1
|
Andolpho GA, Ramalho TC. Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme. J Comput Chem 2024; 45:1303-1315. [PMID: 38363124 DOI: 10.1002/jcc.27328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen-bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE-CWA complex involving Sarin (GB), Cyclosarin (GF), 2-[fluoro(methyl)phosphoryl]oxy-1,1-dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position. The AIM analysis was carried out and consistently revealed the presence of a significant interaction along the PO bond. Investigating the intrinsic nature of the PnB, the NBO and the EDA analysis unearthed the contribution of orbital factors to the overall energy of the system. Strikingly, this observation challenges the conventional σ-hole explanation commonly associated with such interactions. This finding adds a layer of complexity to understanding of PnB, encouraging further exploration into the underlying mechanisms governing these intriguing chemical phenomena.
Collapse
Affiliation(s)
- Gustavo A Andolpho
- Chemistry Department, Institute of Natural Sciences, Universidade Federal de Lavras, Lavras, Brazil
| | - Teodorico C Ramalho
- Chemistry Department, Institute of Natural Sciences, Universidade Federal de Lavras, Lavras, Brazil
- Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| |
Collapse
|
2
|
Ijaz R, Waqas M, Mahal A, Essid M, Zghab I, Khera RA, Alotaibi HF, Al-Haideri M, Alshomrany AS, Zahid S, Alatawi NS, Aloui Z. Tuning the optoelectronic properties of selenophene-diketopyrrolopyrrole-based non-fullerene acceptor to obtain efficient organic solar cells through end-capped modification. J Mol Graph Model 2024; 129:108745. [PMID: 38442441 DOI: 10.1016/j.jmgm.2024.108745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
With the goal of developing a high-performance organic solar cell, nine molecules of A2-D-A1-D-A2 type are originated in the current investigation. The optoelectronic properties of all the proposed compounds are examined by employing the DFT approach and the B3LYP functional with a 6-31G (d, p) basis set. By substituting the terminal moieties of reference molecule with newly proposed acceptor groups, several optoelectronic and photovoltaic characteristics of OSCs have been studied, which are improved to a significant level when compared with reference molecule, i.e., absorption properties, excitation energy, exciton binding energy, band gap, oscillator strength, electrostatic potential, light-harvesting efficiency, transition density matrix, open-circuit voltage, fill factor, density of states and interaction coefficient. All the newly developed molecules (P1-P9) have improved λmax, small band gap, high oscillator strengths, and low excitation energies compared to the reference molecule. Among all the studied compounds, P9 possesses the least binding energy (0.24 eV), P8 has high interaction coefficient (0.70842), P3 has improved electron mobility due to the least electron reorganization energy (λe = 0.009182 eV), and P5 illustrates high light-harvesting efficiency (0.7180). P8 and P9 displayed better Voc results (1.32 eV and 1.33 eV, respectively) and FF (0.9049 and 0.9055, respectively). Likewise, the phenomenon of charge transfer in the PTB7-Th/P1 blend seems to be a marvelous attempt to introduce them in organic photovoltaics. Consequently, the outcomes of these parameters demonstrate that adding new acceptors to reference molecule is substantial for the breakthrough development of organic solar cells (OSCs).
Collapse
Affiliation(s)
- Rimsha Ijaz
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Ahmed Mahal
- Department of Medical Biochemical Analysis, College of Health Technology, Cihan University-Erbil, Erbil, Kurdistan Region, Iraq.
| | - Manel Essid
- Chemistry Department, College of Science, King Khalid University (KKU), Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Imen Zghab
- Department of Physical Sciences, Chemistry Division, College of Science, Jazan University, P.O. Box. 114, Jazan, 45142, Kingdom of Saudi Arabia
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Hadil Faris Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdul Rahman University, Riyadh 11671, Saudi Arabia
| | - Maysoon Al-Haideri
- Pharmacy Department, School of Medicine, University of Kurdistan Hewlêr, Kurdistan Region, Iraq
| | - Ali S Alshomrany
- Department of Physics, College of Sciences, Umm Al-Qura University, Al Taif HWY, Mecca 24381, Saudi Arabia
| | - Saba Zahid
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Naifa S Alatawi
- Physics Department, Faculty of Science, University of Tabuk, Tabuk, 71421, Saudi Arabia
| | - Zouhaier Aloui
- Chemistry Department, College of Science, King Khalid University (KKU), Abha 61413, P.O. Box 9004, Saudi Arabia.
| |
Collapse
|
3
|
Svatunek D. Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions. Top Curr Chem (Cham) 2024; 382:17. [PMID: 38727989 PMCID: PMC11087259 DOI: 10.1007/s41061-024-00461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.
Collapse
Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, Technische Universität Wien (TU Wien), Getreidemarkt 9, 1060, Vienna, Austria.
| |
Collapse
|
4
|
Nikulshin PV, Makarov AY, Koskin IP, Becker CS, Kazantsev MS, Beckmann J, Balmohammadi Y, Grabowsky S, Mebs S, Naumova OV, Protasov DY, Svit KA, Irtegova IG, Radiush EA, Bagryanskaya IY, Shundrin LA, Zibarev AV. 1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials. Chempluschem 2024; 89:e202300692. [PMID: 38052725 DOI: 10.1002/cplu.202300692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.
Collapse
Affiliation(s)
- Pavel V Nikulshin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Alexander Yu Makarov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Igor P Koskin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Christina S Becker
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Maxim S Kazantsev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Stefan Mebs
- Institute for Experimental Physics, Free University of Berlin, 14195, Berlin, Germany
| | - Olga V Naumova
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Dmitry Yu Protasov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Kirill A Svit
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Ekaterina A Radiush
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| |
Collapse
|
5
|
Focke K, De Santis M, Wolter M, Martinez B JA, Vallet V, Pereira Gomes AS, Olejniczak M, Jacob CR. Interoperable workflows by exchanging grid-based data between quantum-chemical program packages. J Chem Phys 2024; 160:162503. [PMID: 38686818 DOI: 10.1063/5.0201701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.
Collapse
Affiliation(s)
- Kevin Focke
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Matteo De Santis
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Jessica A Martinez B
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Valérie Vallet
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | | | - Małgorzata Olejniczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| |
Collapse
|
6
|
Balasubramanian H, Mariappan PR, Poomani K. Crystal structure, intermolecular interactions, charge-density distribution and ADME properties of the acridinium 4-nitrobenzoate and 2-amino-3-methylpyridinium 4-nitrobenzoate salts: a combined experimental and theoretical study. Acta Crystallogr C Struct Chem 2024; 80:115-122. [PMID: 38502537 DOI: 10.1107/s2053229624002250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
Acridines are a class of bioactive agents which exhibit high biological stability and the ability to intercalate with DNA; they have a wide range of applications. Pyridine derivatives have a wide range of biological activities. To enhance the properties of acridine and 2-amino-3-methylpyridine as the active pharmaceutical ingredient (API), 4-nitrobenzoic acid was chosen as a coformer. In the present study, a mixture of acridine and 4-nitrobenzoic acid forms the salt acridinium 4-nitrobenzoate, C13H10N+·C7H4NO4- (I), whereas a mixture of 2-amino-3-methylpyridine and 4-nitrobenzoic acid forms the salt 2-amino-3-methylpyridinium 4-nitrobenzoate, C6H9N2+·C7H4NO4- (II). In both salts, protonation takes place at the ring N atom. The crystal structure of both salts is predominantly governed by hydrogen-bond interactions. In salt I, C-H...O and N-H...O interactions form an infinite chain in the crystal, whereas in salt II, intermolecular N-H...O interactions form an eight-membered R22(8) ring motif. A theoretical charge-density analysis reveals the charge-density distribution of the inter- and intramolecular interactions of both salts. An in-silico ADME analysis predicts the druglikeness properties of both salts and the results confirm that both salts are potential drug candidates with good bioavailability scores and there is no violation of the Lipinski rules, which supports the druglikeness properties of both salts. However, although both salts exhibit drug-like properties, salt I has higher gastrointestinal absorption than salt II and hence it may be considered a potential drug candidate.
Collapse
Affiliation(s)
- Hemalatha Balasubramanian
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Petchi Raman Mariappan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| |
Collapse
|
7
|
Kakalejčíková S, Bazel Y, Fizer M. Extraction-less green spectrofluorimetric method for determination of mercury using an Astra Phloxine fluorophore: Comprehensive experimental and theoretical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123946. [PMID: 38295591 DOI: 10.1016/j.saa.2024.123946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 01/11/2024] [Accepted: 01/21/2024] [Indexed: 02/02/2024]
Abstract
A new sensitive and selective extraction-less method for the spectrofluorimetric determination of Hg2+ has been developed using the polymethine dye Astra Phloxine (AP) with requirements for green analytical chemistry. The principle of this method for analytical use is the formation of an ion associate (IA) in the presence of mercury ions and AP, which causes a change in the electronic structure of the dye cation and its subsequent fluorescence quenching. The IA created during the process was sufficiently stable in aqueous solutions and did not require the use of surfactants or organic solvents, which are typically used for similar analytical systems. The system indicated high selectivity towards Hg2+ in the presence of at least 100-fold higher concentrations of Co2+, Fe2+, Mg2+, Ni2+, Zn2+, Ca2+, Ba2+, K+, Na+. The calibration curve was linear in the range from 0.003 to 0.1 mg L-1. Precision and accuracy were expressed as intra-day and inter-day analysis with RSD values of 2.9 - 4.8 % and recovery of 97.1 - 110.0 %. The proposed method was used for the determination of Hg2+ on the model and real water samples. Theoretical calculations were used to predict the IA structure and to explain the experimentally observed fluorescence spectra. A few theoretical methods were tested for predicting IA emission energies, and the CIS(D) method was found to be the most accurate.
Collapse
Affiliation(s)
- Sofia Kakalejčíková
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, Košice, Slovak Republic.
| | - Yaroslav Bazel
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, Košice, Slovak Republic
| | - Maksym Fizer
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States; Department of Organic Chemistry, Educational Scientific Institute of Chemistry and Ecology, Uzhhorod National University, Fedinets', Str. 53/1, Uzhhorod 88000, Ukraine.
| |
Collapse
|
8
|
Zahoor A, Sadiq S, Khera RA, Essid M, Aloui Z, Alatawi NS, Ibrahim MAA, Hasanin THA, Waqas M. A DFT study for improving the photovoltaic performance of organic solar cells by designing symmetric non-fullerene acceptors by quantum chemical modification on pre-existed LC81 molecule. J Mol Graph Model 2023; 125:108613. [PMID: 37659133 DOI: 10.1016/j.jmgm.2023.108613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023]
Abstract
Minimizing the energy loss and improving the open circuit voltage of organic solar cells is still a primary concern for scientists working in this field. With the aim to enhance the photovoltaic performance of organic solar cells by minimizing energy loss and improving open circuit voltage, seven new acceptor molecules (LC1-LC7) are presented in this work. These molecules are designed by modifying the terminal acceptors of pre-existed "LC81" molecule based on an indacinodithiophene (IDT) fused core. The end-group modification approach is very fruitful in ameliorating the efficacy and optoelectric behavior of OSCs. The newly developed molecules presented remarkable improvements in performance-related parameters and optoelectronic properties. Among all designed molecules, LC7 exhibited the highest absorption maxima (λmax = 869 nm) with the lowest band-gap (1.79 eV), lowest excitation energy (Ex = 1.42 eV), lowest binding energy, and highest excited state lifetime (0.41 ns). The newly designed molecules LC2, LC3, and LC4 exhibited remarkably improved Voc that was 1.84 eV, 1.82 eV, and 1.79 eV accordingly, compared to the LC81 molecule with Voc of 1.74 eV LC2 molecule showed significant improvement in fill factor compared to the previously presented LC81 molecule. LC2, LC6, and LC7 showed a remarkable reduction in energy loss by showing Eloss values of 0.26 eV, 0.18 eV, and 0.25 eV than LC81 molecule (0.37 eV). These findings validate the supremacy of these developed molecules (especially LC2) as potential components of future OSCs.
Collapse
Affiliation(s)
- Amna Zahoor
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Sonia Sadiq
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
| | - Manel Essid
- Chemistry Department, College of Science, King Khalid University (KKU), Abha, P.O. Box 9004, Saudi Arabia
| | - Zouhaier Aloui
- Chemistry Department, College of Science, King Khalid University (KKU), Abha, P.O. Box 9004, Saudi Arabia
| | - Naifa S Alatawi
- Physics Department, Faculty of Science, University of Tabuk, Tabuk, 71421, Saudi Arabia
| | - Mahmoud A A Ibrahim
- Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt; School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4000, South Africa
| | - Tamer H A Hasanin
- Department of Chemistry, College of Science, Jouf University, Sakaka, P.O. Box 2014, Saudi Arabia
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
| |
Collapse
|
9
|
Anisimov AA, Ananyev IV. Electron density-based protocol to recover the interacting quantum atoms components of intermolecular binding energy. J Chem Phys 2023; 159:124113. [PMID: 38127385 DOI: 10.1063/5.0167874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/11/2023] [Indexed: 12/23/2023] Open
Abstract
A new approach for obtaining interacting quantum atoms-defined components of binding energy of intermolecular interactions, which bypasses the use of standard six-dimensional integrals and two-particle reduced density matrix (2-RDM) reconstruction, is proposed. To examine this approach, three datasets calculated within the density functional theory framework using the def2-TZVP basis have been explored. The first two, containing 53 weakly bound bimolecular associates and 13 molecular clusters taken from the crystal, were used in protocol refinement, and the third one containing other 20 bimolecular and three cluster systems served as a validation reference. In addition, to verify the performance of the proposed approach on an exact 2-RDM, calculations within the coupled cluster formalism were performed for part of the first set systems using the cc-pVTZ basis set. The process of optimization of the proposed parametric model is considered, and the role of various energy contributions in the formation of non-covalent interactions is discussed with regard to the obtained trends.
Collapse
Affiliation(s)
- Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str. 28, GSP-1, Moscow 119334, Russian Federation
- National Research University Higher School of Economics, Myasnitskaya Str. 20, Moscow 101000, Russian Federation
| | - Ivan V Ananyev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, Leninsky prospect 31, Moscow 119991, Russian Federation
| |
Collapse
|
10
|
Novoa T, Laplaza R, Peccati F, Fuster F, Contreras-García J. The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. J Chem Inf Model 2023; 63:4483-4489. [PMID: 37537899 DOI: 10.1021/acs.jcim.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.
Collapse
Affiliation(s)
- Trinidad Novoa
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
- Laboratoire Jacques-Louis Lions, LJLL, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Francesca Peccati
- Basque Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Franck Fuster
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
| | | |
Collapse
|
11
|
Jensen CV, Kjaergaard HG. Gas-Phase Room-Temperature Detection of the tert-Butyl Hydroperoxide Dimer. J Phys Chem A 2023; 127:6476-6485. [PMID: 37527456 DOI: 10.1021/acs.jpca.3c03702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
We have detected the tert-butyl hydroperoxide dimer, (t-BuOOH)2, in the gas phase at room temperature using conventional FTIR techniques. The dimer is identified by an asymmetric absorbance band assigned to the fundamental hydrogen-bound OHb-stretch. The weighted band maximum of the dimer OHb-stretch is located at ∼3452 cm-1, red-shifted by ∼145 cm-1 from the monomer OH-stretching band. The gas-phase dimer assignment is supported by Ar matrix isolation FTIR experiments at 12 K and experiments with a partially deuterated sample. Computationally, we find the lowest energy structure of (t-BuOOH)2 to be a doubly hydrogen bound six-membered ring with non-optimal hydrogen bond angles. We estimate the gas-phase constant of dimer formation, K, to be 0.4 (standard pressure of 1 bar) using the experimental integrated absorbance and a theoretically determined oscillator strength of the OHb-stretching band.
Collapse
Affiliation(s)
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen-Ø, Denmark
| |
Collapse
|
12
|
Chavez-Urias I, López-González LE, Plascencia-Martínez DF, García JJ, Flores-Alamo M, Sugich-Miranda R, Medrano F, Picos-Corrales LA, López-Gastélum KA, Velázquez-Contreras EF, Rocha-Alonzo F. l-Isoleucine-Schiff Base Copper(II) Coordination Polymers: Crystal Structure, Spectroscopic, Hirshfeld Surface, and DFT Analyses. ACS OMEGA 2023; 8:24601-24614. [PMID: 37457461 PMCID: PMC10339395 DOI: 10.1021/acsomega.3c02878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
A new copper(II) coordination polymer was synthesized from the l-isoleucine-Schiff base and characterized by elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible (UV-vis) spectroscopy, single-crystal X-ray diffraction (XRD) analysis, electronic paramagnetic resonance, and thermogravimetric analysis. XRD analysis confirmed the square planar coordination geometry of metallic centers and a zipper-like polymer structure. Vibrational, electronic, and paramagnetic spectroscopies and thermal analysis were consistent with the crystal structure. A Hirshfeld surface (HS) and density functional theory (DFT) analyses were employed to gain additional insight into interactions responsible for complex packing. The quantitative examination of two-dimensional (2D) fingerprint plots revealed, among other van der Waals forces, the dominating participation of H···H and H···Cl interactions in the molecular packing. The use of computational methods provided great help in detailing the supramolecular interactions occurring in the crystal, which were mainly van der Waals attractions. The electronic transition analysis helped corroborate the electronic transitions observed experimentally in the absorption spectrum. The frequency and vibrational mode analysis gave a deeper insight into the characterization of the CuLCL complex.
Collapse
Affiliation(s)
- Iván
F. Chavez-Urias
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Luis E. López-González
- Centro
de Investigación Científica y de Educación Superior
de Ensenada, Carretera Tijuana-Ensenada 3918, Zona Playitas, Ensenada, Baja California 22860, México
| | - Damian F. Plascencia-Martínez
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Juventino J. García
- Facultad
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior Cd. Universitaria, Coyoacán,
Ciudad de México, Ciudad de México 04510, México
| | - Marcos Flores-Alamo
- Facultad
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior Cd. Universitaria, Coyoacán,
Ciudad de México, Ciudad de México 04510, México
| | - Rocío Sugich-Miranda
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Felipe Medrano
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Lorenzo A. Picos-Corrales
- Facultad
de Ingeniería Culiacán, Universidad
Autónoma de Sinaloa, Ciudad Universitaria, Culiacán, Sinaloa 80013, México
| | - Karla-Alejandra López-Gastélum
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
- Centro de
Investigación en Alimentación y Desarrollo, Carretera a Ejido La Victoria Km
0.6, Hermosillo, Sonora 83304, México
| | - Enrique F. Velázquez-Contreras
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Fernando Rocha-Alonzo
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| |
Collapse
|
13
|
Sadiq S, Waqas M, Zahoor A, Mehmood RF, Essid M, Aloui Z, Khera RA, Akram SJ. Synergistic modification of end groups in Quinoxaline fused core-based acceptor molecule to enhance its photovoltaic characteristics for superior organic solar cells. J Mol Graph Model 2023; 123:108518. [PMID: 37235903 DOI: 10.1016/j.jmgm.2023.108518] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The competence of organic solar cells (OSCs) could be enhanced by improving the light absorption capabilities as well as the open-circuit voltage (Voc) of utilized molecules. To upgrade overall functionality of OSCs, seven new molecules were designed in this work using an end-cap alteration technique on Quinoxaline fused core-based non-fullerene acceptor (Qx-2) molecule. This technique is known to be quite advantageous in terms of improvement of the effectiveness and optoelectrical behavior of various OSCs. Critical parameters like the absorption maximum, frontier molecular orbitals, excitation energy, exciton binding energy, Voc, and fill factor of molecules were considered for the molecules thus designed. All newly designed molecules showed outstanding improvement in optoelectronic as well as performance-related properties. Out of all scrutinized molecules, Q1 exhibited highest wavelength of absorption peak (λmax = 779 nm) with the reduced band gap (1.90 eV), least excitation energy (Ex = 1.59 eV), along with the highest dipole moment (17.982950 D). Additionally, the newly designed compounds Q4, Q5, and Q6 exhibited significantly improved Vocs that were 1.55, 1.47, and 1.50 eV accordingly, as compared to the 1.37 eV of Qx-2 molecule. These molecules also showed remarkable improvement in fill factor attributed to direct correspondence of Voc with it. Inclusively, these results support the superiority of these newly developed molecules as prospective constituents of upgraded OSCs.
Collapse
Affiliation(s)
- Sonia Sadiq
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Amna Zahoor
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Rana Farhat Mehmood
- Department of Chemistry, Division of Science and Technology, University of Education, Township, Lahore, 54770, Pakistan
| | - Manel Essid
- Chemistry Department, College of Science, King Khalid University (KKU), Abha, P.O. Box 9004, Saudi Arabia
| | - Zouhaier Aloui
- Chemistry Department, College of Science, King Khalid University (KKU), Abha, P.O. Box 9004, Saudi Arabia
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
| | - Sahar Javaid Akram
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
| |
Collapse
|
14
|
Hammud HH, Yar M, Bayach I, Ayub K. Covalent Triazine Framework C 6N 6 as an Electrochemical Sensor for Hydrogen-Containing Industrial Pollutants. A DFT Study. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1121. [PMID: 36986015 PMCID: PMC10053058 DOI: 10.3390/nano13061121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
Industrial pollutants pose a serious threat to ecosystems. Hence, there is a need to search for new efficient sensor materials for the detection of pollutants. In the current study, we explored the electrochemical sensing potential of a C6N6 sheet for H-containing industrial pollutants (HCN, H2S, NH3 and PH3) through DFT simulations. The adsorption of industrial pollutants over C6N6 occurs through physisorption, with adsorption energies ranging from -9.36 kcal/mol to -16.46 kcal/mol. The non-covalent interactions of analyte@C6N6 complexes are quantified by symmetry adapted perturbation theory (SAPT0), quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses. SAPT0 analyses show that electrostatic and dispersion forces play a dominant role in the stabilization of analytes over C6N6 sheets. Similarly, NCI and QTAIM analyses also verified the results of SAPT0 and interaction energy analyses. The electronic properties of analyte@C6N6 complexes are investigated by electron density difference (EDD), natural bond orbital analyses (NBO) and frontier molecular orbital analyses (FMO). Charge is transferred from the C6N6 sheet to HCN, H2S, NH3 and PH3. The highest exchange of charge is noted for H2S (-0.026 e-). The results of FMO analyses show that the interaction of all analytes results in changes in the EH-L gap of the C6N6 sheet. However, the highest decrease in the EH-L gap (2.58 eV) is observed for the NH3@C6N6 complex among all studied analyte@C6N6 complexes. The orbital density pattern shows that the HOMO density is completely concentrated on NH3, while the LUMO density is centred on the C6N6 surface. Such a type of electronic transition results in a significant change in the EH-L gap. Thus, it is concluded that C6N6 is highly selective towards NH3 compared to the other studied analytes.
Collapse
Affiliation(s)
- Hassan H. Hammud
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Muhammad Yar
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, KPK, Islamabad 22060, Pakistan
| | - Imene Bayach
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, KPK, Islamabad 22060, Pakistan
| |
Collapse
|
15
|
Kojasoy V, Tantillo DJ. Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I. J Phys Chem A 2023; 127:2081-2090. [PMID: 36855831 DOI: 10.1021/acs.jpca.2c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.
Collapse
Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| |
Collapse
|
16
|
i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. Commun Chem 2023; 6:31. [PMID: 36797370 PMCID: PMC9935537 DOI: 10.1038/s42004-023-00831-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC5 normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC5 to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.
Collapse
|
17
|
Naserian S, Izadyar M, Ranjbakhsh E. Theoretical evaluation of charge transport properties and mobility of tetraphenyldipyranylidene derivatives in organic field-effect transistors. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
18
|
Novoa T, Contreras-García J, Chaquin P. Conformational preference analysis in C 2H 6 using orbital forces and non-covalent interactions; comparison with related systems. Phys Chem Chem Phys 2023; 25:4276-4283. [PMID: 36688469 DOI: 10.1039/d2cp04913a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Dynamic Orbital Forces (DOF) and Non-Covalent Interactions (NCIs) are used to analyze the attractive/repulsive interactions responsible of the conformational preference of ethane and some related compounds. In ethane, it is found that the stabilization of the staggered conformation with respect to the adiabatic eclipsed one arises from both attractive and repulsive interactions in CH3⋯CH3. Attractive ones are predominant in a ratio 2 : 1, with an important role of a σ MO. On the contrary, the stabilization of the staggered conformation with respect to the vertical eclipsed one arises almost only from repulsive π interactions. Weak long-range H⋯H repulsions also favour the staggered conformation. From the sum of DOFs, yielding intrinsic bond energies, the rotation barrier can be decomposed into a weakening of the C-C bond (ca. 7 kcal mol-1), moderated by a strengthening of C-H ones (ca. 4 kcal mol-1). This evidences the decrease of hyperconjugation in the eclipsed conformation with respect to the staggered one. In the compounds CH3-SiH3, SiH3-SiH3, CH3-CF3 and CF3-CF3, the conformational preference is predominantly or exclusively due to repulsive interactions, with respect as well to adiabatic as to vertical eclipsed structures.
Collapse
Affiliation(s)
- Trinidad Novoa
- Laboratoire de Chimie Théorique (LCT) Sorbonne Université, CNRS, 4, Place Jussieu, F-75005, Paris, France.
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT) Sorbonne Université, CNRS, 4, Place Jussieu, F-75005, Paris, France.
| | - Patrick Chaquin
- Laboratoire de Chimie Théorique (LCT) Sorbonne Université, CNRS, 4, Place Jussieu, F-75005, Paris, France.
| |
Collapse
|
19
|
Wilming FM, Marazzi B, Debes PP, Becker J, Schreiner PR. Probing the Size Limit of Dispersion Energy Donors with a Bifluorenylidene Balance: Magic Cyclohexyl. J Org Chem 2023; 88:1024-1035. [PMID: 36576961 DOI: 10.1021/acs.joc.2c02444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report the synthesis of 14 2,2'-disubstituted 9,9'-bifluorenylidenes as molecular balances for the quantification of London dispersion interactions between various dispersion energy donors. For all balances, we measured ΔGZ/E at 333 K using 1H NMR in seven organic solvents. For various alkyl and aryl substituents, we generally observe a preference for the "folded" Z-isomer due to attractive London dispersion interactions. The cyclohexyl-substituted system shows the largest Z-preference in this study with ΔGZ/E = -0.6 ± 0.05 kcal mol-1 in all solvents, owing to the rotational freedom of cyclohexyl groups paired with their large polarizability that maximizes London dispersion interactions. On the other hand, rigid and sterically more demanding substituents like tert-butyl unexpectedly favor the unfolded E-isomer. This is a result of the close relative position in which the functional groups are positioned in this molecular balance. This close proximity is the reason for the increase of Pauli repulsion in the Z-isomers with large rigid substituents (tert-butyl, adamantyl, and diamantyl) which leads to an equilibrium shift toward the unfolded E-form. While we were able to reproduce most of our experimental trends qualitatively using contemporary computational chemistry methods, quantitative accuracy of the employed methods still needs further improvement.
Collapse
Affiliation(s)
- Finn M Wilming
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Benito Marazzi
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Paul P Debes
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.,Center for Materials Research (ZfM), Justus Liebig University, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| |
Collapse
|
20
|
Recent progress of membrane technology for chiral separation: A comprehensive review. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.123077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
21
|
Experimental and theoretical studies of a thiourea derivative: 1-(4-Chloro-benzoyl)-3-(2-trifluoromethyl-phenyl)thiourea. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
22
|
Complexes of carbon dioxide with methanol and its monohalogen-substituted: Beyond the tetrel bond. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140158] [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]
|
23
|
Ammonia quantum tunneling in cold rare-gas He and Ar clusters and factorial design approach for methodology evaluation. J Mol Model 2022; 28:293. [PMID: 36063224 DOI: 10.1007/s00894-022-05267-9] [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: 06/03/2022] [Accepted: 08/12/2022] [Indexed: 10/14/2022]
Abstract
Quantum tunneling of the ammonia inversion motion and energy level splittings in He and Ar clusters were investigated. It was found that the double well potential (DWP) in He clusters is symmetrical and that the first layer of He atoms is able to model the system. The calculated tunneling splitting was in good agreement with the experimental, 36.4 and 24.6 cm[Formula: see text] respectively. For NH[Formula: see text] in Ar clusters, the DWP becomes slightly asymmetric, which is enough to decrease the resonance and make the symmetric DWP unable to model the system. An asymmetric potential was used and the result was in excellent agreement with the experimental splitting, of 9.0 and 10.6 cm[Formula: see text] respectively. Non-covalent interactions revealed that the asymmetry is caused by dissimilar interactions in each minimum of the double well potential. The effects of different methodologies were analyzed via a design of experiments approach. For the gas-phase NH[Formula: see text] molecule, only diffuse functions were statistically significant while for the NH[Formula: see text] embedded in He cluster both the MP2 method and polarization functions were significant. This tendency suggests higher order polarization functions may be essential to generate accurate barrier heights.
Collapse
|
24
|
Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
Collapse
Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
| |
Collapse
|
25
|
Comprehensive Study of the Chemistry behind the Stability of Carboxylic SWCNT Dispersions in the Development of a Transparent Electrode. NANOMATERIALS 2022; 12:nano12111901. [PMID: 35683756 PMCID: PMC9182667 DOI: 10.3390/nano12111901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are well-known for their excellent electrical conductivity. One promising application for SWCNT-based thin films is as transparent electrodes for uncooled mid-IR detectors (MIR). In this paper, a combination of computational and experimental studies were performed to understand the chemistry behind the stability of carboxylic SWCNTs (SWCNTs-COOH) dispersions in different solvents. A computational study based on the density functional tight-binding (DFTB) method was applied to understand the interactions of COOH-functionalized carbon nanotubes with selected solvents. Attention was focused on understanding how the protonation of COOH groups influences the binding energies between SWCNTs and different solvents. Thin film electrodes were prepared by alternately depositing PEI and SWCNT-COOH on soda lime glass substrates. To prepare a stable SWCNT dispersion, different solvents were tested, such as deionized (DI) water, ethanol and acetone. The SWCNT-COOH dispersion stability was tested in different solvents. Samples were prepared to study the relationship between the number of depositions, transparency in the MIR range (2.5–5 µm) and conductivity, looking for the optimal thickness that would satisfy the application. The MIR transparency of the electrode was reduced by 20% for the thickest SWCNT layers, whereas sheet resistance values were reduced to 150–200 kΩ/sq.
Collapse
|
26
|
De S, Tomiczek BM, Yang Y, Ko K, Ghiviriga I, Roitberg A, Grenning AJ. Diastereoselective Indole-Dearomative Cope Rearrangements by Compounding Minor Driving Forces. Org Lett 2022; 24:3726-3730. [PMID: 35576941 PMCID: PMC10112279 DOI: 10.1021/acs.orglett.2c01381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reported herein is the discovery of a diastereoselective indole-dearomative Cope rearrangement. A suite of minor driving forces promote dearomatization: (i) steric congestion in the starting material, (ii) alkylidene malononitrile and stilbene conjugation events in the product, and (iii) an unexpected intramolecular π-π* stack on the product side of the equilibrium. The key substrates are rapidly assembled from simple starting materials, resulting in many successful examples. The products are structurally complex and bear vicinal stereocenters generated by the dearomative Cope rearrangement. They also contain a variety of functional groups for interconversion to complex architectures.
Collapse
Affiliation(s)
- Subhadip De
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Breanna M Tomiczek
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Yinuo Yang
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Kenneth Ko
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Adrian Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| | - Alexander J Grenning
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32603, United States
| |
Collapse
|
27
|
Ashraf A, Herbert JM, Muhammad S, Farooqi BA, Farooq U, Salman M, Ayub K. Theoretical Approach to Evaluate the Gas-Sensing Performance of Graphene Nanoribbon/Oligothiophene Composites. ACS OMEGA 2022; 7:2260-2274. [PMID: 35071915 PMCID: PMC8772315 DOI: 10.1021/acsomega.1c05863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Composite formation with graphene is an effective approach to increase the sensitivity of polythiophene (nPT) gas sensors. The interaction mechanism between gaseous analytes and graphene/nPT composite systems is still not clear, and density functional theory calculations are used to explore the interaction mechanism between graphene/nPT nanoribbon composites (with n = 3-9 thiophene units) and gaseous analytes CO, NH3, SO2, and NO2. For the studied analytes, the interaction energy ranges from -44.28 kcal/mol for (C54H30-3PT)-NO2 to -2.37 kcal/mol for (C54H30-3PT)-CO at the counterpoise-corrected ωB97M-V/def2-TZVPD level of theory. The sensing mechanism is further evaluated by geometric analysis, ultraviolet-visible spectroscopy, density of-states analysis, calculation of global reactivity indices, and both frontier and natural bond orbital analyses. The variation in the highest occupied molecular orbital/lowest unoccupied molecular orbital gap of the composite indicates the change in conductivity upon complexation with the analyte. Energy decomposition analysis reveals that dispersion and charge transfer make the largest contributions to the interaction energy. The graphene/oligothiophene composite is more sensitive toward these analytes than either component taken alone due to larger changes in the orbital gap. The computational framework established in the present work can be used to evaluate and design graphene/nPT nanoribbon composite materials for gas sensors.
Collapse
Affiliation(s)
- Ayesha Ashraf
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - Shabbir Muhammad
- Department
of Physics, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Bilal Ahmad Farooqi
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Umar Farooq
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Muhammad Salman
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| |
Collapse
|
28
|
Coba‐Jiménez L, Maza J, Guerra M, Deluque‐Gómez J, Cubillán N. Interaction of Ciprofloxacin with Arabinose, Glucosamine, Glucuronic Acid and Rhamnose: Insights from Genetic Algorithm and Quantum Chemistry. ChemistrySelect 2022. [DOI: 10.1002/slct.202103836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ludis Coba‐Jiménez
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Julio Maza
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Mayamarú Guerra
- Laboratorio de Óptica y Procesamiento de Imágenes Facultad de Ciencias Básicas Universidad Tecnológica de Bolívar Turbaco Colombia
| | - Julio Deluque‐Gómez
- Programa de Ingeniería Industrial Facultad de Ingenierías Universidad de la Guajira Riohacha Colombia
| | - Néstor Cubillán
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| |
Collapse
|
29
|
Shachar A, Kallos I, de Vries MS, Bar I. Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations. J Phys Chem Lett 2021; 12:11273-11279. [PMID: 34767362 DOI: 10.1021/acs.jpclett.1c03336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N-H···π and C-H···H-C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.
Collapse
Affiliation(s)
- Afik Shachar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Itai Kallos
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Mattanjah S de Vries
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| |
Collapse
|
30
|
González-Veloso I, Figueiredo NM, Cordeiro MNDS. Unravelling the Interactions of Magnetic Ionic Liquids by Energy Decomposition Schemes: Towards a Transferable Polarizable Force Field. Molecules 2021; 26:molecules26185526. [PMID: 34576997 PMCID: PMC8466702 DOI: 10.3390/molecules26185526] [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: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
This work aims at unravelling the interactions in magnetic ionic liquids (MILs) by applying Symmetry-Adapted Perturbation Theory (SAPT) calculations, as well as based on those to set-up a polarisable force field model for these liquids. The targeted MILs comprise two different cations, namely: 1-butyl-3-methylimidazolium ([Bmim]+) and 1-ethyl-3-methylimidazolium ([Emim]+), along with several metal halides anions such as [FeCl4]−, [FeBr4]−, [ZnCl3]− and [SnCl4]2− To begin with, DFT geometry optimisations of such MILs were performed, which in turn revealed that the metallic anions prefer to stay close to the region of the carbon atom between the nitrogen atoms in the imidazolium fragment. Then, a SAPT study was carried out to find the optimal separation of the monomers and the different contributions for their interaction energy. It was found that the main contribution to the interaction energy is the electrostatic interaction component, followed by the dispersion one in most of the cases. The SAPT results were compared with those obtained by employing the local energy decomposition scheme based on the DLPNO-CCSD(T) method, the latter showing slightly lower values for the interaction energy as well as an increase of the distance between the minima centres of mass. Finally, the calculated SAPT interaction energies were found to correlate well with the melting points experimentally measured for these MILs.
Collapse
|
31
|
Goossen LJ, Koley D, De S, Sivendran N. Isomerization of Functionalized Olefins Using the Dinuclear Catalyst [PdI(μ-Br)(PtBu3)]2: A Mechanistic Study. Chemistry 2021; 27:15226-15238. [PMID: 34387372 PMCID: PMC8596456 DOI: 10.1002/chem.202102554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/13/2022]
Abstract
In a combined experimental and computational study, the isomerization activity of the dinuclear palladium(I) complex [PdI(μ‐Br)(PtBu3)]2 towards allyl arenes, esters, amides, ethers, and alcohols has been investigated. The calculated energy profiles for catalyst activation for two alternative dinuclear and mononuclear catalytic cycles, and for catalyst deactivation are in good agreement with the experimental results. Comparison of experimentally observed E/Z ratios at incomplete conversion with calculated kinetic selectivities revealed that a substantial amount of product must form via the dinuclear pathway, in which the isomerization is promoted cooperatively by two palladium centers. The dissociation barrier towards mononuclear Pd species is relatively high, and once the catalyst enters the energetically more favorable mononuclear pathway, only a low barrier has to be overcome towards irreversible deactivation.
Collapse
Affiliation(s)
- Lukas J Goossen
- Ruhr-Universität Bochum, Organische Chemie I, Universitätsstraße 150, ZEMOS 2/27, 44801, 44801 Bochum, GERMANY
| | - Debasis Koley
- IISER-K: Indian Institute of Science Education and Research Kolkata, Chemical Sciences, Campus Rd, 741 246, Mohanpur, Nadia, INDIA
| | - Sriman De
- IISER-K: Indian Institute of Science Education and Research Kolkata, Chemical Sciences, Campus Rd, 741 246, Mohanpur, Nadia, INDIA
| | - Nardana Sivendran
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Chemistry and Biochemistry, Universitätsstr. 150, ZEMOS, 44795, Bochum, GERMANY
| |
Collapse
|
32
|
Interaction between organic molecules and a gold nanoparticle: a quantum chemical topological analysis. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02821-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
33
|
Van Lommel R, De Borggraeve WM, De Proft F, Alonso M. Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels. Gels 2021; 7:87. [PMID: 34287290 PMCID: PMC8293097 DOI: 10.3390/gels7030087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
Supramolecular gels form a class of soft materials that has been heavily explored by the chemical community in the past 20 years. While a multitude of experimental techniques has demonstrated its usefulness when characterizing these materials, the potential value of computational techniques has received much less attention. This review aims to provide a complete overview of studies that employ computational tools to obtain a better fundamental understanding of the self-assembly behavior of supramolecular gels or to accelerate their development by means of prediction. As such, we hope to stimulate researchers to consider using computational tools when investigating these intriguing materials. In the concluding remarks, we address future challenges faced by the field and formulate our vision on how computational methods could help overcoming them.
Collapse
Affiliation(s)
- Ruben Van Lommel
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem & Tech, P.O. Box 2404, 3001 Leuven, Belgium;
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
| | - Wim M. De Borggraeve
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem & Tech, P.O. Box 2404, 3001 Leuven, Belgium;
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
| |
Collapse
|
34
|
Morales-Toyo M, Kansız S, Dege N, Glidewell C, Fuenmayor-Zafra A, Cubillán N. Polymorphs of 2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetic acid (Diclofenac): Differences from crystallography, Hirshfeld surface, QTAIM and NCIPlots. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
35
|
Sixto-López Y, Correa-Basurto J, Bello M, Landeros-Rivera B, Garzón-Tiznado JA, Montaño S. Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Sci Rep 2021; 11:4659. [PMID: 33633229 PMCID: PMC7907372 DOI: 10.1038/s41598-021-84053-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/11/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus responsible for coronavirus disease 2019 (COVID-19); it become a pandemic since March 2020. To date, there have been described three lineages of SARS-CoV-2 circulating worldwide, two of them are found among Mexican population, within these, we observed three mutations of spike (S) protein located at amino acids H49Y, D614G, and T573I. To understand if these mutations could affect the structural behavior of S protein of SARS-CoV-2, as well as the binding with S protein inhibitors (cepharanthine, nelfinavir, and hydroxychloroquine), molecular dynamic simulations and molecular docking were employed. It was found that these punctual mutations affect considerably the structural behavior of the S protein compared to wild type, which also affect the binding of its inhibitors into their respective binding site. Thus, further experimental studies are needed to explore if these affectations have an impact on drug-S protein binding and its possible clinical effect.
Collapse
Affiliation(s)
- Yudibeth Sixto-López
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | | | - Jose Antonio Garzón-Tiznado
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Sarita Montaño
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico.
| |
Collapse
|
36
|
Lei J, Alessandrini S, Chen J, Zheng Y, Spada L, Gou Q, Puzzarini C, Barone V. Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex. Molecules 2020; 25:E4899. [PMID: 33113920 PMCID: PMC7660205 DOI: 10.3390/molecules25214899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023] Open
Abstract
The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions.
Collapse
Affiliation(s)
- Juncheng Lei
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Junhua Chen
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
| |
Collapse
|