Article
Agronomy
Jian Liu, Yating Shen, Liqiang Luo
Summary: The study showed that EDTA significantly enhances the translocation of Pb from roots to leaves in Bidens pilosa L., with a translocation factor of up to 2.43. EDTA was found to decrease Pb retention in specific root zones and increase the water-soluble Pb fraction in plant cells, thereby enhancing Pb translocation in plant vascular bundles.
Article
Environmental Sciences
L. R. Lokin, J. J. Warmink, S. J. M. H. Hulscher
Summary: River dunes, dynamic bedforms in the river bed, can limit navigable depths and increase bed roughness. Predicting the navigable depth and planning maintenance dredging can be done with a numerical dune development model. Different sediment transport models were used to study the effect on dune shape and propagation. The models were able to simulate dune propagation, with shear stress-based models reshaping the dunes. The models reproduced observed dune celerity and realistic dune shapes for low and median discharges.
WATER RESOURCES RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
K. R. Flores, A. Fahrenholz, P. R. Ferket, T. J. Biggs, J. L. Grimes
Summary: Research found that increasing corn particle size and adding it post-pelleting can save energy during feed milling, but may result in slightly lower body weight in turkeys. A combination of inorganic and chelated zinc and manganese may improve performance and increase total breast meat yields.
Article
Materials Science, Multidisciplinary
K. A. Yasakau, A. Maltseva, S. V. Lamaka, Di Mei, H. Orvi, P. Volovitch, M. G. S. Ferreira, M. L. Zheludkevich
Summary: The corrosion protection and surface properties of magnesium containing different levels of iron were evaluated in NaCl solutions with or without various carboxylates. It was found that the presence of 2,5-pyridinedicarboxylate was effective in inhibiting corrosion of magnesium, while salicylate was efficient in inhibiting corrosion of magnesium with higher iron content.
Article
Chemistry, Multidisciplinary
Fredrik Haeffner, Thomas C. Pickel, April Hou, Donald G. Walker, William F. Kiesman, Xianglin Shi
Summary: Density functional theory (DFT) calculations revealed the reasons for the experimentally observed reaction rate acceleration (>= 500 fold) and enantioselectivity (>= 99% ee) in the three-component Petasis reactions catalyzed by 1,1'-bi-2-naphthol- (BINOL). BINOL accelerates the rate determining step by forming a B-IV chelate and facilitates the subsequent vinyl group transfer to the iminium carbon, resulting in enantiomerically enriched product formation. The mechanism involves C-H-O hydrogen bonding between the iminium C-H and O of (R)-BINOL, explaining both the rapid reaction rate and high enantioselectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Jie Xiao, Yoo Gyeong Park, Ge Guo, Byoung Ryong Jeong
Summary: The growth and development of S. commixta in vitro was affected by both the Fe source and pH, with plantlets showing greener leaves under pH 4.70 and 5.70. Despite higher Fe absorption at pH 4.70, Fe-EDTA combined with pH 5.70 was found to be the most beneficial for the overall growth and development of S. commixta.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Tommaso Baggio, Vincenzo D'Agostino
Summary: The aim of this study is to simulate the effect of check dam collapse in a debris-flow event. The study analyzed a catastrophic debris flow in the Rotian channel and used the simulation tool r.avaflow to reconstruct the event and define three scenarios. The results showed that the method combining the contribution of bed erosion and check dam collapse is of particular relevance for residual risk estimation in aging mitigation structures.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Inorganic & Nuclear
Angelo Frei, Alex Rigby, Thomas T. C. Yue, George Firth, Michelle T. Ma, Nicholas J. Long
Summary: Thallium, known for its toxic properties, has been explored for applications in nuclear diagnostics and medicine. Lack of suitable organic chelators for coordinating Tl ions and delivering them to specific diseased tissue has led to a loss of interest in its use. This study describes the synthesis and characterization of a series of Kryptofix 222-based chelators that can be radiolabeled with Tl-201(i) at high yields. Despite the ability of the Kryptofix system to bind thallium cations, no PSMA-mediated cell uptake was observed with the PSMA-conjugate, suggesting that this targeting moiety may not be suitable for use with Tl-201.
DALTON TRANSACTIONS
(2022)
Article
Pharmacology & Pharmacy
Zhaoqi Ma, Agisilaos Kourmatzis, Liam Milton-McGurk, Hak-Kim Chan, Dino Farina, Shaokoon Cheng
Summary: This study investigates the independent influence of different anatomical features of the human pharynx on airflow dynamics and particle deposition. The findings suggest that widening the space between the oral cavity and oropharynx has the most significant impact on reducing drug deposition in the upper airway. Exclusion of the uvula and epiglottis affects flow dynamics and regional deposition behavior but does not significantly affect the total number of particles deposited in the pharynx. The space adjacent to the soft palate is a key determinant for aerosol deposition in the extrathoracic region.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2022)
Article
Agriculture, Dairy & Animal Science
Erin L. Deters, Allison J. VanDerWal, Katherine R. VanValin, Aubree M. Beenken, Katie J. Heiderscheit, Katherine G. Hochmuth, Trey D. Jackson, Elizabeth M. Messersmith, Jodi L. McGill, Stephanie L. Hansen
Summary: The study evaluated the efficacy of bis-glycinate bound zinc in sheep, showing that different sources and concentrations of zinc have effects on zinc and other mineral absorption and utilization in the body. The chelated form of zinc has a positive impact on plasma zinc concentrations and liver MT1 expression, enhancing the bioavailability of zinc.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agronomy
Haider Addab, Ryan T. Bailey
Summary: This study used the SWAT-Salt model to explore the effects of region-wide implementation of subsurface tile drainage on salinity transport and export from an irrigated semi-arid watershed. The model can simulate salinity transport in tile drained watersheds and evaluate the impact of salinity management practices at various spatial and temporal scales.
AGRICULTURAL WATER MANAGEMENT
(2022)
Article
Materials Science, Ceramics
YanXin Dan, Yu Wang, Atsushi Nakamura, Hidetoshi Saitoh, Hua Li
Summary: This study investigates the structure-property relationships of Er2O3 coatings and their thermal conductivities as a function of thickness. It was found that the 300 μm thick coating exhibited higher thermal insulation capability compared to the 100 μm thick coating, which had lower thermal conductivity due to its unique microstructure with higher porosity.
CERAMICS INTERNATIONAL
(2022)
Article
Chemistry, Applied
Xiaoping Wu, Fangfang Wang, Xixi Cai, Shaoyun Wang
Summary: This study prepared a glycosylated peptide-calcium chelate with calcium absorption promoting activity and demonstrated its ability to improve the gut microbiota structure of calcium-deficient mice, indicating its potential prebiotic effect.
Article
Chemistry, Multidisciplinary
Jian Xu, Sudip Pan, Shenglai Yao, Gernot Frenking, Matthias Driess
Summary: The stable plumbylone {[Si-II(Xant)Si-II]Pb-0} 3 and its isolable carbonyl iron complex {[Si-II(Xant)Si-II](PbFe)-Fe-0(CO)(4)} 4 were obtained by reduction reactions. While compound 4 showed relatively good stability, it decomposed to elemental Pb and {[Si-II(Xant)Si-II]Fe(CO)(3)} 5 at higher temperatures. Reaction of 4 with [Rh(CO)(2)Cl](2) yielded the unusual dimeric [(OC)(2)RhPb(Cl)Fe(CO)(4)] complex 6 with Rh-Pb-Fe bonds. The molecular and electronic structures of 3 and 4 were determined by Density Functional Theory (DFT) calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Engineering, Civil
Mostafa Ramadan Ahmed, Ashraf El Damatty, Kaoshan Dai
Summary: Wind turbines are a rapidly growing source of sustainable energy, but current design codes lack procedures for estimating wind loads on turbines during high-intensity wind events like downbursts. This study aims to develop design load provisions that can simulate the critical effect of downbursts on wind turbines. Through two phases of research, the peak effects of downbursts and their associated critical profiles are identified, and dynamic analyses under turbulence are conducted to determine the downburst gust response factor. These findings are used to create a complete set of design provisions.
ENGINEERING STRUCTURES
(2023)
Article
Chemistry, Medicinal
Gaurav Sharma, Lin Frank Song, Kenneth M. Merz
Summary: This study investigates the influence of the MLN-4760 inhibitor on ACE2 through molecular dynamics simulations. The presence of the inhibitor affects the conformational properties of ACE2 and its interaction with SARS-CoV-2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Zhen Liu, Zi-Yang Qin, Ledong Zhu, Soumitra Athavale, Arkajyoti Sengupta, Zhi-Jun Jia, Marc Garcia-Borras, K. N. Houk, Frances H. Arnold
Summary: Propargyl amines are versatile synthetic intermediates with numerous applications in the pharmaceutical industry. An enzymatic platform for enantioselective propargylic amination of alkynes using a hydroxylamine derivative as the nitrene precursor was developed in this study. The biocatalytic process showed high efficiency and selectivity, making it a promising approach for industrial applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Zhen Li, Kenneth M. Merz
Summary: Diffusion, as a fundamental property of fluids, plays a crucial role in both scientific research and everyday life. While the diffusion properties of many liquids, such as water, have been extensively studied, there has been a lack of theoretical research on transition metal ions. In this study, a workflow called ISAIAH was developed to accurately simulate the diffusion coefficients of 15 monoatomic ions in water. The results showed good agreement with experimental data, which allowed for the theoretical prediction of the diffusion coefficient of 239Pu4+ ion. The use of an augmented 12-6-4 Lennard-Jones potential parameter set showed better results compared to some other parameter sets, indicating that both hydration free energy and ion-oxygen distance play important roles in diffusion.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Gaurav Sharma, Kenneth M. Merz
Summary: Zinc is an essential transition metal ion that plays multiple roles in cellular function. This study used molecular dynamics simulations to explore the structure-function relationship of YiiP protein in a lipid bilayer and proposed a hypothesis on the zinc efflux mechanism. The study revealed the important role of zinc ions in restraining the protein's transmembrane domains and suggested the guiding role of amino acid H153 in transporting zinc ions. Understanding the zinc transport process can provide insights into treating diseases such as diabetes and cancer.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Susanta Das, Kiyoto Aramis Tanemura, Laleh Dinpazhoh, Mithony Keng, Christina Schumm, Lydia Leahy, Carter K. Asef, Markace Rainey, Arthur S. Edison, Facundo M. Fernandez, Kenneth M. Merz
Summary: In this study, an efficient CCS computational workflow was developed to accurately predict unknown structures using a machine learning model and standard DFT methods. TWIMS experiments were performed to validate the experimental values and assess uncertainties. The workflow yielded accurate structural predictions and provided unique insights into preferred conformations.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Madushanka Manathunga, Andreas W. Gotz, Kenneth M. Merz
Summary: Quantum chemistry allows for the study of systems with high accuracy, but its computational expense limits its application to a few atoms. To optimize performance, methods such as implementing quantum mechanical methods on modern hardware and using multiscale approaches have been developed. Simplified QM methods, including the use of machine learning, have also been created to enhance the speed and accuracy of calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Ali Rahnamoun, Kurt A. O'Hearn, Mehmet Cagri Kaymak, Zhen Li, Kenneth M. Merz, Hasan Metin Aktulga
Summary: A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is proposed for molecular dynamics simulations of ions in condensed phases. The model introduces polarization effects by the electronegativity equalization model (EEM) method, allowing charges on the metal ion and its dummy atoms to fluctuate in response to the environment. This model can be coupled with nonpolarizable or polarizable water models and enhances the original fixed charge CDA model by adapting to the local solvent structure.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Abhishek Thakur, Gaurav Sharma, Vishnu Nayak Badavath, Venkatesan Jayaprakash, Kenneth M. Merz, Galia Blum, Orlando Acevedo
Summary: The COVID-19 outbreak has caused massive devastation worldwide, with millions of infections and deaths reported. Using a combination of crystal structures and validated inhibitors, four rules for designing potent inhibitors of SARS-CoV-2 main protease have been proposed. Experimental examination identified a potential lead compound with higher potency than known inhibitors.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Organic
Quan Tran, Arkajyoti Sengupta, K. N. Houk
Summary: The 1,5-sigmatropic hydrogen shift in cyclopentadiene is traditionally believed to be a unimolecular pericyclic reaction, but Yamabe proposed a more complex bimolecular mechanism. Recent computational studies show that the unimolecular mechanism is kinetically more favorable and closer to experimental values compared to the bimolecular mechanism proposed by Yamabe.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Gotz, Jr Kenneth M. Merz
Summary: The researchers have ported and optimized the GPU-accelerated QUICK and AMBER-based QM/MM implementation on AMD GPUs. This includes the entire Fock matrix build and force calculation in QUICK, along with general performance improvements to the QUICK GPU code. Benchmark tests on NVIDIA V100 and AMD MI100 cards show similar performance for standalone HF/DFT calculations and QM/MM molecular dynamics simulations with QUICK and QUICK/AMBER. In addition, significant speedups are observed for QM/MM molecular dynamics simulations compared to the previous release version.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Editorial Material
Chemistry, Medicinal
Kenneth M. Merz, Guo-Wei Wei, Feng Zhu
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian C. C. J. C. Ebert, Paul Labute, Kenneth M. Merz, Darrin M. York
Summary: We propose a framework for optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for softcore potentials. The framework is implemented and tested in the GPU-accelerated AMBER software suite. The optimized pathways integrate important features such as smoothstep functions, power scaling of interactions, LJ pairwise form, and smoothing of the potential at the nonbonded cutoff boundary. The pathways demonstrate superior numerical stability and minimal variance of free energy estimates compared to traditional methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Madelyn Smith, Zhen Li, Luke Landry, Kenneth M. Merz, Pengfei Li
Summary: Atomic radii are important in scientific research and can be derived from crystal structures. However, determining the van der Waals (VDW) radii of ions is a challenge due to the combination of VDW and electrostatic interactions in crystal structures. In this study, VDW radii were determined based on a wavefunction analysis, showing excellent agreement with experimentally determined VDW radii of noble-gas atoms.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Correction
Chemistry, Multidisciplinary
Cooper S. Jamieson, Arkajyoti Sengupta, K. N. Houk
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Arkajyoti Sengupta, K. N. Houk
Summary: This study investigates the reaction mechanism for intramolecular cycloadditions of a heptafulvenyl-fulvene tethered by a trimethylene chain using quantum mechanical calculations and molecular dynamics simulations. The experimental reports of temperature dependence on the periselectivity of intramolecular cycloadditions are explained by the mechanistic details. Furthermore, additional calculations with multireference-based methods highlight the limitations of DFT methods and single-reference wavefunction-based CCSD(T) in describing the complete potential energy surface involving various cycloadditions of the heptafulvenyl-fulvene.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
