Article
Chemistry, Multidisciplinary
Damian Mroz, Ruimin Wang, Ulli Englert, Richard Dronskowski
Summary: This study determined the electron density and displacement parameters of R,R-tartaric acid using X-ray diffraction experiment and density-functional theory. The comparison between experimental and theoretical results showed good agreement, validating the accuracy of the theoretical approach.
Article
Biochemistry & Molecular Biology
Monika Wanat, Maura Malinska, Anna A. Hoser, Krzysztof Wozniak
Summary: Quantum crystallography is a rapidly developing interdisciplinary field within crystallography. This study analyzes the impact of different charge density models, hydrogen atom thermal motion modeling, and the type of radiation used on final results. Results suggest that HAR model better describes geometrical parameters, while MM or TAAM refinement is closer to neutron values for hydrogen bonds. The NoMoRe method demonstrates superiority in describing H-atom ADPs.
Article
Chemistry, Multidisciplinary
Riccardo Destro, Mario Barzaghi, Raffaella Soave, Pietro Roversi, Leonardo Lo Presti
Summary: In this study, the accurate charge density distribution of NCLBA was determined using single crystal X-ray diffraction. The chemical properties of the N-Cl bond were explored. The N-Cl bond in NCLBA was found to be one of the longest reported to date. Modeling of the thermal motion of the molecule's halogen atoms was achieved through accurate measurements of high-order data and the use of low temperature techniques.
Article
Chemistry, Physical
Dong Yan, Yijie Zeng, Yishi Lin, Lingyong Zeng, Junjie Yin, Mebrouka Boubeche, Meng Wang, Yihua Wang, Dao-Xin Yao, Huixia Luo
Summary: The study shows that Zn doping in Cu0.5IrTe2 affects the CDW order negatively but stabilizes the superconducting state with only minor changes in T-c at different x values. The optimal doping composition Zn0.25Cu0.25IrTe2 exhibits superconducting properties close to the BCS value.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Physical
Arnau Vila, Miguel Gonzalez
Summary: In this study, the photodissociation dynamics of Br-2 in doped nanodroplets were investigated using a quantum mechanical hybrid strategy. The results showed significant differences in the photodissociation mechanism, probability, and time scale compared to the study on Cl-2.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
K. Vignesh, D. Sivaganesh, S. Saravanakumar, M. Prema Rani
Summary: The synthesis and characterization of Zn1-xHoxO (X= 0, 0.02, 0.04, 0.06, and 0.08) materials were investigated. It was found that ZnO with 6% Ho3+ doping exhibited the best performance.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Wenjia Sun, Pohua Chen, Mingxuan Zhang, Jian-Xin Ma, Junliang Sun
Summary: Covalent organic frameworks (COFs) have various applications, and their host-guest interactions are crucial for COF functions. However, determining the positions of hydrogen atoms in COFs is challenging due to the difficulty in synthesizing high-quality single crystals. This study demonstrates for the first time that three-dimensional electron diffraction (3D ED) using continuous precession electron diffraction tomography (cPEDT) can locate the hydrogen atoms in COFs, both in the framework and guest molecules, under cryogenic conditions. The locations of the hydrogen atoms provide insights into the host-guest interactions in COFs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Xuecheng Shao, Wenhui Mi, Michele Pavanello
Summary: OE-SCF is an orbital-free DFT solver that extends the applicability of DFT to beyond nanoscale system sizes with high accuracy and fast convergence. It enables large-scale ab initio simulations of silicon-based materials at a low computational cost, and opens up the possibility of adopting more accurate functionals in practical applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Optics
Xiang Li, Rebecca Boll, Daniel Rolles, Artem Rudenko
Summary: A simple model for sequential multiphoton ionization by ultraintense x rays is presented in this study. The ion yield increases according to the power-law behavior typical of multiphoton ionization and saturates at high pulse energies. The calculated average time interval between ionizations for producing ions at a certain charge state is found to be proportional to the pulse duration and independent of all other x-ray pulse parameters, consistent with previous studies.
Article
Chemistry, Physical
Tiancong Zhu, Wei Ruan, Yan-Qi Wang, Hsin-Zon Tsai, Shuopei Wang, Canxun Zhang, Tianye Wang, Franklin Liou, Kenji Watanabe, Takashi Taniguchi, Jeffrey B. Neaton, Alexander Weber-Bargioni, Alex Zettl, Z. Q. Qiu, Guangyu Zhang, Feng Wang, Joel E. Moore, Michael F. Crommie
Summary: The authors used scanning tunnelling microscopy and spectroscopy to study the mirror twin boundaries in single-layer 1H-MoSe2 devices. By adjusting the electron density, they successfully visualized the electronic structure of the mirror twin boundaries and confirmed the presence of density wave excitations and spin-charge separation effects, in agreement with the predictions of the Tomonaga-Luttinger liquid theory.
Article
Optics
Serhiy Rednyk, Petr Dohnal, Michal Hejduk, Juraj Glosik, Radek Plasil
Summary: Experimental studies showed that the reaction rate coefficients of doubly charged carbon cation with O-2, N-2, CO, and HD molecules are almost independent of temperature. At 60K, there are different reaction rate coefficients for each reaction.
Article
Physics, Multidisciplinary
Moatoshi, Sidananda Sarma, J. P. Borah
Summary: Recent economic and environmental concerns have prompted in-depth research into the creation and improvement of rare-earth free permanent magnets, particularly ferrites. In this study, barium hexaferrite co-substituted with transition elements was successfully synthesized using the chemical co-precipitation method. The structure, morphology, vibrational spectrum, and thermal stability of the nanoparticles were characterized, and their magnetic properties were investigated.
Article
Multidisciplinary Sciences
Zhihao Zhao, Linglin Zhou, Shaoxin Li, Di Liu, Yanhong Li, Yikui Gao, Yuebo Liu, Yejing Dai, Jie Wang, Zhong Lin Wang
Summary: This study provides a set of rules for selecting triboelectric materials for DC-TENG, with polyvinyl chloride selected as the triboelectric layer, achieving a high effective charge density in microstructure-designed DC-TENG. This work offers a basic guideline for triboelectric materials selection and promotes the practical applications of DC-TENG.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Li Long, Wenlin Liu, Zhao Wang, Wencong He, Gui Li, Qian Tang, Hengyu Guo, Xianjie Pu, Yike Liu, Chenguo Hu
Summary: This study introduces a floating self-excited sliding TENG which solves the issue of low output in traditional floating TENG, achieving high charge density and output, and can continuously power small electronics.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Hui Sun, Bing Yang, Han-Yi Wang, Zhao-Yu Zhou, Guo-Xian Su, Han-Ning Dai, Zhen-Sheng Yuan, Jian-Wei Pan
Summary: Quantum antiferromagnets are important for studying exotic many-body states and here, a one-dimensional Heisenberg antiferromagnet was successfully created using ultracold bosons. By manipulating the spin-exchange interaction in a two-component Bose-Hubbard system, an isotropic antiferromagnetic Heisenberg model was realized in a 70-site chain, demonstrating the establishment of antiferromagnetism. Ultracold gases in optical lattices offer advantages for exploring bosonic magnetism and spin dynamics due to their microscopic engineering and measurement capabilities.
Article
Chemistry, Multidisciplinary
Malgorzata Katarzyna Cabaj, Paulina Maria Dominiak
Summary: The structures of hypoxanthinium nitrate monohydrate crystals were determined at 15 different temperatures ranging from 20 to 285 K, revealing a phase transition from a twinned, low temperature phase to a high temperature phase. As temperature increases, the layers of the crystals shift against each other, leading to negative thermal expansion in one direction and positive expansion in the perpendicular direction. This phenomenon ceases at the phase transition point when the asymmetry in interactions in the structure disappears.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Prashant Kumar, Paulina Maria Dominiak
Summary: Computational analysis of protein-ligand interactions is crucial for drug discovery, with assessment of ligand binding energy providing a glimpse of binding potential. Electrostatic interactions, which are highly directional, dominate molecular packing and contribute significantly to differences in inhibition strength among enzyme inhibitors.
Article
Biochemistry & Molecular Biology
Monika Wanat, Maura Malinska, Anna A. Hoser, Krzysztof Wozniak
Summary: Quantum crystallography is a rapidly developing interdisciplinary field within crystallography. This study analyzes the impact of different charge density models, hydrogen atom thermal motion modeling, and the type of radiation used on final results. Results suggest that HAR model better describes geometrical parameters, while MM or TAAM refinement is closer to neutron values for hydrogen bonds. The NoMoRe method demonstrates superiority in describing H-atom ADPs.
Article
Chemistry, Multidisciplinary
Bruno Landeros-Rivera, Julia Contreras-Garcia, Paulina M. Dominiak
Summary: The synergy between theory and experiment in X-ray wavefunction refinement (XWR) makes it a compelling technique for chemical physics, but its reliance on the quality of empirical and theoretical data is a weakness. The study found that refinement strategies and manipulation of input data can impact the physical properties obtained from XWR, with a proposed solution to the instability in the X-ray constrained wavefunction fitting (XCW) by using distinct constraints for each resolution interval.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Anna Agnieszka Hoser, Toms Rekis, Anders Ostergaard Madsen
Summary: This article focuses on the structure and relative stability of four pyrazinamide polymorphs. Experimental and computational methods are used to analyze and predict the stability order of the polymorphs as a function of temperature.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2022)
Article
Chemistry, Medicinal
Paulina Maria Rybicka, Marta Kulik, Michal Leszek Chodkiewicz, Paulina Maria Dominiak
Summary: The multipole model is a non-spherical method that accurately describes electron density. The MATTS database collects parameters for atom types in proteins, nucleic acids, and organic molecules. By clustering using topology and multipole parameters, it was found that the element of the central atom, the number of first neighbors, and planarity of the group have the biggest impact on multipole parameters. Similar spatial distribution of electron density reveals distinct and unique atom types. Improving the quality of existing types requires better parametrization and local coordinate systems. The future development of the MATTS database will provide a wider range of atom types for constructing the electron density of any molecule.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Kunal Kumar Jha, Barbara Gruza, Aleksandra Sypko, Prashant Kumar, Michal Leszek Chodkiewicz, Paulina Maria Dominiak
Summary: A fast and accurate operational model of electron density is crucial in many scientific disciplines. The MATTS2021 database provides a comprehensive coverage of atom types in various molecular structures and materials, allowing for accurate description and analysis.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Marta Kulik, Michal Leszek Chodkiewicz, Paulina Maria Dominiak
Summary: This study applies the transferable aspherical atom model (TAAM) in combination with the University at Buffalo Data Bank (UBDB) to calculate theoretical electrostatic potential maps for lysozyme and proteinase K. The results are compared with experimental maps from 3D electron diffraction (3D ED). The findings show that UBDB is capable of accurately reproducing the molecular electrostatic potential, outperforming the commonly used neutral spherical models. Additionally, the study highlights the potential of the computational method to aid in the interpretation of less resolved regions in cryo-electron microscopy density maps and facilitate the distinction between different ions/water molecules in the active sites of macromolecules in high-resolution structures, which is valuable for drug-design purposes.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Urszula Anna Budniak, Natalia Katarzyna Karolak, Marta Kulik, Krzysztof Mlynarczyk, Maria Wiktoria Gorna, Paulina Maria Dominiak
Summary: This study proposes a method called UBDB+EPMM for characterizing electrostatic interactions in biological systems. The method allows for qualitative and quantitative analysis of protein-RNA interactions, and also identifies the contribution of charge penetration to electrostatic interactions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Slawomir Antonii Bojarowski, Barbara Gruza, Damian Trzybinski, Radoslaw Kaminski, Anna Agnieszka Hoser, Prashant Kumar, Krzysztof Wozniak, Paulina Maria Dominiak
Summary: Pseudoatom databanks are collections of parameters used for crystal structure refinements and rapid electrostatic energy calculations. The databanks provide a more accurate Transferable Aspherical Atom Model (TAAM) compared to the Independent Atom Model. This study proposes a new model, the P-v kappa | P-lm kappa' model, which shows promising properties for both TAAM refinements and electrostatic energy estimations.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2022)
Article
Chemistry, Physical
Bruno Landeros-Rivera, David Ramirez-Palma, Fernando Cortes-Guzman, Paulina M. Dominiak, Julia Contreras-Garcia
Summary: In this study, the effects of different levels of HF exchange on the HAR of urea and oxalic acid dihydrate using hybrid density functionals are investigated. The influence of basis sets, methods, and cluster sizes is also examined. The results show that changing the amount of HF exchange mainly affects the refinement of H atoms in the HAR. Unlike pure quantum mechanical calculations, the best match with neutron diffraction reference values is not necessarily obtained with intermediate HF exchange mixtures in the HAR. Additionally, the X-H bond lengths increase proportionally to the HF exchange.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Kunal Kumar Jha, Florian Kleemiss, Michal Leszek Chodkiewicz, Paulina Maria Dominiak
Summary: Aspherical atom refinement is crucial for accurate structure models and analysis of various parameters. Different quantum crystallographic methods like HAR and TAAM have their advantages and limitations. NoSpherA2 has made it possible to overcome some limitations and improve refinement statistics. A hybrid refinement approach allows a combination of IAM, HAR, and TAAM in one structure refinement, reducing computational costs without compromising accuracy.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
Article
Biochemistry & Molecular Biology
Mohammed Hawash, Derar Al-Smadi, Anil Kumar, Barbara Olech, Paulina Maria Dominiak, Nidal Jaradat, Sarah Antari, Sarah Mohammed, Ala'a Nasasrh, Murad Abualhasan, Ahmed Musa, Shorooq Suboh, Irfan Capan, Mohammad Qneibi, Hiba Natsheh
Summary: In this study, benzodioxol carboxamide derivatives were synthesized and their potential as antidiabetic agents was investigated. Compounds IIa and IIc showed potent inhibition against alpha-amylase in vitro, with negligible effects on normal cells, indicating their safety. Compound IId exhibited significant activity against multiple cancer cell lines. In vivo experiments demonstrated that compound IIc effectively lowered blood glucose levels in mice. These findings highlight the potential of benzodioxol derivatives as candidates for the development of synthetic antidiabetic drugs.
Article
Chemistry, Multidisciplinary
Marcin Ziemniak, Sylwia Pawledzio, Anna Zawadzka-Kazmierczuk, Paulina M. Dominiak, Damian Trzybinski, Wiktor Kozminski, Rafal Zielinski, Izabela Fokt, Waldemar Priebe, Krzysztof Wozniak, Beata Pajak
Summary: The structural studies of two bromo-substituted derivatives of 2-deoxy-D-glucose revealed that bromine substitution has a significant impact on the crystal structure, leading to a layered supramolecular landscape containing hydrogen bonds involving the bromine atom. Periodic DFT calculations supported these findings, while NMR studies showed similarities in anomeric equilibria and pyranose ring puckering compared to 2-DG.
Article
Chemistry, Multidisciplinary
Anna A. Hoser, Marcin Sztylko, Damian Trzybinski, Anders O. Madsen
Summary: This study presents a novel framework for estimating the thermodynamic properties of molecular crystals, which shows good agreement with experimental data.
CHEMICAL COMMUNICATIONS
(2021)
