1
|
Pinto CB, Dos Santos LHR, Rodrigues BL. Experimental charge density and topological analysis of tetraaquabis(hydrogenmaleato)nickel(II): a comparison with Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:281-295. [PMID: 37402161 DOI: 10.1107/s2052520623004377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/20/2023] [Indexed: 07/06/2023]
Abstract
Experimental charge density analysis is conducted on the coordination compound tetraaquabis(hydrogenmaleato)nickel(II), which exhibits a short intramolecular hydrogen bond. Through topological analysis, the nature of Ni-O bonds is concluded to be intermediate between ionic and covalent, but mainly presenting an ionic character, while the short hydrogen bond is classified as covalent in nature. The compound was also analysed after Hirshfeld atom refinement performed using NoSpherA2. A topological analysis was conducted on the molecular wavefunction and the results are compared with those obtained from experiment. In general, there is good agreement between the refinements, and the chemical bonds involving H atoms are in better agreement with what is expected from neutron data after HAR than they are after multipole refinement.
Collapse
Affiliation(s)
- Camila B Pinto
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Leonardo H R Dos Santos
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Bernardo L Rodrigues
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| |
Collapse
|
2
|
Genoni A. Elucidating the nature of chemical bonds in a coordination compound through quantum crystallographic techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:253-254. [PMID: 37561073 DOI: 10.1107/s2052520623006364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
Investigations simultaneously involving multiple techniques of quantum crystallography could be very useful to prove the consistency of obtained results or to highlight different facets of the same scientific phenomenon or problem. Pinto et al. [Acta Cryst. (2023), B79, 282-296] exploit three different quantum crystallographic techniques (Hansen & Coppens multipole model refinement, QTAIM analysis of the electron density, and Hirshfeld atom refinement) to characterize the nature of chemical bonds and of intra/intermolecular interactions in an organometallic compound.
Collapse
Affiliation(s)
- Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57070, France
| |
Collapse
|
3
|
Song Z, Liu X, Ochani A, Shen S, Li Q, Sun Y, Ruggiero MT. Low-frequency vibrational spectroscopy: a new tool for revealing crystalline magnetic structures in iron phosphate crystals. Phys Chem Chem Phys 2021; 23:22241-22245. [PMID: 34610061 DOI: 10.1039/d1cp03424c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, the strong-dependence of low-frequency (terahertz) vibrational dynamics on weak and long-range forces in crystals is leveraged to determine the bulk magnetic configuration of iron phosphate - a promising material for cathodes in lithium ion batteries. We demonstrate that terahertz time-domain spectroscopy - coupled with quantum mechanical simulations - can discern between various spin configurations in FePO4. Furthermore, the results of this work unambiguously show that the well-accepted space group symmetry for FePO4 is incorrect, and the low-frequency spectroscopic measurements provide a clearer picture of the correct structure over the gold-standard of X-ray diffraction. This work opens the door for characterizing, predicting, and interpreting crystalline magnetic ordering using low-frequency vibrational spectroscopy.
Collapse
Affiliation(s)
- Zihui Song
- Department of Chemistry, 82 University Place, University of Vermont, Burlington, VT, 05405, USA.
| | - Xudong Liu
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Anish Ochani
- Department of Chemistry, SUNY College at Old Westbury, Old Westbury, NY 11568, USA
| | - Suling Shen
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Qiqi Li
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yiwen Sun
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Michael T Ruggiero
- Department of Chemistry, 82 University Place, University of Vermont, Burlington, VT, 05405, USA.
| |
Collapse
|
4
|
Banks PA, Burgess L, Ruggiero MT. The necessity of periodic boundary conditions for the accurate calculation of crystalline terahertz spectra. Phys Chem Chem Phys 2021; 23:20038-20051. [PMID: 34518858 DOI: 10.1039/d1cp02496e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Terahertz vibrational spectroscopy has emerged as a powerful spectroscopic technique, providing valuable information regarding long-range interactions - and associated collective dynamics - occurring in solids. However, the terahertz sciences are relatively nascent, and there have been significant advances over the last several decades that have profoundly influenced the interpretation and assignment of experimental terahertz spectra. Specifically, because there do not exist any functional group or material-specific terahertz transitions, it is not possible to interpret experimental spectra without additional analysis, specifically, computational simulations. Over the years simulations utilizing periodic boundary conditions have proven to be most successful for reproducing experimental terahertz dynamics, due to the ability of the calculations to accurately take long-range forces into account. On the other hand, there are numerous reports in the literature that utilize gas phase cluster geometries, to varying levels of apparent success. This perspective will provide a concise introduction into the terahertz sciences, specifically terahertz spectroscopy, followed by an evaluation of gas phase and periodic simulations for the assignment of crystalline terahertz spectra, highlighting potential pitfalls and good practice for future endeavors.
Collapse
Affiliation(s)
- Peter A Banks
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA.
| | - Luke Burgess
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA.
| | - Michael T Ruggiero
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA.
| |
Collapse
|
5
|
Fingerprint characterization of M-EDTA complexes and iron compounds using terahertz time-domain spectroscopy. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
6
|
Sergienko VS, Koksharova TV, Surazhskaya MD, Mandzii TV, Churakov AV. Synthesis, Crystal Structure, and Molecular Structure of Maleate Tris(Benzohydrazide) Cobalt(II) Tetrahydrate [Co(L1)3](Mal) · 4H2O and Maleate Tris(Phenylacethydrazide) Nikel(II) Monohydrate [Ni(L2)3](Mal) · H2O. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619110172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Li Q, Zaczek AJ, Korter TM, Zeitler JA, Ruggiero MT. Methyl-rotation dynamics in metal–organic frameworks probed with terahertz spectroscopy. Chem Commun (Camb) 2018; 54:5776-5779. [DOI: 10.1039/c8cc02650e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In ZIF-8 and its cobalt analogue ZIF-67, the imidazolate methyl-groups, which point directly into the void space, have been shown to freely rotate – even down to cryogenic temperatures.
Collapse
Affiliation(s)
- Qi Li
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Adam J. Zaczek
- Department of Chemistry, Syracuse University
- 1-014 Center for Science and Technology
- Syracuse
- USA
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University
- 1-014 Center for Science and Technology
- Syracuse
- USA
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
- Department of Chemistry
| |
Collapse
|
8
|
Ruggiero MT, Sibik J, Erba A, Zeitler JA, Korter TM. Quantification of cation–anion interactions in crystalline monopotassium and monosodium glutamate salts. Phys Chem Chem Phys 2017; 19:28647-28652. [DOI: 10.1039/c7cp05544g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific anion–cation orbital interactions lead to the large structural and spectral differences observed in crystalline monosodium and monopotassium glutamates.
Collapse
Affiliation(s)
- Michael T. Ruggiero
- Department of Chemistry
- Syracuse University
- 1-104 Center for Science and Technology
- Syracuse
- USA
| | - Juraj Sibik
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Alessandro Erba
- Dipartimento di Chimica and Centre of Excellence Nanostructured Interfaces and Surfaces, Universita di Torino
- Torino
- Italy
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Timothy M. Korter
- Department of Chemistry
- Syracuse University
- 1-104 Center for Science and Technology
- Syracuse
- USA
| |
Collapse
|
9
|
Ruggiero MT, Zeitler JA. Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations. J Phys Chem B 2016; 120:11733-11739. [PMID: 27766874 DOI: 10.1021/acs.jpcb.6b10248] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.
Collapse
Affiliation(s)
- Michael T Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - J Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| |
Collapse
|
10
|
Ruggiero MT, Sibik J, Zeitler JA, Korter TM. Examination of l-Glutamic Acid Polymorphs by Solid-State Density Functional Theory and Terahertz Spectroscopy. J Phys Chem A 2016; 120:7490-5. [PMID: 27588684 DOI: 10.1021/acs.jpca.6b05702] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of l-glutamic acid to crystallize in two different forms has long been the subject of study due to its commercial importance. While a solvent-mediated phase transformation between the α and β polymorphs is the prevailing theory, recent reports indicate a thermal solid-solid transformation between the two may be possible. However, determining accurate thermodynamic stabilities of these crystals has been challenging. Here new low-temperature single-crystal X-ray diffraction data coupled to solid-state density functional theory simulations have enabled a detailed description to be achieved for the energetic parameters governing the stabilization of the two l-glutamic acid solids. The temperature-dependent Gibbs free-energy curves show that α-glutamic acid is the preferred form at low temperatures (<222 K) and the β form is most stable at ambient temperatures. Terahertz time-domain spectroscopy was utilized to evaluate the quality of the intermolecular force modeling as well as to provide characteristic low-frequency spectral data that can be used for quantification of polymorph mixtures or crystal growth monitoring.
Collapse
Affiliation(s)
- Michael T Ruggiero
- Department of Chemistry, Syracuse University , 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States
| | - Juraj Sibik
- Department of Chemical Engineering and Biotechnology, University of Cambridge , New Museums Site, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - J Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge , New Museums Site, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - Timothy M Korter
- Department of Chemistry, Syracuse University , 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States
| |
Collapse
|