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Manna D, Lo R, Vacek J, Miriyala VM, Bouř P, Wu T, Osifová Z, Nachtigallová D, Dračinský M, Hobza P. The Stability of Hydrogen-Bonded Ion-Pair Complex Unexpectedly Increases with Increasing Solvent Polarity. Angew Chem Int Ed Engl 2024; 63:e202403218. [PMID: 38497312 DOI: 10.1002/anie.202403218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The generally observed decrease of the electrostatic energy in the complex with increasing solvent polarity has led to the assumption that the stability of the complexes with ion-pair hydrogen bonds decreases with increasing solvent polarity. Besides, the smaller solvent-accessible surface area (SASA) of the complex in comparison with the isolated subsystems results in a smaller solvation energy of the latter, leading to a destabilization of the complex in the solvent compared to the gas phase. In our study, which combines Nuclear Magnetic Resonance, Infrared Spectroscopy experiments, quantum chemical calculations, and molecular dynamics (MD) simulations, we question the general validity of this statement. We demonstrate that the binding free energy of the ion-pair hydrogen-bonded complex between 2-fluoropropionic acid and n-butylamine (CH3CHFCOO-…NH3But+) increases with increased solvent polarity. This phenomenon is rationalized by a substantial charge transfer between the subsystems that constitute the ion-pair hydrogen-bonded complex. This unexpected finding introduces a new perspective to our understanding of solvation dynamics, emphasizing the interplay between solvent polarity and molecular stability within hydrogen-bonded systems.
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Affiliation(s)
- Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
- Faculty of Science, Palacký University Olomouc, 17. Listopadu 1192/12, 779 00, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
| | - Martin Dračinský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, 160 00, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
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2
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Sarmah A, Hobza P, Chandra AK, Mitra S, Nakajima T. Many-body Effects on Electronic Transport in Molecular Junctions: A Quantum Perspective. Chemphyschem 2024:e202300938. [PMID: 38469938 DOI: 10.1002/cphc.202300938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/13/2024]
Abstract
This concept delves into quantum particle transport at the nanoscale, with a particular focus on how electrons move through molecular circuits. The thriving field of single molecular electronics benefits from the unique electrical and other properties of nanostructures. It concentrates on single molecular junctions that serve as bridges between electrodes. In this context, the electronic correlation-induced many-body effect gives rise to resonant states. These states, along with conductance, depend on electron spin. Thus, the field acts as a bridge between quantum and macroscopic worlds, unveiling unique behaviors of electrons. Additionally, external factors, such as magnetic fields and voltages, offer means to control the electron correlation in these junctions.
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Affiliation(s)
- Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Asit K Chandra
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Sivaprasad Mitra
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimi-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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3
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Manna D, Lo R, Miriyala VM, Nachtigallová D, Trávníček Z, Hobza P. Impact of dielectric constant of solvent on the formation of transition metal-ammine complexes. J Comput Chem 2024; 45:204-209. [PMID: 37752737 DOI: 10.1002/jcc.27230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023]
Abstract
The DFT-level computational investigations into Gibbs free energies (ΔG) demonstrate that as the dielectric constant of the solvent increases, the stabilities of [M(NH3 )n ]2+/3+ (n = 4, 6; M = selected 3d transition metals) complexes decrease. However, there is no observed correlation between the stability of the complex and the solvent donor number. Analysis of the charge transfer and Wiberg bond indices indicates a dative-bond character in all the complexes. The solvent effect assessed through solvation energy is determined by the change in the solvent accessible surface area (SASA) and the change in the charge distribution that occurs during complex formation. It has been observed that the SASA and charge transfer are different in the different coordination numbers, resulting in a variation in the solvent effect on complex stability in different solvents. This ultimately leads to a change between the relative stability of complexes with different coordination numbers while increasing the solvent polarity for a few complexes. Moreover, the findings indicate a direct relationship between ΔΔG (∆Gsolvent -∆Ggas ) and ΔEsolv , which enables the computation of ΔG for the compounds in a particular solvent using only ΔGgas and ΔEsolv . This approach is less computationally expensive.
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Affiliation(s)
- Debashree Manna
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Rabindranath Lo
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic
| | - Dana Nachtigallová
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Zdeněk Trávníček
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic
| | - Pavel Hobza
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
- IT4Innovations, VŠB-Technical University of Ostrava, Ostrava, Czech Republic
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4
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Lo R, Manna D, Miriyala VM, Nachtigallová D, Hobza P. Trends in the stability of covalent dative bonds with variable solvent polarity depend on the charge transfer in the Lewis electron-pair system. Phys Chem Chem Phys 2023; 25:25961-25964. [PMID: 37727041 DOI: 10.1039/d3cp03445c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
In general, the stability of neutral complexes with dative bonds increases as the polarity of the solvent increases. This is based on the fact that the dipole moment of the complex increases as the charge transferred from the donor to the acceptor increases. As a result, the solvation energy of the complex becomes greater than that of subsystems, causing an increase in the stabilization energy with increasing solvent polarity. Our research confirms this assumption, but only when the charge transfer is sufficiently large. If it is below a certain threshold, the increase in the complex's dipole moment is insufficient to result in a higher solvation energy than subsystems. Thus, the magnitude of the charge transfer in the Lewis electron-pair system determines the stability trends of dative bonds with varying solvent polarity. We used molecular dynamics (MD) simulations based on an explicit solvent model, which is considered more reliable, to verify the results obtained with a continuous solvent model.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16000, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, Olomouc 77900, Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16000, Czech Republic.
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16000, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, Olomouc 77900, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16000, Czech Republic.
- IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba 70800, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16000, Czech Republic.
- IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba 70800, Czech Republic
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5
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Sutradhar D, Sarmah A, Hobza P, Chandra AK. Strong Be-N Interaction Induced Complementary Chemical Tuning to Design a Dual-gated Single Molecule Junction. Chemistry 2023; 29:e202301473. [PMID: 37401206 DOI: 10.1002/chem.202301473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
The interaction between pyridines and the π-hole of BeH2 leads to the formation of strong beryllium-bonded complexes. Theoretical investigations demonstrate that the Be-N bonding interaction can effectively regulate the electronic current through a molecular junction. The electronic conductance exhibits distinct switching behavior depending on the substituent groups at the para position of pyridine, highlighting the role of Be-N interaction as a potent chemical gate in the proposed device. The complexes exhibit short intermolecular distances ranging from 1.724 to 1.752 Å, emphasizing their strong binding. Detailed analysis of electronic rearrangements and geometric perturbations upon complex formation provides insights into the underlying reasons for the formation of such strong Be-N bonds, with bond strengths varying from -116.25 to -92.96 kJ/mol. Moreover, the influence of chemical substituents on the local electronic transmission of the beryllium-bonded complex offers valuable insights for the implementation of a secondary chemical gate in single-molecule devices. This study paves the way for the development of chemically gateable, functional single-molecule transistors, advancing the design and fabrication of multifunctional single-molecule devices in the nanoscale regime.
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Affiliation(s)
- Dipankar Sutradhar
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, 466114, India
| | - Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu, 1192/12, 771 46, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Asit K Chandra
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
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6
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Mallada B, Ondráček M, Lamanec M, Gallardo A, Jiménez-Martín A, de la Torre B, Hobza P, Jelínek P. Visualization of π-hole in molecules by means of Kelvin probe force microscopy. Nat Commun 2023; 14:4954. [PMID: 37587123 PMCID: PMC10432393 DOI: 10.1038/s41467-023-40593-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Submolecular charge distribution significantly affects the physical-chemical properties of molecules and their mutual interaction. One example is the presence of a π-electron-deficient cavity in halogen-substituted polyaromatic hydrocarbon compounds, the so-called π-holes, the existence of which was predicted theoretically, but the direct experimental observation is still missing. Here we present the resolution of the π-hole on a single molecule using the Kelvin probe force microscopy, which supports the theoretical prediction of its existence. In addition, experimental measurements supported by theoretical calculations show the importance of π-holes in the process of adsorption of molecules on solid-state surfaces. This study expands our understanding of the π-hole systems and, at the same time, opens up possibilities for studying the influence of submolecular charge distribution on the chemical properties of molecules and their mutual interaction.
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Affiliation(s)
- B Mallada
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic
- Department of Physical Chemistry, Palacký University Olomouc, Tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - M Ondráček
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - M Lamanec
- Department of Physical Chemistry, Palacký University Olomouc, Tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000, Prague, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
| | - A Gallardo
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - A Jiménez-Martín
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic
| | - B de la Torre
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - P Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000, Prague, Czech Republic.
- IT4Innovations, VŠB - Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic.
| | - P Jelínek
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic.
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7
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Manna D, Lo R, Nachtigallová D, Trávníček Z, Hobza P. The Impact of the Solvent Dielectric Constant on A← NH3 Dative Bond Depends on the Nature of the Lewis Electron-Pair Systems. Chemistry 2023:e202300635. [PMID: 37066846 DOI: 10.1002/chem.202300635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 04/18/2023]
Abstract
The present work aims to determine to what extent the value of the dielectric constant of the solvent can influence the dative bond in Lewis electron pair bonding systems. For this purpose, two different systems, namely H3B¬NH3 and {Zn¬(NH3)}2+, were studied in selected solvents with significantly different dielectric constants. Based on the results resulting from state-of-the-art computational methods using DFT, constrained DFT, energy decomposition analyses, solvent accessible surface area, and charge transfer calculations, we found that the stability of the neutral H3B¬NH3 system increases with increasing solvent polarity. In contrast, the opposite trend is observed for the positively charged {Zn¬(NH3)}2+. The observed changes are attributed to different charge redistributions in neutral and charged complexes, which are reflected by a different response to the solvent and are quantified by changes in solvation energies.
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Affiliation(s)
- Debashree Manna
- IOCB CAS: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Non-covalent interactions, CZECH REPUBLIC
| | - Rabindranath Lo
- IOCB CAS: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Non=covalent Interactions, CZECH REPUBLIC
| | - Dana Nachtigallová
- IOCB CAS: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Non-covalent interactions, CZECH REPUBLIC
| | - Zdeněk Trávníček
- UPOL: Univerzita Palackeho v Olomouci, Regional Centre of Advanced Technologies and Materials, CZECH REPUBLIC
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Computational Chemistry, Flemingovo nam. 2, 16610, Prague 6, CZECH REPUBLIC
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8
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Civiš S, Lamanec M, Špirko V, Kubišta J, Špet'ko M, Hobza P. Hydrogen Bonding with Hydridic Hydrogen-Experimental Low-Temperature IR and Computational Study: Is a Revised Definition of Hydrogen Bonding Appropriate? J Am Chem Soc 2023. [PMID: 37036315 PMCID: PMC10119939 DOI: 10.1021/jacs.3c00802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Spectroscopic characteristics of Me3Si-H···Y complexes (Y = ICF3, BrCN, and HCN) containing a hydridic hydrogen were determined experimentally by low-temperature IR experiments based on the direct spectral measurement of supersonically expanded intermediates on a cold substrate or by the technique of argon-matrix isolation as well as computationally at harmonic and one-dimensional anharmonic levels. The computations were based on DFT-D, MP2, MP2-F12, and CCSD(T)-F12 levels using various extended AO basis sets. The formation of all complexes related to the redshift of the Si-H stretching frequency upon complex formation was accompanied by an increase in its intensity. Similar results were obtained for another 10 electron acceptors of different types, positive σ-, π-, and p-holes and cations. The formation of HBe-H···Y complexes, studied only computationally and again containing a hydridic hydrogen, was characterized by the blueshift of the Be-H stretching frequency upon complexation accompanied by an increase in its intensity. The spectral shifts and stabilization energies obtained for all presently studied hydridic H-bonded complexes were comparable to those in protonic H-bonded complexes, which has prompted us to propose a modification of the existing IUPAC definition of H-bonding that covers, besides the classical protonic form, the non-classical hydridic and dihydrogen forms.
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Affiliation(s)
- Svatopluk Civiš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Náměstí 542/2, 160 00 Prague, Czech Republic
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Náměstí 542/2, 160 00 Prague, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
- Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Vladimír Špirko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Náměstí 542/2, 160 00 Prague, Czech Republic
| | - Jiří Kubišta
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic
| | - Matej Špet'ko
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Náměstí 542/2, 160 00 Prague, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
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9
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Lo R, Mašínová A, Lamanec M, Nachtigallová D, Hobza P. The unusual stability of H-bonded complexes in solvent caused by greater solvation energy of complex compared to those of isolated fragments. J Comput Chem 2023; 44:329-333. [PMID: 35616117 DOI: 10.1002/jcc.26928] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 01/03/2023]
Abstract
Here, the effect of solvent on the stability of non-covalent complexes, was studied. These complexes were from previously published S22, S66, and X40 datasets, which include hydrogen-, halogen- and dispersion-bonded complexes. It was shown that the charge transfer in the complex determines whether the complex is stabilized or destabilized in solvent.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Mašínová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
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10
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Miriyala VM, Lo R, Bouř P, Wu T, Nachtigallová D, Hobza P. Unexpected Strengthening of the H-Bond Complexes in a Polar Solvent Due to a More Efficient Solvation of the Complex Compared to Isolated Monomers. J Phys Chem A 2022; 126:7938-7943. [PMID: 36263696 DOI: 10.1021/acs.jpca.2c05992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is generally assumed that hydrogen-bonded complexes are less stable in solvents than in the gas phase and that their stability decreases with increasing solvent polarity. This assumption is based on the size of the area available to the solvent, which is always smaller in the complex compared to the subsystems, thereby reducing the solvation energy. This reduction prevails over the amplification of the electrostatic hydrogen bond by the polar solvent. In this work, we show, using experimental IR spectroscopy and DFT calculations, that there are hydrogen-bonded complexes whose stability becomes greater with increasing solvent polarity. The explanation for this surprising stabilization is based on the analysis of the charge redistribution in the complex leading to increase of its dipole moment and solvation energy. Constrained DFT calculations have shown a dominant role of charge transfer over polarization effects for dipole moment and solvation energy.
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Affiliation(s)
- Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 77900 Olomouc, Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 77900 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - Tau Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava, Poruba, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava, Poruba, Czech Republic
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11
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Abstract
Phosphorous-doped graphene can form a covalent dative bond with the electron acceptor, C60 molecule. On the other hand, C60 on graphene and N-doped graphene surfaces can only form vdW complexes. State-of-the-art quantum-chemical techniques have been used to characterise the nature of the P-C dative bond. A considerable amount of charge transfer from the P-Gr surface to C60 has been observed. This complex formation may enable enhancement in the optical limiting response with potential application in energy harvesting. The stability of the P-C dative bond has been assessed using DFT-D molecular dynamics simulations at 300 K for 10 ps.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic. .,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, Olomouc 77900, Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic. .,Maulana Abul Kalam Azad Universsity of Technology, West Bengal (formerly known as West Bengal University of Technology) Simhat, Haringhata-741249, WB, India
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic. .,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
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12
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Mallada B, Gallardo A, Lamanec M, de la Torre B, Špirko V, Hobza P, Jelinek P. Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy. Science 2021; 374:863-867. [PMID: 34762455 DOI: 10.1126/science.abk1479] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- B Mallada
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - A Gallardo
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - M Lamanec
- Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - B de la Torre
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - V Špirko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 12116 Prague, Czech Republic
| | - P Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - P Jelinek
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371 Olomouc, Czech Republic.,Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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13
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Otava T, Šála M, Li F, Fanfrlík J, Devkota K, Perveen S, Chau I, Pakarian P, Hobza P, Vedadi M, Boura E, Nencka R. The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors. ACS Infect Dis 2021; 7:2214-2220. [PMID: 34152728 PMCID: PMC8265718 DOI: 10.1021/acsinfecdis.1c00131] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 12/23/2022]
Abstract
In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases (MTases), nsp14. This MTase catalyzes the transfer of the methyl group from S-adenosyl-l-methionine (SAM) to cap the guanosine triphosphate moiety of the newly synthesized viral RNA, yielding the methylated capped RNA and S-adenosyl-l-homocysteine (SAH). As the crystal structure of SARS-CoV-2 nsp14 is unknown, we have taken advantage of its high homology to SARS-CoV nsp14 and prepared its homology model, which has allowed us to identify novel SAH derivatives modified at the adenine nucleobase as inhibitors of this important viral target. We have synthesized and tested the designed compounds in vitro and shown that these derivatives exert unprecedented inhibitory activity against this crucial enzyme. The docking studies nicely explain the contribution of an aromatic part attached by a linker to the position 7 of the 7-deaza analogues of SAH.
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Affiliation(s)
- Tomáš Otava
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
- Faculty of Food and Biochemical Technology,
University of Chemistry and Technology, 166 28, Prague 6,
Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Fengling Li
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Kanchan Devkota
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Paknoosh Pakarian
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Masoud Vedadi
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
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14
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Lo R, Manna D, Lamanec M, Wang W, Bakandritsos A, Dračínský M, Zbořil R, Nachtigallová D, Hobza P. Addition Reaction between Piperidine and C 60 to Form 1,4-Disubstituted C 60 Proceeds through van der Waals and Dative Bond Complexes: Theoretical and Experimental Study. J Am Chem Soc 2021; 143:10930-10939. [PMID: 34266233 DOI: 10.1021/jacs.1c01542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A combined computational and experimental study reveals the character of the C60 complexes with piperidine formed under different reaction conditions. The IR and NMR experiments detect the dative bond complex, which according to NMR, is stable in the oxygen-free environment and transforms to the adduct complex in the presence of O2. Computational studies on the character of reaction channels rationalize the experimental observations. They show that the piperidine dimer rather than a single piperidine molecule is required for the complex formation. The calculations reveal significant differences in the dative bond and adduct complexes' character, suggesting a considerable versatility in their electronic properties modulated by the environment. This capability offers new application potential in several fields, such as in energy storage devices.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, 77900 Olomouc, Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Department of Physical Chemistry, Palacký University Olomouc, tr. 17. listopadu 12, 77146 Olomouc, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China
| | - Aristides Bakandritsos
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, 77900 Olomouc, Czech Republic.,Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic
| | - Radek Zbořil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Křížkovského 511/8, 77900 Olomouc, Czech Republic.,Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000 Prague, Czech Republic.,IT4Innovations, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 70800 Ostrava-Poruba, Czech Republic
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15
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Abstract
The newly synthesized C18 ring is demonstrated as the smallest all-carbon acceptor that exhibits strong electron acceptance. This study provides a quantum-chemical investigation of the electron-acceptance behavior of monocyclic carbon rings with a particular emphasis on C18 through the formation of a dative bond with piperidine. The results show that Cn rings form strong dative bonds with piperidine, whereas the respective van der Waals (vdW) complexes are higher in energy. The main driving force is the release of angle strain of cyclo[n]carbons caused by the change in hybridization from sp to sp2 associated with the formation of the dative bond. On the contrary, other sp allotropes, diynes, favorably form vdW complexes. Molecular dynamics (MD) simulations support the stability of the dative bond throughout a simulation of 20 ps. This opens up the possibility of stabilizing highly reactive C18 through dative/covalent functionalization.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16000 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 77900 Olomouc, Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16000 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16000 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 77900 Olomouc, Czech Republic
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16
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Abstract
The P-C dative/covalent bonds formed in R3P-C60 complexes (R = OCH3, N(CH3)2, NC4H8) have been affected by the nature of the R group. The highest stabilisation (18.7 kcal mol-1) has been found in the last system. The contribution of dispersion energies in the stabilisation also varies depending on the R group. The nature of the P→C bond has been characterised using state-of-the-art quantum-chemical techniques including NBO, AIM and ELF. The P→C dative bond is significantly different from the prototype dative bonds appearing in H3N→BH3 as well as in the fullerene - secondary-amine complexes previously studied by us. The findings obtained through electron structure theory have been supported by 10 ps DFT-D MD simulations.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6 16610, Czech Republic.
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17
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Lo R, Lamanec M, Wang W, Manna D, Bakandritsos A, Dračínský M, Zbořil R, Nachtigallová D, Hobza P. Structure-directed formation of the dative/covalent bonds in complexes with C 70piperidine. Phys Chem Chem Phys 2021; 23:4365-4375. [PMID: 33589890 DOI: 10.1039/d0cp06280d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The combined experimental-computational study has been performed to investigate the complexes formed between C70 carbon allotrope and piperidine. The results of FT-IR, H-NMR, and C-NMR measurements, together with the calculations based on the DFT approach and molecular dynamics simulations, prove the existence of dative/covalent bonding in C70piperidine complexes. The dative bond forms not only at the region of five- and six-membered rings, observed previously with C60, but also at the region formed of six-membered rings. The structure, i.e., nonplanarity, explains the observed dative bond formation. New findings on the character of interaction of secondary amines with C70 bring new aspects for the rational design of modified fullerenes and their applications in electrocatalysis, spintronics, and energy storage.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and Department of Physical Chemistry, Palacký University Olomouc, Tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Aristides Bakandritsos
- CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic and Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Šlechtitelů 27, 78371, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic.
| | - Radek Zbořil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic and Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Šlechtitelů 27, 78371, Czech Republic and Nanotechnology Centre, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
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18
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Kolařík J, Bakandritsos A, Bad'ura Z, Lo R, Zoppellaro G, Kment Š, Naldoni A, Zhang Y, Petr M, Tomanec O, Filip J, Otyepka M, Hobza P, Zbořil R. Carboxylated Graphene for Radical-Assisted Ultra-Trace-Level Water Treatment and Noble Metal Recovery. ACS Nano 2021; 15:3349-3358. [PMID: 33464824 DOI: 10.1021/acsnano.0c10093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sorption technologies, enabling removal of heavy metals, play a pivotal role in meeting the global demands for unrestricted access to drinking water. Standard sorption technologies suffer from limited efficiency related to the weak sorbent-metal interaction. Further challenges include the development of technologies enabling smart metal recovery and sorbent regeneration. To this end, a densely functionalized graphene, with 33% by mass content of carboxyl groups, linked through direct C-C bonds (graphene acid, GA) represents a previously unexplored solution to this challenge. GA revealed excellent efficiency for removal of highly toxic metals, such as Cd2+ and Pb2+. Due to its selective chemistry, GA can bind heavy metals with high affinity, even at concentrations of 1 mg L-1 and in the presence of competing ions of natural drinking water, and reduce them down to drinking water allowance levels of a few μg L-1. This is not only due to carboxyl groups but also due to the stable radical centers of the GA structure, enabling metal ion-radical interactions, as proved by EPR, XPS, and density functional theory calculations. GA offers full structural integrity during the highly acidic and basic treatment, which is exploited for noble metal recovery (Ga3+, In3+, Pd2+) and sorbent regeneration. Owing to these attributes, GA represents a fully reusable metal sorbent, applicable also in electrochemical energy technologies, as illustrated with a GA/Pt catalyst derived from Pt4+-contaminated water.
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Affiliation(s)
- Jan Kolařík
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Aristides Bakandritsos
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Zdeněk Bad'ura
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Department of Experimental Physics, Faculty of Science, Palacký University Olomouc, 17. Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Rabindranath Lo
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Giorgio Zoppellaro
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Štěpán Kment
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Alberto Naldoni
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Yu Zhang
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Martin Petr
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Ondřej Tomanec
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Jan Filip
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Pavel Hobza
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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19
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Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Sárosi MB, Hnyk D, Hobza P. Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods. Chemphyschem 2020; 21:2599-2604. [PMID: 33179424 DOI: 10.1002/cphc.202000729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Indexed: 12/31/2022]
Abstract
The success of approximate computational methods, such as molecular mechanics, or dispersion-corrected density functional theory, in the description of non-covalent interactions relies on accurate parameterizations. Benchmark data sets are thus required. This area is well developed for organic molecules and biomolecules but practically non-existent for boron clusters, which have been gaining in importance in modern drug as well as material design. To fill this gap, we have introduced two data sets featuring the most common non-covalent interaction of boron clusters, the dihydrogen bond, and calculated reference interaction energies at the "golden standard" CCSD(T)/CBS level. The boron clusters studied interact with formamide, methanol, water and methane at various distances and in two geometrical arrangements. The performance of the tested approximate methods is variable and recommendations for further use are given.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Istituto Italiano di Tecnologia, Molecular Modeling and Drug Discovery, Via Morego 30, 161 63, Genoa, Italy
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Menyhárt B Sárosi
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 25068, Husinec-Řež, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 77146, Olomouc, Czech Republic
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20
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Lamanec M, Lo R, Nachtigallová D, Bakandritsos A, Mohammadi E, Dračínský M, Zbořil R, Hobza P, Wang W. The Existence of a N→C Dative Bond in the C
60
–Piperidine Complex. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Department of Physical Chemistry Palacký University Olomouc tr. 17 listopadu 12 771 46 Olomouc Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Aristides Bakandritsos
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Elmira Mohammadi
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
| | - Radek Zbořil
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- CATRIN, Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- CATRIN, Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials Luoyang Normal University Luoyang 471934 China
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21
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Lamanec M, Lo R, Nachtigallová D, Bakandritsos A, Mohammadi E, Dračínský M, Zbořil R, Hobza P, Wang W. The Existence of a N→C Dative Bond in the C
60
–Piperidine Complex. Angew Chem Int Ed Engl 2020; 60:1942-1950. [DOI: 10.1002/anie.202012851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Department of Physical Chemistry Palacký University Olomouc tr. 17 listopadu 12 771 46 Olomouc Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Aristides Bakandritsos
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Elmira Mohammadi
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
| | - Radek Zbořil
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- CATRIN, Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo Námĕstí 542/2 16000 Prague Czech Republic
- CATRIN, Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials Luoyang Normal University Luoyang 471934 China
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22
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2361. [PMID: 32986310 DOI: 10.1002/cplu.202000627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Invited for this month's cover is the group of Prof. Pavel Hobza, Czech Academy of Sciences, Prague. The cover picture shows a powerful automated quantum mechanics based SQM/COSMO approach to protein-ligand scoring. It comprises thorough preparation of ligand structures, extensive generation of binding complexes, fast geometry relaxation and reliable affinity prediction. Read the full text of the Minireview at 10.1002/cplu.202000120.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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23
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. Front Cover: SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design (ChemPlusChem 11/2020). Chempluschem 2020. [DOI: 10.1002/cplu.202000628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
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24
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Groborz O, Poláková L, Kolouchová K, Švec P, Loukotová L, Miriyala VM, Francová P, Kučka J, Krijt J, Páral P, Báječný M, Heizer T, Pohl R, Dunlop D, Czernek J, Šefc L, Beneš J, Štěpánek P, Hobza P, Hrubý M. Chelating Polymers for Hereditary Hemochromatosis Treatment. Macromol Biosci 2020; 20:e2000254. [PMID: 32954629 DOI: 10.1002/mabi.202000254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Indexed: 12/17/2022]
Abstract
Hemochromatosis (iron overload) encompasses a group of diseases that are characterized by a toxic hyperaccumulation of iron in parenchymal organs. Currently, only few treatments for this disease have been approved; however, all these treatments possess severe side effects. In this study, a paradigm for hemochromatosis maintenance/preventive therapy is investigated: polymers with negligible systemic biological availability form stable complexes with iron ions in the gastrointestinal tract, which reduces the biological availability of iron. Macroporous polymer beads are synthesized with three different iron-chelating moieties (benzene-1,2-diol, benzene-1,2,3-triol, and 1,10-phenanthroline). The polymers rapidly chelate iron ions from aqueous solutions in vitro in the course of minutes, and are noncytotoxic and nonprooxidant. Moreover, the in vivo biodistribution and pharmacokinetics show a negligible uptake from the gastrointestinal tract (using 125 I-labeled polymer and single photon emission computed tomography/computed tomography), which generally prevents them from having systemic side effects. The therapeutic efficacy of the prepared polymers is successfully tested in vivo, and exhibits a significant inhibition of iron uptake from the gastrointestinal tract without any noticeable signs of toxicity. Furthermore, an in silico method is developed for the prediction of chelator selectivity. Therefore, this paradigm can be applied to the next-generation maintenance/preventive treatment for hemochromatosis and/or other diseases of similar pathophysiology.
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Affiliation(s)
- Ondřej Groborz
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic.,Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, Salmovská 1, 120 00, Prague 2, Czech Republic
| | - Lenka Poláková
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
| | - Kristýna Kolouchová
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Pavel Švec
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Lenka Loukotová
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 162 06, Prague 6, Czech Republic
| | - Pavla Francová
- Center for Advanced Preclinical Imaging (CAPI), First Faculty of Medicine, Charles University, Salmovská 3, 120 00, Prague 2, Czech Republic
| | - Jan Kučka
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
| | - Jan Krijt
- Institute of Pathophysiology, First Faculty of Medicine, Charles University, U Nemocnice 5, 128 53, Prague 2, Czech Republic
| | - Petr Páral
- Center for Advanced Preclinical Imaging (CAPI), First Faculty of Medicine, Charles University, Salmovská 3, 120 00, Prague 2, Czech Republic
| | - Martin Báječný
- Center for Advanced Preclinical Imaging (CAPI), First Faculty of Medicine, Charles University, Salmovská 3, 120 00, Prague 2, Czech Republic
| | - Tomáš Heizer
- Center for Advanced Preclinical Imaging (CAPI), First Faculty of Medicine, Charles University, Salmovská 3, 120 00, Prague 2, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 162 06, Prague 6, Czech Republic
| | - David Dunlop
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 162 06, Prague 6, Czech Republic
| | - Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
| | - Luděk Šefc
- Center for Advanced Preclinical Imaging (CAPI), First Faculty of Medicine, Charles University, Salmovská 3, 120 00, Prague 2, Czech Republic
| | - Jiří Beneš
- Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, Salmovská 1, 120 00, Prague 2, Czech Republic
| | - Petr Štěpánek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 162 06, Prague 6, Czech Republic
| | - Martin Hrubý
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, 162 06, Prague 6, Czech Republic
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25
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Sarmah A, Hobza P. Mechanical force-induced manipulation of electronic conductance in a spin-crossover complex: a simple approach to molecular electronics. Nanoscale Adv 2020; 2:2907-2913. [PMID: 36132398 PMCID: PMC9417810 DOI: 10.1039/d0na00285b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 06/15/2023]
Abstract
The atomic-scale technological sophistication from the last half-decade provides new avenues for the atom-by-atom fabrication of nanostructures with extraordinary precision. This urges the appraisal of the fabrication scheme layout for a modular nanoelectronic device based on an individual molecular complex. The mechanical force-induced distortion to the metal coordination sphere triggers a low-spin (LS) to high-spin (HS) electronic transition in the complex. The controlled structural distortions (relative to a specific bond-angle) are deemed to be the switching parameter for the observed spin-transitions. Mechanical stretching is the key to engineering a spin-state switch in the proposed molecular device. The spin-dependent reversible variation in the electronic conductance concurrent to the unique spin-states can be understood from the state-of-the-art Nonequilibrium Green's Function (NEGF) calculations. Combined with NEGF calculations, the DFT study further provides a qualitative perception of the electronic conductance in the two-terminal device architecture. From the transport calculations, there is also evidence of considerable fluctuation in the spin-dependent electronic conductance at the molecular junction with relative variations in the scattering limit. Subsequently, the present study shows significant advances in the transmission probabilities for the high-spin state of the Fe(ii) complex. The results empower the progress of nanoelectronics at the single molecule level.
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Affiliation(s)
- Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic +420731015016
- Department of Physical Chemistry, Palacký University CZ-77146 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic +420731015016
- Department of Physical Chemistry, Palacký University CZ-77146 Olomouc Czech Republic
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26
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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27
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Nachtigallová D, Antalík A, Lo R, Sedlák R, Manna D, Tuček J, Ugolotti J, Veis L, Legeza Ö, Pittner J, Zbořil R, Hobza P. Corrigendum: An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground‐State: A Nexus between Theory and Experiment. Chemistry 2020; 26:1691. [DOI: 10.1002/chem.201905698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Antalík A, Nachtigallová D, Lo R, Matoušek M, Lang J, Legeza Ö, Pittner J, Hobza P, Veis L. Ground state of the Fe(ii)-porphyrin model system corresponds to quintet: a DFT and DMRG-based tailored CC study. Phys Chem Chem Phys 2020; 22:17033-17037. [DOI: 10.1039/d0cp03086d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe(ii)-porphyrins play an important role in many reactions, due to their closely lying spin states. We present a thorough study of a Fe(ii)-porphyrin model system, in which we examine how the geometrical parameters influence its spin state ordering.
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Affiliation(s)
- Andrej Antalík
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
- Faculty of Mathematics and Physics
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Mikuláš Matoušek
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
- Faculty of Mathematics and Physics
| | - Jakub Lang
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
| | - Örs Legeza
- Strongly Correlated Systems “Lendület” Research group
- Wigner Research Centre for Physics
- Budapest
- Hungary
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
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29
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Manna D, Lo R, Hobza P. Spin modification of iron(ii) complexes via covalent (dative) and dispersion guided non-covalent bonding with N-heterocyclic carbenes: DFT, DLPNO-CCSD(T) and MCSCF studies. Dalton Trans 2020; 49:164-170. [DOI: 10.1039/c9dt04334a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spin crossover from high spin Fe(ii)-phthalocyanine to low or intermediate spin via either dative covalent or non-covalent interaction by just varying the substituent using the same core ligand.
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Affiliation(s)
- Debashree Manna
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
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30
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Eyrilmez SM, Köprülüoğlu C, Řezáč J, Hobza P. Impressive Enrichment of Semiempirical Quantum Mechanics‐Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. Chemphyschem 2019; 20:2721. [DOI: 10.1002/cphc.201900975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsPalacký University 77146 Olomouc CzechRepublic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsPalacký University 77146 Olomouc CzechRepublic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsPalacký University 77146 Olomouc CzechRepublic
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31
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Macháčková K, Mlčochová K, Potalitsyn P, Hanková K, Socha O, Buděšínský M, Muždalo A, Lepšík M, Černeková M, Radosavljević J, Fábry M, Mitrová K, Chrudinová M, Lin J, Yurenko Y, Hobza P, Selicharová I, Žáková L, Jiráček J. Mutations at hypothetical binding site 2 in insulin and insulin-like growth factors 1 and 2 result in receptor- and hormone-specific responses. J Biol Chem 2019; 294:17371-17382. [PMID: 31558604 PMCID: PMC6873181 DOI: 10.1074/jbc.ra119.010072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/23/2019] [Indexed: 11/26/2022] Open
Abstract
Information on how insulin and insulin-like growth factors 1 and 2 (IGF-1 and -2) activate insulin receptors (IR-A and -B) and the IGF-1 receptor (IGF-1R) is crucial for understanding the difference in the biological activities of these peptide hormones. Cryo-EM studies have revealed that insulin uses its binding sites 1 and 2 to interact with IR-A and have identified several critical residues in binding site 2. However, mutagenesis studies suggest that Ile-A10, Ser-A12, Leu-A13, and Glu-A17 also belong to insulin's site 2. Here, to resolve this discrepancy, we mutated these insulin residues and the equivalent residues in IGFs. Our findings revealed that equivalent mutations in the hormones can result in differential biological effects and that these effects can be receptor-specific. We noted that the insulin positions A10 and A17 are important for its binding to IR-A and IR-B and IGF-1R and that A13 is important only for IR-A and IR-B binding. The IGF-1/IGF-2 positions 51/50 and 54/53 did not appear to play critical roles in receptor binding, but mutations at IGF-1 position 58 and IGF-2 position 57 affected the binding. We propose that IGF-1 Glu-58 interacts with IGF-1R Arg-704 and belongs to IGF-1 site 1, a finding supported by the NMR structure of the less active Asp-58–IGF-1 variant. Computational analyses indicated that the aforementioned mutations can affect internal insulin dynamics and inhibit adoption of a receptor-bound conformation, important for binding to receptor site 1. We provide a molecular model and alternative hypotheses for how the mutated insulin residues affect activity.
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Affiliation(s)
- Kateřina Macháčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Květoslava Mlčochová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Pavlo Potalitsyn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Kateřina Hanková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Anja Muždalo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Michaela Černeková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jelena Radosavljević
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Czech Academy of Sciences, 166 37 Prague 6, Czech Republic
| | - Katarína Mitrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Martina Chrudinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jingjing Lin
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Yevgen Yurenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
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Eyrilmez SM, Köprülüoğlu C, Řezáč J, Hobza P. Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. Chemphyschem 2019; 20:2759-2766. [PMID: 31460692 DOI: 10.1002/cphc.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Indexed: 12/11/2022]
Abstract
This paper describes the excellent performance of a newly developed scoring function (SF), based on the semiempirical QM (SQM) PM6-D3H4X method combined with the conductor-like screening implicit solvent model (COSMO). The SQM/COSMO, Amber/GB and nine widely used SFs have been evaluated in terms of ranking power on the HSP90 protein with 72 biologically active compounds and 4469 structurally similar decoys. Among conventional SFs, the highest early and overall enrichment measured by EF1 and AUC% obtained using single-scoring-function ranking has been found for Glide SP and Gold-ASP SFs, respectively (7, 75 % and 3, 76 %). The performance of other standard SFs has not been satisfactory, mostly even decreasing below random values. The SQM/COSMO SF, where P-L structures were optimised at the advanced Amber level, has resulted in a dramatic enrichment increase (47, 98 %), almost reaching the best possible receiver operator characteristic (ROC) curve. The best SQM frame thus inserts about seven times more active compounds into the selected dataset than the best standard SF.
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Affiliation(s)
- Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
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Affiliation(s)
- Pavel Hobza
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsDepartment of Physical Chemistry, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71 Olomouc Czech Republic
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Nachtigallová D, Antalík A, Lo R, Sedlák R, Manna D, Tuček J, Ugolotti J, Veis L, Legeza Ö, Pittner J, Zbořil R, Hobza P. Cover Feature: An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground-State: A Nexus between Theory and Experiment (Chem. Eur. J. 51/2018). Chemistry 2018. [DOI: 10.1002/chem.201804158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Andrej Antalík
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
- Faculty of Mathematics and Physics; Charles University Prague; 11636 Prague Czech Republic Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Robert Sedlák
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jiří Tuček
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Juri Ugolotti
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Örs Legeza
- Strongly Correlated Systems “ Lendület” Research group; Wigner Research Centre for Physics; 1525 Budapest Hungary
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
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Nachtigallová D, Antalík A, Lo R, Sedlák R, Manna D, Tuček J, Ugolotti J, Veis L, Legeza Ö, Pittner J, Zbořil R, Hobza P. An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground-State: A Nexus between Theory and Experiment. Chemistry 2018; 24:13413-13417. [DOI: 10.1002/chem.201803380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/31/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Andrej Antalík
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
- Faculty of Mathematics and Physics; Charles University Prague; 11636 Prague Czech Republic Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Robert Sedlák
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jiří Tuček
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Juri Ugolotti
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Örs Legeza
- Strongly Correlated Systems “ Lendület” Research group; Wigner Research Centre for Physics; 1525 Budapest Hungary
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
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de la Torre B, Švec M, Hapala P, Redondo J, Krejčí O, Lo R, Manna D, Sarmah A, Nachtigallová D, Tuček J, Błoński P, Otyepka M, Zbořil R, Hobza P, Jelínek P. Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene. Nat Commun 2018; 9:2831. [PMID: 30026582 PMCID: PMC6053383 DOI: 10.1038/s41467-018-05163-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Nitrogen doping of graphene significantly affects its chemical properties, which is particularly important in molecular sensing and electrocatalysis applications. However, detailed insight into interaction between N-dopant and molecules at the atomic scale is currently lacking. Here we demonstrate control over the spin state of a single iron(II) phthalocyanine molecule by its positioning on N-doped graphene. The spin transition was driven by weak intermixing between orbitals with z-component of N-dopant (pz of N-dopant) and molecule (dxz, dyz, dz2) with subsequent reordering of the Fe d-orbitals. The transition was accompanied by an electron density redistribution within the molecule, sensed by atomic force microscopy with CO-functionalized tip. This demonstrates the unique capability of the high-resolution imaging technique to discriminate between different spin states of single molecules. Moreover, we present a method for triggering spin state transitions and tuning the electronic properties of molecules through weak non-covalent interaction with suitably functionalized graphene.
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Affiliation(s)
- Bruno de la Torre
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Martin Švec
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Prokop Hapala
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic
| | - Jesus Redondo
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic
| | - Ondřej Krejčí
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Debashree Manna
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Amrit Sarmah
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Dana Nachtigallová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Jiří Tuček
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Piotr Błoński
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic.
| | - Pavel Hobza
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.
| | - Pavel Jelínek
- Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10, 16200, Prague 6, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic.
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37
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Sarmah A, Hobza P. Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes. Phys Chem Chem Phys 2018; 20:18718-18728. [PMID: 29956698 DOI: 10.1039/c8cp02027b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In recent years, magnetic or electric field induced modulations on the electronic environment of single molecular systems are common practice. In this particular study, we have instigated the possibility of controlling the electronic and spin-dependent properties of hydrogen-terminated graphene fragments, so-called graphene nanoflakes (GNF), using weak non-covalent interactions as the external stimuli. The topological frustration in the graphene fragment appreciated the compelling electronic behavior of the system. This leads to some unorthodox spin-distribution in the system and it is possible to synchronize this electronic perturbation switching through a non-covalent interaction. These findings institute a new avenue for sculpting such donor-acceptor composites as self-regulated spintronic devices in next generation electronics.
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Affiliation(s)
- Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic. and Department of Physical Chemistry, Palacký University, CZ-77146 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic. and Department of Physical Chemistry, Palacký University, CZ-77146 Olomouc, Czech Republic
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38
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Stasyuk OA, Sedlak R, Guerra CF, Hobza P. Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions. J Chem Theory Comput 2018; 14:3440-3450. [PMID: 29926727 DOI: 10.1021/acs.jctc.8b00034] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interaction energies computed with density functional theory can be divided into physically meaningful components by symmetry-adapted perturbation theory (DFT-SAPT) or the canonical energy decomposition analysis (EDA). In this work, the decomposition results obtained by these schemes were compared for more than 200 hydrogen-, halogen-, and pnicogen-bonded, dispersion-bound, and mixed complexes to investigate their similarity in the evaluation of the nature of noncovalent interactions. BLYP functional with D3(BJ) correction was used for the EDA scheme, whereas asymptotically corrected PBE0 functional for DFT-SAPT provided some of the best combinations for description of noncovalent interactions. Both schemes provide similar results concerning total interaction energies and insight into the individual energy components. For most complexes, the dominant energetic term was identified equally by both decomposition schemes. Because the canonical EDA is computationally less demanding than the DFT-SAPT, the former can be especially used in cases where the systems investigated are very large.
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Affiliation(s)
- Olga A Stasyuk
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic
| | - Robert Sedlak
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry , Palacký University , 771 46 Olomouc , Czech Republic
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling , VU Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , P.O. Box 9502, 2300 RA Leiden , The Netherlands
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry , Palacký University , 771 46 Olomouc , Czech Republic
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39
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Ajani H, Jansa J, Köprülüoğlu C, Hobza P, Kryštof V, Lyčka A, Lepsik M. Imidazo[1,2-c
]pyrimidin-5(6H
)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring. J Mol Recognit 2018; 31:e2720. [DOI: 10.1002/jmr.2720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Josef Jansa
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Department of Organic Chemistry, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University and Institute of Experimental Botany; Olomouc Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Faculty of Science; University of Hradec Králové; Hradec Králové Czech Republic
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40
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Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J. Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Chemphyschem 2018; 19:873-879. [PMID: 29316128 DOI: 10.1002/cphc.201701104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/11/2022]
Abstract
Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (Ki ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Magdalena Hořejší
- Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
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41
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Sarmah A, Hobza P. Sequential BN-doping induced tuning of electronic properties in zigzag-edged graphene nanoribbons: a computational approach. RSC Adv 2018; 8:10964-10974. [PMID: 35541531 PMCID: PMC9078980 DOI: 10.1039/c8ra00386f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/06/2018] [Indexed: 11/21/2022] Open
Abstract
We employed first-principles methods to elaborate doping induced electronic and magnetic perturbations in one-dimensional zigzag graphene nanoribbon (ZGNR) superlattices. Consequently, the incorporation of alternate boron and nitrogen (hole–electron) centers into the hexagonal network instituted substantial modulations to electronic and magnetic properties of ZGNR. Our theoretical analysis manifested some controlled changes to electronic and magnetic properties of the ZGNR by tuning the positions (array) of impurity centers in the carbon network. Subsequent DFT based calculations also suggested that the site-specific alternate electron–hole (B/N) doping could regulate the band-gaps of the superlattices within a broad range of energy. The consequence of variation in the width of ZGNR in the electronic environment of the system was also tested. The systematic analysis of various parameters such as the structural orientations, spin-arrangements, the density of states (DOS), band structures, and local density of states envisioned a basis for the band-gap engineering in ZGNR and attributed to its feasible applications in next generation electronic device fabrication. Incorporation of an alternate impurity array in the ZGNR don't break the spin-degeneracy, providing the freedom to tune the electronic behaviors without affecting the spin-dependent properties.![]()
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Affiliation(s)
- Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Czech Republic
- Department of Physical Chemistry
- Palacký University
- CZ–77146 Olomouc
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42
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Sedlak R, Eyrilmez SM, Hobza P, Nachtigallova D. The role of the σ-holes in stability of non-bonded chalcogenide⋯benzene interactions: the ground and excited states. Phys Chem Chem Phys 2018; 20:299-306. [DOI: 10.1039/c7cp05537d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Different characters of molecular electrostatic potential (MEP) in the ground and excited states of chalcogenides are responsible for changes in conformer stability of T-shape and stacked non-bonded chalcogenide–benzene complexes upon electronic excitation.
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Affiliation(s)
- Robert Sedlak
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Department of Physical Chemistry
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Dana Nachtigallova
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
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43
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Holub J, Růžičková Z, Hobza P, Fanfrlík J, Hnyk D, Růžička A. Various types of non-covalent interactions contributing towards crystal packing of halogenated diphospha-dicarbaborane with an open pentagonal belt. NEW J CHEM 2018. [DOI: 10.1039/c8nj00450a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have synthesized and crystalized 3-Cl-10-I-nido-7,8,9,11-P2C2B7H7. Quantum chemical calculations have demonstrated that the obtained crystal structure is stabilized by hydrogen, dihydrogen and pnictogen bonds.
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Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- 250 68 Husinec-Řež
- Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- 53210 Pardubice
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- 250 68 Husinec-Řež
- Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- 53210 Pardubice
- Czech Republic
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44
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Jia C, Zuo W, Yang D, Chen Y, Cao L, Custelcean R, Hostaš J, Hobza P, Glaser R, Wang YY, Yang XJ, Wu B. Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box. Nat Commun 2017; 8:938. [PMID: 29038482 PMCID: PMC5643546 DOI: 10.1038/s41467-017-00915-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 08/04/2017] [Indexed: 11/15/2022] Open
Abstract
In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. This similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives, as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, l-carnitine, and glycine betaine effectively. The choline-binding protein ChoX exhibits a synergistic dual-site binding mode that allows it to discriminate choline over structural analogues. Here, the authors design a biomimetic triple anion helicate receptor whose selectivity for choline arises from a similar binding mechanism.
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Affiliation(s)
- Chuandong Jia
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Wei Zuo
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Dong Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Yanming Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Liping Cao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Radu Custelcean
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6119, USA
| | - Jiří Hostaš
- Institute of Organic Chemistry and Biochemistry, 16010, Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 12843, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, 16010, Prague 6, Czech Republic.,Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Robert Glaser
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Yao-Yu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Xiao-Juan Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China.
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45
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Ajani H, Pecina A, Eyrilmez SM, Fanfrlík J, Haldar S, Řezáč J, Hobza P, Lepšík M. Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking. ACS Omega 2017; 2:4022-4029. [PMID: 30023710 PMCID: PMC6044937 DOI: 10.1021/acsomega.7b00503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/18/2017] [Indexed: 06/08/2023]
Abstract
General and reliable description of structures and energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency of scoring functions (SFs) by the systematic development of corrected semiempirical quantum mechanical (SQM) methods, which correctly describe all types of noncovalent interactions and are fast enough to treat systems of thousands of atoms. Two most accurate SQM methods, PM6-D3H4X and SCC-DFTB3-D3H4X, are coupled with the conductor-like screening model (COSMO) implicit solvation model in so-called "SQM/COSMO" SFs and have shown unique recognition of native ligand poses in cognate docking in four challenging PL systems, including metalloprotein. Here, we apply the two SQM/COSMO SFs to 17 diverse PL complexes and compare their performance with four widely used classical SFs (Glide XP, AutoDock4, AutoDock Vina, and UCSF Dock). We observe superior performance of the SQM/COSMO SFs and identify challenging systems. This method, due to its generality, comparability across the chemical space, and lack of need for any system-specific parameters, gives promise of becoming, after comprehensive large-scale testing in the near future, a useful computational tool in structure-based drug design and serving as a reference method for the development of other SFs.
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Affiliation(s)
- Haresh Ajani
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Adam Pecina
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Saltuk M. Eyrilmez
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Jindřich Fanfrlík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Susanta Haldar
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Jan Řezáč
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Pavel Hobza
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacký University, 77146 Olomouc, Czech Republic
| | - Martin Lepšík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
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46
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Karlický F, Otyepková E, Lo R, Pitoňák M, Jurečka P, Pykal M, Hobza P, Otyepka M. Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite. J Chem Theory Comput 2017; 13:1328-1340. [PMID: 28145699 PMCID: PMC5352977 DOI: 10.1021/acs.jctc.6b01130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 11/28/2022]
Abstract
Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from -7 to -13 kcal/mol and are by 1-2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy.
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Affiliation(s)
- František Karlický
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Eva Otyepková
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Rabindranath Lo
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166
10 Prague 6, Czech Republic
| | - Michal Pitoňák
- Department
of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, 842 15 Bratislava, Slovakia
- Computing Center
of the Slovak Academy of Sciences, Dúbravská cesta č. 9, 845 35 Bratislava, Slovakia
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Martin Pykal
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
| | - Pavel Hobza
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166
10 Prague 6, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký
University Olomouc, tř.
17. listopadu 12, 77 146 Olomouc, Czech Republic
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47
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Affiliation(s)
- Pavel Hobza
- Academy of Sciences of the Czech Republic, Prague
| | - Jan Řezáč
- Academy of Sciences of the Czech Republic, Prague
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48
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Sigwalt D, Šekutor M, Cao L, Zavalij PY, Hostaš J, Ajani H, Hobza P, Mlinarić-Majerski K, Glaser R, Isaacs L. Unraveling the Structure–Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids. J Am Chem Soc 2017; 139:3249-3258. [DOI: 10.1021/jacs.7b00056] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- David Sigwalt
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Marina Šekutor
- Department
of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Liping Cao
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Peter Y. Zavalij
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jiří Hostaš
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Praha 6, Czech Republic
| | - Haresh Ajani
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Praha 6, Czech Republic
- Regional
Center of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, 77146 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Praha 6, Czech Republic
- Regional
Center of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, 77146 Olomouc, Czech Republic
| | - Kata Mlinarić-Majerski
- Department
of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Robert Glaser
- Department
of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Lyle Isaacs
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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49
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Nekardová M, Vymětalová L, Khirsariya P, Kováčová S, Hylsová M, Jorda R, Kryštof V, Fanfrlík J, Hobza P, Paruch K. Structural Basis of the Interaction of Cyclin-Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles. Chemphyschem 2017; 18:785-795. [DOI: 10.1002/cphc.201601319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Michaela Nekardová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Faculty of Mathematics and Physics; Charles University in Prague; Ke Karlovu 3 Prague 2 121 16 Czech Republic
| | - Ladislava Vymětalová
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
| | - Silvia Kováčová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Michaela Hylsová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
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50
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Pecina A, Haldar S, Fanfrlík J, Meier R, Řezáč J, Lepšík M, Hobza P. SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses. J Chem Inf Model 2017; 57:127-132. [DOI: 10.1021/acs.jcim.6b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Adam Pecina
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - René Meier
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Palacký University, 77146 Olomouc, Czech Republic
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