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
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
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, 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
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, Inorganic & Nuclear
Jason D. Masuda, Leila Mokhtabad Amrei, Rene T. Boere
Summary: This paper presents definitive structural evidence for N,P(III)-monophosphaamidines in both P=C and N=C isomeric forms using new syntheses, single-crystal X-ray diffraction (SC-XRD), solid-state NMR and FTIR methods. Computational investigations using DFT methods were also conducted to understand the tautomeric structure preferences. The study suggests that phospha(III)amidines and -guanidines can be treated as new types of functional groups distinct from their organic analogues.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2023)
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
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
Chemistry, Multidisciplinary
Yoshio Yano, Toshikazu Ono, Takashi Ohhara, Yoshio Hisaeda
Summary: The relationship between the optical properties and degree of protonation in acid-base complexes was studied using X-ray diffraction, neutron diffraction, and theoretical calculations. The presence or absence of guests in the acid-base complexes affected the emission color by altering the hydrogen bond strength. The accurate N...H distances between the pyridyl moiety and the carboxy group varied between guest-free and guest-inclusion crystals at different temperatures, contributing to a better understanding of photofunction and proton dynamics in acid-base complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Sylwia Pawledzio, Maura Malinska, Florian Kleemiss, Simon Grabowsky, Krzysztof Wozniak
Summary: This article presents the details of validating disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound. It discusses the impact of refining disorder on HAR results through an analysis of dynamic structure factor differences. The article also compares the role of disorder modelling with the effect of treating hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom.
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, 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
Materials Science, Multidisciplinary
K. Sujatha, S. Israel, C. Anzline, R. A. J. R. Sheeba
Summary: Experimental charge density analysis of two isostructural transition metal difluorides, CoF2 and NiF2, reveals that the difluoride of nickel has more covalent nature compared to the difluoride of cobalt. Additionally, a comparative study on fluorine bonding in low valent binary fluorides shows an increase in covalent nature as the oxidation state of metals ascends.
MATERIALS CHEMISTRY AND PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Giulia Novelli, Charles J. McMonagle, Florian Kleemiss, Michael Probert, Horst Puschmann, Simon Grabowsky, Helen E. Maynard-Casely, Garry J. McIntyre, Simon Parsons
Summary: The crystal structure of the monoclinic polymorph of l-histidine has been determined for the first time using single-crystal neutron diffraction, while the orthorhombic polymorph has been reinvestigated to improve experimental precision and accuracy. The study reveals differences in hydrogen bond energy and geometry between the two polymorphs, with molecular packing interpreted by intermolecular interaction energies calculated using the Pixel method. The precision and accuracy of the new Hirshfeld atom refinement method implemented in NoSpherA2 were probed, showing good agreement with neutron structural models.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Monika Wanat, Maura Malinska, Matthias J. Gutmann, Richard Cooper, Krzysztof Wozniak
Summary: The article introduces the use of the Independent Atom Model (IAM) and the multipole model of electron density in electron density analysis, comparing their advantages and disadvantages. By refining Mo K alpha and Cu K alpha data of different model compounds, the study found that the application of new methods has a more significant influence on the results for Cu K alpha data.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Georg Niggemeyer, Anastasia Knyazeva, Raphael Gasper, Dale Corkery, Pia Bodenbinder, Julian J. Holstein, Sonja Sievers, Yao-Wen Wu, Herbert Waldmann
Summary: Design and synthesis of pseudo-natural products through recombination of natural product fragments enables the discovery of novel biologically relevant chemical matter. In this study, the combination of this principle with macrocycle formation was described, leading to the efficient synthesis of 163 macrocyclic pseudo-natural products. Biological investigation revealed their potent inducers of autophagy-related processes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Bin Chen, Julian J. Holstein, Andre Platzek, Laura Schneider, Kai Wu, Guido H. Clever
Summary: Recently developed self-assembly strategies allow for a rational reduction in the symmetry of metallosupramolecular architectures. In addition, it is now possible to combine multiple ligand types without creating compound mixtures. Coordination Sphere Engineering (CSE), which utilizes secondary repulsive or attractive interactions near the metal nodes, is an effective approach to achieve non-statistical heteroleptic assembly. This study introduces a new subtype of CSE that achieves trans-[Pd2L2L2'] and [Pd2L3L'] cages by balancing hydrogen bonding and repulsive interactions between ligands carrying quinoline and 1,8-naphthyridine donors, with the assistance of templation of encapsulated fullerenes. The formation, structure, and fullerene binding ability of these metallosupramolecular hosts were investigated using NMR, mass spectrometry, and single crystal X-ray diffraction.
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
Andre Platzek, Selina Juber, Cem Yurtseven, Shota Hasegawa, Laura Schneider, Christoph Drechsler, Kristina E. Ebbert, Robin Rudolf, Qian-Qian Yan, Julian J. Holstein, Lars Schafer, Guido H. Clever
Summary: A series of heteroleptic [Pd(2)A(2)B(2)] coordination cages were self-assembled from a library of shape complementary ligands, which selectively bind phosphate diesters. Molecular dynamics simulations were conducted to understand the mechanistic relationships behind guest affinities.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
David Van Craen, Malavika G. Kalarikkal, Julian J. Holstein
Summary: The field of anion recognition chemistry relies on either the formation of covalent bonds resulting in organic and often neutral host species or metal-driven self-assembly for the formation of charged receptors. However, the combination of these two approaches to design charge-neutral metal-assembled stable anion receptors is lacking. In this study, a fluorescent and uncharged double-stranded hydroxyquinoline-based zinc(II) helicate is presented, which can bind environmentally relevant dicarboxylate anions with high fidelity in dimethyl sulfoxide (DMSO) at nanomolar concentrations. These dianions are pinned between zinc(II) centers with binding constants up to 145,000,000 M-1. The presented investigation exemplifies a pathway to bridge the two design approaches and combine their strength in one structural motif as an efficient anion receptor.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Witold M. Bloch, Shinnosuke Horiuchi, Julian J. Holstein, Christoph Drechsler, Axel Wuttke, Wolf Hiller, Ricardo A. Mata, Guido H. Clever
Summary: Helicity is an important structural motif in biological systems that contributes to molecular recognition in DNA. However, the relationship between helicity and guest encapsulation in artificial supramolecular hosts is not well understood. This study explores a coiled-up Pd2L4 metallohelicate and its tight anion binding capability, demonstrating that the coiled-up cage has an oblate/prolate cavity expansion that allows for strong host-guest interactions, confirmed by various analytical techniques.
Article
Chemistry, Multidisciplinary
Justus Reitz, Patrick W. Antoni, Julian J. Holstein, Max M. Hansmann
Summary: Recently, stable diazoalkenes have gained attention in organic chemistry as a new substance class. A general synthetic approach using a Regitz-type diazo transfer with azides is established, which allows for the synthesis of pyridine diazoalkenes. This approach is applicable to weakly polarized olefins as well. The properties of these pyridine-derived diazoalkenes are distinct from previously reported classes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(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
Irene Regeni, Rituparno Chowdhury, Kai Terlinden, Shinnosuke Horiuchi, Julian J. J. Holstein, Sascha Feldmann, Guido H. H. Clever
Summary: This article introduces a strategy to engineer the stacking of diketopyrrolopyrrole (DPP) dyes based on non-statistical metallosupramolecular self-assembly. Different discrete assemblies can be formed by adding Pd(II) to the DPP backbone equipped with nitrogen-based donors, distinguished by the number of π-stacked chromophores. We obtained and systematically investigated a Pd3L6 three-ring, a heteroleptic Pd2L2L’2 ravel composed of two crossing DPPs (flanked by two carbazoles), and two unprecedented self-penetrated motifs (a Pd2L3 triple and a Pd2L4 quadruple stack). With increasing counts of stacked chromophores, UV/Vis absorptions red-shift and emission intensities decrease, except for compound Pd2L2L’2, which has an exceptional photoluminescence quantum yield of 51% explainable by an intra-assembly FRET process. The modular design and synthesis of soluble multi-chromophore building blocks offer potential for the preparation of nanodevices and materials with applications in sensing, photo-redox catalysis, and optics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(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, Organic
Sudhakar Ganta, Jan-Hendrik Borter, Christoph Drechsler, Julian J. Holstein, Dirk Schwarzer, Guido H. Clever
Summary: A [Pd2L4] coordination cage, consisting of electron-rich phenothiazine-based ligands and encapsulating an electron-deficient anthraquinone-based disulfonate guest, has been reported. Transient absorption spectroscopy reveals photoinduced electron transfer from the host's chromophores to the guest, as indicated by characteristic spectral features. The host-guest complex was characterized using various techniques, and spectroelectrochemical experiments and DFT calculations support the proposed light-induced charge separation.
ORGANIC CHEMISTRY FRONTIERS
(2022)
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)