Article
Crystallography
Rene T. Boere
Summary: New structure determinations of CuCl2·2H2O and NiCl2·6H2O were conducted using 100 K X-Ray diffraction experiments with Mo Kα and Cu Kα radiation. The Hirshfeld atom refinements (HAR) were performed using combined density functional theory (ORCA) and non-spherical atomic scattering factor (NoSpherA2) computations with custom atom scattering factors based on accurately polarized atom electron densities. The refinements of water hydrogen atoms revealed longer O-H bond lengths compared to previous X-ray diffraction experiments, but were consistent with legacy neutron diffraction studies. Anisotropic displacement factors were utilized for the first time in these compounds. The outcomes of using different X-ray sources with the new HAR method were compared, and the precision of H-atom refinements was evaluated where possible.
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
Piotr A. Gunka, Anna Olejniczak, Samuele Fanetti, Roberto Bini, Ines E. Collings, Volodymyr Svitlyk, Kamil F. Dziubek
Summary: The high-pressure behavior of hexamethylenetetramine was studied using XRD and FTIR, revealing significant damping of molecular librations and atomic thermal motion at 4 GPa, and a first-order phase transition to a tetragonal structure at 12.5 GPa. This behavior only occurs in non-hydrostatic conditions and was modeled using DFT computations and Hirshfeld atom refinements.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Lorraine A. Malaspina, Alessandro Genoni, Simon Grabowsky
Summary: In quantum crystallography, software capable of both quantum-mechanical calculations and crystallographic refinements is essential, with Tonto being the only known program currently able to do so. The lamaGOET interface successfully integrates popular quantum-chemical software with Tonto's refinement capabilities, showcasing different styles of quantum-crystallographic refinements.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Chemistry, Physical
B. Pramodh, K. N. Chethan Prathap, M. K. Hema, Ismail Warad, N. K. Lokanath
Summary: Three novel thiophene derivatives containing benzenesulfonyl hydrazide were synthesized and characterized using various spectroscopic techniques. Intermolecular hydrogen bonds formed different supramolecular motifs, with dispersion energy being dominant in all compounds. The derivatives exhibited antibacterial activity against both Staphylococcus aureus and Escherichia coli.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Multidisciplinary
Paul Niklas Ruth, Nico Graw, Tobias Ernemann, Regine Herbst-Irmer, Dietmar Stalke
Summary: This paper demonstrates the application of indium K alpha radiation in independent-atom model refinement and approaches using aspherical atomic form factors in MetalJet source. The results vary greatly depending on the detector employed, with Eiger2 CdTe providing a solution to the energy contamination problem of MetalJet In radiation that Photon III detector cannot provide.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
Article
Chemistry, Multidisciplinary
Lorraine A. Malaspina, Alessandro Genoni, Dylan Jayatilaka, Michael J. Turner, Kunihisa Sugimoto, Eiji Nishibori, Simon Grabowsky
Summary: This article discusses the application of quantum crystallography methods in treating hydrogen bonds, using three different compound classes as test cases. It examines the differences in quantum-mechanical electron densities among the methods and how these variances affect the refinement results.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Chemistry, Multidisciplinary
Sylwia Pawledzio, Maura Malinska, Magdalena Woinska, Jakub Wojciechowski, Lorraine Andrade Malaspina, Florian Kleemiss, Simon Grabowsky, Krzysztof Wozniak
Summary: The study aims to validate relativistic Hirshfeld atom refinement for high-resolution X-ray diffraction datasets of an organo-gold compound, showing that relativistic effects have significant influence on the electron density of the gold atom in both core and bonding regions.
Article
Chemistry, Physical
Hemat M. Dardeer, Mohamed Y. Mahgoub, Joao Ferreira da Silva, Elghareeb E. Elboray
Summary: A set of new N-substituted chlorindylimides and a chlorendic acid sodium-coordination polymer were synthesized, with the crystal networks explored based on Hirshfeld surface analysis showing the involvement of chlorine atoms in at least 70% of the total intermolecular interactions. The predominance of Cl···Cl interactions over C-H···Cl interactions is due to the structural features of the incorporated imide, resulting in the formation of a sodium 1D-polymer.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Multidisciplinary
Michal Chodkiewicz, Sylwia Pawledzio, Magdalena Woinska, Krzysztof Wozniak
Summary: Hirshfeld atom refinement (HAR) is an effective method for obtaining accurate structural parameters for hydrogen atoms. However, it is computationally expensive. This study explores a fragmentation approach as a solution to this problem, significantly improving computation time for larger organic and metal-organic systems with minor differences in calculated structural parameters. Fragmentation also provides a solution for polymeric and disordered systems when applying HAR. The concept of fragmentation is related to the transferable aspherical atom model (TAAM), providing insight into improving TAAM. Hybrid approaches combining fragmentation and atomic density transfer were tested. An efficient handling of intermolecular interactions was introduced. The fragHAR approach improved efficiency in calculations. The study highlights the importance of load-balancing for lowering computational time.
Article
Chemistry, Multidisciplinary
Michal L. Chodkiewicz, Roman Gajda, Barbara Lavina, Sergey Tkachev, Vitali B. Prakapenka, Przemyslaw Dera, Krzysztof Wozniak
Summary: Water is essential for living organisms, and the structures of ice crystals have many unresolved problems. This study presents accurate crystal structures of H2O, D2O, and mixed ice VI using Hirshfeld atom refinement combined with X-ray diffraction. The results show that X-ray diffraction combined with HAR can compete with neutron diffraction in detailed studies of ice polymorphs.
Article
Chemistry, Multidisciplinary
Max L. Davidson, Simon Grabowsky, Dylan Jayatilaka
Summary: The paper reviews the X-ray constrained wavefunction (XCW) procedure and distinguishes between the two-center probability distribution model and the newer one-center probability distribution model. It introduces the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure and its efficient implementation. The paper also refines the definition of the related X-ray wavefunction refinement (XWR) method and reviews the work on the key halting problem for the XCW method.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2022)
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, Physical
Praveen B. Managutti, Sumitra N. Mangasuli, Shivanand S. Malaganvi
Summary: The synthesis, crystal structure, and electronic structure of newly synthesized coumarin-theophylline hybrids with high anti-TB activity were investigated using experiments and quantum chemical calculations. The compound was found to crystallize in the monoclinic system with space group P21/c, and it exhibited strong and weak intra-/inter-molecular hydrogen bonding for stabilization. The crystal structure was consistent with the optimized geometry calculated using density functional theory. The compounds showed significant in vitro anti-tuberculosis activity against Mycobacterium tuberculosis, making them potential candidates for anti-TB drugs.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Physical
Ligia R. Gomes, John N. Low, James L. Wardell
Summary: This study reports the crystal structures and intermolecular interactions of two new compounds. The compounds exhibit larger interplanar angles due to steric hindrance. The PIXEL calculations reveal that dispersion energy is the largest contributor to the total energy distribution in the crystal packing.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Karolina Stryjska, Izabela Korona-Glowniak, Lilianna Checinska, Joachim Kusz, Justyn Ochocki
Summary: The synthesis of two novel silver(I) complexes of miconazole with new counter ions was conducted, showing significant antimicrobial activity against Gram-positive bacteria and yeasts, surpassing silver sulfadiazine and silver salts. The complex containing the nitrate counter ion exhibited the highest antimicrobial activity, while all silver(I) complexes of miconazole demonstrated better inhibition of yeast growth compared to silver sulfadiazine, silver salts, and miconazole. Additionally, the synthesized complexes showed good or moderate activity against Gram-negative bacteria when compared to the free ligand.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Dominik Zyro, Lidia Radko, Agnieszka Sliwinska, Lilianna Checinska, Joachim Kusz, Izabela Korona-Glowniak, Agata Przekora, Michal Wojcik, Andrzej Posyniak, Justyn Ochocki
Summary: This study aimed to compare the chemical, cytotoxic and antimicrobial properties of metronidazole complexes with silver(I) nitrate and silver(I) sulfate to metronidazole and pure silver(I) salts. The results showed that silver(I) complexes present higher photo-stability, cytotoxicity, and antimicrobial activity in comparison to metronidazole and, to a certain extent, to silver(I) salts.
Article
Chemistry, Physical
Rumpa Pal, Dylan Jayatilaka, Eiji Nishibori
Summary: This study investigates the static structure factors and charge density of metallic aluminum through periodic calculations and comparisons with experimental data. The results reveal the importance of high-resolution structure factors in determining the detailed bonding description of metallic aluminum.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Max L. Davidson, Simon Grabowsky, Dylan Jayatilaka
Summary: The paper reviews the X-ray constrained wavefunction (XCW) procedure and distinguishes between the two-center probability distribution model and the newer one-center probability distribution model. It introduces the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure and its efficient implementation. The paper also refines the definition of the related X-ray wavefunction refinement (XWR) method and reviews the work on the key halting problem for the XCW method.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Max L. Davidson, Simon Grabowsky, Dylan Jayatilaka
Summary: The reproducibility of the Hirshfeld atom-based X-ray constrained wavefunction fitting (HA-XCW) procedure is tested and the information content of the fitted wavefunction is critically assessed. Fourteen different alpha-oxalic acid dihydrate data sets are used for this purpose, and the first joint fitting to 12 of these data sets is reported. The results show systematic features in the electron density obtained from all data sets, agreeing with higher level benchmark calculations, but also many other systematic features that disagree with the reference calculations.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Hanna Kaspiaruk, Lilianna Checinska
Summary: The crystal structures of miconazole and its solvatomorphs were compared, showing that solvent molecules influence the molecular conformation of miconazole. Dispersion forces were found to predominate over electrostatic forces.
ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Tomasz Pore, Stefano Racioppi, Gaston Garbarino, Wolfgang Morgenroth, Mohamed Mezouar
Summary: The structural evolution of cesium triiodide under high pressures has been studied using synchrotron single-crystal X-ray diffraction. A first-order phase transition from an orthorhombic to a trigonal system was observed above 1.24(3) GPa. This transition is accompanied by a significant reorganization of the polyiodide network from layered to three-dimensional architecture.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Aleksandra Felczak, Urszula Kalinowska-Lis, Joachim Kusz, Lilianna Checinska
Summary: The crystal structure of danofloxacin (DFX) as a zwitterionic dihydrate has been determined, and the stability of the crystal structure is ensured by hydrogen bonds. The zwitterionic molecules of DFX are packed in stacks, and a survey of the Cambridge Structural Database revealed that neutral molecules are preferred over zwitterions in the crystalline state of fluoroquinolones (FQs).
ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY
(2022)
Article
Crystallography
Prabhakar Priyanka, Bidarur K. Jayanna, Thayamma R. Divakara, Gejjalagere P. Suresha, Yeriyur B. Basavaraju, Hemmige S. Yathirajan, Sean R. Parkin, Lilianna Checinska
Summary: The crystal structures of three salts, including their ionic components, water molecules, and hydrogen bonding patterns, have been determined and compared. The results reveal the formation of infinite chains running parallel to the [100] direction through a combination of N-H···O and O-H···O hydrogen bonds. Additionally, the presence of C-H···O, C-H···π(arene), and O-H···O interactions leads to the propagation of these chains into di-periodic layers or tri-periodic networks in one of the salts.
Article
Physics, Multidisciplinary
Alexander G. Gavriliuk, Viktor V. Struzhkin, Anna G. Ivanova, Vitali B. Prakapenka, Anna A. Mironovich, Sergey N. Aksenov, Ivan A. Troyan, Wolfgang Morgenroth
Summary: The insulator-metal transition and collapse of spin and magnetism in NiO are important topics in the study of strong electronic correlations. This study reports an iso-structural transition in NiO accompanying the observed transition to the metallic state, providing resolution to experimental controversies and confirming recent theoretical models. The findings stimulate further efforts to understand this prototype Mott insulator.
COMMUNICATIONS PHYSICS
(2023)
Article
Crystallography
Holehundi J. Shankara Prasad, Devaraju, Subbaiah M. Murthy, Hanna Kaspiaruk, Hemmige S. Yathirajan, Sabine Foro, Lilianna Checinska
Summary: The synthesis and crystal structures of two molecular salts of 4-(4-nitrophenyl)piperazine with trifluoroacetate and trichloroacetate are reported and compared. The anions in both structures show partial positional disorder. The piperazine rings adopt a chair conformation in both structures, but the positions of the nitrophenyl group on the piperazine ring differ. The supramolecular assemblies in both structures are mono-periodic based on chain-of-rings motifs supported by aromatic pi-pi interactions. Hirshfeld surface analysis reveals the dominant contacts in the crystals.
ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Emanuel Hupf, Florian Kleemiss, Tobias Borrmann, Rumpa Pal, Joanna M. M. Krzeszczakowska, Magdalena Woinska, Dylan Jayatilaka, Alessandro Genoni, Simon Grabowsky
Summary: In X-ray constrained wavefunction (XCW) fitting, external information is incorporated into the isolated-molecule wavefunction to extract electron correlation and polarization effects accurately. This method is validated by comparing to theoretical reference calculations, and it is shown that fitting to single-crystal x-ray diffraction measurements can provide qualitatively similar results and separate the physical effects despite their inherent convolution in the experiment. The XCW fitting also has a significant impact on the exchange-correlation potentials, which could be used for method development in quantum chemistry, albeit with some remaining challenges.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Sean Li, Bjoern Bohman, Gavin R. Flematti, Dylan Jayatilaka
Summary: This study proposes a method for identifying the correct candidate formula of an unidentified natural product from its mass spectrum. The method involves scoring the plausibility of parent candidate formulae based on a parent subformula graph (PSG) and introduces the two-dimensional fragmentation plot (2DFP) for visualizing PSGs. The method reliably identifies the correct parent formula even when the mass information is ambiguous and can also identify the associated fragments.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Sean Li, Bjorn Bohman, Dylan Jayatilaka
Summary: This paper presents an algorithm to solve the compomer problem in mass spectrometry, which can generate all possible solutions efficiently and reduce memory requirements using heuristics.
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Dylan Jayatilaka, Amir Karton
Summary: Density functional theory is currently at its prime, but there are limitations in terms of occupied and unoccupied orbitals. Each rung of Jacob's Ladder includes multiple functionals and lacks a clear pathway for improvement. This article provides an overview of a new method for calculating the exchange-correlation hole and its potential for developing better functionals.
AUSTRALIAN JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Abu Talha Aqueel Ahmed, Sankar Sekar, Shubhangi S. Khadtare, Nurul Taufiqu Rochman, Bathula Chinna, Abu Saad Ansari
Summary: In this study, MnCo2S4 nanosheet catalyst was successfully synthesized and found to exhibit superior performance in hydrogen evolution. Compared to MnCo2S4, MnCo2S4 showed low overpotentials, moderate Tafel slope, and excellent sustainability. The outstanding performance can be attributed to the increased number of electrochemically active sites and enhanced electronic conductivity on the catalyst surface.
Article
Chemistry, Multidisciplinary
Victor V. Maltsev, Elena A. Volkova, Elizaveta V. Koporulina, Diana D. Mitina, Vladimir L. Kosorukov, Anna I. Jiliaeva, Daniil A. Naprasnikov, Konstantin N. Gorbachenya, Viktor E. Kisel
Summary: The phase relationships, crystal properties and luminescence kinetics of two complex systems were studied, including unit cell parameters, segregation coefficients of impurities, and lifetimes of energy levels.
Article
Chemistry, Multidisciplinary
Xiaoman Zhang, Wangwang Xu, W. J. Meng, Andrew C. Meng
Summary: This study successfully grew high-quality single crystal AlScN nanowires through ultra-high vacuum reactive sputtering technique and characterized their structure and properties. The nanowires exhibit significantly reduced mosaic spread and predominantly single ferroelectric domains, as well as a high piezoelectric constant.
Article
Chemistry, Multidisciplinary
Tom E. de Vries, Elias Vlieg, Rene de Gelder
Summary: Networks are important for describing relationships between people, roads between cities, reactions between chemicals, and other interactions. Bipartiteness, dividing the network into two groups, can facilitate the study of the network's structure. We have developed an algorithm that can find a near-optimal bipartisation within a reasonable time frame and used it to uncover the hidden structure of the CSD cocrystal network.
Article
Chemistry, Multidisciplinary
Chuchu Han, Jing Yang, Xin Zhang, Aisen Li, Jiang Peng
Summary: An elastic crystal based on a photo-reactive acylhydrazone derivative is reported, which exhibits reversible bending behavior under UV irradiation and heating. The crystal undergoes reversible E<->Z isomerization under light and heating conditions. The crystal demonstrates excellent elastic properties and the bending can be controlled to control the output direction of red light.
Article
Chemistry, Multidisciplinary
Lingfeng Zhang, Yu Wang, Yefeng Wang, Shuai Liu, Na Zhang, Mingmin Yang, Haixia Ma, Zhaoqi Guo
Summary: This study designs and synthesizes a series of high-energy salts compounds without heavy metal ions and azide groups. The molecular structures and stability of the compounds are confirmed through single-crystal X-ray diffraction and intermolecular interaction analysis. Furthermore, the thermal stability, energetic properties, and electrical initiation properties of the compounds are investigated, suggesting their potential as primary explosives.