Article
Chemistry, Physical
Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A. Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma
Summary: The study of non-covalent interactions of post-transcriptionally modified bases in RNA is crucial for understanding RNA structure and function. However, these interactions are understudied. To address this, we analyzed the stacking of biologically relevant modified bases in high-resolution RNA crystal structures and classified them geometrically. By incorporating quantum chemical calculations and analyzing the structural context, we provide a map of stacking conformations available to modified bases in RNA. This analysis is expected to facilitate structural research on altered RNA bases.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Yusuke Sato, Yoshihide Takaku, Toshiaki Nakano, Ken Akamatsu, Dai Inamura, Seiichi Nishizawa
Summary: A fluorescent probe, Dimethyllumazine (DML)-thiazole orange (TO) conjugate, has been developed for detecting thymine glycol (Tg)-containing DNAs by selectively recognizing the A nucleobase opposite the Tg residue. Moreover, this conjugate exhibits inhibitory activity against endonuclease III, a DNA repair enzyme, via competitive binding to Tg-containing DNAs.
CHEMICAL COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Mohammed S. Abu-Jafar, Vincent Leonhardi, Raed Jaradat, Ahmad A. Mousa, Samah Al-Qaisi, Nada T. Mahmoud, Ahmed Bassalat, R. Khenata, A. Bouhemadou
Summary: This study investigates the properties of Scandium Carbide compound using first-principles calculations, revealing that NaCl and NiAs structures are mechanically and dynamically stable phases, while ZB and CsCl structures are unstable. The electronic structures of all considered structures show metallic character.
RESULTS IN PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Mumtaz Manzoor, Debidatta Behera, Ramesh Sharma, Muhammad Waqas Iqbal, S. K. Mukherjee
Summary: In this report, the structural, electronic, mechanical, thermoelectric, and thermodynamic responses of ScSb with external pressure were investigated using FP-LAPW and DFT. The structure of the ScSb compound was computed and found to be dynamically stable. Different approximations were used to accurately consider exchange and correlation effects in electronic properties. The transport properties were studied using the Boltzmann equation, considering temperature, chemical potential, and carriers concentrations under external pressure. The thermodynamic properties of the material were also computed across a wide temperature range. The material showed a large power factor, indicating its potential as a thermoelectric material in high-temperature applications.
MATERIALS SCIENCE AND ENGINEERING B-ADVANCED FUNCTIONAL SOLID-STATE MATERIALS
(2023)
Article
Multidisciplinary Sciences
Yaxin Lv, Junfeng Lin, Kai Song, Xuwei Song, Hongjun Zang, Yaping Zang, Daoben Zhu
Summary: The conjugated macrocycles cycloparaphenylenes (CPPs) exhibit high conductance and large tunneling attenuation coefficient, especially at small ring sizes. Radially pi-conjugated molecular systems offer a larger conductance modulation range than standard linear molecules, making them a potential platform for building molecular devices with highly tunable transport behaviors.
Article
Chemistry, Physical
Maria Isabel Menendez, Nicolas Montenegro-Pohlhammer, Ricardo Pino-Rios, Rodrigo Urzua-Leiva, Simone Morales-Lovera, Merlys Borges-Martinez, Kevin Granados-Tavera, Ramon Lopez, Gloria Cardenas-Jiron
Summary: The photophysical, photovoltaic, and charge transport properties of fused core-modified expanded porphyrins were investigated using density functional theory and time-dependent density functional theory. The compounds showed absorption in the range of 700-970 nm for their Q bands and 500-645 nm for their Soret bands. The presence of thiophene rings in the macrocycle led to a bathochromic shift in the absorption wavelength, resulting in near-infrared absorptions. The charge transport study showed that pentaphyrin 1 and octaphyrin 4 were more conductive than hexaphyrin 2 or heptaphyrin 3.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Xin Song, Zhicun Zhou, Xinchen Peng, Xinbang Liu, Dianrong Han, Hang Zhang, Xiaoqing Liu, Li Wang, Huihui Kong
Summary: Delicate control over structural phase transition enables the fabrication of desired nanoarchitectures. The addition of metal adatoms in pure organic systems facilitates the phase transition by capturing surface metal adatoms. However, the transition at high molecular concentration is limited due to poor migration ability. In this study, the phase transition of PT molecules on Au(111) surface from row-like nanostructures to metal-organic honeycomb networks was observed, and the key to phase transition was identified to be the identical molecular density of the two nanostructures.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Materials Science, Multidisciplinary
Xie Huang, Qiao Wu, Rong Dai, Jing Ning, Lei Zhang, Wei Wang, Suqing Xue, Junfeng Yan, Fuchun Zhang, Weibin Zhang
Summary: Based on first-principles density functional theory, the electronic structure, optical and lattice dynamical properties of AgGaS2 crystal were calculated. The results demonstrate that AgGaS2 is a promising infrared nonlinear optical crystal with good nonlinear optical coefficient and suitable birefringence.
RESULTS IN PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
HaiYing Wu, YaHong Chen, Zi Jiang Liu, XiangYu Han, PengFei Yin
Summary: In this study, the high-pressure behavior of magnesium dicarbide was investigated using first-principle methods. Three stable structures were identified, and the P-3m1 structure showed potential as a hard material.
PHILOSOPHICAL MAGAZINE
(2023)
Article
Chemistry, Physical
Yulong Chen, Haohao Xu, Yangwei Ma, Jun Liu, Liqun Zhang
Summary: The dynamics of polymer-grafted nanoparticles (PGNPs) in melts of unentangled linear chains were studied using coarse-grained molecular dynamics simulations. The results showed that the relaxation of graft monomers near the particle surface is slower due to surface constraint and neighboring chain confinement. This heterogeneous relaxation perturbs particle motion, leading to subdiffusive dynamics in an intermediate-time stage. For long-time Fickian diffusion, the diffusivity decreases with increasing grafting density, grafted chain length, and matrix chain length. These findings are significant for understanding the anomalous dynamics of PGNPs in various polymers.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Electrochemistry
Canlong Wu, Li Zhang, Guangyu Zhao, Xianbo Yu, Chao Liu, Junjie He, Kening Sun, Naiqing Zhang
Summary: By incorporating water molecules into MoS2, hydrous MoS2 (H-MoS2) demonstrates enhanced Mg diffusion kinetics, high capacity, excellent rate performance, and outstanding cycling stability.
Article
Engineering, Chemical
Moritz A. Junker, Wiebe M. de Vos, Joris de Grooth, Rob G. H. Lammertink
Summary: A novel method of making nanofiltration membranes is to use the Layer-by-Layer method, which involves coating polyelectrolytes alternately on a porous ultrafiltration membrane to form a controllable nanometer-thin separation layer known as Polyelectrolyte Multilayer (PEM). Understanding the structural properties of PEMs and their relationship to coating conditions and membrane performance is crucial for membrane optimization. In this study, the separation performance of NF PEM membranes based on different polymer systems (PDADMAC/PSS and PAH/PAA) was investigated by analyzing the structure of the membrane, particularly the pore size distribution.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Chemistry, Physical
Tsai-Wei Lin, Baicheng Mei, Kenneth S. Schweizer, Charles E. Sing
Summary: The role of cross-linked network polymers in governing the molecular motion of penetrants is investigated using molecular simulation. The results show that cross-links primarily affect molecular diffusion through the modification of the matrix glass transition, and penetrant transport is affected by dynamic heterogeneity at low temperatures. This research provides important insights for the design of materials for applications such as coatings and membranes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Energy & Fuels
Zhen Zhu, Shang Li, Lichang Zhang, Xin Lu, Pengtao Huang, Yadong Wang, Mu Pan
Summary: In this study, poly(1,5-diaminoanthraquinone) (P15DAAQ) was deposited on carbon fiber of gas diffusion backing (GDB) to improve the water management ability of the gas diffusion layer (GDL). The morphology of carbon fibers and the pore structure of GDBs were characterized. Performance and water management capabilities of proton exchange membrane fuel cells were studied. The results show that P15DAAQ-GDL exhibits better oxygen mass transfer and water management capabilities than PTFE-GDL.
Article
Chemistry, Physical
Wulan Zeng, Xia Wang, Youwang Li, Xueao Li, Yuxing Zhang
Summary: Two new spirocompounds were synthesized by two different routes, and their structures and properties were analyzed using X-ray diffraction and DFT optimization.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Nanoscience & Nanotechnology
Eric S. Muckley, Rama Vasudevan, Bobby G. Sumpter, Rigoberto C. Advincula, Ilia N. Ivanov
Summary: In this study, we have developed an integrated machine-intelligent experimental system that allows simultaneous testing of the electrical, optical, gravimetric, and viscoelastic properties of materials under a programmable dynamic environment. The system is controlled by specially designed software that enables on-the-fly extensive data analysis, real-time iterative feedback, and rapid visualization of experimental results. This system provides a viable platform for AI-centered material characterization and has the potential to accelerate the discovery of multifunctional materials when coupled with an AI-controlled synthesis system.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Nanoscience & Nanotechnology
Daniel Salatto, Zhixing Huang, Peter Todd Benziger, Jan-Michael Y. Carrillo, Yashasvi Bajaj, Aiden Gauer, Leonidas Tsapatsaris, Bobby G. Sumpter, Ruipeng Li, Mikihito Takenaka, Wei Yin, David G. Thanassi, Maya Endoh, Tadanori Koga
Summary: Synergistic nanostructured surfaces combining bactericidal and bacteria-releasing properties were reported in this study. A diblock copolymer was used to fabricate vertically oriented cylindrical structures on silicon substrates. The results demonstrate that these surfaces exhibit highly effective bactericidal and bacteria-releasing properties against Escherichia coli and Listeria monocytogenes. Molecular dynamics simulations were performed to understand the mechanisms underlying these properties.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nuria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that forms two different i-motif structures depending on pH and temperature. At neutral pH, the major structure is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated i-motif structure with C:C+ base pairs and G:T:G:T tetrads is observed. Molecular dynamics calculations showed that the conformational transition between the two structures is driven by the protonation state of key cytosines. This study reveals the pH-dependent plasticity and conformational switch of i-motif structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Instruments & Instrumentation
Sebin Varghese, Jake Dudley Mehew, Alexander Block, David Saleta Reig, Pawel Wozniak, Roberta Farris, Zeila Zanolli, Pablo Ordejon, Matthieu J. Verstraete, Niek F. van Hulst, Klaas-Jan Tielrooij
Summary: Diffusion, a ubiquitous transport phenomenon, can be experimentally tracked by point spreading. A spatiotemporal pump-probe microscopy technique is introduced here to study diffusion. By utilizing the temperature profile obtained through transient reflectivity, this technique allows for nanometer accuracy in probing the diffusion of long-lived excitations. It also enables the quantification of thermal transport without the need for material input parameters or strong heating.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Physics, Applied
Olha Popova, Steven J. Randolph, Sabine M. Neumayer, Liangbo Liang, Benjamin Lawrie, Olga S. Ovchinnikova, Robert J. Bondi, Matthew J. Marinella, Bobby G. Sumpter, Petro Maksymovych
Summary: This study investigates resistive switching phenomena using scanning microwave impedance microscopy and cathodoluminescence microscopy. The results show that even at the lowest doses, helium ions can modify the nature of bonds but the conductive properties of the films remain stable. Additionally, the study explores a method of electroforming with lower dissipated power and provides information on characteristic impurity levels through calculations.
APPLIED PHYSICS LETTERS
(2023)
Article
Chemistry, Physical
Jan-Michael Carrillo, Yangyang Wang, Rajeev Kumar, Bobby G. Sumpter
Summary: This study investigates the behavior of charged polyelectrolytes in semidilute solutions using explicit-solvent coarse-grained molecular dynamics simulations. The results highlight the importance of explicit-solvent effects in understanding polyelectrolyte solution behavior, particularly in semidilute solutions.
EUROPEAN PHYSICAL JOURNAL E
(2023)
Article
Chemistry, Medicinal
Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Summary: The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Zhiqiang Shen, Jan-Michael Y. Carrillo, Bobby G. Sumpter, Yangyang Wang
Summary: The collective density-density and hydrostatic pressure-pressure correlations of glass-forming liquids were investigated using molecular dynamics simulations. It was found that below the Arrhenius temperature, there is a slow nonhydrodynamic collective dynamics that is closely related to the local structural dynamics. This result highlights the importance of understanding the dynamic crossover phenomenon.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Polymer Science
Catalin Gainaru, Rajeev Kumar, Ivan Popov, Md Anisur Rahman, Michelle Lehmann, Eric Stacy, Vera Bocharova, Bobby G. Sumpter, Tomonori Saito, Kenneth S. Schweizer, Alexei P. Sokolov
Summary: This study investigates the mechanisms controlling the energy barrier for ion hopping in conducting polymers. It is found that the Arrhenius fit of the temperature dependence of conductivity relaxation time for polymer electrolytes leads to unphysical values, and the energy barrier for charge transport in these polymers has strong temperature dependence even below their glass transition temperature. Significant temperature variations of dielectric permittivity and instantaneous shear modulus in the glassy state of these polymers are also observed. The proposed approach reveals that the energy barrier for ion hopping in polymer electrolytes is significantly lower than previously estimated using traditional Arrhenius fit.
Article
Multidisciplinary Sciences
Zhen Xu, Nuwayo Eric Munyaneza, Qikun Zhang, Mengqi Sun, Carlos Posada, Paul Venturo, Nicholas A. Rorrer, Joel Miscall, Bobby G. Sumpter, Guoliang Liu
Summary: Conversion of plastic wastes to fatty acids is an attractive and economically viable method for supplementing the sourcing of high-value chemicals. Our method achieves a conversion rate of up to 80% and produces fatty acids with high molar masses. The process can be applied to municipal PE and PP wastes, and the resulting fatty acids can be further converted into high-value surfactants without the need for subsidies.
Article
Chemistry, Physical
William J. Zamora, Antonio Viayna, Silvana Pinheiro, Carles Curutchet, Laia Bisbal, Rebeca Ruiz, Clara Rafols, F. Javier Luque
Summary: In recent years, the use of partition systems other than n-octanol/water has gained attention in studying the lipophilicity of compounds. The difference between n-octanol/water and toluene/water partition coefficients has been found to be valuable in understanding intramolecular hydrogen bonds and chameleon-like properties that affect solubility and permeability. This study reports the experimental toluene/water partition coefficients for a series of drugs and investigates the performance of two computational strategies for predicting log P-tol/w.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Dustin Eby, Mikolaj Jakowski, Valeria Lauter, Mathieu Doucet, Panchapakesan Ganesh, Miguel Fuentes-Cabrera, Rajeev Kumar
Summary: Diblock copolymers undergo microphase separation due to repulsive interactions between dissimilar monomers. In thin films, additional effects make microphase separation more complicated. Physics-based models have been used to extract interaction parameters, but they are time-intensive and prone to errors. This work develops an alternative method using neural networks to extract parameters from neutron scattering length density profiles, paving the way for automated analysis using machine learning tools.
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nu'ria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that can form two different i-motif structures, with their stability depending on pH and temperature. The structure at neutral pH is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated structure consisting of C:C+ base pairs and G:T:G:T tetrads is observed. The transition between these two structures is driven by the protonation state of key cytosines.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Qiushi Deng, Jose Maria Castillo-Robles, Ernane de Freitas Martins, Pablo Ordejon, Jan-Niclas Gorges, Philipp Eiden, Xiao-Bo Chen, Patrick Keil, Ivan Cole
Summary: This study investigates the distinct adsorption behaviors induced by different chemical functionalities on the corrosion of zinc steel. The results show that both inhibitors exhibit corrosion inhibition effects on zinc steel through different mechanisms.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Xiangyi Jiang, Jing Li, Antonio Viayna, F. Javier Luque, Molly Woodson, Lanlan Jing, Shenghua Gao, Fabao Zhao, Minghui Xie, Karoly Toth, John Tavis, Ann E. Tollefson, Xinyong Liu, Peng Zhan
Summary: Compounds D1N8 and D1N52 have shown excellent inhibitory activity against SARS-CoV-2 3CL(pro) with low cytotoxicity, providing a foundation for the research of novel anti-SARS-CoV-2 agents.
RSC MEDICINAL CHEMISTRY
(2023)
