Article
Chemistry, Medicinal
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz
Summary: The new water models and ion parameter sets accurately reproduce experimental data, demonstrating improved performance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Kara K. Grotz, Nadine Schwierz
Summary: Research has made progress in accurately simulating magnesium ions in physiological processes through optimized force fields, providing a new approach to address the shortcomings of existing 12-6 Lennard-Jones potential force fields. These parameters can accurately reproduce experimental results in various water models.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Polymer Science
Jiafu Shen, Yu Dai, Fan Xia, Xiaojin Zhang
Summary: This article reviews the synthesis and theoretical simulation of M2 +-hydrogels, the effect of M2 + on hydrogels, and their applications in energy storage, sensing, biomedicine, resource utilization, and environmental remediation. The challenges of M2 +-hydrogels are also discussed.
PROGRESS IN POLYMER SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Khalid Z. Elwakeel, Marwan M. Ahmed, Abdullah Akhdhar, Huda M. Alghamdi, Mohamed G. M. Sulaiman, Mohammed F. Hamza, Ziya A. Khan
Summary: In this study, gum Arabic was associated with alginate to produce magnetic beads for the adsorption of metal ions from water. The magnetic beads exhibited superior adsorption performance compared to regular beads, with uptake capacities of 1.33 mmol g^-1 for Cu(II), 1.59 mmol g^-1 for Cd(II), and 1.43 mmol g^-1 for Pb(II).
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Engineering, Environmental
J. Tapiador, E. Garcia-Rojas, P. Lopez-Paton, Guillermo Calleja, Gisela Orcajo, Carmen Martos, Pedro Leo
Summary: The concentration of carbon dioxide has reached unprecedented levels. The valorization of CO2 into high value-added chemicals can stabilize the concentration of this atmospheric pollutant. The influence of metal in the catalytic reaction is key, with Zn-MOF-74 showing the highest catalytic activity and selectivity values above 93% regardless of the epoxides studied.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Chemistry, Analytical
Evangelos Skotadis, Evangelos Aslanidis, Georgios Tsekenis, Chryssi Panagopoulou, Annita Rapesi, Georgia Tzourmana, Stella Kennou, Spyridon Ladas, Angelos Zeniou, Dimitris Tsoukalas
Summary: A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is developed for the detection of Pb2+, Cd2+, and Cr3+. This sensor combines the selective interaction of DNAzymes with heavy metal ions and metallic nanoparticles. The sensor shows promising results for the detection of all three target ions in concentrations below their maximum permitted levels in tap water. It has great potential for integration in autonomous and remote sensing systems due to its low power, simple fabrication, and easy automation.
Article
Chemistry, Multidisciplinary
Yajie Wang, Feihong Meng, Tong Lu, Chunyun Wang, Fei Li
Summary: This study reveals the significant role of divalent metal ions in the aggregation and cytotoxicity of hIAPP, with metal-associated hIAPP oligomers showing reduced ability to damage lipid membranes. The interaction between metal ions and hIAPP oligomers can affect the extent of membrane damage, depending on the peptide-to-metal ratio. Additionally, the abundance of oligomer species with altered disruptive ability can influence the membrane damage caused by hIAPP oligomers.
Article
Biochemical Research Methods
Christina Bergonzo, Baikuntha Aryal, V. Ashutosh Rao
Summary: The toxicity caused by off-pathway reactions can limit the dosing and efficacy of chemotherapeutic drugs. Metal-catalyzed oxidative damage of cardiac myosin binding protein C (cMyBP-C) in cardiac tissue is one potential mechanism for such toxicity. This study investigates the ion environment surrounding specific subunits of cMyBP-C responsible for actin binding and reveals the potential interruption of actin-cMyBP-C binding due to protein carbonylation in these subunits.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Agricultural Engineering
Tengxia He, Mengping Chen, Chenyu Ding, Qifeng Wu, Manman Zhang
Summary: The key denitrifying gene nirB of Pseudomonas taiwanensis J488 was determined through draft genome sequencing. The nitrification of ammonium by the strain was not affected by high concentrations of divalent metal ions, and the efficiency of nitrate removal was significantly enhanced by the addition of various doses of divalent metal ions, promoting bacterial growth in both nitrifying and denitrifying processes. Overall, the results indicate that divalent metal ions do not severely limit the strain's capacity to purify nitrogen-polluted wastewater.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Physical
Nathalia Salles Vernin, Dirk Gillespie
Summary: This study investigates the role of divalent ions in charge regulation by coupling charge regulation with classical density functional theory (DFT). It is found that the size of divalent ions has significant consequences on surface charge density and should not be neglected. At low concentrations, ion correlations play a second-order but non-negligible role; at high concentrations, ion correlations play a dominant role by creating charge inversion.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Analytical
Joana Galhano, Goncalo A. Marcelo, Hugo M. Santos, Jose Luis Capelo-Martinez, Carlos Lodeiro, Elisabete Oliveira
Summary: A new metal ion sensor was synthesized, which showed sensitive reactions to different metal ions and exhibited visible color changes. The sensor combined with nanomaterials also demonstrated high sensitivity in detecting Cu2+ ions in water.
Article
Engineering, Environmental
Cuijuan Feng, Michael Huang, Chin-pao Huang
Summary: A gamma-Fe2O3-biochar was synthesized using ferrate as precursor, which increased surface acidity and magnetism strength, enhancing metal ion adsorption and enabling easy magnetic separation. The adsorption of selected metal ions onto gamma-Fe2O3-biochar was well fitted by the Langmuir adsorption model, with significantly high monolayer metal coverage capacity. Metal ion adsorption reactions involved surface complex formation and the dominating component for adsorption was specific chemical energy.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Xiao Xu, Xu Jia, Yuejun Zhang
Summary: The study investigates the structural and electrostatic properties of charged dendrimers, focusing on the pharmaceutically important dendritic polyglycerol sulfate (dPGS) macromolecule equilibrated with monovalent and divalent salts. It is observed that the sequential replacement of condensed monovalent cations (MCs) with divalent cations (DCs) leads to a decrease in the effective charge of dPGS. Additionally, the release of monovalent cations remains favorable for complexation, while the release of divalent cations only occurs above a certain concentration with a smaller number of ions released compared to monovalent cations.
Article
Chemistry, Physical
Mohammed Ashraf Uddin, Malik Abdul Rub, Shamim Mahbub, Md Farhad Hossain, Shahed Rana, Md Anamul Hoque, Naved Azum, Abdullah M. Asiri
Summary: The study found differences in the binding of levofloxacin hemihydrate with alkali earth metal ions and transition metal ions, with hydrophobic interactions being the key force for binding with alkali earth metal ions while electrostatic, dipole-dipole, ion-dipole, and hydrogen bonding playing key roles in binding with transition metal ions. The thermodynamic parameters reveal that binding phenomena are spontaneous in nature, and the DFT study provides valuable insights into the structural and electronic properties of the drug-metal complexes.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Multidisciplinary
Fatma Hussain Emamy, Ali Bumajdad, Jerzy P. Lukaszewicz
Summary: By optimizing the physicochemical properties of chitosan-based activated carbon, the performance towards heavy metal removal can be enhanced. Through testing the removal of Cr(VI) and Pb(II) under different conditions, it was found that the prepared Ch-ACs showed promising results, making them suitable for wastewater treatment.
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, 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)
Article
Chemistry, Medicinal
Madelyn Smith, Pengfei Li
Summary: Calcium-binding proteins play critical roles in various biological processes. Understanding the ion binding mechanism of EF-hand motif in calcium-binding proteins is important for inhibitor design. This study systematically investigates the ion binding affinity of four calcium-binding peptides containing the EF-hand loop. The results provide molecular insights into the ion binding and the importance of the E-helix motif in this regulation.
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, Multidisciplinary
Theodore Gerard, Yang Wei, Erwin Weerawardhana, Adriana Lugosan, Matthias Zeller, Diane A. Dickie, Pengfei Li, Wei-Tsung Lee
Summary: A Zn2+ based complex, 3, exhibits enhanced fluorescence emission in the presence of Mg2+. Both fluorescent and computational studies reveal that 3 selectively interacts with Mg2+ due to the optimal cavity size formed by two uncoordinated pyrazole side arms. This research presents a novel approach to the development of fluorescent chemosensors.
Article
Biochemistry & Molecular Biology
Ajay Sharma, Chris Whittington, Mohammed Jabed, S. Gage Hill, Anastasiia Kostenko, Tao Yu, Pengfei Li, Peter E. Doan, Brian M. Hoffman, Adam R. Offenbacher
Summary: We report the active-site structure of the MoLOX substrate complex, which provides insight into reactivity differences across the LOX family and can guide the development of MoLOX inhibitors. The ENDOR-guided MD approach used in this study demonstrates its robustness in describing LOX-substrate structures.
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)
Article
Chemistry, Multidisciplinary
Wenhan Fang, Shishi Feng, Zhihui Jiang, Wanzhen Liang, Pengfei Li, Binju Wang
Summary: pH buffer plays a critical role in accelerating the degradation of lignin substrate in lignin peroxidase (LiP). The pH buffer of tartaric acid stabilizes the Trp171H·+ cation radical and enhances the oxidizing power of the enzyme, facilitating the thermodynamics of the reaction and increasing the rate of lignin degradation. These findings provide valuable insights into pH-dependent redox reactions and tryptophan-mediated biological electron transfer reactions.
