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Tikhonov DS. Regularized weighted sine least-squares spectral analysis for gas electron diffraction data. J Chem Phys 2023; 159:174101. [PMID: 37909450 DOI: 10.1063/5.0168417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Here, we present a new approach for obtaining radial distribution functions (RDF) from the electron diffraction data using a regularized weighted sine least-squares spectral analysis. It allows for explicitly transferring the measured experimental uncertainties in the reduced molecular scattering function to the produced RDF. We provide a numerical demonstration, discuss the uncertainties and correlations in the RDFs, and suggest a regularization parameter choice criterion. The approach is also applicable for other diffraction data, e.g., for x-ray or neutron diffraction of liquid samples.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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2
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Tikhonov DS, Vishnevskiy YV. Describing nuclear quantum effects in vibrational properties using molecular dynamics with Wigner sampling. Phys Chem Chem Phys 2023. [PMID: 37401424 DOI: 10.1039/d3cp01007d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
In this work we discuss the generally applicable Wigner sampling and introduce a new, simplified Wigner sampling method, for computationally effective modeling of molecular properties containing nuclear quantum effects and vibrational anharmonicity. For various molecular systems test calculations of (a) vibrationally averaged rotational constants, (b) vibrational IR spectra and (c) photoelectron spectra have been performed. The performance of Wigner sampling has been assessed by comparing with experimental data and with results of other theoretical models, including harmonic and VPT2 approximations. The developed simplified Wigner sampling method shows advantages in application to large and flexible molecules.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Yury V Vishnevskiy
- 2Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany.
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3
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Equilibrium molecular structure and intramolecular interactions of picolinic acid hydrazide. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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4
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Equilibrium molecular structure of nicotinic acid hydrazide: joint study by means of gas electron diffraction and quantum chemistry. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kolesnikova IN, Rykov AN, Shishkov IF. Conformation and equilibrium molecular structure of isoniazid in the gas phase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Weddeling JH, Vishnevskiy YV, Neumann B, Stammler HG, Mitzel NW. Inter- and Intramolecular Aryl-Aryl Interactions in Partially Fluorinated Ethylenedioxy-bridged Bisarenes*. Chemistry 2020; 26:16111-16121. [PMID: 32845047 PMCID: PMC7756350 DOI: 10.1002/chem.202003259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 01/10/2023]
Abstract
Several ethylenedioxy‐bridged bisarenes with a variety of type and number of aryl groups were synthesized to study non‐covalent dispersion‐driven inter‐ and intramolecular aryl–aryl interactions in the solid state and gas phase. Intramolecular interactions are preferably found in the gas phase. DFT calculations with and without dispersion correction show larger interacting aromatic groups increase the stabilization energy of folded conformers and decrease the intermolecular centroid–centroid distance. Single‐molecule structures generally adopt folded conformations with short intramolecular aryl–aryl contacts. Gas electron diffraction experiments were performed exemplarily for 1‐(pentafluorophenoxy)‐2‐(phenoxy)ethane. A new procedure for structure refinement was developed to deal with the conformational complexity of such molecules. The results are an experimental confirmation of the existence of folded conformations of this molecule with short intramolecular aryl–aryl distances in the gas phase. Solid‐state structures are dominated by stretched structures without intramolecular aryl–aryl interactions but interactions with neighboring molecules.
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Affiliation(s)
- Jan-Henrik Weddeling
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yury V Vishnevskiy
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Beate Neumann
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hans-Georg Stammler
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert W Mitzel
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
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8
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Otlyotov AA, Girichev GV, Rykov AN, Glodde T, Vishnevskiy YV. Molecular Structure of Pyrazinamide: A Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories. J Phys Chem A 2020; 124:5204-5211. [DOI: 10.1021/acs.jpca.0c03531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arseniy A. Otlyotov
- Ivanovo State University of Chemistry and Technology, Department of Physics, Sheremetievskiy Avenue, 7, 153000 Ivanovo, Russian Federation
| | - Georgiy V. Girichev
- Ivanovo State University of Chemistry and Technology, Department of Physics, Sheremetievskiy Avenue, 7, 153000 Ivanovo, Russian Federation
| | - Anatolii N. Rykov
- M. V. Lomonosov Moscow State University, Department of Chemistry, 119992 GSP-2, Vorob’evy gory 1, Building 3, Moscow, Russian Federation
| | - Timo Glodde
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Yury V. Vishnevskiy
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
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9
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Fatima M, Maué D, Pérez C, Tikhonov DS, Bernhard D, Stamm A, Medcraft C, Gerhards M, Schnell M. Structures and internal dynamics of diphenylether and its aggregates with water. Phys Chem Chem Phys 2020; 22:27966-27978. [DOI: 10.1039/d0cp04104a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report on a detailed multi-spectroscopic analysis of the structures and internal dynamics of diphenylether and its aggregates with up to three water molecules by employing molecular beam experiments.
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Affiliation(s)
- M. Fatima
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Pérez
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. S. Tikhonov
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Bernhard
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Medcraft
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Schnell
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
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10
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Internal rotation and intramolecular hydrogen bonding in thiosalicylamide: gas phase electron diffraction study supported by quantum chemical calculations. Struct Chem 2019. [DOI: 10.1007/s11224-019-01369-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Baše T, Holub J, Fanfrlík J, Hnyk D, Lane PD, Wann DA, Vishnevskiy YV, Tikhonov D, Reuter CG, Mitzel NW. Icosahedral Carbaboranes with Peripheral Hydrogen-Chalcogenide Groups: Structures from Gas Electron Diffraction and Chemical Shielding in Solution. Chemistry 2019; 25:2313-2321. [DOI: 10.1002/chem.201805145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/27/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Tomáš Baše
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of, the Czech Academy of Sciences; 166 10 Praha 6 Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Paul D. Lane
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
- Present address: School of Engineering and Physical Sciences; Heriot-Watt University; Edinburgh EH14 4AS UK
| | - Derek A. Wann
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
| | - Yury V. Vishnevskiy
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Denis Tikhonov
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
- Present addresses: Department of Physical Chemistry; M. V. Lomonosov Moscow State University; GSP-1, 1-3 Leninskiye Gory 119991 Moscow Russian Federation
- FS-SMP Deutsches Elektronen-Synchrotron (DESY); Notkestrasse 85, Building 25f, Room 353 22607 Hamburg Germany
| | - Christian G. Reuter
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert W. Mitzel
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
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Tikhonov DS, Sharapa DI, Otlyotov AA, Solyankin PM, Rykov AN, Shkurinov AP, Grikina OE, Khaikin LS. Nitroxoline Molecule: Planar or Not? A Story of Battle between π–π Conjugation and Interatomic Repulsion. J Phys Chem A 2018; 122:1691-1701. [DOI: 10.1021/acs.jpca.7b11364] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Denis S. Tikhonov
- Department of Physical
Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3
Leninskie Gory, 119991 Moscow, Russian Federation
| | - Dmitry I. Sharapa
- Lehrstuhl
für Physikalische und Theoretische Chemie, Friedrich-Alexander-Universität Erlangen−Nürnberg, Egerlandstraße 3, 91058 Erlangen, Germany
| | - Arseniy A. Otlyotov
- Ivanovo State University of Chemistry and Technology, Ivanovo 153000, Russia
| | - Peter M. Solyankin
- Department of Physics and International
Laser Center, Lomonosov Moscow State University, GSP-1, 1-62 Leninskie Gory, Moscow 119992, Russia
- Institute on Laser and Information Technologies of the Russian Academy of Sciences, Branch of the FSRC “Crystallography and Photonics” RAS, Svyatoozerskaya 1, 140700 Shatura, Moscow Region, Russia
| | - Anatolii N. Rykov
- Department of Physical
Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3
Leninskie Gory, 119991 Moscow, Russian Federation
| | - Alexander P. Shkurinov
- Department of Physics and International
Laser Center, Lomonosov Moscow State University, GSP-1, 1-62 Leninskie Gory, Moscow 119992, Russia
- Institute on Laser and Information Technologies of the Russian Academy of Sciences, Branch of the FSRC “Crystallography and Photonics” RAS, Svyatoozerskaya 1, 140700 Shatura, Moscow Region, Russia
| | - Olga E. Grikina
- Department of Physical
Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3
Leninskie Gory, 119991 Moscow, Russian Federation
| | - Leonid S. Khaikin
- Department of Physical
Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3
Leninskie Gory, 119991 Moscow, Russian Federation
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Tikhonov DS, Sharapa DI, Schwabedissen J, Rybkin VV. Application of classical simulations for the computation of vibrational properties of free molecules. Phys Chem Chem Phys 2018; 18:28325-28338. [PMID: 27722605 DOI: 10.1039/c6cp05849c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.
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Affiliation(s)
- Denis S Tikhonov
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany. and M. V. Lomonosov Moscow State University, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia
| | - Dmitry I Sharapa
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Jan Schwabedissen
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany.
| | - Vladimir V Rybkin
- ETH Zurich, Department of Materials, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland.
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Fokin AA, Zhuk TS, Blomeyer S, Pérez C, Chernish LV, Pashenko AE, Antony J, Vishnevskiy YV, Berger RJF, Grimme S, Logemann C, Schnell M, Mitzel NW, Schreiner PR. Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers. J Am Chem Soc 2017; 139:16696-16707. [PMID: 29037036 DOI: 10.1021/jacs.7b07884] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The covalent diamantyl (C28H38) and oxadiamantyl (C26H34O2) dimers are stabilized by London dispersion attractions between the dimer moieties. Their solid-state and gas-phase structures were studied using a multitechnique approach, including single-crystal X-ray diffraction (XRD), gas-phase electron diffraction (GED), a combined GED/microwave (MW) spectroscopy study, and quantum chemical calculations. The inclusion of medium-range electron correlation as well as the London dispersion energy in density functional theory is essential to reproduce the experimental geometries. The conformational dynamics computed for C26H34O2 agree well with solution NMR data and help in the assignment of the gas-phase MW data to individual diastereomers. Both in the solid state and the gas phase the central C-C bond is of similar length for the diamantyl [XRD, 1.642(2) Å; GED, 1.630(5) Å] and the oxadiamantyl dimers [XRD, 1.643(1) Å; GED, 1.632(9) Å; GED+MW, 1.632(5) Å], despite the presence of two oxygen atoms. Out of a larger series of quantum chemical computations, the best match with the experimental reference data is achieved with the PBEh-3c, PBE0-D3, PBE0, B3PW91-D3, and M06-2X approaches. This is the first gas-phase confirmation that the markedly elongated C-C bond is an intrinsic feature of the molecule and that crystal packing effects have only a minor influence.
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Affiliation(s)
- Andrey A Fokin
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine.,Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Tatyana S Zhuk
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Sebastian Blomeyer
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Cristóbal Pérez
- Max-Planck-Institut für Struktur und Dynamik der Materie , Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Lesya V Chernish
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Alexander E Pashenko
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Jens Antony
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Yury V Vishnevskiy
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Raphael J F Berger
- Materialchemie, Paris-Lodron Universität Salzburg , Hellbrunner Str. 34, A-5020 Salzburg, Austria
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Christian Logemann
- Institute of Inorganic and Analytical Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Melanie Schnell
- Max-Planck-Institut für Struktur und Dynamik der Materie , Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Norbert W Mitzel
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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Sandwisch JW, Holmes J, Nibler JW, Hedberg K. Improved methods and calibration technique in gas-phase electron-diffraction experiments: Use of nitrogen as a wavelength standard. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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