1
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Shenderovich IG. The Scope of the Applicability of Non-relativistic DFT Calculations of NMR Chemical Shifts in Pyridine-Metal Complexes for Applied Applications. Chemphyschem 2024; 25:e202300986. [PMID: 38259119 DOI: 10.1002/cphc.202300986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Heavy metals are toxic, but it is impossible to stop using them. Considering the variety of molecular systems in which they can be present, the multicomponent nature and disorder of the structure of such systems, one of the most effective methods for studying them is NMR spectroscopy. This determines the need to calculate NMR chemical shifts for expected model systems. For elements beyond the third row of the periodic table, corrections for relativistic effects are necessary when calculating NMR parameters. Such corrections may be necessary even for light atoms due to the shielding effect of a neighboring heavy atom. This work examines the extent to which non-relativistic DFT calculations are able to reproduce experimental 15N and 113Cd NMR chemical shift tensors in pyridine-metal coordination complexes. It is shown that while for the calculation of 15N NMR chemical shift tensors there is no real need to consider relativistic corrections, for 113Cd, on the contrary, none of the tested calculation methods could reproduce the experimentally obtained tensor to any extent correctly.
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Affiliation(s)
- Ilya G Shenderovich
- NMR Department, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040, Regensburg, Germany
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2
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Franco BA, Luciano ER, Sarotti AM, Zanardi MM. DP4+App: Finding the Best Balance between Computational Cost and Predictive Capacity in the Structure Elucidation Process by DP4+. Factors Analysis and Automation. JOURNAL OF NATURAL PRODUCTS 2023; 86:2360-2367. [PMID: 37721602 DOI: 10.1021/acs.jnatprod.3c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
DP4+ is one of the most popular methods for the structure elucidation of natural products using NMR calculations. While the method is simple and easy to implement, it requires a series of procedures that can be tedious, coupled with the fact that its computational demand can be high in certain cases. In this work, we made a substantial improvement to these limitations. First, we deeply explored the effect of molecular mechanics architecture on the DP4+ formalism (MM-DP4+). In addition, a Python applet (DP4+App) was developed to automate the entire process, requiring only the Gaussian NMR output files and a spreadsheet containing the experimental NMR data and labels. The script is designed to use the statistical parameters from the original 24 levels of theory (employing B3LYP/6-31G* geometries) and the new 36 levels explored in this work (over MMFF geometries). Furthermore, it enables the development of customizable methods using any desired level of theory, allowing for a free choice of test molecules.
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Affiliation(s)
- Bruno A Franco
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Ezequiel R Luciano
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - María M Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
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3
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Shenderovich IG. Weak, Broken, but Working-Intramolecular Hydrogen Bond in 2,2'-bipyridine. Int J Mol Sci 2023; 24:10390. [PMID: 37373539 DOI: 10.3390/ijms241210390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
From an academic and practical point of view, it is desirable to be able to assess the possibility of the proton exchange of a given molecular system just by knowing the positions of the proton acceptor and the proton donor. This study addresses the difference between intramolecular hydrogen bonds in 2,2'-bipyridinium and 1,10-phenanthrolinium. Solid-state 15N NMR and model calculations show that these hydrogen bonds are weak; their energies are 25 kJ/mol and 15 kJ/mol, respectively. Neither these hydrogen bonds nor N-H stretches can be responsible for the fast reversible proton transfer observed for 2,2'-bipyridinium in a polar solvent down to 115 K. This process must have been caused by an external force, which was a fluctuating electric field present in the solution. However, these hydrogen bonds are the grain that tips the scales precisely because they are an integral part of a large system of interactions, including both intramolecular interactions and environmental influence.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany
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4
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Imamura K, Yokogawa D, Higashi M, Sato H. Reference interaction site model self-consistent field with constrained spatial electron density approach for nuclear magnetic shielding in solution. J Chem Phys 2022; 157:204105. [DOI: 10.1063/5.0122326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We propose a new hybrid approach combining quantum chemistry and statistical mechanics of liquids for calculating the nuclear magnetic resonance (NMR) chemical shifts of solvated molecules. Based on the reference interaction site model self-consistent field with constrained spatial electron density distribution (RISM–SCF–cSED) method, the electronic structure of molecules in solution is obtained, and the expression for the nuclear magnetic shielding tensor is derived as the second-order derivative of the Helmholtz energy of the solution system. We implemented a method for calculating chemical shifts and applied it to an adenine molecule in water, where hydrogen bonding plays a crucial role in electronic and solvation structures. We also performed the calculations of 17O chemical shifts, which showed remarkable solvent dependence. While converged results could not be sometimes obtained using the conventional method, in the present framework with RISM–SCF–cSED, an adequate representation of electron density is guaranteed, making it possible to obtain an NMR shielding constant stably. This introduction of cSED is key to extending the method’s applicability to obtain the chemical shift of various chemical species. The present demonstration illustrates our approach’s superiority in terms of numerical robustness and accuracy.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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5
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Streitferdt V, Tiefenthaler SM, Shenderovich IG, Gärtner S, Korber N, Gschwind RM. NMR‐Spectroscopic Detection of an Elusive Protonated and Coinage Metalated Silicide [NHC
Dipp
Cu(η
4
‐Si
9
)H]
2−
in Solution. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Verena Streitferdt
- Institute of Organic Chemistry University of Regensburg 93040 Regensburg Germany
| | | | | | - Stefanie Gärtner
- Central Analytics University of Regensburg 93040 Regensburg Germany
| | - Nikolaus Korber
- Institute of Inorganic Chemistry University of Regensburg 93040 Regensburg Germany
| | - Ruth M. Gschwind
- Institute of Organic Chemistry University of Regensburg 93040 Regensburg Germany
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6
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Shenderovich IG, Denisov GS. Modeling of the Response of Hydrogen Bond Properties on an External Electric Field: Geometry, NMR Chemical Shift, Spin-Spin Scalar Coupling. Molecules 2021; 26:molecules26164967. [PMID: 34443575 PMCID: PMC8399935 DOI: 10.3390/molecules26164967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡15N-1H⋯X, 1J(15N1H) depends exclusively on the N-H distance, while δ(15N) is also slightly influenced by the nature of X.
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Affiliation(s)
- Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russia;
- Correspondence:
| | - Gleb S. Denisov
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russia;
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7
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NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The isotopically enriched cyanide anion, (13C≡15N)−, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of 15N≡13CH···X and 13C≡15NH···X hydrogen bonding complexes in solution, where X = 19F, 15N, and O=31P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic 13C and 15N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. 1J(15N13C) strongly correlates with the length of the N≡C bond.
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8
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Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State. Symmetry (Basel) 2021. [DOI: 10.3390/sym13050756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).
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9
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Shenderovich IG. 1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution. Molecules 2021; 26:molecules26051390. [PMID: 33806666 PMCID: PMC7961616 DOI: 10.3390/molecules26051390] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its 31P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this 31P chemical shift. This approach has been tested on a variety of the metals of groups 8-12 and molecular structures. General recommendations for appropriate basis sets are reported.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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10
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Modeling of Solute-Solvent Interactions Using an External Electric Field-From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides. Molecules 2021; 26:molecules26051283. [PMID: 33652943 PMCID: PMC7956811 DOI: 10.3390/molecules26051283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 12/18/2022] Open
Abstract
An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute-solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.
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11
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Abstract
Magnetic shielding depends on molecular structure and noncovalent interactions. This study shows that it is also measurably dependent on the electric field generated by surrounding molecules. This effect has been observed explicitly for 31P nucleus using the adduct under field approach. The results obtained indicate that the field strength experienced by molecules in crystals consisting of molecules with large dipole moments is similar to that in polar solvents. Therefore, magnetic shielding should explicitly depend on solvent polarity. It is important to note that this effect cannot be reproduced correctly within the polarizable continuum model approach.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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12
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Jóźwiak K, Jezierska A, Panek JJ, Goremychkin EA, Tolstoy PM, Shenderovich IG, Filarowski A. Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates. Molecules 2020; 25:E4720. [PMID: 33066679 PMCID: PMC7587347 DOI: 10.3390/molecules25204720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 01/18/2023] Open
Abstract
Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.
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Affiliation(s)
- Kinga Jóźwiak
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
| | - Eugene A. Goremychkin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia;
| | - Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.)
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13
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Shenderovich IG. For Whom a Puddle Is the Sea? Adsorption of Organic Guests on Hydrated MCM-41 Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11383-11392. [PMID: 32900200 DOI: 10.1021/acs.langmuir.0c02327] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermal and hydration effects on the mobility of compact and branched organic molecules and a bulky pharmaceutical substance loaded in submonolayer amounts onto mesoporous silica have been elucidated using 1H and 31P solid-state NMR. In all cases, the ambient hydration has a stronger effect than an increase in temperature to 370 K for water-free silica. The effect of hydration depends on the guest and ranges from complete solvation to a silica-water-guest sandwich structure to a silica-guest/silica-water pattern. The mobility of the guests under different conditions has been described. The specific structure of the MCM-41 surface allows one to study very slow surface diffusion, a diffusivity of about 10-15-10-16 m2/s. The data reported are relevant to any nonfunctionalized silica, while the method used is applicable to any phosphor-containing guest on any host.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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14
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Shenderovich IG. Experimentally Established Benchmark Calculations of
31
P NMR Quantities. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/cmtd.202000033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ilya G. Shenderovich
- Ilya G. Shenderovich Institute of Organic Chemistry University of Regensburg Universitaetstrasse 31 93053 Regensburg Germany
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15
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Kaczmarek-Kędziera A. Gas Phase Computational Study of Diclofenac Adsorption on Chitosan Materials. Molecules 2020; 25:molecules25112549. [PMID: 32486148 PMCID: PMC7321203 DOI: 10.3390/molecules25112549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental pollution with non-steroidal anti-inflammatory drugs and their metabolites exposes living organisms on their long-lasting, damaging influence. Hence, the ways of non-steroidal anti-inflammatory drugs (NSAIDs) removal from soils and wastewater is sought for. Among the potential adsorbents, biopolymers are employed for their good availability, biodegradability and low costs. The first available theoretical modeling study of the interactions of diclofenac with models of pristine chitosan and its modified chains is presented here. Supermolecular interaction energy in chitosan:drug complexes is compared with the the mutual attraction of the chitosan dimers. Supermolecular interaction energy for the chitosan-diclofenac complexes is significantly lower than the mutual interaction between two chitosan chains, suggesting that the diclofenac molecule will encounter problems when penetrating into the chitosan material. However, its surface adsorption is feasible due to a large number of hydrogen bond donors and acceptors both in biopolymer and in diclofenac. Modification of chitosan material introducing long-distanced amino groups significantly influences the intramolecular interactions within a single polymer chain, thus blocking the access of diclofenac to the biopolymer backbone. The strongest attraction between two chitosan chains with two long-distanced amino groups can exceed 120 kcal/mol, while the modified chitosan:diclofenac interaction remains of the order of 20 to 40 kcal/mol.
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Affiliation(s)
- Anna Kaczmarek-Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
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16
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Shenderovich IG, Denisov GS. Adduct under Field-A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding. Molecules 2020; 25:molecules25030436. [PMID: 31973045 PMCID: PMC7037398 DOI: 10.3390/molecules25030436] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF3/CDClF2. With some limitations, they can be applied to the chemically similar CHCl3 and CH2Cl2. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters.
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Affiliation(s)
- Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
- Correspondence: ; Tel.:+49-941-9434027
| | - Gleb S. Denisov
- Department of Physics, Saint-Petersburg State University, 198504 Saint-Petersburg, Russia;
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17
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Shenderovich IG, Denisov GS. Solvent effects on acid-base complexes. What is more important: A macroscopic reaction field or solute-solvent interactions? J Chem Phys 2019; 150:204505. [PMID: 31153188 DOI: 10.1063/1.5096946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Can the geometry of an acid-base complex in solution be reproduced in calculations using an implicit accounting for the solvent effect in the form of a macroscopic reaction field? The answer is, "Yes, it can." Is this field equal to the real electric field experienced by the complex in solution? The answer is, "No, it is not." How can the geometry be correct under wrong conditions? This question is answered using density functional theory modeling of geometric and NMR parameters of pyridine⋯HF⋯(HCF3)n adducts in the absence and presence of an external electric field. This adduct under field approach shows that the N⋯H distance is a function of the H-F distance whatever method is used to change the geometry of the latter. An explicit account for solute-solvent interactions is required to get a realistic value of the solvent reaction field. Besides that, this approach reveals how certain NMR parameters depend on the solvent reaction field, the solute-solvent interactions, and the geometry of the N⋯H-F hydrogen bond. For some of them, the obtained dependences are far from self-evident.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Gleb S Denisov
- Department of Physics, St.Petersburg State University, Saint Petersburg, Russia
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18
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Chernyshov IY, Vener MV, Shenderovich IG. Local-structure effects on 31P NMR chemical shift tensors in solid state. J Chem Phys 2019; 150:144706. [PMID: 30981271 DOI: 10.1063/1.5075519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The effect of the local structure on the 31P NMR chemical shift tensor (CST) has been studied experimentally and simulated theoretically using the density functional theory gauge-independent-atomic-orbital approach. It has been shown that the dominating impact comes from a small number of noncovalent interactions between the phosphorus-containing group under question and the atoms of adjacent molecules. These interactions can be unambiguously identified using the Bader analysis of the electronic density. A robust and computationally effective approach designed to attribute a given experimental 31P CST to a certain local morphology has been elaborated. This approach can be useful in studies of surfaces, complex molecular systems, and amorphous materials.
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Affiliation(s)
- Ivan Yu Chernyshov
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany
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19
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Zanardi MM, Sortino MA, Sarotti AM. On the effect of intramolecular H-bonding in the configurational assessment of polyhydroxylated compounds with computational methods. The hyacinthacines case. Carbohydr Res 2019; 474:72-79. [DOI: 10.1016/j.carres.2019.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 01/04/2023]
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