Article
Physics, Fluids & Plasmas
Vincent Giovangigli
Summary: A compressible Cahn-Hilliard fluid model is derived from the kinetic theory of dense gas mixtures, involving various energy and flux terms. Chapman-Enskog method and Taylor expansion are used to obtain the Cahn-Hilliard fluid model, which includes viscous, heat, and diffusive fluxes.
Article
Engineering, Environmental
Thomas Krumpolc, D. W. Trahan, D. A. Hickman, L. T. Biegler
Summary: Applications of fixed-effects models for kinetic parameter estimation assume independence among batches, but biased residuals often exist in multiple longitudinal batch experiments with time series data. Nonlinear mixed-effects models provide an alternative approach to address the two types of random experimental variation resulting from longitudinal experiments: measurement error for each data point and random batch-to-batch variation. In our case study, implementing a mixed-effects model using nonlinear programming for a batch reactor system yields parameter estimates with less bias compared to a fixed-effects model. Additionally, the Bayesian notion of probability shares is applied to discriminate between several candidate mixed-effects models, demonstrating the ability to elucidate additional model information when fixed-effects models are inappropriate.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Chemistry, Physical
Jinghan Li, Ilaria Maresi, Yanwei Lum, Joel W. Ager
Summary: The study developed a lattice KMC method for electrocatalytic CO2 reduction, analyzing the impact of surface diffusion on isotope fractions and site selectivity. Results showed that the size of active sites and surface coverage play a crucial role in the observed isotope fractions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Computer Science, Artificial Intelligence
Paravee Maneejuk
Summary: Motivated by advancements in parameter estimation in linear models using regularization methods like Ridge and Lasso, the study focuses on regularization in Generalized Maximum Entropy, showing its superior performance and potential for further theoretical research. An application of the method is demonstrated with data from Thailand on the impact of education on economic growth.
Article
Biophysics
Shashank K. Gahlaut, Anisha Pathak, Banshi D. Gupta, J. P. Singh
Summary: The platform utilizes specific antibodies for early detection of Dengue virus NS1 antigen, providing high sensitivity and detection limit. The technology shows potential for very early detection in infected blood samples.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Physics, Multidisciplinary
Emanuele Bernardi, Lorenzo Pareschi, Giuseppe Toscani, Mattia Zanella
Summary: This paper examines the impact of vaccination campaigns on economic improvement during the COVID-19 pandemic. It evaluates the economic trends and wealth distribution using mathematical models, highlighting the positive effects of vaccination in reducing economic inequalities in society.
Article
Nanoscience & Nanotechnology
Zhenzi Yu, Dylan M. Anstine, Salah Eddine Boulfelfel, Chenkai Gu, Coray M. Colina, David S. Sholl
Summary: The study investigates various simulation methods for predicting molecule adsorption in metal-organic frameworks (MOFs), finding that adsorption-relaxation simulations are necessary for quantitative predictions in many MOFs, although standard calculations based on rigid structures can also provide useful information.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Mathematics, Applied
Megala Anandan, S. V. Raghurama Rao
Summary: This paper investigates the entropy conserving scheme for vector kinetic model and its corresponding entropy stable scheme for macroscopic model, filling the gap in numerical methods. The schemes are validated through benchmark tests, demonstrating the conservation/stability of both the kinetic and macroscopic entropies.
APPLIED MATHEMATICS AND COMPUTATION
(2024)
Article
Computer Science, Interdisciplinary Applications
Kyungjoo Kim, Oscar H. Diaz-Ibarra, Habib N. Najm, Judit Zador, Cosmin Safta
Summary: TChem is a performance portable software toolkit for analyzing complex kinetic mechanisms. It provides tools for gas-phase and surface chemistry, thermodynamic properties, and implements formulations for several reactor models. The software uses automatic differentiation to compute analytical derivatives and achieves portability across multiple computing platforms using the Kokkos framework. Efficient evaluations of chemical source terms and thermodynamic properties are enabled through a hierarchical parallelism framework. Parallel efficiency results on Intel Xeon CPUs and NVIDIA Volta GPUs are analyzed.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Shi-Qin Xiang, Shu-Ting Gao, Jun-Lin Shi, Wei Zhang, Liu-Bin Zhao
Summary: A micro-kinetic model was developed to study the influences of solution pH and electrode potential on the reaction rate, pathways, and product distribution of electrocatalytic CO2 conversion. The study investigated competing proton-electron transfer pathways and pathways controlled by thermodynamics and kinetics, showing that different mechanisms occur at different pH levels and electrode potentials. Manipulating solution pH and electrode potential can effectively modulate the electrocatalytic activity and selectivity.
JOURNAL OF CATALYSIS
(2021)
Article
Chemistry, Physical
Sen Yang, Xiantang Liu, Gang Yang
Summary: This study uses molecular dynamics simulations to investigate cation exchange mechanisms at clay interfaces, revealing different selectivities for various binary ion systems and highlighting the strong coupling between thermodynamics, kinetics, and confinement effects. The results provide new insights into cation exchange processes at clay interfaces and offer explanations for experimental observations at the molecular level.
APPLIED CLAY SCIENCE
(2021)
Article
Chemistry, Applied
Yongting Chen, Junxiang Chen, Shengli Chen
Summary: Electrocatalysis plays a crucial role in energy and environmental technologies, and volcano relations are commonly used tools for predicting activity trends. Modern electrocatalytic volcano relations are typically based on kinetic models, but important factors impacting reaction kinetics are often overlooked. Constructing more rational volcano relations is a current research direction in this field.
CHINESE JOURNAL OF CATALYSIS
(2022)
Article
Materials Science, Ceramics
Hongchen Guo, Jianxing Shen, Tailin Wang, Chuanbing Cheng, Hongyan Yao, Xiujun Han, Qiuju Zheng
Summary: The research successfully prepared HEO@G composite material, providing high capacity and cycling stability for lithium-ion batteries, and deeply analyzed the influence of graphene on the electrochemical properties of the composite electrode.
CERAMICS INTERNATIONAL
(2022)
Review
Biochemical Research Methods
Charles J. Foster, Lin Wang, Hoang Dinh, Patrick F. Suthers, Costas D. Maranas
Summary: Kinetic formalisms of metabolism provide a mechanistic link across heterogeneous omics datasets to inform metabolic engineering strategies. Despite challenges in identifying physiologically relevant values for parameters, recent progress in computational power, gene annotation coverage, and formalism standardization have enabled significant advancements. Careful interpretation of model predictions, limited metabolic flux datasets, and assessment of parameter sensitivity remain as challenges that need to be addressed.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Florian Schneider, Tobias Leibner
Summary: This paper presents a second-order realizability-preserving scheme for moment models of linear kinetic equations. The scheme is applied to a variety of continuous and discontinuous models in different geometries, and it is shown that the new models can achieve competitive or even better performance than the classical full-moment models in reasonable test cases.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Chemistry, Organic
Harjeet S. Soor, Diego B. Diaz, Ka Yi Tsui, Karina Calvopina, Marcin Bielinski, Dean J. Tantillo, Christopher J. Schofield, Andrei K. Yudin
Summary: Amidoboronic acid-containing peptidomimetics, a crucial scaffold in chemistry and drug discovery, have been synthesized using a new methodology to prepare constrained alpha- and beta-amidoboronic acids. Quantum chemical calculations have revealed rate-limiting steps for different ring sizes, and a potential application of beta-amidoboronic acid derivatives as novel VIM-2 metallo-beta-lactamase inhibitors has been demonstrated.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Organic
Croix J. Laconsay, Tyler C. Rho, Dean J. Tantillo
Summary: In this study, the hyperconjugation/conjugation through-bond stereoelectronic effects in 3-azabicyclo[3.3.1]nonanes were investigated using density functional theory to explain the puzzling differences in reactivity between a vinylogous chloride and a vinylogous ester.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Prajyot Jayadev Nagtilak, Manoj V. Mane, Supreeth Prasad, Luigi Cavallo, Dean J. Tantillo, Manmohan Kapur
Summary: This study reports the reactivity of propargyl alcohols as Three-Carbon Synthons in a Rh(III)-catalyzed C-H functionalization. This method allows for the efficient synthesis of diverse molecular frameworks, with good functional group tolerance and unique regioselectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Organic
Yoshimitsu Hashimoto, Dean J. Tantillo
Summary: Density functional theory calculations were performed to investigate the reaction mechanism of (4 + 2) and (2 + 2) cycloadditions of benzyne with classical dienes. The results indicate that the (4 + 2) products are formed via concerted pathways, while the (2 + 2) products are formed through stepwise pathways with diradical intermediates. These diradical intermediates are generated through isomerization of carbene intermediates. Distortion/interaction analysis of the key steps provides insights into the origin of selectivity, revealing that the slight distortion in the very early [4 + 2] transition structure, coupled with entropic favorability, controls the selective (4 + 2) cycloaddition.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yusef G. Ahmed, Dean J. Tantillo
Summary: The [3s,5s]-sigmatropic shift is selectively favored in Pd-II-complexed systems with strategically placed substituents, due to key stereoelectronic effects, as demonstrated by density functional theory calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Gilberto E. Fernandez, Debabrata Maiti, Dean J. Tantillo
Summary: The template-directed C-H insertion of alpha,beta-unsaturated esters into quinoline was studied using computational quantum chemistry. A feasible mechanism for this complex transformation was elucidated, taking into account conformational flexibility and alternative ligand binding modes. The selectivity was found to be correlated with distortion from a tetrahedral geometry, which can guide future template design.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Organic
Adam J. Youman, Samantha N. Rokey, Jacob P. Grabowski, Wentao Guo, Qing Sun, Susanna N. Angles, John R. Goodell, Dean J. Tantillo, T. Andrew Mitchell
Summary: The reactivity of silyloxypyrone-based (5 + 2) cycloadditions was found to be highly dependent on the dipolarophile. Neutral alkenes were least reactive, while both electron-deficient and electron-rich dipolarophiles showed higher reactivity, indicating the presence of ambident oxidopyrylium intermediates. Qualitative rate studies, Hammett linear free energy relationships, and theoretical calculations revealed a spectrum of reactivity that encompasses both concerted and stepwise pathways.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Organic
Croix J. Laconsay, Dean J. Tantillo
Summary: We study the escape channels of dirhodium carbene intermediates from cycloheptatrienyl diazo compounds using density functional theory. In principle, intramolecular cyclopropanation could provide a novel pathway to semibullvalenes (SBVs). Our analysis of the potential energy surface reveals that methylating carbon-7 can suppress a competing β-hydride migration pathway, increasing the likelihood of SBV formation. Additionally, we discover unusual spirononatriene, spironorcaradiene, and metal-stabilized 9-barbaralyl cation structures as local minima during our explorations.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Miao Hu, Hao Ding, William DeSnoo, Dean J. Tantillo, Zackaria Nairoukh
Summary: Nitrogen heterocycles, including aromatic and aliphatic architectures, play an important role in pharmaceuticals and natural products. This article proposes a stepwise dearomative functionalization reaction for synthesizing highly decorated piperidine derivatives. The challenges related to site-selectivity, regio- and diastereoselectivity are discussed, and the reaction mechanism is studied through experiments and computational calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Neha Jha, Wentao Guo, Wang-Yeuk Kong, Dean J. Tantillo, Manmohan Kapur
Summary: A site-selective C(3)/C(4)-alkylation of N-pyridylisoquinolones is achieved through C-C bond activation of cyclopropanols under Ru(II)-catalyzed/Cu(II)-mediated conditions. The regioisomeric ratios of the products depend on the electronic nature of the cyclopropanols and isoquinolones used. The methodology has the potential for synthesizing relevant scaffolds.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Joseph P. Mancinelli, Wang-Yeuk Kong, Wentao Guo, Dean J. Tantillo, Sidney M. Wilkerson-Hill
Summary: In this study, a method for synthesizing tert-alkyl cyclopropanes through C-F bond functionalization of gem-difluorocyclopropenes using tris(pentafluorophenyl)borane catalysis is disclosed. The reaction proceeds through the intermediacy of a fluorocyclopropenium ion, which was confirmed by the isolation of [Ph-2(C6D5)C-3](+)[(C6F5)(3)BF](-). It was found that silylketeneacetal nucleophiles were optimal reaction partners, yielding fully substituted cyclopropenes functionalized with two α-tert-alkyl centers (63-93% yield).
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Andre Sanchez, Anjali Gurajapu, Wentao Guo, Wang-Yeuk Kong, Croix J. Laconsay, Nicholas S. Settineri, Dean J. Tantillo, Thomas J. Maimone
Summary: Polycyclic ring systems are crucial for the function of biologically active small molecules and organic materials, and slight changes in their molecular shape and connectivity can greatly impact their properties. By utilizing unique molecular topology involving pi-orbital interactions, a common skeletal ancestor can evolve into a complex network of valence isomers, allowing for controllable and continuous isomerization processes with just two chemical steps. Computational and photophysical studies provide insight into the reactivity and mechanism of these isomer networks, which can inform the design and synthesis of new dynamic and shapeshifting systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Susanna N. Angles, Wentao Guo, Kwabena Darko, Marymoud Erzuah, Kenneth G. Pauley, Ifeanyichukwu E. Promise, John R. Goodell, Dean J. Tantillo, T. Andrew Mitchell
Summary: This study demonstrates that the reactivity of silyloxypyrone-based (5+2) cycloadditions can be enhanced by introducing amides, and the reaction rate is influenced by steric and electronic factors. Specifically, amides enable the powerful transformation of dearomative oxidopyrylium-indole (5+2) cycloadditions, and a one-pot acylation/(5+2) cycloaddition/nucleophilic lactam opening can be achieved by using amides.
Article
Chemistry, Multidisciplinary
Claire S. Harmange Magnani, Jose R. Hernandez-Melendez, Dean J. Tantillo, Thomas J. Maimone
Summary: This article documents the evolution of a synthetic program aimed at accessing the unusual sulfonamide-containing natural product altemicidin. The study found that the biosynthetic pathway of altemicidin is similar to the presumed abiotic synthetic strategy. The synthesis of altemicidin proved challenging due to the manipulation of multiple functional groups present on the highly polar scaffold.
Article
Chemistry, Multidisciplinary
Mingchun Gao, Jose M. Ruiz, Emily Jimenez, Anna Lo, Croix J. Laconsay, James C. Fettinger, Dean J. Tantillo, Jared T. Shaw
Summary: Substrates designed for 1,4-C-H insertion to produce benzocyclobutenes underwent a unique elimination reaction, resulting in the formation of ortho-quinone dimethide (o-QDM) intermediates that further participated in Diels-Alder or hetero-Diels-Alder cycloadditions. The analogous benzylic acetals or ethers, on the other hand, bypassed the C-H insertion pathway and, after hydride transfer, underwent a de-aromatizing elimination reaction to form o-QDM at ambient temperature. The resulting dienes exhibited high diastereo- and regio-selectivity when involved in various cycloaddition reactions. This method represents a rare example of catalytic o-QDM generation without the involvement of a benzocyclobutene, and it offers a mild and ambient temperature approach to access these valuable intermediates. DFT calculations provided support for the proposed mechanism. Furthermore, this methodology was successfully applied to the synthesis of (+/-)-isolariciresinol with an overall yield of 41%.