Article
Chemistry, Physical
Keerti Chauhan, Amit Raj Singh, Sanjay Kumar, Rony Granek
Summary: This research investigates the kinetics of DNA sequence melting using molecular dynamic simulations and the Gaussian binding energy model. Two major partial denaturation states are identified, and their influence on the dynamics of base pair opening and closing is analyzed. The study demonstrates that multi-step relaxation can be observed by tagging specific base pairs at certain temperatures. It also suggests which base pairs should be tagged in order to observe this behavior. The results show that the Gaussian binding energy model can reliably predict the dynamics of long DNA sequences, where molecular dynamic simulations may be limited.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Sha Wang, Wenjun Lu, Yafei Wang, Ying Guan, Yongjun Zhang
Summary: Protein-imprinted polymers with a novel peptide crosslinker can achieve complete template removal under mild conditions and significantly improve the imprinting efficiency. The reversible helix-coil transition of peptide segments controlled by pH enables the release and recognition of template proteins. The peptide-crosslinked polymer shows high adsorption capacity, selectivity, reusability, and preservation of protein secondary structures, making it a promising candidate for bioseparation applications.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Surahit Chewle, Franziska Emmerling, Marcus Weber
Summary: Crystallization is a complex phenomenon that has significant implications for the production and formulation of active pharmaceutical ingredients. This study reveals the intricate dynamics of paracetamol crystallization intermediate phases, which vary with the choice of solvent. The novel approach of using objective function-based non-negative matrix factorization for time-resolved Raman spectroscopy data analysis, in conjunction with time-lapse photography, is demonstrated to be effective.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Biochemistry & Molecular Biology
Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina
Summary: Molecular dynamics simulations were performed to study protein folding. By applying rotational force to the C-terminal amino acid while restricting the movement of the N-terminal amino acid, the folding of four protein domains was accelerated at least by an order of magnitude. These results suggest that external forces and constraints can bias the motions of the polypeptide and facilitate the attainment of stable fold.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Unmesh D. Chowdhury, B. L. Bhargava
Summary: The study examines the conformational and dynamical changes of Aβ monomers in coordination with Zn2+ ions using all-atom molecular dynamics simulations. The presence of Zn2+ ions leads to differential intra-peptide interactions and shifts in hydrogen bonding, resulting in structural and dynamical variations in Aβ monomers. The transition from an alpha-helix dominated structure to an unfolded coil structure highlights the impact of Zn2+ ions on Aβ monomers under fibrillation-like conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Optics
Manita Rai, Wesley E. Deeg, Baozhu Lu, Katrina Brandmier, Ashtyn M. Miller, Darius H. Torchinsky
Summary: We propose a novel time-resolved, optical pump/NIR supercontinuum probe spectrometer suitable for oscillators. A NIR supercontinuum probe spectrum is generated in a photonic crystal fiber, dispersed and raster scanned into a single element detector. Simultaneous measurement of bare reflectance R and its photoinduced change Delta R is achieved through dual modulation of pump and probe beams at disparate frequencies, allowing for continuously self-normalized measurement of Delta R/R. Example data on a germanium wafer sample demonstrate high spectral resolution, temporal resolution pre-recompression, and sensitivity comparable to standard time-resolved, amplifier-based pump-probe techniques.
Article
Endocrinology & Metabolism
Yanwu Yang, Michael D. Glidden, Balamurugan Dhayalan, Alexander N. Zaykov, Yen-Shan Chen, Nalinda P. Wickramasinghe, Richard D. DiMarchi, Michael A. Weiss
Summary: This article investigates the toxic misfolding of diabetes-associated proteins in beta-cells, and proposes a peptide model for classifying related mutations. The study found that the mutant variants exhibit successive structural perturbations, which are correlated with the phenotypic differences in diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Chemistry, Physical
Ruth Chau-Ting Chan, Chensheng Ma, Allen Ka-Wa Wong, Chris Tsz-Leung Chan, Joshua Chiu-Lok Chow, Wai-Ming Kwok
Summary: In contrast to the extensive research on electronically excited DNA, little is known about the excited states of RNA. In this study, the intrinsic fluorescence and overall dynamics of a homopolymeric adenine center dot uracil RNA duplex with the A-form structure were investigated using ultrafast broadband time-resolved fluorescence and fluorescence anisotropy. The results revealed complex deactivation processes mediated by states of varied energy, involving charge transfer and lifetimes ranging from sub-picosecond to nanoseconds. Unique features, such as an unprecedented kinetic isotopic effect and unusual proton transfer, were observed. Additionally, a high-energy nanosecond emission with fluorescence anisotropy was attributed to long-lived weakly emissive excitons specific to the A-form conformation of the adenine center dot uracil double helix.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Shunki Takaramoto, Yusuke Nakasone, Kei Sadakane, Shinsaku Maruta, Masahide Terazima
Summary: In this study, the interaction dynamics between alpha Syn and SDS micelles was investigated using time-resolved measurements with a micro-stopped-flow system. The gradual change in diffusion triggered by the presence of SDS micelles was revealed, suggesting an interesting discovery of the diffusion coefficient decreasing in an intermediate state and then increasing to the final state in the binding reaction.
Article
Chemistry, Multidisciplinary
Wenbo Zhang, Mingwei Liu, Yang Wang, Xin Wang, Ruonan Wang, Shuyuan Li, Lanlan Yu, Feiyi Zhang, Chenxuan Wang
Summary: Transferring structural information from amino acid sequence to macroscale assembly is achieved by designing two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and using scanning tunneling microscopy (STM) to determine their folding structure and beta-sheet supramolecular organization. The structural variations in beta-strand length distribution between QNL-His and QNL-Arg lead to distinguishable outcomes in their beta-sheet assembled fibrils and phase transitions. The comparison of their structures and macroscopic properties reveals the role of assembly in amplifying the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.
Article
Chemistry, Physical
Stavros Katsiaounis, Andrey Sharkov, Eugeniy Khoroshilov, Georgios Paterakis, John Parthenios, Konstantinos Papagelis
Summary: Phonon lifetimes are crucial parameters in phonon transport of two-dimensional materials. The presence of a substrate significantly reduces the lifetimes of exfoliated graphene, while CVD graphene tends to have systematically lower lifetimes due to structural defects. Additionally, the electronphonon coupling strength of graphite is found to be in excellent agreement with theoretical predictions for graphene.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biochemical Research Methods
Ferenc Zsila
Summary: A simple spectrophotometric approach is proposed for detecting conformational transitions of peptide/protein sequences. Helix formation leads to intensity reduction, while unfolding events result in intensity increase of the absorption band. This method has the potential to be widely used in the field of protein science.
ANALYTICAL BIOCHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Yuan Zhang, Junfeng Dai, Xiangli Zhong, Dongwen Zhang, Gaokuo Zhong, Jiangyu Li
Summary: Ferroelectric materials have been a key research topic due to their wide range of modern electronic and photonic applications. The ultrafast dynamics of ferroelectrics, explored through time-resolved pump-probe spectroscopy, have drawn considerable attention for their potential in understanding and utilizing dynamic processes. Through studying the ultrafast dynamics, insights can be gained to advance next-generation devices.
Article
Chemistry, Multidisciplinary
Shiny Maity, Brad D. D. Price, C. Blake Wilson, Arnab Mukherjee, Matthieu Starck, David Parker, Maxwell Z. Z. Wilson, Janet E. E. Lovett, Songi Han, Mark S. S. Sherwin
Summary: We propose a time-resolved Gd-Gd electron paramagnetic resonance (TiGGER) technique at 240 GHz to monitor inter-residue distances in proteins' mechanical cycles in solution state. TiGGER utilizes Gd-sTPATCN spin labels with favorable properties, including spin-7/2 EPR-active center, short linker, narrow intrinsic linewidth, and minimal anisotropy at high fields. By applying TiGGER, we observed that the C-terminus and N-terminus of AsLOV2 separate within 1 s upon light activation and relax back to equilibrium with a time constant of approximately 60 s. TiGGER also revealed that the light-induced long-range mechanical motion is decelerated in the Q513A variant of AsLOV2, which is correlated with the slowed relaxation of the optically excited chromophore as reported in recent literature. TiGGER has the potential to complement existing methods for studying triggered functional dynamics in proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Physics, Multidisciplinary
Xiangpeng Luo, Dimuthu Obeysekera, Choongjae Won, Suk Hyun Sung, Noah Schnitzer, Robert Hovden, Sang-Wook Cheong, Junjie Yang, Kai Sun, Liuyan Zhao
Summary: Using EQ RA-SHG, we demonstrate the ferro-rotational nature of CCDW in 1T-TaS2 and observe a photoinduced transient CDW phase at high pump fluence.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Khulud Almasabi, Xiaopeng Zheng, Bekir Turedi, Abdullah Y. Alsalloum, Muhammad Naufal Lintangpradipto, Jun Yin, Luis Gutierrez-Arzaluz, Konstantinos Kotsovos, Aqil Jamal, Issam Gereige, Omar F. Mohammed, Osman M. Bakr
Summary: The difficulty of growing perovskite single crystals suitable for efficient photovoltaic devices has been a challenge. Here, we report the growth of mixed-cation FA0.6MA0.4PbI3 perovskite single crystals on a hydrophilic self-assembled monolayer. The single crystals exhibit enhanced stability and power conversion efficiencies up to 23.1%, setting a new benchmark for perovskite solar cells.
ACS ENERGY LETTERS
(2023)
Article
Chemistry, Physical
Shorooq A. Alomar, Luis Gutierrez-Arzaluz, Issatay Nadinov, Ru He, Xiaodan Wang, Jian-Xin Wang, Jiangtao Jia, Osama Shekhah, Mohamed Eddaoudi, Husam N. Alshareef, Kirk S. Schanze, Omar F. Mohammed
Summary: Structural modifications to molecular systems that control photon emission processes are crucial for the development of fluorescence sensors, X-ray imaging scintillators, and OLEDs. This study explored the effects of slight changes in chemical structure on interfacial excited-state transfer processes using two donor-acceptor systems. The results showed efficient energy transfer in the SDZ-TADF system and both energy and electron transfer processes in the Ac-SDZ-TADF system. Transient absorption measurements and TD-DFT calculations confirmed the occurrence of photoinduced electron transfer in the Ac-SDZ-TADF system. This work provides a straightforward approach to modulate excited-state energy/charge transfer processes at donor-acceptor interfaces.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Ren-Wu Huang, Xin Song, Shulin Chen, Jun Yin, Partha Maity, Jiayi Wang, Bingyao Shao, Hongwei Zhu, Chunwei Dong, Peng Yuan, Taimoor Ahmad, Omar F. F. Mohammed, Osman M. M. Bakr
Summary: Zero-dimensional (0D) scintillation materials are of great interest for the fabrication of flexible high-energy radiation scintillation screens. Challenges still persist in the development of 0D scintillators, but a strategy based on metal nanoclusters shows promise in overcoming these limitations. This work demonstrates the synthesis and self-assembly of atomically precise nanoclusters with high phosphorescence quantum yield, AIEE behavior, and intense radioluminescence. The self-assembled nanoclusters can be used as building blocks for flexible particle-deposited scintillation films with high-resolution X-ray imaging performance.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Prakash T. Parvatkar, Sharath Kandambeth, Aslam C. Shaikh, Issatay Nadinov, Jun Yin, Vinayak S. Kale, George Healing, Abdul-Hamid Emwas, Osama Shekhah, Husam N. Alshareef, Omar F. Mohammed, Mohamed Eddaoudi
Summary: Heterogeneous photocatalysis is an ecofriendly and sustainable method for addressing energy and environmental issues. Heterogeneous photocatalysts based on covalent organic frameworks (COFs) have gained attention due to their performance and recyclability, offering a prospective alternative to homogeneous photocatalysts based on precious metal/organic dyes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Shulin Chen, Jiayi Wang, Simil Thomas, Wasim J. J. Mir, Bingyao Shao, Jianxun Lu, Qingxiao Wang, Peng Gao, Omar F. F. Mohammed, Yu Han, Osman M. M. Bakr
Summary: Inorganic halide perovskite nanocrystals (NCs) are extensively studied as next-generation optoelectronic materials. The atomic structure at the surface of CsPbBr3 NCs is directly observed, revealing a Cs-Br terminated surface with a significantly decreased Cs-Cs bond length, inducing compressive strain and polarization. Density functional theory calculations suggest that this reconstructed surface contributes to the separation of holes and electrons. These findings enhance our understanding of the surface structure and provide insights for designing stable and efficient optoelectronic devices.
Article
Optics
Kostiantyn Sakhatskyi, Bekir Turedi, Gebhard J. Matt, Erfu Wu, Anastasiia Sakhatska, Vitalii Bartosh, Muhammad Naufal Lintangpradipto, Rounak Naphade, Ivan Shorubalko, Omar F. Mohammed, Sergii Yakunin, Osman M. Bakr, Maksym V. Kovalenko
Summary: We demonstrate single-photon counting and long-term stability of perovskite X-ray detectors in the photovoltaic mode, using thick and uniform methylammonium lead iodide single-crystal films (up to 300 μm) and solution directly grown on hole-transporting electrodes. These findings pave the path for the implementation of hybrid perovskites in low-cost, low-dose commercial detector arrays for X-ray imaging with single-photon sensitivity.
Article
Chemistry, Physical
Zhiming Zhao, Binbin Nian, Yongjiu Lei, Yizhou Wang, Lin Shi, Jian Yin, Omar F. Mohammed, Husam N. Alshareef
Summary: Nanoscale Zn2+ channels have been successfully engineered in a plastic-crystal electrolyte, enabling fast Zn2+ solid-state transport and high conductivity. This work offers new perspectives for developing super multivalent ion conductors.
ADVANCED ENERGY MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Razan O. Nughays, Chen Yang, Sarvarkhodzha Nematulloev, Jun Yin, George T. Harrison, Jianfeng Zhao, Shadi Fatayer, Osman M. Bakr, Omar F. Mohammed
Summary: Understanding charge carrier dynamics at the nanometer and femtosecond scales is crucial for optimizing light-conversion devices. The authors used ultrafast scanning electron microscopy (USEM) to investigate the effect of surface orientations and termination on charge carriers in MAPbI(3) perovskite single crystals. Results showed facet-dependent diffusion, surface trap density, surface work function, and carrier concentration. Optimization of perovskite surfaces based on these findings could lead to more efficient and stable solar-cell devices.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Nikita Kolobov, Abdelali Zaki, Katarzyna Swirk, Partha Maity, Luis Garzon-Tovar, Giasemi K. Angeli, Alla Dikhtiarenko, G. Delahay, Pantelis N. Trikalitis, Abdul-Hamid Emwas, Amandine Cadiau, Omar F. Mohammed, Christopher H. Hendon, Karim Adil, Jorge Gascon
Summary: Despite efforts to develop efficient Ti-based metal-organic framework (MOF) photocatalysts, MIL-125-NH2 remains the benchmark, and few design principles have been offered to improve photocatalytic performance. Linker functionalization in Ti MOFs has been shown to enhance photocatalysis under visible light by closing the electronic band gap and improving charge carrier lifetimes. The role of node nuclearity and topology on photocatalytic activity in known Ti-based MOFs is still unclear. Here, we report a new MOF, ICGM-1, with a 3D-connected framework featuring 1D Ti-O rods. Photocatalytic hydrogen evolution experiments reveal a significant difference in activity, solely attributed to node geometry. Time-resolved spectroscopy and DFT calculations explain these differences in terms of electronic and geometric properties, paving the way for the development of Ti-MOF photocatalysts.
ACS MATERIALS LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Jian-Xin Wang, Yue Wang, Maram Almalki, Jun Yin, Osama Shekhah, Jiangtao Jia, Luis Gutierrez-Arzaluz, Youdong Cheng, Omar Alkhazragi, Vijay K. Maka, Tien Khee Ng, Osman M. Bakr, Boon S. Ooi, Mohamed Eddaoudi, Omar F. Mohammed
Summary: Metal-organic frameworks (MOFs) are excellent platforms for high-speed and multichannel data transmission in optical wireless communications (OWCs) due to their tunable optical behaviors. In this study, a novel approach using a combination of organic linkers and metal clusters in MOFs was demonstrated to achieve a tunable wide modulation bandwidth and high net data rate. The engineered MOFs showed outstanding performance in color conversion and color-pure wavelength-division multiplexing (WDM), significantly improving the data transmission capacity and security.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Yongjiu Lei, Wenli Zhao, Jun Yin, Yinchang Ma, Zhiming Zhao, Jian Yin, Yusuf Khan, Mohamed Nejib Hedhili, Long Chen, Qingxiao Wang, Youyou Yuan, Xixiang Zhang, Osman M. Bakr, Omar F. Mohammed, Husam N. Alshareef
Summary: The three-proton intercalation mechanism in α-molybdenum trioxide is uncovered using a specially designed electrolyte, leading to an improved specific discharge capacity. Experimental and theoretical evidence verifies the semiconductor-to-metal transition behavior and the expansion of lattice interlayers after proton trapping. Fracture behavior is observed during the proton intercalation process, creating diffusion channels for hydronium ions. Additionally, an additional redox behavior at low potential is observed, contributing to an enhanced specific discharge capacity of α-molybdenum trioxide.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Yang Zhou, Tengyue He, Peng Yuan, Jun Yin, Shulin Chen, Luis Gutierrez-Arzaluz, Lijie Wang, Osman M. Bakr, Omar F. Mohammed
Summary: Copper halide clusters have garnered attention in light-emitting diodes and optical sensors due to their unique physicochemical properties and diverse chemical structures. Recently, they have also been explored as promising scintillation materials because of their large absorption cross section for X-ray radiation. However, research on copper halide cluster scintillators is still in its early stages and their performance lags behind that of perovskite and its related metal halide structures.
ACS MATERIALS LETTERS
(2023)
Article
Materials Science, Multidisciplinary
Jian-Xin Wang, Indranil Dutta, Jun Yin, Tengyue He, Luis Gutierrez-Arzaluz, Osman M. Bakr, Mohamed Eddaoudi, Kuo-Wei Huang, Omar F. Mohammed
Summary: In this study, a highly efficient and reabsorption-free transparent X-ray imaging scintillator was fabricated by utilizing an efficient triplet-triplet energy transfer strategy between TADF-Br and Ir-OMC. The experiments and calculations showed that efficient energy transfer from TADF-Br to Ir-OMC can be achieved, leading to enhanced triplet-state radioluminescence upon X-ray irradiation. The fabricated scintillator achieved a high X-ray imaging resolution of 19.8 lp mm -1 .
Article
Chemistry, Multidisciplinary
Lijie Wang, Hong Wang, Razan Nughays, Wojciech Ogieglo, Jun Yin, Luis Gutierrez-Arzaluz, Xinyuan Zhang, Jian-Xin Wang, Ingo Pinnau, Osman M. Bakr, Omar F. Mohammed
Summary: This study reveals the significant contribution of hot phonons to the photo-induced transient bandgap renormalization in MAPbBr(3) single crystals, as evidenced by asymmetric spectral evolutions and transient reflection spectral shifts in the picosecond timescale. Moreover, it identifies a strong correlation between surface charge carrier diffusion and transient bandgap renormalization in time. These findings highlight the need to re-evaluate current theories on photo-induced bandgap renormalization and provide a new approach for precisely controlling the optical and electronic properties of perovskite materials, enabling the design and fabrication of high-performance optoelectronic devices with exceptional efficiency and unique properties.
MATERIALS HORIZONS
(2023)
Article
Engineering, Chemical
Nawader Alqadhi, Mohamed H. Abdellah, Sarvarkhodzha Nematulloev, Omar F. Mohammed, Mahmoud A. Abdulhamid, Gyorgy Szekely
Summary: Polymer engineering can improve the properties and performance of membranes. In this study, two customized PEEKs were synthesized and green membrane preparation methods were used. The effects of polymer structure, green solvent, and crosslinking on membrane performance were investigated, as well as the molecular interaction between organic solvents and PEEKs. The membranes showed high permeance and long-term stability in acetone, making them suitable for active pharmaceutical ingredient purification.
SEPARATION AND PURIFICATION TECHNOLOGY
(2024)
