Article
Agronomy
Wei Zhang, Shengxin Guo, Ya Wang, Yikun Wu, Lijiao Yu, Jian Wu
Summary: Novel compounds S1-S28 were synthesized and evaluated for their curative effects against CMV. Compound S8 showed a strong binding affinity to CMV-coat protein and impacted the self-assemble of CMV particles, making it a potential lead compound for discovering a new anti-plant virus candidate.
PEST MANAGEMENT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Rie Nygaard, Chris L. B. Graham, Meagan Belcher Dufrisne, Jonathan D. Colburn, Joseph Pepe, Molly A. Hydorn, Silvia Corradi, Chelsea M. Brown, Khuram U. Ashraf, Owen N. Vickery, Nicholas S. Briggs, John J. Deering, Brian Kloss, Bruno Botta, Oliver B. Clarke, Linda Columbus, Jonathan Dworkin, Phillip J. Stansfeld, David I. Roper, Filippo Mancia
Summary: Peptidoglycan is a crucial component of bacterial cell wall synthesized during cell division and elongation. It is targeted by antibiotics and its assembly requires the involvement of glycosyltransferase and penicillin binding protein.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yao Zhang, Jingyi Yu, Xuan Wang, Daniel M. Durachko, Sulin Zhang, Daniel J. Cosgrove
Summary: Plants have evolved complex nanofibril-based cell walls to meet diverse biological and physical constraints, with cellulose and matrix polysaccharides playing important mechanical roles. By simulating the assembly and tensile mechanics of cell walls, researchers found that fibril-fibril sliding in cellulose networks leads to plasticity, revealing design principles of biomaterials.
Article
Chemistry, Multidisciplinary
Wanhao Cai, Miriam Jaeger, Jakob T. Bullerjahn, Thorsten Hugel, Steffen Wolf, Bizan N. Balzer
Summary: In this study, the rupture force and friction of the biotin-streptavidin complex under a externally applied force were investigated using AFM-based single molecule force spectroscopy and molecular dynamics simulations. Anisotropic friction, arising from an experimentally uncontrolled orientation parameter, was identified. The study suggests that anisotropic friction should be taken into account for a complete understanding of friction in biomolecular dynamics and anisotropic mechanical environments.
Article
Biochemistry & Molecular Biology
Mastaneh Shokri, Sajad Moradi, Sabrieh Amini, Mohsen Shahlaei, Farzad Seidi, Shahab Saedi
Summary: A novel amino cellulose derivative was synthesized and its antibacterial activity and interaction with a model membrane were studied experimentally and by molecular dynamics simulation.
BIOORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Marco Klement, Sangmin Lee, Joshua A. Anderson, Michael Engel
Summary: Polyhedral nanocrystals are essential building blocks for nanostructured materials used in catalysis and plasmonics. Computer simulations, mainly using Monte Carlo methods, help predict phase equilibria. The Newtonian event-chain algorithm offers a speedup in simulation for hard polyhedra.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Materials Science, Paper & Wood
Zikang Deng, Guohui Zhou, Timing Fang, Kuanjun Fang, Xiaomin Liu
Summary: The dissolution and regeneration process of cellulose in NMMO aqueous solution was studied using molecular dynamics simulation. The concentration of NMMO aqueous solution has a significant impact on the structure of cellulose.
Article
Chemistry, Applied
Changyue Deng, Chuan Cao, Yingying Zhang, Jingwei Hu, Yongqiang Gong, Mingming Zheng, Yibin Zhou
Summary: The formation and stabilization mechanisms of inclusion complexes between beta-cyclodextrin and five C10 aroma molecules were investigated using experimental methods and molecular dynamics simulation. The inclusion complexes had a new crystal structure and better thermal stability. The aroma molecules induced conformational changes in the inclusion complexes, with van der Waals interactions being the main driving force for their spontaneous entry into the cavity.
FOOD HYDROCOLLOIDS
(2022)
Article
Biochemistry & Molecular Biology
Yasaman Mahmoodi, Faramarz Mehrnejad, Somayeh Khanmohammadi, Masoud Shahriari, Fereshteh Rahimi, Mohammad Reza Vakili, Afsaneh Lavasanifar
Summary: In this study, we investigated the influence of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz) using computational and spectroscopic methods. Our findings indicate that static quenching is the main mechanism for the formation of a stable CNC-hLyz complex, driven by electrostatic interactions. The structural elements and tertiary structure of the enzyme were mostly unaffected, except for the loop regions, in the presence of cellulose nanocrystals.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Jihad Sebhaoui, Youness El Bakri, Chin-Hung Lai, Subramani Karthikeyan, El Hassane Anouar, Joel T. Mague, El Mokhtar Essassi
Summary: Three new compounds were synthesized and characterized by single crystal X-ray diffraction. Theoretical parameters were calculated using density functional theory and compared with experimental ones obtained by XRD. Intermolecular interactions in crystal packing were rationalized by Hirshfeld surface analysis, and binding modes within Tyrosine-protein kinase JAK2 were investigated using molecular docking and molecular dynamics simulation studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Polymer Science
Jiachen Wang, Zhanqiang Li, Majid Basharat, Shaojun Wu, Shuangkun Zhang, Xinfang Zhang, Hanlin Ma, Wei Liu, Dezhen Wu, Zhanpeng Wu
Summary: This study focuses on adjusting the Tg of polyphosphazenes by introducing ethoxy substituents to improve overall performance. Molecular dynamics simulations show that the Tg of the polymers gradually decreases with an increase in ethoxy content, in good agreement with experimental values.
Article
Chemistry, Physical
Sophie Baker, Joshua Pagotto, Timothy T. Duignan, Alister J. Page
Summary: Neural network potentials have proven to be an efficient tool for accelerating ab initio molecular dynamics simulations. This study explores the use of existing DFTB molecular dynamics data to train graph neural network potentials and accurately reproduce solvation structures in NaCl solutions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Materials Science, Paper & Wood
Ryota Matsuba, Hiroyuki Kubota, Nobuyuki Matubayasi
Summary: An all-atom analysis of cellulose acetate was conducted using molecular dynamics simulation, examining the intermolecular interactions, energetics of dissolution, and the underlying structures. The results showed that DS strongly influenced the hydrogen bonding and packing of cellulose acetate, with dissolution being more favorable for H2O compared to CO2 and CH4. The electrostatic component was found to play a crucial role in the DS dependence of dissolution free energy for H2O, as well as the difference in affinity between CO2 and CH4.
Article
Chemistry, Physical
Thitiya Boonma, Bodee Nutho, Bunleu Sungthong, Ployvadee Sripadung, Thanyada Rungrotmongkol, Nadtanet Nunthaboot
Summary: The atomistic molecular dynamics simulation shows that scandenin tends to form inclusion complexes with different types of cyclodextrin, with some cyclodextrins exhibiting higher inclusivity than others. The calculations indicate that modified cyclodextrins have a stronger binding affinity to scandenin compared to the parent host molecule.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Saina Kishani, Tobias Benselfelt, Lars Wagberg, Jakob Wohlert
Summary: This study investigated the thermodynamics of the adsorption of xyloglucan (XG) to cellulose surfaces at different temperatures using molecular dynamics simulations. The results showed that adsorption near room temperature is an endothermic process driven by the entropy of released interfacial water molecules. In the case of native cellulose, adsorption became exothermic at higher temperatures, while the interactions between water and charged groups of oxidized cellulose hindered this transition.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Physical
Sabila K. Pinky, Albert L. Kwansa, Buang Zhang, Adrienne D. Stiff-Roberts, Yaroslava G. Yingling
Summary: The morphology of conjugated polymer thin films is influenced by the emulsion characteristics, but the understanding of how these characteristics control the film properties and device performance is still unclear. In this study, molecular dynamics simulations were conducted on emulsions containing polyfluorene (PFO) polymer and various solvents to investigate the relationship between emulsion properties and the morphology of deposited PFO thin films. The results showed that a primary solvent with low solubility-in-water and high non-bonded interaction energy ratio among the solvent, polymer, and water produced smoother and denser films.
Review
Chemistry, Analytical
Hind A. Al-Abadleh, James D. Kubicki, Nicholas Meskhidze
Summary: With the increasing recognition of the need for interdisciplinary communication in addressing research questions related to climate change and pollution, this article focuses on the chemical reactivity of Fe-containing minerals in air, water, and the air-sea interface. The reactions driven by Fe have significant impacts on respiratory organs and aerosol properties, and the deposition of aerosol particles affects ocean biogeochemical processes. Enhancing the predictive power of atmospheric and ocean models is emphasized.
ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS
(2023)
Article
Materials Science, Biomaterials
Atrouli Chatterjee, Preeta Pratakshya, Albert L. Kwansa, Nikhil Kaimal, Andrew H. Cannon, Barbara Sartori, Benedetta Marmiroli, Helen Orins, Zhijing Feng, Samantha Drake, Justin Couvrette, LeAnn Le, Sigrid Bernstorff, Yaroslava G. Yingling, Alon A. Gorodetsky
Summary: By combining experimental and computational methods, we systematically mapped the three-dimensional refractive index distributions of model self-assembled reflectin-based structures, which can improve understanding of squid skin cell functionality and enhance characterization of protein-based optical materials.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Buang Zhang, Sabila K. Pinky, Albert L. Kwansa, Spencer Ferguson, Yaroslava G. Yingling, Adrienne D. Stiff-Roberts
Summary: Thin films of polyfluorene (PFO) were successfully deposited using the emulsion based resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) method. It was found that the selection of surfactant can increase the crystalline-fi phase content and improve the color purity of light emission. Comparison of blue light-emitting diodes (LEDs) with different surfactants showed the significant impact of surfactant on device performance.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Akhlak U. Mahmood, Mehedi H. Rizvi, Joseph B. Tracy, Yaroslava G. Yingling
Summary: Inorganic colloidal nanoparticle (NP) properties can be controlled by stripping stabilizing ligands using a poor solvent. This study investigates the stripping process of oleylamine ligands from magnetite (Fe3O4) NPs in different ethanol/hexane mixtures. The results reveal the complex interactions between ethanol and system components, and suggest the existence of a threshold concentration of ethanol for effective ligand stripping. The study provides insights into the ligand-solvent interactions and offers a computational approach for studying ligand stripping from colloidal NPs.
Article
Polymer Science
Albert L. L. Kwansa, Rakhee C. C. Pani, Joseph A. A. DeLoach, Arianna Tieppo, Eric J. J. Moskala, Steven T. T. Perri, Yaroslava G. G. Yingling
Summary: Plasticizers improve the flexibility and durability of polymer materials by reducing glass transition and cold flex temperatures. However, the migration and exudation of plasticizers from polymer materials have hindered the development of efficient and safe plasticizers. This study used molecular dynamics simulations validated by experiment to investigate the molecular mechanism of exudation of different plasticizers from PVC, and found that plasticizer-PVC compatibility was the main determinant of exudation.
Article
Multidisciplinary Sciences
Joshua T. Del Mundo, Sintu Rongpipi, Hui Yang, Dan Ye, Sarah N. Kiemle, Stephanie L. Moffitt, Charles L. Troxel, Michael F. Toney, Chenhui Zhu, James D. Kubicki, Daniel J. Cosgrove, Esther W. Gomez, Enrique D. Gomez
Summary: In this study, grazing-incidence wide-angle X-ray scattering (GIWAXS) with a humidity chamber was used to investigate the properties of onion cell walls. The results showed that the lattice spacing of cellulose (110/110) slightly decreased upon drying, while the lattice parameters of (200) remained unchanged. The intensity of (110/110) diffraction increased relative to (200) in hydrated samples. Density functional theory models confirmed the changes in crystalline properties during drying. GIWAXS also revealed a peak attributed to pectin chain aggregation.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
Juseok Choi, Albert L. Kwansa, Yaroslava G. Yingling, Seong H. Kim
Summary: Vibrational sum frequency generation (SFG) spectroscopy is commonly used to analyze the structural information of molecular functional groups at two-dimensional interfaces in gas or liquid mediums. However, interpreting the measured intensity in terms of molecular orientation with respect to laboratory coordinates is challenging. This study utilized density functional theory to calculate the polarizability and dipole derivative tensors of different molecules, allowing for the theoretical calculation of their SFG intensities in relation to the tilt angle of the CH3 group with respect to the surface normal direction. The findings suggest that the vibrational coupling among neighboring functional groups is significant and should not be ignored in SFG experiments.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Daniel Mejia-Rodriguez, Hoshin Kim, Natalie Sadler, Xiaolu Li, Pavlo Bohutskyi, Marat Valiev, Wei-Jun Qian, Margaret S. Cheung
Summary: Post-translational modification (PTM) of a protein involves chemical modifications of specific amino acid residues and plays a central role in regulating molecular interactions. This study introduces a workflow called PTM-Psi that allows users to interpret how PTMs affect a protein's properties, dynamics, and interactions with binding partners based on inferred or experimentally determined protein structure.
Article
Biochemistry & Molecular Biology
Preeti Verma, Albert L. Kwansa, Ruoya Ho, Yaroslava G. Yingling, Jochen Zimmer
Summary: Cellulose, a major component of plant cell walls, is synthesized by cellulose synthase through translocation. In this study, cryogenic electron microscopy structures of the substrate and product bound to cellulose synthase isoform-8 from aspen were presented. UDP-glucose binds to a catalytic pocket adjacent to a transmembrane channel, and the glucosyl unit of the substrate is coordinated by conserved residues and amphipathic interface helices. Mutagenesis of a conserved gating loop revealed its critical role in catalytic activity. Molecular dynamics simulations showed prolonged interactions between the gating loop and the substrate, facilitating proper positioning for glycosyl transfer and cellulose translocation.
Article
Chemistry, Multidisciplinary
Alireza Namayandeh, Olaf J. Borkiewicz, Nefeli M. Bompoti, Steven K. Watson, James D. Kubicki, Maria Chrysochoou, F. Marc Michel
Summary: This study used synchrotron scattering methods and chemical analysis to investigate the impact of oxyanion surface loading on the transformation of Fh. The results showed that adsorption of oxyanions decreased the transformation rate and favored the formation of Hm over Gt. The inhibitory effect of PO43- surface loading on Fh transformation was greater.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Thomas J. Oweida, Yaroslava G. Yingling
Summary: This study presents a method that integrates experimental small-angle X-ray scattering data and all-atom molecular modeling data using a genetic algorithm method for the determination of the atomistic representation of poly-Thymine DNA in solution. The results validate the performance of various AMBER force fields and implicit solvent models for ssDNA and enable a better understanding of the behavior of ssDNA in solution.
ADVANCED THEORY AND SIMULATIONS
(2023)
Article
Chemistry, Physical
Izaac Sit, Mark A. Young, James D. Kubicki, Vicki H. Grassian
Summary: This study investigates the surface chemistry of nucleotides adsorbed on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. The results show preferential adsorption of the phosphate group to either surface. The experimental absorption frequencies were compared to DFT calculations, revealing differences in the binding modes of nucleotides to the two mineral surfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biophysics
Michael J. Taylor, Hoshin Kim, William Kew, Amity Andersen, Arunima Bhattacharjee, Mark H. Engelhard, Christopher R. Anderton
Summary: In beam-based ionization methods, the substrate plays a crucial role in the desorption mechanism of molecules from surfaces. Atomistic simulations combined with density functional theory calculations were used to study the desorption of a sphingolipid from a model surface. The results provide insights into the effects of biointerfacial lipid ordering on SIMS imaging.
Article
Environmental Sciences
James S. Peerless, Alexey Gulyuk, Nina J. B. Milliken, Gyu Dong Kim, Elliot Reid, Jae Woo Lee, Dooil Kim, Zachary Hendren, Young Chul Choi, Yaroslava G. Yingling
Summary: Brine desalination is important for reducing the environmental impact of contaminated wastewater, but current techniques require high energy. We tested 10 organic solvents for solvent-based desalination efficacy using experiments and simulations. Solvents that form partial nanoscale phases effectively remove salt ions and capture water molecules. Our results contribute to the rational design of solvents for efficient desalination and low-cost fresh water production.