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Jabłoński M. A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions. Molecules 2020; 25:molecules25235512. [PMID: 33255559 PMCID: PMC7728086 DOI: 10.3390/molecules25235512] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
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Lu J, Scheiner S. Relationships between Bond Strength and Spectroscopic Quantities in H-Bonds and Related Halogen, Chalcogen, and Pnicogen Bonds. J Phys Chem A 2020; 124:7716-7725. [DOI: 10.1021/acs.jpca.0c05936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jia Lu
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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Sarkar R, Kundu TK. Nonbonding interaction analyses on PVDF/[BMIM][BF 4] complex system in gas and solution phase. J Mol Model 2019; 25:131. [PMID: 31025122 DOI: 10.1007/s00894-019-4020-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022]
Abstract
The present study provides a detailed quantum chemical description of the physicochemical interactions between poly-vinylidene fluoride (PVDF) and 1-butyl-3-methyl-imidazolium tetrafluoro borate ([BMIM][BF4]) ionic liquid (IL). Geometry optimization and frequency calculations are carried out for four monomer units of α- and β-PVDF, [BMIM][BF4], and PVDF/[BMIM][BF4] using dispersion corrected density functional theory. The effects of solvation on the systems under study are demonstrated for three polar aprotic solvents, namely tetra-hydrofuran (THF), acetone, and n,n-dimethyl formamide (DMF) using the integral equation formalism polarizable continuum model (IEFPCM). Calculated negative solvation free energy values suggest solution phase stability of the systems under study. Binding and interaction energies for β-PVDF/IL are found higher in magnitude than those for α-PVDF/IL. The nonbonding interaction phenomenon of β-PVDF/[BMIM][BF4] is elucidated on the basis of natural bond orbital (NBO), Bader's quantum theory of atoms in molecules (QTAIM), delocalization indices, Hirshfeld surface, and reduced density gradient (RDG) analyses. Both anions and cations of ionic liquids are found to show weak van der Waals interaction with PVDF molecule but the anion ([BF4]-)/PVDF interaction is found to be stronger than cation ([BMIM]+)/PVDF interaction. Inter-unit C-H⋯F type hydrogen bonds are found to show improper (causing blue shifts in vibrational frequencies) nature. Frontier molecular orbital analysis is carried out, and different chemical parameters like electronegativity, chemical potential, chemical hardness and softness, and electrophilicity index are calculated using Koopmans' theorem. Thermochemical calculations are also performed, and the variation in different standard thermodynamic parameters with temperature is formulated. Graphical abstract (a) Hirshfeld surface mapped onto electron density and (b) NCI isosurfaces showing inter-unit interactions of β-PVDF/[BMIM][BF4].
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Affiliation(s)
- Ranjini Sarkar
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - T K Kundu
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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An insight into intramolecular blue-shifting C H⋯π hydrogen bonds in 1,3-hexadien-5-yne and its halogen-substituted derivatives. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sun W, Lozada IB, van Wijngaarden J. Fourier Transform Microwave Spectroscopic and ab Initio Study of the Rotamers of 2-Fluorobenzaldehyde and 3-Fluorobenzaldehyde. J Phys Chem A 2018; 122:2060-2068. [DOI: 10.1021/acs.jpca.7b11673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenhao Sun
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Issiah Byen Lozada
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR. Molecules 2016; 21:molecules21111426. [PMID: 27801801 PMCID: PMC6274571 DOI: 10.3390/molecules21111426] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/30/2022] Open
Abstract
The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.
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Sarkar A, Bhattacharyya S, Mukherjee A. Colorimetric detection of fluoride ions by anthraimidazoledione based sensors in the presence of Cu(ii) ions. Dalton Trans 2016; 45:1166-75. [DOI: 10.1039/c5dt03209a] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A thioimidazole bearing anthraimidazoledione detects fluoride selectively in the presence of Cu2+with a detection limit of 0.04 ppm. The results show that the change of thioimidazole to imidazole leads to no detection.
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Affiliation(s)
- Amrita Sarkar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Sudipta Bhattacharyya
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Arindam Mukherjee
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
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Sutradhar D, Zeegers-Huyskens T, Chandra AK. Theoretical study of the interaction between pyridine derivatives and atomic chlorine. Substituent effect and nature of the bonding. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1014440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Jabłoński M. Red and blue shifted hydridic bonds. J Comput Chem 2014; 35:1739-47. [DOI: 10.1002/jcc.23678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/14/2014] [Accepted: 06/18/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry; Nicolaus Copernicus University; 7-Gagarina St. PL-87 100 Toruń Poland
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Rodziewicz P, Meyer B. Interplay between molecule–molecule and molecule–substrate interactions: first-principles study of fluoroform aggregates on a hexagonal ice (0001) surface. Phys Chem Chem Phys 2014; 16:940-54. [DOI: 10.1039/c3cp53829j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jabłoński M, Monaco G. Different zeroes of interaction energies as the cause of opposite results on the stabilizing nature of C-H···O intramolecular interactions. J Chem Inf Model 2013; 53:1661-75. [PMID: 23768311 DOI: 10.1021/ci400085t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interaction energy of the C-H···O intramolecular interaction is estimated by several methods for a large group of systems possessing a quasi-cyclic six-membered ring. In the case of the geometry corrected method (GCM), the related rotamers method (RRM), and Espinosa's method (EM), the linear correlations between interaction energies and the electron density at the bond critical point have close slopes. The first and the last two methods yield almost systematically opposite results concerning the stabilizing/destabilizing character of the interaction, and their main difference is their zero of the interaction energy. An investigation on the limitations of reference energies has led to the introduction of the geometry corrected related rotamers method (GCRRM), estimating both stabilizing and destabilizing C-H···O interactions. An extension of EM is proposed.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Nicolaus Copernicus University, 7-Gagarina St., PL-87 100 Toruń, Poland.
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The halogenoxygen interaction in 3-halogenopropenal revisited – The dimer model vs. QTAIM indications. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sigalov MV, Doronina EP, Sidorkin VF. CAr–H···O Hydrogen Bonds in Substituted Isobenzofuranone Derivatives: Geometric, Topological, and NMR Characterization. J Phys Chem A 2012; 116:7718-25. [DOI: 10.1021/jp304009g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mark V. Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, 84105 Beer-Sheva,
Israel
| | - Evgeniya P. Doronina
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
| | - Valery F. Sidorkin
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
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Jabłoński M. Energetic and Geometrical Evidence of Nonbonding Character of Some Intramolecular Halogen···Oxygen and Other Y···Y Interactions. J Phys Chem A 2012; 116:3753-64. [DOI: 10.1021/jp300993b] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Mirosl̷aw Jabłoński
- Department of Quantum Chemistry, Nicolaus Copernicus University, 7-Gagarina
Street, PL-87 100 Toruń, Poland
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Zhang R, Wu WJ, Huang JM, Meng X. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution. CHINESE J CHEM PHYS 2011. [DOI: 10.1088/1674-0068/24/06/691-696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Jabłoński M, Solà M. Influence of confinement on hydrogen bond energy. The case of the FH···NCH dimer. J Phys Chem A 2011; 114:10253-60. [PMID: 20738112 DOI: 10.1021/jp104968x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of the external pressure on the energy of the intermolecular hydrogen bond is investigated by modeling the pressure effects with helium atoms located at fixed points in space around the hydrogen bonded dimer. Several methods of estimating the energy of the H···N hydrogen bond in the He···FH···NCH···He model system are proposed. They show that the energy of the H···N hydrogen bond in this confined dimer decreases continuously with the reduction of the He···He distance, thus with the increase of the pressure effect exerted on the confined dimer.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Nicolaus Copernicus UniVersity, PL-87 100 Toruń, Poland.
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Selvam L, Chen F, Wang F. Solvent effects on blue shifted improper hydrogen bond of C–H⋯O in deoxycytidine isomers. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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van der Veken B, Delanoye S, Michielsen B, Herrebout W. A cryospectroscopic study of the blue-shifting C–H⋯O bonded complexes of pentafluoroethane with dimethyl ether-d6, acetone-d6 and oxirane-d4. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.02.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chen F, Selvam L, Wang F. Blue shifted intramolecular C−H···O improper hydrogen bonds in conformers of zidovudine. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Zhou PP, Qiu WY. Red- and Blue-Shifted Hydrogen Bonds in theCis-TransNoncyclic Formic Acid Dimer. Chemphyschem 2009; 10:1847-58. [DOI: 10.1002/cphc.200800870] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jabłoński M, Sadlej AJ. Influence of the external pressure on improper character of intramolecular C–H⋯O interactions. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Solvation of Hydrogen Bonded Systems: CH···O, OH···O, and Cooperativity. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8270-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Mondal P, Karmakar A, Singh WM, Baruah JB. Crystal packing in some flexible carboxylic acids and esters attached to a naphthalene ring. CrystEngComm 2008. [DOI: 10.1039/b808399a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Jabłoński M. Blue-shifting intramolecular CH⋯O(S) contacts in sterically strained systems. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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