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Ćeranić K, Milovanović B, Petković M. Density functional theory study of crown ether-magnesium complexes: from a solvated ion to an ion trap. Phys Chem Chem Phys 2023; 25:32656-32665. [PMID: 38010878 DOI: 10.1039/d3cp03991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Metal ion detection rests on host-guest recognition. We propose a theoretical protocol for designing an optimal trap for a desired metal cation. A host for magnesium ions was sought for among derivatives of crown ethers 12-crown-4, 15-crown-5, and 18-crown-6. Mg-crown complexes and their hydrated counterparts with water molecules bound to the cation were optimized using density functional theory. Based on specific geometric criteria, Interacting quantum atoms analysis and density functional theory-based molecular dynamics of Mg-crown complexes immersed in water, crown ethers for optimal accommodation of Mg2+ in aqueous solution were identified. Selectivity of the chosen crowns towards Na+, K+, and Ca2+ ions is addressed.
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Affiliation(s)
- Katarina Ćeranić
- Innovative Centre of the Faculty of Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Branislav Milovanović
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Milena Petković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
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Osifová Z, Šála M, Dračínský M. Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives. ACS OMEGA 2023; 8:25538-25548. [PMID: 37483191 PMCID: PMC10357537 DOI: 10.1021/acsomega.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for life on Earth. Canonical nucleobases form base pairs according to two main geometries: Watson-Crick pairing, which enables the static functions of nucleic acids, such as the storing of genetic information; and Hoogsteen pairing, which facilitates the dynamic functions of these biomacromolecules. This precisely tuned system can be affected by oxidation or substitution of nucleobases, leading to changes in their hydrogen-bonding patterns. This paper presents an investigation into the intermolecular interactions of various 8-substituted purine derivatives with their hydrogen-bonding partners. The systems were analyzed using nuclear magnetic resonance spectroscopy and density functional theory calculations. Our results demonstrate that the stability of hydrogen-bonded complexes, or base pairs, depends primarily on the number of intermolecular H-bonds and their donor-acceptor alternation. No strong preferences for a particular geometry, either Watson-Crick or Hoogsteen, were found.
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Affiliation(s)
- Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
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Hercigonja M, Milovanović B, Etinski M, Petković M. Decorated crown ethers as selective ion traps: Solvent’s role in crown’s preference towards a specific ion. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides. Int J Mol Sci 2022; 23:ijms232113514. [PMID: 36362296 PMCID: PMC9654426 DOI: 10.3390/ijms232113514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base–base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated.
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Martínez FA, Adler NS, Cavasotto CN, Aucar GA. Solvent effects on the NMR shieldings of stacked DNA base pairs. Phys Chem Chem Phys 2022; 24:18150-18160. [PMID: 35861154 DOI: 10.1039/d2cp00398h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).
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Affiliation(s)
- Fernando A Martínez
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Chemistry Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina
| | - Natalia S Adler
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Centro de Investigaciones en BioNanociencias (CIBION), CONICET, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
| | - Gustavo A Aucar
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina.
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Pavković N, Milovanović B, Stanojević A, Etinski M, Petković M. Proton leap: shuttling of protons onto benzonitrile. Phys Chem Chem Phys 2022; 24:3958-3969. [PMID: 35099492 DOI: 10.1039/d1cp04338b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed description of chemical transformations in the interstellar medium allows deciphering the origin of a number of small and medium - sized organic molecules. We present density functional theory analysis of proton transfer from the trihydrogen cation and the ethenium cation to benzonitrile, a recently discovered species in the Taurus Molecular Cloud 1. Detailed energy transformations along the reaction paths were analyzed using the interacting quantum atoms methodology, which elucidated how the proton carrier influences the lightness to deliver the proton to benzonitrile's nitrogen atom. The proton carriers' deformation energy represents the largest destabilizing effect, whereas a proton's promotion energy, the benzonitrile-proton Coulomb attraction, as well as non-classical benzonitrile-proton and carrier-proton interaction are the dominant stabilizing energy components. As two ion-molecule reactions proceed without energy barriers, rate constants were estimated using the classical capture theory and were found to be an order of magnitude larger for the reaction with the trihydrogen cation compared to that with the ethenium cation (∼10-8 and 10-9 cm3 s-1, respectively). These results were obtained both with quantum chemical and ab initio molecular dynamics simulations (the latter performed at 10 K and 100 K), confirming that up to 100 K both systems choose energetically undemanding routes by tracking the corresponding minimum energy paths. A concept of a turning point is introduced, which is an equivalent to the transition state in barrierless reactions.
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Affiliation(s)
- Nemanja Pavković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Branislav Milovanović
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Ana Stanojević
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Mihajlo Etinski
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Milena Petković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
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Chen L, Feng Q, Wang C, Yin S, Mo Y. Classical Electrostatics Remains the Driving Force for Interanion Hydrogen and Halogen Bonding. J Phys Chem A 2021; 125:10428-10438. [PMID: 34818021 DOI: 10.1021/acs.jpca.1c09250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interanion hydrogen bonding (IAHB) and halogen bonding (IAXB) have emerged as a counterintuitive linker in a range of fascinating applications. Despite the overall repulsive (positive) binding energy, anions are trapped in a local minimum with its corresponding transition state (TS) preventing dissociation. In other words, the adduct of anions is metastable. Seemingly, the electrostatic paradigm and force field description of hydrogen/halogen bonding (HB/XB) are challenged, because of the preconceived Coulombic repulsion. Aiming at an insightful understanding of these interanion phenomena, we employed the energy decomposition approach based on the block-localized wavefunction method (BLW-ED) to investigate a series of exemplary interanion complexes. As expected, the key distinction from the conventional HB/XB lies in the electrostatic interaction, which is not increasingly repulsive as anions gradually approach to each other. Rather, there is a Coulombic barrier at a certain point. After this point, the electrostatic repulsion diminishes with the decreasing distance between anions. Differently, other energy components vary monotonically just like in conventional cases. The nonmonotonic characteristic of the electrostatic interaction in interanion complexes was reproduced using the multipole expansion in AMOEBA polarizable force field in which the state-specified atomic multipoles were adopted. This suggests that the nonmonotonicity can be well interpreted by classical electrostatic theory and there is no conceptual difference between conventional HB/XB and IAHB/IAXB. The stability of IAHB/IAXB depends on the competition between the local attractive HB/XB and the global Coulombic repulsion of net charges, though there is cooperativity between these two contrasting forces. This concise model was supported by the attractive IAHB/IAXB in modified molecular capsules, which exhibit strong quadruple HB/XBs and a considerable distance between charged substituents.
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Affiliation(s)
- Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qiuyan Feng
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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