1
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Masoumifeshani E, Korona T. Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules. J Comput Chem 2024. [PMID: 38946399 DOI: 10.1002/jcc.27429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.
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Affiliation(s)
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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2
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Pichierri F. Comment on “Revealing the new structure of B8N8 nanocage and comparison of hydrogen storage capacity” [Chem. Phys. 559 (2022) 111540]. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Saroj A, Venkatnarayan R, Mishra BK, Panda AN, Narayanasami S. Improved Estimates of Host‐Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations. Chemphyschem 2022; 23:e202200413. [DOI: 10.1002/cphc.202200413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/18/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Arti Saroj
- IIT BHU: Indian Institute of Technology BHU Varanasi Chemistry 221005 Varanasi INDIA
| | | | | | - Aditya N. Panda
- IIT Guwahati: Indian Institute of Technology Guwahati Chemistry 781039 INDIA
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4
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Jaworski A, Hedin N. Local energy decomposition analysis and molecular properties of encapsulated methane in fullerene (CH 4@C 60). Phys Chem Chem Phys 2021; 23:21554-21567. [PMID: 34550137 DOI: 10.1039/d1cp02333k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane has been successfully encapsulated within cages of C60 fullerene, which is an appropriate model system to study confinement effects. Its chemistry and physics are also relevant for theoretical model descriptions. Here we provide insights into intermolecular interactions and predicted spectroscopic responses of the CH4@C60 complex and compared them with results from other methods and with data from the literature. Local energy decomposition analysis (LED) within the domain-based local pair natural orbital coupled cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) framework was used, and an efficient protocol for studies of endohedral complexes of fullerenes is proposed. This approach allowed us to assess energies in relation to electronic and geometric preparation, electrostatics, exchange, and London dispersion for the CH4@C60 endohedral complex. The calculated stabilization energy of CH4 inside the C60 fullerene was -13.5 kcal mol-1 and its magnitude was significantly larger than the latent heat of evaporation of CH4. Evaluation of vibrational frequencies and polarizabilities of the CH4@C60 complex revealed that the infrared (IR) and Raman bands of the endohedral CH4 were essentially "silent" due to the dielectric screening effect of C60, which acted as a molecular Faraday cage. Absorption spectra in the UV-vis domain and ionization potentials of C60 and CH4@C60 were predicted. They were almost identical. The calculated 1H/13C NMR shifts and spin-spin coupling constants were in very good agreement with experimental data. In addition, reference DLPNO-CCSD(T) interaction energies for complexes with noble gases (Ng@C60; Ng = He, Ne, Ar, Kr) were calculated. The values were compared with those derived from supramolecular MP2/SCS-MP2 calculations and estimates with London-type formulas by Pyykkö and coworkers [Phys. Chem. Chem. Phys., 2010, 12, 6187-6203], and with values derived from DFT-based symmetry-adapted perturbation theory (DFT-SAPT) by Hesselmann & Korona [Phys. Chem. Chem. Phys., 2011, 13, 732-743]. Selected points at the potential energy surface of the endohedral He2@C60 trimer were considered. In contrast to previous theoretical attempts with the DFT/MP2/SCS-MP2/DFT-SAPT methods, our calculations at the DLPNO-CCSD(T) level of theory predicted the He2@C60 trimer to be thermodynamically stable, which is in agreement with experimental observations.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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5
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Yifru A, Dare G, Demissie TB, Mehretie S, Admassie S. Cheap and sensitive polymer/bismuth film modified electrode for simultaneous determination of Pb(II) and Cd(II) ions. Heliyon 2021; 7:e08215. [PMID: 34926845 PMCID: PMC8648549 DOI: 10.1016/j.heliyon.2021.e08215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/24/2021] [Accepted: 10/15/2021] [Indexed: 10/31/2022] Open
Abstract
Different aminonaphetalenesulphonic acid derivatives like 5-aminonaphthalene-1-sulphonic acid (5AN1SA), 2-aminonaphthalene-1-sulphonic acid (2AN1SA), 8-aminonaphthalene-2-sulphonic acid (8AN2SA) and 4-amino-3-hydroxynaphthalene-1-sulphonic acid (4A3HN1SA) were used to construct polymer/bismuth film modified electrode for simultaneous determination of Pb(II) and Cd(II) ions with the aim of developing a cheaper and sensitive electrode that could possibly replace Nafion. Among the different modified electrodes, poly (8AN2SA)/bismuth film modified electrodes showed the highest electrochemical response for both ions. These electrochemical results were also supported by density functional theory (DFT) calculations. Based on these experimental and theoretical results, poly (8AN2SA)/bismuth film glassy carbon modified electrode was further investigated to develop a simple and sensitive electrochemical method for the simultaneous determination of Pb(II) and Cd(II) ions. After optimizing the different experimental parameters, the proposed method gave a linear range of 1-40 μg/L with the detection limit of 0.38 and 0.08 μg/L for the simultaneous determination of Pb(II) and Cd(II) ions, respectively.
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Affiliation(s)
- Alemayehu Yifru
- Department of Chemistry, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Gossa Dare
- Department of Chemistry, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Taye B. Demissie
- Materials Science Program, Department of Chemistry, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Solomon Mehretie
- Department of Chemistry, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Shimelis Admassie
- Department of Chemistry, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
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6
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Suárez M, Makowski K, Lemos R, Almagro L, Rodríguez H, Herranz MÁ, Molero D, Ortiz O, Maroto E, Albericio F, Murata Y, Martín N. An Androsterone-H 2 @C 60 hybrid: Synthesis, Properties and Molecular Docking Simulations with SARS-Cov-2. Chempluschem 2021; 86:972-981. [PMID: 33540487 PMCID: PMC8014820 DOI: 10.1002/cplu.202000770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/21/2021] [Indexed: 01/13/2023]
Abstract
We report the synthesis and characterization of a fullerene‐steroid hybrid that contains H2@C60 and a dehydroepiandrosterone moiety synthesized by a cyclopropanation reaction with 76 % yield. Theoretical calculations at the DFT‐D3(BJ)/PBE 6‐311G(d,p) level predict the most stable conformation and that the saturation of a double bond is the main factor causing the upfield shielding of the signal appearing at −3.13 ppm, which corresponds to the H2 located inside the fullerene cage. Relevant stereoelectronic parameters were also investigated and reinforce the idea that electronic interactions must be considered to develop studies on chemical‐biological interactions. A molecular docking simulation predicted that the binding energy values for the protease‐hybrid complexes were −9.9 kcal/mol and −13.5 kcal/mol for PLpro and 3CLpro respectively, indicating the potential use of the synthesized steroid‐H2@C60 as anti‐SARS‐Cov‐2 agent.
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Affiliation(s)
- Margarita Suárez
- Laboratorio de Síntesis Orgánica, Facultad de Química, Universidad de la Habana, 10400, La Habana, Cuba
| | - Kamil Makowski
- Departament of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) and CIBER-BBN, Barcelona, Spain
| | - Reinier Lemos
- Laboratorio de Síntesis Orgánica, Facultad de Química, Universidad de la Habana, 10400, La Habana, Cuba
| | - Luis Almagro
- Laboratorio de Síntesis Orgánica, Facultad de Química, Universidad de la Habana, 10400, La Habana, Cuba
| | - Hortensia Rodríguez
- Yachay Tech University, School of Chemical Sciences and Engineering, 100119-, Urququi, Ecuador
| | - María Ángeles Herranz
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040-, Madrid, Spain
| | - Dolores Molero
- CAI RMN Universidad Complutense de Madrid 28040 Madrid (Spain)
| | - Orlando Ortiz
- Laboratorio de Síntesis Orgánica, Facultad de Química, Universidad de la Habana, 10400, La Habana, Cuba
| | - Enrique Maroto
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040-, Madrid, Spain
| | - Fernando Albericio
- School of Chemistry and Physics, University of KwaZul-Natal, Durban, South Africa
| | - Yasujiro Murata
- Institute for Chemical Research, Kyoto University Uji, Kyoto, 611-0011, Japan
| | - Nazario Martín
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040-, Madrid, Spain
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7
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Breslavskaya NN, Buchachenko AL. Isotope Effects Induced by Molecular Compression. J Phys Chem A 2020; 124:6352-6355. [PMID: 32663008 DOI: 10.1021/acs.jpca.0c05567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zero-point energies (ZPEs) of hydroxyl ion and hydrogen and water molecules, free and compressed in C60 cages, are computed; the excess energy acquired by molecules under compression is in the range 2-3 kcal/mol and depends on the isotopes. The differences in ZPE of compressed isotopic molecules strongly exceed those of the free molecules, resulting in the large deuterium and tritium isotope effects. These effects induced by compression are suggested as a probe for testing molecular compression of enzymatic sites; they may be important for understanding enormously large isotope effects observed in some enzymatic reactions, where they are attributed to the tunneling.
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Affiliation(s)
- Natalia N Breslavskaya
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 117907, Russia.,Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Anatoly L Buchachenko
- Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russian Federation.,Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation.,Scientific Center of the Russian Academy of Sciences, Chernogolovka 142432, Russian Federation.,Moscow State University, Moscow 119992, Russian Federation
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8
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Influence of the second layer on geometry and spectral properties of doped two-dimensional hexagonal boron nitride. J Mol Model 2020; 26:216. [PMID: 32719904 PMCID: PMC7384999 DOI: 10.1007/s00894-020-04456-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/21/2020] [Indexed: 11/08/2022]
Abstract
Influence of the additional layer of hexagonal boron nitride (h-BN) on structure, energetics, and electronic spectra of a layer doped with magnesium, silicon, phosphorus, aluminum, or carbon atoms has been examined by theoretical methods. The h-BN layers are modeled as BN clusters of over thirty atoms with the defect in the center. The calculations show that atom positions undergo some modifications in the presence of the second layer, which in several cases lead to significant changes in electronic spectra, like (i) modifications of the character of some states from local excitation to a partial charge transfer; (ii) redshift of the majority of lowest excitations; (iii) absence or appearance of new states in comparison with the monolayers. For instance, a zero-intensity excitation below 4 eV for the carbon atom in place of boron transforms into a dipole-allowed one in the presence of the second layer. A comparison of the interaction energies of doped and undoped clusters shows a strong dependence of the stabilizing of destabilizing effect on the dopant atom, the replaced atom, and in some cases also on the stacking type (AA’ or AB). The stabilization energy per BN pair, calculated for two undoped clusters, is equal to − 31 and − 28 meV for the AA’ and AB stacking, respectively, thus confirming a larger stability of the AA’ stacking for the h-BN case.
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9
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Zeinalinezhad A, Sahnoun R. Encapsulation of Hydrogen Molecules in C 50 Fullerene: An ab Initio Study of Structural, Energetic, and Electronic Properties of H 2@C 50 and 2H 2@C 50 Complexes. ACS OMEGA 2020; 5:12853-12864. [PMID: 32548469 PMCID: PMC7288600 DOI: 10.1021/acsomega.0c00601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Various DFT functionals, including those containing long-range interactions and dispersion, together with HF and MP2 theoretical methods, were used to identify the number of H2 molecules that can be encapsulated inside a C50 cage. It is demonstrated that the 2H2@C50 complex is thermodynamically unstable based on its positive complexation energy. Some discrepancies, however, were found with respect to the stability of the H2@C50 complex. Indeed, SVWN5, PBEPBE, MP2, B2PLYP, and B2PLYPD calculations confirmed that the H2@C50 complex is thermodynamically stable, while HF, BP86, B3LYP, BHandHLYP, LC-wPBE, CAM-B3LYP, and wB97XD showed that this complex is thermodynamically unstable. Nevertheless, examination of strain and dispersion energies further supported the fact that one H2 molecule can indeed be encapsulated inside the C50 cage. Other factors, such as the host-guest interactions and bond dissociation energy, were analyzed and discussed.
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Affiliation(s)
| | - Riadh Sahnoun
- Department
of Chemistry, Faculty of Computing and Applied Sciences, Baze University Abuja, Plot 686 Cadastral Zone C00, Kuchigoro, Abuja, Nigeria
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10
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Werner HJ, Knowles PJ, Manby FR, Black JA, Doll K, Heßelmann A, Kats D, Köhn A, Korona T, Kreplin DA, Ma Q, Miller TF, Mitrushchenkov A, Peterson KA, Polyak I, Rauhut G, Sibaev M. The Molpro quantum chemistry package. J Chem Phys 2020; 152:144107. [PMID: 32295355 DOI: 10.1063/5.0005081] [Citation(s) in RCA: 475] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Molpro is a general purpose quantum chemistry software package with a long development history. It was originally focused on accurate wavefunction calculations for small molecules but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding, and anharmonic vibrational spectra. In addition to conventional input-file specification of calculations, Molpro calculations can now be specified and analyzed via a new graphical user interface and through a Python framework.
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Affiliation(s)
- Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Peter J Knowles
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Frederick R Manby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joshua A Black
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Klaus Doll
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Andreas Heßelmann
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Daniel Kats
- Max-Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Andreas Köhn
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, L. Pasteura 1 St., 02-093 Warsaw, Poland
| | - David A Kreplin
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
| | - Iakov Polyak
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Guntram Rauhut
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Marat Sibaev
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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11
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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12
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Yourdkhani S, Jabłoński M. Physical nature of silane⋯carbene dimers revealed by state-of-the-art ab initio calculations. J Comput Chem 2019; 40:2643-2652. [PMID: 31441520 DOI: 10.1002/jcc.26043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/06/2022]
Abstract
Using the SAPT2 + 3(CCD)δMP2 method in complete basis set (CBS) limit, it is shown that the interactions in the recently studied silane⋯carbene dimers are mainly dispersive in nature. Consequently, slow convergence of dispersion energy also forces slow convergence of the interaction energy. Therefore, obtaining very accurate values requires extrapolation of the correlation part to the CBS limit. The most accurate values obtained at the CCSD(T)/CBS level of theory show that the studied silane⋯carbene dimers are rather weakly bound, with interaction energies ranging from about -1.9 to -1.3 kcal/mol. Comparing to CCSD(T)/CBS, it will be shown that SCS-MP2 and MP2C methods clearly underestimate and methods based on SAPT2+ and having some third-order corrections, as well as the MP2 method, overestimate values of interaction energies. Popular SAPT(DFT) method performs better than SCS-MP2 and MP2C; nevertheless, underestimation is still considerable. The underestimation is slightly quenched if third-order dispersion energy and its exchange counterpart is added to the SAPT(DFT). The closest value of CCSD(T)/CBS has been given by the SAPT2 + (3)(CCD)δMP2 method in quadruple-ζ basis set. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Sirous Yourdkhani
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3,CZ-12116, Prague 2, Czech Republic
| | - Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7-Gagarina St, 87-100, Toruń, Poland
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Chojecki M, Rutkowska-Zbik D, Korona T. Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules-Theoretical Study. J Chem Inf Model 2019; 59:2123-2140. [PMID: 30998013 DOI: 10.1021/acs.jcim.8b00984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A dimerization of methyl chlorophyllide a molecules and a role of water in stabilization and properties of methyl chlorophyllide a dimers were studied by means of symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), density-functional theory (DFT), and time-dependent DFT approaches. The quantification of various types of interactions, such as π-π stacking, coordinative, and hydrogen bonding by applying the F-SAPT energy decomposition scheme shows the major role of the magnesium atom and the pheophytin macrocycle in the stability of the complex. The examination of interaction energy components with respect to a mutual orientation of monomers and in the presence or absence of water molecules reveals that the dispersion energy is the main binding factor of the interaction, while water molecules tend to weaken the attraction between methyl chlorophyllide a species. The dimerization can be seen in computed UV-vis spectra, and results in a doubling of the lowest peaks, as compared to the monomer spectrum, and in an intensity rise of the lowest 1.8 and 2.4 eV peaks at a cost of the 3.5 eV peaks for the majority of dimer configurations. The complexation of water has little effect on the peaks' position; however, it affects the overall shape of simulated spectra through changes in peak intensities, which is strongly dependent on the structure of the complex. The VCD spectra for the dimers show several characteristic features attributed to the interaction of substituting groups and/or water ligand attached to macrocycle groups belonging to different monomers. VCD is sensitive to the type of the formed dimer, but not to the number of water molecules it contains. This and several other features, as well as the differential UV-vis spectra, may serve as the indicator of the presence of a given dimer structure in the experiment.
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Affiliation(s)
- Michał Chojecki
- Faculty of Chemistry , University of Warsaw , ul. Pasteura 1 , 02-093 Warsaw , Poland
| | - Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , ul. Niezapominajek 8 , 30-239 Cracow , Poland
| | - Tatiana Korona
- Faculty of Chemistry , University of Warsaw , ul. Pasteura 1 , 02-093 Warsaw , Poland
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14
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Stöhr M, Van Voorhis T, Tkatchenko A. Theory and practice of modeling van der Waals interactions in electronic-structure calculations. Chem Soc Rev 2019; 48:4118-4154. [PMID: 31190037 DOI: 10.1039/c9cs00060g] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.
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Affiliation(s)
- Martin Stöhr
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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15
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Abstract
The potential energy surfaces for the interior rotation of a series of pairs of noble gas atoms encapsulated in the C70 cavity have been explored.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore
- Classe di Scienze
- 56126 Pisa
- Italy
| | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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16
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Pastorczak E, Corminboeuf C. Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions. J Chem Phys 2018; 146:120901. [PMID: 28388098 DOI: 10.1063/1.4978951] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.
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Affiliation(s)
- Ewa Pastorczak
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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17
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Suresh CH, Mohan N, Della TD. A Noncovalent Binding Strategy to Capture Noble Gases, Hydrogen and Nitrogen. J Comput Chem 2018; 39:901-908. [PMID: 29356043 DOI: 10.1002/jcc.25167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/01/2018] [Accepted: 01/05/2018] [Indexed: 12/22/2022]
Abstract
A molecular design strategy to develop receptor systems for the entrapment of noble gases, H2 and N2 is described using M06L-D3/6-311++G(d,p)//M06L/6-311++G(d,p) DFT method. These receptors made with two-, three-, four- and five-fluorinated benzene cores, linked with methelene units viz. RI , RII , RIII and RIV as well as the corresponding non-fluorinated hydrocarbons viz. RIH , RIIH , RIIIH and RIVH show a steady and significant increase in binding energy (Eint ) with increase in the number of aromatic rings in the receptor. A stabilizing "cage effect" is observed in the cyclophane type receptors RIV and RIVH which is 26-48% of total Eint for all except the larger sized Kr, Xe and N2 complexes. Eint of RIV …He, RIV …Ne, RIV …Ar, RIV …Kr, RIV …H2 and RIV …N2 is 4.89, 7.03, 6.49, 6.19, 8.57 and 8.17 kcal/mol, respectively which is 5- to9-fold higher than that of hexafluorobenzene. Similarly, compared to benzene, multiple fold increase in Eint is observed for RIVH receptors with noble gases, H2 and N2 . Fluorination of the aromatic core has no significant impact on Eint (∼ ±0.5 kcal/mol) for most of the systems with a notable exception of the cage receptor RIV for N2 where fluorination improves Eint by 1.61 kcal/mol. The Eint of the cage receptors may be projected as one of the highest interaction energy ranges reported for noble gases, H2 and N2 for a neutral carbon framework. Synthesis of such systems is promising in the study of molecules in confined environment. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695 019, India.,Academy of Scientific & Innovative Research (AcSIR), New Delhi, 110020, India
| | - Neetha Mohan
- Chemical Sciences and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695 019, India
| | - Therese Davis Della
- Chemical Sciences and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695 019, India.,Academy of Scientific & Innovative Research (AcSIR), New Delhi, 110020, India
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18
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Kawatsu T, Tachikawa M. Quantum fluctuations of a fullerene cage modulate its internal magnetic environment. Phys Chem Chem Phys 2018; 20:1673-1684. [PMID: 29264598 DOI: 10.1039/c7cp06401b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To investigate the effect of quantum fluctuations on the magnetic environment inside a C60 fullerene cage, we have calculated the nuclear magnetic shielding constant of protons in H2@C60 and HD@C60 systems by on-the-fly ab initio path integral simulation, including both thermal and nuclear quantum effects. The most dominant upfield from an isolated hydrogen molecule occurs due to the diamagnetic current of the C60 cage, which is partly cancelled by the paramagnetic current, where the paramagnetic contribution is enlarged by the zero-point vibrational fluctuation of the C60 carbon backbone structure via a widely distributed HOMO-LUMO gap. This quantum modulation mechanism of the nuclear magnetic shielding constant is newly proposed. Because this quantum effect is independent of the difference between H2 and HD, the H2/HD isotope shift occurs in spite of the C60 cage. The nuclear magnetic constants computed for H2@C60 and HD@C60 are 32.047 and 32.081 ppm, respectively, which are in reasonable agreement with the corresponding values of 32.19 and 32.23 ppm estimated from the experimental values of the chemical shifts.
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Affiliation(s)
- Tsutomu Kawatsu
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan.
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19
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Demissie TB, Ruud K, Hansen JH. Cryptophanes for Methane and Xenon Encapsulation: A Comparative Density Functional Theory Study of Binding Properties and NMR Chemical Shifts. J Phys Chem A 2017; 121:9669-9677. [PMID: 29178799 DOI: 10.1021/acs.jpca.7b10595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The host-guest chemistry of cryptophanes is an active research area because of its applications in sensor design, targeting small molecules and atoms in environmental and medical sciences. As such, the computational prediction of binding energies and nuclear magnetic resonance (NMR) properties of different cryptophane complexes are of interest to both theoreticians and experimentalists working in host-guest based sensor development. Herein we present a study of 10 known and some newly proposed cryptophanes using density functional theory (DFT) calculations. We benchmark the description of nonbonding interactions by different DFT functionals against spin-component-scaled, second-order Møller-Plesset theory (SCS-MP2) and predict novel host molecules with enhanced affinity toward methane and Xenon, two representative systems of high interest. We demonstrate the power and limitations of the different computational methods in describing the binding and NMR properties of these established and novel host systems. The results show the importance of including dispersion corrections in the DFT functionals. The overall analysis of the dispersion corrections indicated that results obtained from pure DFT functionals should be used cautiously when conclusions are drawn for molecular systems with considerable weak interactions. Proposed analogues of cryptophane-A, where the alkoxy bridges are replaced by alkyl chains, are predicted to display enhanced affinity toward both methane and Xenon.
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Affiliation(s)
- Taye B Demissie
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway.,Organic Chemistry Group, Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
| | - Jørn H Hansen
- Organic Chemistry Group, Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway
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20
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Yourdkhani S, Jabłoński M, Echeverría J. Attractive PHHP interactions revealed by state-of-the-art ab initio calculations. Phys Chem Chem Phys 2017; 19:28044-28055. [PMID: 28994835 DOI: 10.1039/c7cp04412g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report in this work a combined structural and state-of-the-art computational study of homopolar P-HH-P intermolecular contacts. Database surveys have shown the abundance of such surprisingly unexplored contacts, which are usually accompanied by other weak interactions in the solid state. By means of a detailed theoretical study utilizing SAPT(DFT), MP2, SCS-MP2, MP2C and CCSD(T) methods and both aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, Q, 5) basis sets as well as extrapolation to the CBS limit, we have shown that P-HH-P contacts are indeed attractive and considerably strong. SAPT(DFT) calculations have revealed the dispersive nature of the P-HH-P interaction with only minor contribution of the inductive term, whereas the first-order electrostatic term is clearly overbalanced by the first-order exchange energy. In general the computed interaction energies follow the trend: E ≈ E < E < E. Our results have also shown that the aug-cc-pVDZ (or aug-cc-pCVDZ) basis set is not yet well balanced and that the second-order dispersion energy term is the slowest converging among all SAPT(DFT) energy components. Compared to aug-cc-pVXZ basis sets, their core-correlation counterparts have a modest influence on all supermolecular interaction energies and a negligible influence on both the SAPT(DFT) interaction energy and its components.
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Affiliation(s)
- Sirous Yourdkhani
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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21
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Yourdkhani S, Jabłoński M. Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods. J Comput Chem 2017; 38:773-780. [PMID: 28145082 DOI: 10.1002/jcc.24739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/26/2023]
Abstract
The physical nature of charge-inverted hydrogen bonds in H3 XH ⋯YH3 (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: EintSAPT<EintSCS-MP2≤EintMP2C<EintMP2≈EintCCSD(T). It is confirmed that the aug-cc-pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole-ζ quality. Considerably large binding energies suggest potential usefulness of charge-inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ- and π-hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge-inverted hydrogen bond would become the first described case of a hydride-triel bond. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sirous Yourdkhani
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7-Gagarina St, Toruń, 87-100, Poland
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22
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Dolgonos GA, Peslherbe GH. Can two H2 molecules be inserted into C60 – an accurate first-principles exploration of structural, energetic and vibrational properties of the 2H2@C60 complex. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Calvo F, Yurtsever E. Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes. J Chem Phys 2016; 145:084304. [PMID: 27586919 DOI: 10.1063/1.4961159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.
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Affiliation(s)
- F Calvo
- Université Grenoble Alpes, LIPHY, F-38000 Grenoble, France and CNRS, LIPHy, F-38000 Grenoble, France
| | - E Yurtsever
- Koç University, Rumelifeneriyolu, Sariyer, Istanbul 34450, Turkey
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24
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Roztoczyńska A, Kozłowska J, Lipkowski P, Bartkowiak W. Hydrogen bonding inside and outside carbon nanotubes: HF dimer as a case study. Phys Chem Chem Phys 2016; 18:2417-27. [PMID: 26701220 DOI: 10.1039/c5cp04153h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this theoretical work we analyze the noncovalent interactions of molecular complexes formed between the hydrogen bonded HF dimer and single-walled carbon nanotubes (SWCNTs) of different diameters. In particular, the interaction energies of: (i) spatially confined hydrogen fluoride molecules and (ii) HF dimer and the exterior or interior of SWCNTs are investigated. The computations are carried out in a supermolecular manner using the M06-2X exchange-correlation functional. In order to establish the influence of mutual orientation of the hydrogen fluoride dimer and molecular carbon cages on the analyzed energetic parameters energy scans are performed. Furthermore, changes in the charge distribution of the investigated endo- and exohedral complexes are studied employing the Natural Bond Orbital analysis. Among others, the position of the HF dimer with respect to the carbon cages proves to have a significant influence on the analyzed quantities. The results of our study also indicate that the HF dimer interacts stronger with the interior rather than the exterior of SWCNTs. Moreover, a substantial enhancement of the basis set superposition error is disclosed.
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Affiliation(s)
- Agnieszka Roztoczyńska
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Justyna Kozłowska
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
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25
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Dodziuk H, Ruud K, Korona T, Demissie TB. Chiral recognition by fullerenes: CHFClBr enantiomers in the C82cage. Phys Chem Chem Phys 2016; 18:26057-26068. [DOI: 10.1039/c6cp05030a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical studies of complexes of the enantiomers of CHFClBr with C82-3 show that the too large guests are stabilized in the C82cage by electrostatic interactions. The sign of v(CH) stretching vibration of S-CHFClBr@C82-3 in the VCD spectrum is reversed as compared to that of the free guest. Spectra of the complexes exhibit differences.
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Affiliation(s)
- Helena Dodziuk
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-264 Warsaw
- Poland
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- UiT The Arctic University of Norway
- 9037 Tromsø
- Norway
| | - Tatiana Korona
- Faculty of Chemistry
- University of Warsaw
- 02-093 Warsaw
- Poland
| | - Taye B. Demissie
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- UiT The Arctic University of Norway
- 9037 Tromsø
- Norway
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26
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Usvyat D. High precision quantum-chemical treatment of adsorption: Benchmarking physisorption of molecular hydrogen on graphane. J Chem Phys 2015; 143:104704. [DOI: 10.1063/1.4930851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Denis Usvyat
- Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg, Germany
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27
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Yourdkhani S, Korona T, Hadipour NL. Structure and Energetics of Complexes of B12N12 with Hydrogen Halides—SAPT(DFT) and MP2 Study. J Phys Chem A 2015; 119:6446-67. [DOI: 10.1021/acs.jpca.5b01756] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Tatiana Korona
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Nasser L. Hadipour
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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28
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Heßelmann A, Korona T. Intermolecular symmetry-adapted perturbation theory study of large organic complexes. J Chem Phys 2015; 141:094107. [PMID: 25194364 DOI: 10.1063/1.4893990] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.
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Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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29
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Duarte Alaniz V, Rocha-Rinza T, Cuevas G. Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer. J Comput Chem 2014; 36:361-75. [DOI: 10.1002/jcc.23798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Víctor Duarte Alaniz
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
| | - Tomás Rocha-Rinza
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
| | - Gabriel Cuevas
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
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30
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Felker PM. Fully quantal calculation of H2 translation-rotation states in the (p-H2)2@51264 clathrate hydrate inclusion compound. J Chem Phys 2014; 141:184305. [DOI: 10.1063/1.4901057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Dolgonos GA, Peslherbe GH. Encapsulation of diatomic molecules in fullerene C60: implications for their main properties. Phys Chem Chem Phys 2014; 16:26294-305. [DOI: 10.1039/c4cp04069d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Korona T, Rutkowska-Zbik D. A theoretical study on elementary building blocks for organic solar cells – Influence of a donor molecule on electronic spectrum of PCBM. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Lipkowski P, Kozłowska J, Roztoczyńska A, Bartkowiak W. Hydrogen-bonded complexes upon spatial confinement: structural and energetic aspects. Phys Chem Chem Phys 2014; 16:1430-40. [DOI: 10.1039/c3cp53583e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Kozłowska J, Zaleśny R, Bartkowiak W. On the nonlinear electrical properties of molecules in confined spaces – From cylindrical harmonic potential to carbon nanotube cages. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2013.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Density functional theory based molecular dynamics simulations of C70O3 doped with light molecules. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2013.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Korona T. A coupled cluster treatment of intramonomer electron correlation within symmetry-adapted perturbation theory: benchmark calculations and a comparison with a density-functional theory description. Mol Phys 2013. [DOI: 10.1080/00268976.2012.746478] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Rastrelli F, Frezzato D, Lawler RG, Li Y, Turro NJ, Bagno A. Predicting the paramagnet-enhanced NMR relaxation of H₂ encapsulated in endofullerene nitroxides by density-functional theory calculations. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110634. [PMID: 23918714 DOI: 10.1098/rsta.2011.0634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We have investigated the structure and nuclear magnetic resonance (NMR) spectroscopic properties of some dihydrogen endofullerene nitroxides by means of density-functional theory (DFT) calculations. Quantum versus classical roto-translational dynamics of H₂ have been characterized and compared. Geometrical parameters and hyperfine couplings calculated by DFT have been input to the Solomon-Bloembergen equations to predict the enhancement of the NMR longitudinal relaxation of H₂ due to coupling with the unpaired electron. Estimating the rotational correlation time via computed molecular volumes leads to a fair agreement with experiment for the simplest derivative; the estimate is considerably improved by recourse to the calculation of the diffusion tensor. For the other more flexible congeners, the agreement is less good, which may be due to an insufficient sampling of the conformational space. In all cases, relaxation by Fermi contact and Curie mechanisms is predicted to be negligible.
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Affiliation(s)
- Federico Rastrelli
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo, 35131 Padova, Italy
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38
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Kaiser A, Leidlmair C, Bartl P, Zöttl S, Denifl S, Mauracher A, Probst M, Scheier P, Echt O. Adsorption of hydrogen on neutral and charged fullerene: experiment and theory. J Chem Phys 2013; 138:074311. [PMID: 23445013 DOI: 10.1063/1.4790403] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Helium droplets are doped with fullerenes (either C60 or C70) and hydrogen (H2 or D2) and investigated by high-resolution mass spectrometry. In addition to pure helium and hydrogen cluster ions, hydrogen-fullerene complexes are observed upon electron ionization. The composition of the main ion series is (H2)(n)HC(m)(+) where m = 60 or 70. Another series of even-numbered ions, (H2)(n)C(m)(+), is slightly weaker in stark contrast to pure hydrogen cluster ions for which the even-numbered series (H2)(n)(+) is barely detectable. The ion series (H2)(n)HC(m)(+) and (H2)(n)C(m)(+) exhibit abrupt drops in ion abundance at n = 32 for C60 and 37 for C70, indicating formation of an energetically favorable commensurate phase, with each face of the fullerene ion being covered by one adsorbate molecule. However, the first solvation layer is not complete until a total of 49 H2 are adsorbed on C60(+); the corresponding value for C70(+) is 51. Surprisingly, these values do not exhibit a hydrogen-deuterium isotope effect even though the isotope effect for H2/D2 adsorbates on graphite exceeds 6%. We also observe doubly charged fullerene-deuterium clusters; they, too, exhibit abrupt drops in ion abundance at n = 32 and 37 for C60 and C70, respectively. The findings imply that the charge is localized on the fullerene, stabilizing the system against charge separation. Density functional calculations for C60-hydrogen complexes with up to five hydrogen atoms provide insight into the experimental findings and the structure of the ions. The binding energy of physisorbed H2 is 57 meV for H2C60(+) and (H2)2C60(+), and slightly above 70 meV for H2HC60(+) and (H2)2HC60(+). The lone hydrogen in the odd-numbered complexes is covalently bound atop a carbon atom but a large barrier of 1.69 eV impedes chemisorption of the H2 molecules. Calculations for neutral and doubly charged complexes are presented as well.
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Affiliation(s)
- A Kaiser
- Institut für Ionenphysik und Angewandte Physik, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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39
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Zaleśny R, Góra RW, Kozłowska J, Luis JM, Ågren H, Bartkowiak W. Resonant and Nonresonant Hyperpolarizabilities of Spatially Confined Molecules: A Case Study of Cyanoacetylene. J Chem Theory Comput 2013; 9:3463-72. [DOI: 10.1021/ct400410m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Robert Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wyb. Wyspiańskiego 27, PL−50370 Wrocław, Poland
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wyb. Wyspiańskiego 27, PL−50370 Wrocław, Poland
| | - Justyna Kozłowska
- Theoretical Chemistry Group, Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wyb. Wyspiańskiego 27, PL−50370 Wrocław, Poland
| | - Josep M. Luis
- Institut de Química Computacional
i Catàlisi and Departament de Química, Universitat de Girona, E−17071 Girona, Catalonia,
Spain
| | - Hans Ågren
- Department of Theoretical
Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE−10691 Stockholm,
Sweden
| | - Wojciech Bartkowiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wyb. Wyspiańskiego 27, PL−50370 Wrocław, Poland
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40
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Kaiser A, Zöttl S, Bartl P, Leidlmair C, Mauracher A, Probst M, Denifl S, Echt O, Scheier P. Methane adsorption on aggregates of fullerenes: site-selective storage capacities and adsorption energies. CHEMSUSCHEM 2013; 6:1235-44. [PMID: 23744834 PMCID: PMC3799018 DOI: 10.1002/cssc.201300133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Indexed: 05/13/2023]
Abstract
Methane adsorption on positively charged aggregates of C60 is investigated by both mass spectrometry and computer simulations. Calculated adsorption energies of 118-281 meV are in the optimal range for high-density storage of natural gas. Groove sites, dimple sites, and the first complete adsorption shells are identified experimentally and confirmed by molecular dynamics simulations, using a newly developed force field for methane-methane and fullerene-methane interaction. The effects of corrugation and curvature are discussed and compared with data for adsorption on graphite, graphene, and carbon nanotubes.
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Affiliation(s)
- Alexander Kaiser
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Samuel Zöttl
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Peter Bartl
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Christian Leidlmair
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Andreas Mauracher
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Michael Probst
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
| | - Olof Echt
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
- Department of Physics, University of New HampshireDurham, NH 03824 (USA)
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität InnsbruckTechniker Str. 25, 6020 Innsbruck (Austria)
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41
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Felker PM. Nuclear-orbital/configuration-interaction study of coupled translation-rotation states in (H2)2@C70. J Chem Phys 2013; 138:044309. [PMID: 23387586 DOI: 10.1063/1.4776262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantal translation-rotation states of two endohedral H(2) moieties in C(70) are computed by means of a nuclear-orbital/configuration-interaction method. H(2) "nuclear orbitals" are calculated as the translation-rotation eigenfunctions of one H(2) molecule interacting with C(70) and the mean field of the second H(2) molecule. Configurations are constructed as symmetrized bilinear products of these orbitals. These configurations are employed as the basis in which the matrix of the translation-rotation Hamiltonian of the cluster is computed and diagonalized. We show that this scheme allows for an efficient means to calculate the Hamiltonian matrix elements. We show that the configuration basis states represent excellent first approximations to the eigenstates of the species. Finally, we present results pertaining to the (H(2))(2)@C(70) low-energy translation-rotation level structure that can be understood in terms of a small number of H(2) excitation types.
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Affiliation(s)
- Peter M Felker
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA.
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42
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Dodziuk H, Korona T, Lomba E, Bores C. Carbon Nanotube Container: Complexes of C50H10 with Small Molecules. J Chem Theory Comput 2012; 8:4546-55. [DOI: 10.1021/ct300546c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helena Dodziuk
- Institute of Physical Chemistry,
Polish Academy of Sciences, ul. Kasprzaka 44, 01-224 Warsaw, Poland
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw,
Poland
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43
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Rutkowska-Zbik D, Korona T. How Many Ligands Can Be Bound by Magnesium–Porphyrin? A Symmetry-Adapted Perturbation Theory Study. J Chem Theory Comput 2012; 8:2972-82. [DOI: 10.1021/ct300281p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface
Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239
Cracow, Poland
| | - Tatiana Korona
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw,
Poland
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44
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Ravinder P, Subramanian V. Role of Encapsulation of Na+ and F– Ions on the Diels–Alder Reactivity of C32. J Phys Chem A 2012; 116:6870-8. [DOI: 10.1021/jp3015244] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- P. Ravinder
- Chemical Laboratory, CSIR-Central Leather Research Institute, Council of Scientific and Industrial
Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Council of Scientific and Industrial
Research, Adyar, Chennai 600 020, India
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45
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Podeszwa R, Cencek W, Szalewicz K. Efficient Calculations of Dispersion Energies for Nanoscale Systems from Coupled Density Response Functions. J Chem Theory Comput 2012; 8:1963-9. [DOI: 10.1021/ct300200m] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rafał Podeszwa
- Institute of Chemistry, University
of Silesia, Szkolna 9, 40-006 Katowice, Poland
- Department of Physics and Astronomy,
University of Delaware, Newark, Delaware 19716, United States
| | - Wojciech Cencek
- Department of Physics and Astronomy,
University of Delaware, Newark, Delaware 19716, United States
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy,
University of Delaware, Newark, Delaware 19716, United States
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46
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Waller MP, Kruse H, Mück-Lichtenfeld C, Grimme S. Investigating inclusion complexes using quantum chemical methods. Chem Soc Rev 2012; 41:3119-28. [DOI: 10.1039/c2cs15244d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Dabbagh HA, Zamani M, Farrokhpour H. DFT investigation of endohedral boron oxide nanocapsules: Encapsulation of He, Ne, Ar, H, N, and Cl atoms. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Ravinder P, Subramanian V. Studies on the Encapsulation of Various Anions in Different Fullerenes Using Density Functional Theory Calculations and Born–Oppenheimer Molecular Dynamics Simulation. J Phys Chem A 2011; 115:11723-33. [DOI: 10.1021/jp203421v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pawar Ravinder
- Chemical Laboratory, Council of Scientific and Industrial Research, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - Venkatesan Subramanian
- Chemical Laboratory, Council of Scientific and Industrial Research, Central Leather Research Institute, Adyar, Chennai 600 020, India
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49
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Dolgonos GA, Peslherbe GH. Conventional and density-fitting local Møller–Plesset theory calculations of C60 and its endohedral H2@C60 and 2H2@C60 complexes. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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50
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Szalewicz K. Symmetry-adapted perturbation theory of intermolecular forces. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.86] [Citation(s) in RCA: 357] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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