoglucosenone (LGO) using a combination of dilute sulfuric acid and propylsulfonic acid functionalized SBA-15 (PS-SBA-15) in tetrahydrofuran (THF). The addition of small amounts of liquid acid catalyst such as sulfuric acid was found to complement the use of solid acid catalyst for cellulose conversion, leading to an increase in LGO yield. The main role of the solid Bronsted acid catalyst was to dehydrate the generated levoglucosan (LGA) into LGO, demonstrating a more environmentally friendly approach for LGO production.
BIOMASS & BIOENERGY
(2022)
Article
Chemistry, Multidisciplinary
Elise B. Gilcher, Hochan Chang, George W. Huber, James A. Dumesic
Summary: The hydrogenation of a biomass-derived platform molecule, 5-hydroxymethyl furfural (HMF)-acetone-HMF (HAH), was studied over Pd, Ru, and Cu based catalysts at temperatures ranging from 313-393 K. Different catalysts exhibited varying levels of selectivity and reaction pathways for hydrogenation. Kinetic modeling was used to quantify the behavior of the hydrogenation reactions. This study provides insights for optimizing catalyst selection and reaction conditions to improve the yield of hydrogenation products.
Article
Chemistry, Multidisciplinary
Raka G. Dastidar, Peter H. Galebach, Michael P. Lanci, Chengrong Wang, Yi Du, George W. Huber
Summary: Cellulose upgrading with methanol to produce fuel-range alcohols involves complex reactions, such as C-C coupling, C-O scission, and C-C scission, as observed in the conversion of 1,2-propanediol and methanol over CuMgAlOx catalyst. The selectivity of different products is influenced by the reaction orders with respect to hydrogen, 1,2-propanediol, and methanol, as well as the apparent activation energies for various pathways. The rate determining step in C-C coupling is found to be associated with the nucleophilic attack by 1,2-propanediol, and the co-feeding of formaldehyde affects the rates of C-C coupling, direct C-C scission, and esterification reactions.
Article
Chemistry, Physical
Paolo A. Cuello-Penaloza, Raka G. Dastidar, Shao-Chun Wang, Yi Du, Michael P. Lanci, Bradley Wooler, Christine E. Kliewer, Ive Hermans, James A. Dumesic, George W. Huber
Summary: A series of calcined MgAl mixed metal oxide catalysts with low Cu loadings were tested for ethanol oligomerization to distillate-range molecules. The low Cu loading catalysts showed high selectivity to linear chain alcohols and esters, with diesel fuel precursor selectivities over 75%.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2022)
Article
Biotechnology & Applied Microbiology
Lisa Je, George W. Huber, Reid C. Van Lehn, Victor M. Zavala
Summary: Computational workflows combining molecular dynamics simulations and data-centric methods can expedite the screening and analysis of solvent systems. By utilizing data representations derived from MD simulations, DC techniques enable predictive modeling and experimental design for solvent effects on reaction outcomes.
CURRENT OPINION IN CHEMICAL ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Feng Cheng, Sarah Liu, Steven D. Karlen, Hoon Kim, Fachuang Lu, John Ralph, Leida Vazquez M. Ramos, George W. Huber, James A. Dumesic
Summary: This paper describes an approach for producing high quality and high quantity of lignin through studying the structural change of lignin during treatment of poplar wood in gamma-valerolactone (GVL). The results show that multiple-step cycling of cosolvent-assisted hydrolysis can help preserve more of the virgin ether-bond structures of GVL-extracted poplar lignin.
Article
Chemistry, Multidisciplinary
Aurora del Carmen Munguia-Lopez, Dilara Goreke, Kevin L. Sanchez-Rivera, Horacio A. Aguirre-Villegas, Styliani Avraamidou, George W. Huber, Victor M. Zavala
Summary: Food packaging often uses multilayer plastic films to achieve specific food protection goals. However, the production of these films generates large amounts of unrecyclable plastic waste. A proposed technology called STRAP enables the separation and recycling of the polymers in the films. This study evaluates the environmental benefits of STRAP compared to virgin film production using life cycle assessment methods.
Correction
Chemistry, Multidisciplinary
Houqian Li, Horacio A. Aguirre-Villegas, Robert D. Allen, Xianglan Bai, Craig H. Benson, Gregg T. Beckham, Sabrina L. Bradshaw, Jessica L. Brown, Robert C. Brown, Victor S. Cecon, Julia B. Curley, Greg W. Curtzwiler, Son Dong, Soumika Gaddameedi, John E. Estela-Garcia, Ive Hermans, Min Soo Kim, Jiaze Ma, Lesli O. Mark, Manos Mavrikakis, Olumide O. Olafasakin, Tim A. Osswald, Konstantinos G. Papanikolaou, Harish Radhakrishnan, Marco Antonio Sanchez Castillo, Kevin L. Sanchez-Rivera, Khairun N. Tumu, Reid C. Van Lehn, Keith L. Vorst, Mark M. Wright, Jiayang Wu, Victor M. Zavala, Panzheng Zhou, George W. Huber
Summary: This article mainly discusses the chemical aspects, technology status, and challenges of expanding plastics recycling technologies.
Article
Chemistry, Physical
Juan-Manuel Restrepo-Florez, Paolo Cuello-Penaloza, Emmanuel Canales, Dustin Witkowski, David A. Rothamer, George W. Huber, Christos T. Maravelias
Summary: This article introduces a sustainable approach of catalytic upgrading ethanol into diesel fuel through Guerbet coupling and etherification reactions, showing experimentally the feasibility of producing diesel fuel with superior properties. The use of lignocellulosic ethanol may lead to more than 50% reduction in greenhouse gas emissions, and in some instances, carbon neutral diesel fuel production is possible.
SUSTAINABLE ENERGY & FUELS
(2023)
Review
Chemistry, Multidisciplinary
Houqian Li, Horacio A. Aguirre-Villegas, Robert D. Allen, Xianglan Bai, Craig H. Benson, Gregg T. Beckham, Sabrina L. Bradshaw, Jessica L. Brown, Robert C. Brown, Victor S. Cecon, Julia B. Curley, Greg W. Curtzwiler, Son Dong, Soumika Gaddameedi, John E. Garcia, Ive Hermans, Min Soo Kim, Jiaze Ma, Lesli O. Mark, Manos Mavrikakis, Olumide O. Olafasakin, Tim A. Osswald, Konstantinos G. Papanikolaou, Harish Radhakrishnan, Marco Antonio Sanchez Castillo, Kevin L. Sanchez-Rivera, Khairun N. Tumu, Reid C. Van Lehn, Keith L. Vorst, Mark M. Wright, Jiayang Wu, Victor M. Zavala, Panzheng Zhou, George W. Huber
Summary: Globally, less than 10% of plastics are recycled, with new technologies for chemical recycling offering hope. Chemists and chemical engineers need to strengthen their understanding of these technologies, while options for managing plastic waste are explored.
Article
Chemistry, Physical
Elise B. Gilcher, Hochan Chang, Michael Rebarchik, George W. Huber, James A. Dumesic
Summary: In this study, lumped reaction schemes were developed to investigate the hydrogenation of HAH over different catalysts. The addition of water was found to have different effects on the hydrogenation reactions of HAH over Pd, Ru, and Cu catalysts, altering the selectivity and yield of the products while providing a new pathway to increase the production rates of specific products.
Correction
Chemistry, Multidisciplinary
Houqian Li, Horacio A. Aguirre-Villegas, Robert D. Allen, Xianglan Bai, Craig H. Benson, Gregg T. Beckham, Sabrina L. Bradshaw, Jessica L. Brown, Robert C. Brown, Victor S. Cecon, Julia B. Curley, Greg W. Curtzwiler, Son Dong, Soumika Gaddameedi, John E. Estela-Garcia, Ive Hermans, Min Soo Kim, Jiaze Ma, Lesli O. Mark, Manos Mavrikakis, Olumide O. Olafasakin, Tim A. Osswald, Konstantinos G. Papanikolaou, Harish Radhakrishnan, Marco Antonio Sanchez Castillo, Kevin L. Sanchez-Rivera, Khairun N. Tumu, Reid C. Van Lehn, Keith L. Vorst, Mark M. Wright, Jiayang Wu, Victor M. Zavala, Panzheng Zhou, George W. Huber
Article
Chemistry, Multidisciplinary
Raka G. Dastidar, Min Soo Kim, Panzheng Zhou, Zaneta Luo, Changxia Shi, Kevin J. Barnett, Daniel J. McClelland, Eugene Y. -X. Chen, Reid C. Van Lehn, George W. Huber
Summary: This study successfully synthesized THP with high selectivity and yield. THP exhibited excellent thermal, chemical, and peroxidative stability, making it a potential alternative solvent to THF. The minimum selling price of THP was competitive with the market price of THF. Simulation studies showed that THP could be used for plastic dissolution, especially for common plastics.
Article
Chemistry, Multidisciplinary
Mark J. Lindsay, Michael S. Molitor, Tejas B. Goculdas, Jikai Zhao, Jarryd R. Featherman, Mengting Li, James B. Miller, Styliana Avraamidou, Scott A. Rankin, James A. Dumesic, George W. Huber
Summary: Greek yogurt acid whey is a byproduct with unsustainable disposal methods. A new process has been developed to produce multiple products from it, with positive economic and environmental impacts.
Article
Chemistry, Physical
Alvin Jonathan, Raka G. Dastidar, Chengrong Wang, James A. Dumesic, George W. Huber
Summary: The oligomerization activity of a carbon-supported cobalt oxide catalyst is nearly double when supported on a less oxidized carbon, and this difference is unrelated to the cobalt phase. The oxygen content and oxidized surface functional groups impact the activity, and increasing the support particle size has minimal effect on selectivities. A carbon support with fewer impurities plays a crucial role in enhancing oligomerization activity.
CATALYSIS SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Physical
Yifan Sun, Ye Lv, Wei Li, Jinli Zhang, Yan Fu
Summary: In this study, PtRu electrocatalysts were fabricated on carbon paper via cyclic electrodeposition for the electrocatalytic hydrogenation (ECH) of phenol. The Pt3Ru3 catalyst exhibited excellent activity and stability for the conversion of phenol to cyclohexanol at ambient temperature and various current densities. The in situ Raman spectroscopy and kinetic study revealed the hydrogenation mechanism of phenol over Pt3Ru3 in acidic electrolyte, providing an effective electrochemical strategy for the facile construction of durable electrode materials and efficient phenol hydrogenation.
JOURNAL OF CATALYSIS
(2024)
Article
Chemistry, Physical
Amir Shahzad, Khezina Rafiq, Muhammad Zeeshan Abid, Naseem Ahmad Khan, Syed Shoaib Ahmad Shah, Raed H. Althomali, Abdul Rauf, Ejaz Hussain
Summary: Photocatalytic hydrogen production through water splitting is an effective method for meeting future energy demands. In this study, researchers synthesized a 1 % Ag2S/Cu2S co-doped CdZnS catalyst and found that it can produce hydrogen at a higher rate. The co-doping of Ag2S and Cu2S in the CdZnS catalyst showed a synergistic effect, with Ag2S promoting oxidation reactions and Cu2S promoting reduction reactions.
JOURNAL OF CATALYSIS
(2024)
