1
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Xu J, Li K, Liu L, Ma J, Zhang H. Tannic acid - a bridge and suspending agent for lithium cobalt oxide and reduced graphene oxide: a lodestar for lithium-ion batteries. Environ Technol 2024; 45:2486-2492. [PMID: 36727477 DOI: 10.1080/09593330.2023.2176790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
ABSTRACTLithium cobalt oxide (LCO) has been employed as cathode material for 40 years. However, the low solubility of LCOs in water and strong electrostatic force and H-bonding between the LCOs particles limited the use of the aqueous binders in the LCO system. We report a feasible and universal approach to fabricating a complex cathode of LCO and reduced graphene oxide (RGO). Tannic acid (TA) could simultaneously disperse LCO and RGO particles. Meanwhile, the branched polyphenol TA acts as a 'bridge' molecule for connecting the LCO and RGO, confirmed by the SEM test. The rheology properties of the PVDF slurry of cathode materials (LCO, LCO/, RGO, and TA/LCO/RGO) were also determined. It could be found that the TA could act as a crosslinking agent for the LCO and RGO particles, increasing the viscosity and storage modulus of the slurry. The cell employed the TA/LCO/RGO slurry as the cathode material, have a higher areal capacity, and had a higher redox potential than employed LCO/RGO and LCO as cathode materials, all of which could be attributed to the addition of the TA. This green molecule can be used to fabricate environmentally friendly and possibly biodegradable electrochemical energy storage devices.
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Affiliation(s)
- Juan Xu
- Research Institute of Highland Forestry, Chinese Academy of Forestry, Kunming, People's Republic of China
| | - Kai Li
- Faculty of Chemical Engineering and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Lanxiang Liu
- Research Institute of Highland Forestry, Chinese Academy of Forestry, Kunming, People's Republic of China
| | - Jinju Ma
- Research Institute of Highland Forestry, Chinese Academy of Forestry, Kunming, People's Republic of China
| | - Hong Zhang
- Research Institute of Highland Forestry, Chinese Academy of Forestry, Kunming, People's Republic of China
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2
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Fernández Z, Sánchez L, Santhosh Babu S, Fernández G. Oligo(phenyleneethynylene)s: Shape-Tunable Building Blocks for Supramolecular Self-Assembly. Angew Chem Int Ed Engl 2024; 63:e202402259. [PMID: 38421233 DOI: 10.1002/anie.202402259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/02/2024]
Abstract
Oligo(phenyleneethynylene)s (OPEs) have attracted widespread attention due to their remarkable (opto)electronic and photophysical properties, which have enabled numerous applications. The versatile functionalization possibilities of OPEs make them unique candidates to form various shape-persistent geometries, including linear, triangular, rectangular, hexagonal and macrocyclic. However, as a result of this structural variety, it is oftentimes challenging to correlate molecular design with self-assembly properties. In this minireview, we have classified OPEs based on their molecular shapes and correlated them with their self-assembly behavior in solution. Particularly, we provide important insights into the aggregation propensity of the different molecular shapes and how to tune the association strength using various non-covalent interactions. Our classification will enable a better understanding of the structure-property correlation in OPEs, which is key to develop supramolecular functional materials.
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Affiliation(s)
- Zulema Fernández
- Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
| | - Luis Sánchez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Sukumaran Santhosh Babu
- Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
- CSIR, National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
| | - Gustavo Fernández
- Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
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3
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Bogdanowicz KA, Iwan A, Dysz K, Przybyl W, Marzec M, Cichy K, Świerczek K. Air-Stable and Eco-Friendly Symmetrical Imine with Thiadiazole Moieties in Neutral and Protonated form for Perovskite Photovoltaics. Materials (Basel) 2024; 17:1909. [PMID: 38673266 PMCID: PMC11052309 DOI: 10.3390/ma17081909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
This paper proposes molecular and supramolecular concepts for potential application in perovskite solar cells. New air-stable symmetrical imine, with thiadiazole moieties PPL2: (5E,6E)-N2,N5-bis(4-(diphenylamino)benzylidene)-1,3,4-thiadiazole-2,5-diamine), as a hole-transporting material was synthesised in a single-step reaction, starting with commercially available and relatively inexpensive reagents, resulting in a reduction in the cost of the final product compared to Spiro-OMeTAD. Moreover, camphorsulfonic acid (CSA) in both enantiomeric forms was used to change the HOMO-LUMO levels and electric properties of the investigated imine-forming complexes. Electric, optical, thermal, and structural studies of the imine and its complexes with CSA were carried out to characterise the new material. Imine and imine/CSA complexes were also characterised in depth by the proton Nuclear Magnetic Resonance 1H NMR method. The position of nitrogen in the thidiazole ring influences the basicity of donor centres, which results in protonation in the imine bond. Simple devices of ITO/imine (with or without CSA(-) or CSA(+))/Ag/ITO architecture were constructed, and a thermographic camera was used to find the defects in the created devices. Electric behaviour was also studied to demonstrate conductivity properties under the forward current. Finally, the electrical properties of imine and its protonated form with CSA were compared with Spiro-OMeTAD. In general, the analysis of thermal images showed a very similar response of the samples to the applied potential in terms of the homogeneity of the formed organic layer. The TGA analysis showed that the investigated imine exhibits good thermal stability in air and argon atmospheres.
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Affiliation(s)
| | - Agnieszka Iwan
- Military Institute of Engineer Technology, Obornicka 136 Str., 50-961 Wroclaw, Poland; (K.D.); (W.P.)
| | - Karolina Dysz
- Military Institute of Engineer Technology, Obornicka 136 Str., 50-961 Wroclaw, Poland; (K.D.); (W.P.)
| | - Wojciech Przybyl
- Military Institute of Engineer Technology, Obornicka 136 Str., 50-961 Wroclaw, Poland; (K.D.); (W.P.)
| | - Monika Marzec
- Institute of Physics, Jagiellonian University, Prof. S. Lojasiewicza 11, 30-348 Krakow, Poland;
| | - Kacper Cichy
- Faculty of Energy and Fuels, AGH University of Krakow, Al. A. Mickiewicza 30, 30-059 Krakow, Poland; (K.C.); (K.Ś.)
| | - Konrad Świerczek
- Faculty of Energy and Fuels, AGH University of Krakow, Al. A. Mickiewicza 30, 30-059 Krakow, Poland; (K.C.); (K.Ś.)
- AGH Centre of Energy, AGH University of Krakow, Ul. Czarnowiejska 36, 30-054 Krakow, Poland
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4
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Thorley KJ, Nielsen CB. Conformational Analysis of Conjugated Organic Materials: What Are My Heteroatoms Really Doing? Chempluschem 2024:e202300773. [PMID: 38598306 DOI: 10.1002/cplu.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/20/2024] [Indexed: 04/12/2024]
Abstract
Organic semiconductor small molecules and polymers often incorporate heteroatoms into their chemical structures to affect the electronic properties of the material. A particular design philosophy has been to use these heteroatoms to influence torsional potentials, since the overlap of adjacent π-orbitals is most efficient in planar systems and is critical for charge delocalization in these systems. Since these design rules became popular, the messages from the earlier works have become lost in a sea of reports of "conformational locks", where the non-covalent interactions have relatively small contributions to planarizing torsional potentials. Greater influences can be found in the stabilization by extended conjugation, consideration of steric repulsion, and the interactions involving solubilizing chains and neighboring molecules or polymer chains in condensed phases.
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Affiliation(s)
- Karl J Thorley
- Center for Applied Energy Research, University of Kentucky, Lexington, KY 40511, USA
| | - Christian B Nielsen
- Department of Chemistry, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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5
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Kasprzak A. Supramolecular Chemistry of Sumanene. Angew Chem Int Ed Engl 2024; 63:e202318437. [PMID: 38231540 DOI: 10.1002/anie.202318437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/20/2023] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Sumanene is a buckybowl molecule that is continuously attracting the attention of the scientific community because of its unique geometrical and physicochemical properties. This Minireview systematically summarizes advances and considerations regarding the applied supramolecular chemistry of sumanene. This work highlights the major fields in which potential or real applications of sumanene molecule have been reported to date, such as the design of sumanene-containing functional supramolecular materials and architectures, sumanene-based drug-delivery systems, or sumanene-tethered ion-selective molecular receptors. An assessment of the current status in the applied supramolecular chemistry of sumanene is provided, together with an emphasis on the key advances being made. Discussion on those milestones that are still to be achieved within this emerging field is also provided.
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Affiliation(s)
- Artur Kasprzak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego Str. 3, 00-664, Warsaw, Poland
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6
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Martínez-Orts M, Pujals S. Responsive Supramolecular Polymers for Diagnosis and Treatment. Int J Mol Sci 2024; 25:4077. [PMID: 38612886 PMCID: PMC11012635 DOI: 10.3390/ijms25074077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Stimuli-responsive supramolecular polymers are ordered nanosized materials that are held together by non-covalent interactions (hydrogen-bonding, metal-ligand coordination, π-stacking and, host-guest interactions) and can reversibly undergo self-assembly. Their non-covalent nature endows supramolecular polymers with the ability to respond to external stimuli (temperature, light, ultrasound, electric/magnetic field) or environmental changes (temperature, pH, redox potential, enzyme activity), making them attractive candidates for a variety of biomedical applications. To date, supramolecular research has largely evolved in the development of smart water-soluble self-assemblies with the aim of mimicking the biological function of natural supramolecular systems. Indeed, there is a wide variety of synthetic biomaterials formulated with responsiveness to control and trigger, or not to trigger, aqueous self-assembly. The design of responsive supramolecular polymers ranges from the use of hydrophobic cores (i.e., benzene-1,3,5-tricarboxamide) to the introduction of macrocyclic hosts (i.e., cyclodextrins). In this review, we summarize the most relevant advances achieved in the design of stimuli-responsive supramolecular systems used to control transport and release of both diagnosis agents and therapeutic drugs in order to prevent, diagnose, and treat human diseases.
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Affiliation(s)
| | - Silvia Pujals
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain;
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7
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Dukhnovsky EA, Novikov AS, Kubasov AS, Borisov AV, Sikaona ND, Kirichuk AA, Khrustalev VN, Kritchenkov AS, Tskhovrebov AG. Halogen Bond-Assisted Supramolecular Dimerization of Pyridinium-Fused 1,2,4-Selenadiazoles via Four-Center Se 2N 2 Chalcogen Bonding. Int J Mol Sci 2024; 25:3972. [PMID: 38612782 PMCID: PMC11011651 DOI: 10.3390/ijms25073972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
The synthesis and structural characterization of α-haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles with various counterions is reported herein, demonstrating a strategy for directed supramolecular dimerization in the solid state. The compounds were obtained through a recently discovered 1,3-dipolar cycloaddition reaction between nitriles and bifunctional 2-pyridylselenyl reagents, and their structures were confirmed by the X-ray crystallography. α-Haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles exclusively formed supramolecular dimers via four-center Se···N chalcogen bonding, supported by additional halogen bonding involving α-haloalkyl substituents. The introduction of halogens at the α-position of the substituent R in the selenadiazole core proved effective in promoting supramolecular dimerization, which was unaffected by variation of counterions. Additionally, the impact of cocrystallization with a classical halogen bond donor C6F3I3 on the supramolecular assembly was investigated. Non-covalent interactions were studied using density functional theory calculations and topological analysis of the electron density distribution, which indicated that all ChB, XB and HB interactions are purely non-covalent and attractive in nature. This study underscores the potential of halogen and chalcogen bonding in directing the self-assembly of functional supramolecular materials employing 1,2,4-selenadiazoles derived from recently discovered cycloaddition between nitriles and bifunctional 2-pyridylselenyl reagents.
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Affiliation(s)
- Evgeny A. Dukhnovsky
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russia
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 31, Moscow 119334, Russia
| | - Alexander V. Borisov
- Department of Chemistry, R.E. Alekseev Nizhny Novgorod State Technical University, Minin St., 24, Nizhny Novgorod 603155, Russia
| | - Nkumbu Donovan Sikaona
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Anatoly A. Kirichuk
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Victor N. Khrustalev
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119334, Russia
| | - Andreii S. Kritchenkov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Alexander G. Tskhovrebov
- Research Institute of Chemistry, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
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Rondelli M, Pasán J, Fernández I, Martín T. Predisposition in Dynamic Covalent Chemistry: The Role of Non-Covalent Interactions in the Assembly of Tetrahedral Boronate Cages. Chemistry 2024:e202400896. [PMID: 38507133 DOI: 10.1002/chem.202400896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
Directional bonding strategies guide the design of complex molecular architectures, yet challenges arise due to emergent behavior. Rigid structures face geometric constraints and sensitivity to mismatches, hindering the efficient assembly of molecular organic cages (MOCs). Harnessing intramolecular non-covalent interactions offers a promising solution, broadening geometrical possibilities and enhancing adaptability to boost assembly yields. However, identifying these interactions remains challenging, with their full potential sometimes latent until final assembly. This study explores these challenges by synthesizing boronic acid tripods with varied oxygen positions at the tripodal feet and investigating their role in assembling tetrahedral boronate MOCs. Our results reveal substantial differences in the assembly efficiency among tripods. While the building blocks with oxygen in the benzylic position relative to the central aromatic ring form the MOCs in high yields, those with the oxygen atom directly bound to the central aromatic ring, only yield traces. Through X-ray crystallography and DFT analyses, we elucidate how intramolecular interactions profoundly influence the geometry of the building blocks and cages in a relay-like fashion, highlighting the importance of considering intramolecular interactions in the rational design of (supra)molecular architectures.
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Affiliation(s)
- Manuel Rondelli
- Molecular Science Department, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Cientícas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez 3, 38206, La Laguna, Tenerife, Spain
| | - Jorge Pasán
- Departamento de Química, Facultad de Ciencias, Laboratorio de Materiales para Análisis Químico (MAT4LL) Universidad de La Laguna, 38200, Tenerife, Spain
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Tomás Martín
- Molecular Science Department, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Cientícas (IPNA-CSIC) Avda. Astrofísico Francisco Sánchez 3, 38206, La Laguna, Tenerife, Spain
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9
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Plett C, Grimme S, Hansen A. Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules. J Comput Chem 2024; 45:419-429. [PMID: 37982322 DOI: 10.1002/jcc.27248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1 . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.
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Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
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10
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Kalebina TS, Rekstina VV, Pogarskaia EE, Kulakovskaya T. Importance of Non-Covalent Interactions in Yeast Cell Wall Molecular Organization. Int J Mol Sci 2024; 25:2496. [PMID: 38473742 DOI: 10.3390/ijms25052496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
This review covers a group of non-covalently associated molecules, particularly proteins (NCAp), incorporated in the yeast cell wall (CW) with neither disulfide bridges with proteins covalently attached to polysaccharides nor other covalent bonds. Most NCAp, particularly Bgl2, are polysaccharide-remodeling enzymes. Either directly contacting their substrate or appearing as CW lipid-associated molecules, such as in vesicles, they represent the most movable enzymes and may play a central role in CW biogenesis. The absence of the covalent anchoring of NCAp allows them to be there where and when it is necessary. Another group of non-covalently attached to CW molecules are polyphosphates (polyP), the universal regulators of the activity of many enzymes. These anionic polymers are able to form complexes with metal ions and increase the diversity of non-covalent interactions through charged functional groups with both proteins and polysaccharides. The mechanism of regulation of polysaccharide-remodeling enzyme activity in the CW is unknown. We hypothesize that polyP content in the CW is regulated by another NCAp of the CW-acid phosphatase-which, along with post-translational modifications, may thus affect the activity, conformation and compartmentalization of Bgl2 and, possibly, some other polysaccharide-remodeling enzymes.
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Affiliation(s)
- Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Valentina V Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elizaveta E Pogarskaia
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tatiana Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino 142290, Russia
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11
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Yin S, Duan M, Zhang J, Zhang T, Zhao G. Interactions between paramyosin and actin greatly improve their thermostability and gel properties. J Sci Food Agric 2024; 104:1564-1571. [PMID: 37807842 DOI: 10.1002/jsfa.13035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/20/2023] [Accepted: 10/09/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Myofibrillar proteins, the main contributors to the quality of meat products, are the main structural protein component of muscle and have functional properties such as the formation of a 3D protein gel network and water binding. The susceptibility of meat-derived proteins to heat-induced aggregation is the functional constraint that hinders their applications in industry, and so establishing an effective but simple method to improve their thermostability of the proteins is of great importance. RESULTS In the present study, we describe an easy approach to perform high colloidal thermostability of both paramyosin and actin by mixing them at low ionic strength. The improvement in thermal stability was found to be derived from intermolecular interactions between these two different proteins through non-covalent binding with each other. Consequently, such interactions protected each of them from thermal-induced degradation compared to individual components. Notably, this binary native protein mixture rather than single paramyosin or actin component has the ability to form protein hydrogels with a shear-thinning and reversible sol-gel transformation behavior, which is markedly different from most of reported heat-induced, denatured protein hydrogels. CONCLUSION The present study not only presents a facile and effective strategy for improvement of the thermal stability and gel properties of a binary paramyosin and actin mixture, but also enhances our understanding of how mutual interactions of protein components affect their physicochemical and functional properties. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Shuhua Yin
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Maoping Duan
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Jian Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
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12
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Platzer G, Ptaszek AL, Böttcher J, Fuchs JE, Geist L, Braun D, McConnell DB, Konrat R, Sánchez-Murcia PA, Mayer M. Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution. Chemphyschem 2024; 25:e202300636. [PMID: 37955910 DOI: 10.1002/cphc.202300636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/23/2023] [Indexed: 11/14/2023]
Abstract
The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with limited information on protein flexibility. An experimentally verified structural model of the binding interface in the native solution-state would support medicinal chemists in their molecular design decisions. Here we demonstrate that protein-bound ligand 1 H NMR chemical shifts are highly sensitive and accurate probes for the immediate chemical environment of protein-ligand interfaces. By comparing the experimental ligand 1 H chemical shift values with those computed from the X-ray structure using quantum mechanics methodology, we identify significant disagreements for parts of the ligand between the two experimental techniques. We show that quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) ensembles can be used to refine initial X-ray co-crystal structures resulting in a better agreement with experimental 1 H ligand chemical shift values. Overall, our findings highlight the usefulness of ligand 1 H NMR chemical shift information in combination with a QM/MM MD workflow for generating protein-ligand ensembles that accurately reproduce solution structural data.
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Affiliation(s)
- Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
- MAG-LAB GmbH, Karl-Farkas-Gasse 22, 1030-, Vienna, Austria
| | - Aleksandra L Ptaszek
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
- Laboratory for Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University Graz, Neue Stiftingtalstrasse 6/III, 8010-, Graz, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Daniel Braun
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
| | - Pedro A Sánchez-Murcia
- Laboratory for Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University Graz, Neue Stiftingtalstrasse 6/III, 8010-, Graz, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
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13
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Li W, Maris A, Melandri S, Lesarri A, Evangelisti L. The Structure of 2,6-Di- tert-butylphenol-Argon by Rotational Spectroscopy. Molecules 2023; 28:8111. [PMID: 38138596 PMCID: PMC10745844 DOI: 10.3390/molecules28248111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The molecular structure of a van der Waals-bonded complex involving 2,6-di-tert-butylphenol and a single argon atom has been determined through rotational spectroscopy. The experimentally derived structural parameters were compared to the outcomes of quantum chemical calculations that can accurately account for dispersive interactions in the cluster. The findings revealed a π-bound configuration for the complex, with the argon atom engaging the aromatic ring. The microwave spectrum reveals both fine and hyperfine tunneling components. The main spectral doubling is evident as two distinct clusters of lines, with an approximate separation of 179 MHz, attributed to the torsional motion associated with the hydroxyl group. Additionally, each component of this doublet further splits into three components, each with separations measuring less than 1 MHz. Investigation into intramolecular dynamics using a one-dimensional flexible model suggests that the main tunneling phenomenon originates from equivalent positions of the hydroxyl group. A double-minimum potential function with a barrier of 1000 (100) cm-1 effectively describes this extensive amplitude motion. However, the three-fold fine structure, potentially linked to internal motions within the tert-butyl group, requires additional scrutiny for a comprehensive understanding.
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Affiliation(s)
- Wenqin Li
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias—I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain;
| | - Assimo Maris
- Department of Chemistry “G. Ciamician”, University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (A.M.); (S.M.)
| | - Sonia Melandri
- Department of Chemistry “G. Ciamician”, University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (A.M.); (S.M.)
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias—I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain;
| | - Luca Evangelisti
- Department of Chemistry “G. Ciamician”, University of Bologna, Via S. Alberto 163, 48123 Ravenna, Italy
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14
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Matveev EY, Dontsova OS, Avdeeva VV, Kubasov AS, Zhdanov AP, Nikiforova SE, Goeva LV, Zhizhin KY, Malinina EA, Kuznetsov NT. Synthesis and Structures of Lead(II) Complexes with Substituted Derivatives of the Closo-Decaborate Anion with a Pendant N 3 Group. Molecules 2023; 28:8073. [PMID: 38138563 PMCID: PMC10746007 DOI: 10.3390/molecules28248073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
In this work, we studied lead(II) and cobalt(II) complexation of derivatives [2-B10H9O(CH2)2O(CH2)2N3]2- and [2-B10H9O(CH2)5N3]2- of the closo-decaborate anion containing pendant azido groups in the presence of 1,10-phenanthroline and 2,2'-bipyridyl. Mononuclear [PbL2{An}] and binuclear [Pb2L4(NO3)2{An}] lead complexes (where {An} is the N3-substituted boron cluster) were isolated and studied by IR spectroscopy and elemental analysis. The mononuclear lead(II) complex [Pb(phen)2[B10H9O(CH2)2O(CH2)2N3] and the binuclear lead(II) complex [Pb2(phen)4(NO3)2[B10H9O(CH2)5)N3] were determined by single-crystal X-ray diffraction. In complex [Pb2(phen)4(NO3)2[B10H9O(CH2)5)N3], the boron cluster is coordinated by the metal atom only via the 3c2e MHB bonds. In complex [Pb(phen)2[B10H9O(CH2)2O(CH2)2N3], the coordination environment of the metal includes BH groups of the boron cluster and the oxygen atom of the exo-polyhedral substituent. When the reaction was performed in a CH3CN/water mixture, the binuclear lead(II) complex [(Pb(bipy)NO3)(Pb(bipy)2NO3)(B10H9O(CH2)2O(CH2)2N3)]·CH3CN·H2O was isolated, where the boron cluster acts as a bridging ligand between lead atoms coordinated by the boron cage via the O atoms of the substituent and/or the BH groups. In the course of cobalt(II) complexation, the starting compound (Ph4P)2[B10H9O(CH2)5N3] was isolated and its structure was also determined by X-ray diffraction. Although a number of lead(II) complexes with coordinated N3 are known from the literature, no complexes with the boron cluster coordinated by the pendant N3 group involved in the metal coordination have been isolated.
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Affiliation(s)
- Evgenii Yu. Matveev
- Institute of Fine Chemical Technologies Named after M. V. Lomonosov, MIREA—Russian Technological University, Vernadskogo pr. 86, Moscow 119571, Russia; (E.Y.M.); (O.S.D.); (K.Y.Z.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Olga S. Dontsova
- Institute of Fine Chemical Technologies Named after M. V. Lomonosov, MIREA—Russian Technological University, Vernadskogo pr. 86, Moscow 119571, Russia; (E.Y.M.); (O.S.D.); (K.Y.Z.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Varvara V. Avdeeva
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Andrey P. Zhdanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Svetlana E. Nikiforova
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Lyudmila V. Goeva
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Konstantin Yu. Zhizhin
- Institute of Fine Chemical Technologies Named after M. V. Lomonosov, MIREA—Russian Technological University, Vernadskogo pr. 86, Moscow 119571, Russia; (E.Y.M.); (O.S.D.); (K.Y.Z.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Elena A. Malinina
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
| | - Nikolay T. Kuznetsov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia; (A.S.K.); (A.P.Z.); (S.E.N.); (L.V.G.); (E.A.M.); (N.T.K.)
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15
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Wei X, Cui L, Liu C, Shen K, Xu J, Dilworth J, Xiao T, Cao F. The Calculation of Both Electrostatic and Van der Waals Effects to Probe the Efficiency of Solvent Extraction of Heterocyclic Aromatics from Heavy Oil. Chemistry 2023; 29:e202301954. [PMID: 37665039 DOI: 10.1002/chem.202301954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/05/2023]
Abstract
Due to the complex composition and similar structure, the extraction denitrification of aromatic rich oil is faced with the contradiction problem of denitrification efficiency and aromatic loss which cannot be efficiently solved by experiments. However, the complex interactions involved can be analyzed from the perspective of calculation, and the prediction criteria and methods are proposed. Based on rigorous density functional theory calculation data, Simple models based on electrostatic potential (ESP) and Van der Waals potential (VdWP)-based calculations were established and validated. The twofold model provided the best prediction for interactions between extractants and nitrogen compounds and between extractants and aromatics, which determines denitrification efficiency and aromatic loss, respectively, due to the most complete description of both electrostatic and VdW force. This provides a powerful tool for evaluating the non-covalent interactions and thence tuning the efficiency of the separation process. Thus, high denitrification efficiency (43.2~66.3 %) and moderate aromatic loss (1.7~4.4 %) were obtained using screened deep eutectic solvents (DESs). This ideal observation provided the potential for mild hydrodesulfurization and manufacture of high-grade carbon materials.
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Affiliation(s)
- Xingguo Wei
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Lingrui Cui
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Cao Liu
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Kaili Shen
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jun Xu
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jon Dilworth
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Tiancun Xiao
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Fahai Cao
- School of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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16
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Nolasco MM, Parker SF, Vaz PD, Ribeiro-Claro PJA. Intermolecular Interactions in 3-Aminopropyltrimethoxysilane, N-Methyl-3-aminopropyltrimethoxysilane and 3-Aminopropyltriethoxysilane: Insights from Computational Spectroscopy. Int J Mol Sci 2023; 24:16634. [PMID: 38068957 PMCID: PMC10706811 DOI: 10.3390/ijms242316634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
In this work, a computational spectroscopy approach was used to provide a complete assignment of the inelastic neutron scattering spectra of three title alkoxysilane derivatives-3-aminopropyltrimethoxysilane (APTS), N-methyl-3-aminopropyltrimethoxysilane (MAPTS), and 3-aminopropyltriethoxysilane (APTES). The simulated spectra obtained from density functional theory (DFT) calculations exhibit a remarkable match with the experimental spectra. The description of the experimental band profiles improves as the number of molecules considered in the theoretical model increases, from monomers to trimers. This highlights the significance of incorporating non-covalent interactions, encompassing classical NH···N, N-H···O, as well as C-H···N and C-H···O hydrogen bond contacts, to achieve a comprehensive understanding of the system. A distinct scenario emerges when considering optical vibrational techniques, infrared and Raman spectroscopy. In these instances, the monomer model provides a reasonable description of the experimental spectra, and no substantial alterations are observed in the simulated spectra when employing dimer and trimer models. This observation underscores the distinctive ability of neutron spectroscopy in combination with DFT calculations in assessing the structure and dynamics of molecular materials.
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Affiliation(s)
- Mariela M. Nolasco
- CICECO—Instituto de Materiais de Aveiro, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal;
| | - Stewart F. Parker
- ISIS Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, UK;
| | - Pedro D. Vaz
- Champalimaud Foundation, Champalimaud Centre for the Unknown, 1400-038 Lisboa, Portugal;
| | - Paulo J. A. Ribeiro-Claro
- CICECO—Instituto de Materiais de Aveiro, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal;
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17
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Burguera S, Bauzá A, Frontera A. Tuning the Nucleophilicity and Electrophilicity of Group 10 Elements through Substituent Effects: A DFT Study. Int J Mol Sci 2023; 24:15597. [PMID: 37958580 PMCID: PMC10648789 DOI: 10.3390/ijms242115597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
In this study, a series of electron donor (-NH2, -NMe2 and -tBu) and electron-withdrawing substituents (-F, -CN and -NO2) were used to tune the nucleophilicity or electrophilicity of a series of square planar Ni2+, Pd2+ and Pt2+ malonate coordination complexes towards a pentafluoroiodobenzene and a pyridine molecule. In addition, Bader's theory of atoms in molecules (AIM), noncovalent interaction plot (NCIplot), molecular electrostatic potential (MEP) surface and natural bond orbital (NBO) analyses at the PBE0-D3/def2-TZVP level of theory were carried out to characterize and discriminate the role of the metal atom in the noncovalent complexes studied herein. We hope that the results reported herein may serve to expand the current knowledge regarding these metals in the fields of crystal engineering and supramolecular chemistry.
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Affiliation(s)
| | | | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa Km 7.5, 07122 Palma, Baleares, Spain; (S.B.); (A.B.)
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18
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Kizior B, Jezierska A, Szyja BM. Partial Methane Oxidation to Methanol on Ru-Porphyrins - on the Role of Non-Innocent Ligands and Spin Crossover. Chemphyschem 2023:e202300499. [PMID: 37875788 DOI: 10.1002/cphc.202300499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Indexed: 10/26/2023]
Abstract
The partial oxidation reaction of CH4 led to the formation of CH3 OH in the presence of Ru-porphyrin oxo complexes (denoted as POR, POR-O and POR-OH where in the case of the last two, oxygen atom and the OH group were attached to the active site, respectively), in which Ru was present on different oxidation states. The simulations were performed based on Density Functional Theory (DFT) with extended geometric and electronic structure analyses of each reaction step. Moreover, the reaction pathways were investigated in different spin states. The Spin Crossover (SCO) phenomenon was found to play an important role in the kinetics of the reaction in the presence of POR and POR-O. Harmonic Oscillator Model of Aromaticity (HOMA) index was applied for different spin states to estimate the aromaticity changes of the pyrrole rings in the Ru-porphyrin complexes. In order to characterize the nature of bonding, the Natural Bond Orbitals (NBO) analysis including the Wiberg Bond Index (WBI) and Natural Population Analysis (NPA) was carried out. Finally, the Non-Covalent Interactions (NCI) index was employed to gain insight into interactions between the components of the reaction. It was found that the non-covalent interactions cannot be neglected in the studied reaction paths.
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Affiliation(s)
- Beata Kizior
- Wrocław University of Science and Technology, Faculty of Chemistry, ul. Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland
| | - Aneta Jezierska
- University of Wrocław, Faculty of Chemistry, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Bartłomiej M Szyja
- Wrocław University of Science and Technology, Faculty of Chemistry, ul. Wybrzeże Wyspiańskiego 27, 50-370, Wroclaw, Poland
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19
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Zhang S, Yu M, Zhang G, He G, Ji Y, Dong J, Zheng H, Qian L. Revealing the Control Mechanisms of pH on the Solution Properties of Chitin via Single-Molecule Studies. Molecules 2023; 28:6769. [PMID: 37836611 PMCID: PMC10574145 DOI: 10.3390/molecules28196769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Chitin is one of the most common polysaccharides and is abundant in the cell walls of fungi and the shells of insects and aquatic organisms as a skeleton. The mechanism of how chitin responds to pH is essential to the precise control of brewing and the design of smart chitin materials. However, this molecular mechanism remains a mystery. Results from single-molecule studies, including single-molecule force spectroscopy (SMFS), AFM imaging, and molecular dynamic (MD) simulations, have shown that the mechanical and conformational behaviors of chitin molecules show surprising pH responsiveness. This can be compared with how, in natural aqueous solutions, chitin tends to form a more relaxed spreading conformation and show considerable elasticity under low stretching forces in acidic conditions. However, its molecular chain collapses into a rigid globule in alkaline solutions. The results show that the chain state of chitin can be regulated by the proportions of inter- and intramolecular H-bonds, which are determined via the number of water bridges on the chain under different pH values. This basic study may be helpful for understanding the cellular activities of fungi under pH stress and the design of chitin-based drug carriers.
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Affiliation(s)
- Song Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China;
| | - Guoqiang Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Guanmei He
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Yunxu Ji
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Juan Dong
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China
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Řezáč J, de la Lande A. On the Role of Charge Transfer in Many-Body Non-Covalent Interactions. Chemphyschem 2023; 24:e202300329. [PMID: 37405855 DOI: 10.1002/cphc.202300329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes. In polar interactions such as hydrogen bonds, it can contribute ten or several tens of percent of the interaction energy. Less is known about its importance in higher-order interactions in many-body systems, mainly because of the lack of methods applicable to this problem. In this work, we extend our method for the quantification of the charge-transfer energy based on constrained DFT to many-body cases and apply it to model trimers extracted from molecular crystals. Our calculations show that charge transfer can account for a large fraction of the total three-body interaction energy. This also has implications for DFT calculations of many-body interactions in general as it is known that many DFT functionals struggle to describe charge-transfer effects correctly.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague, Czech Republic
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 91405, Orsay, France
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21
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Keot N, Lama B, Singh HK, Bhattacharyya HP, Sarma M. Unveiling the Noncovalent Interaction of Thiazol-2-ylidene and Its Derivatives as N-heterocyclic Carbene with Different Proton Donor Molecules. Chemphyschem 2023:e202300413. [PMID: 37712533 DOI: 10.1002/cphc.202300413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
The importance of noncovalent interaction has gained attention in various domains covering drug and novel catalyst design. The present study mainly characterizes the role of hydrogen bond (H-bond) and other intermolecular interactions in different (1 : 1) complex analogues formed between the N-aryl-thiazol-2-ylidene (YR) and five proton donor (HX) molecules. The analysis of the singlet-triplet energy gap (Δ E S - T ${{\rm{\Delta }}E_{\left( {S - T} \right)} }$ ) confirmed the stability of the singlet state for this class of N-aryl-thiazol-2-ylidenes than the triplet state. The interaction energy values of the YR-HX complexes follow the order: YR-NH3
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Affiliation(s)
- Niharika Keot
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039
| | - Bittu Lama
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039
| | - Haobam Kisan Singh
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039
| | | | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039
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22
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Komisarek D, Demirbas F, Haj Hassani Sohi T, Merz K, Schauerte C, Vasylyeva V. Polymorphism and Multi-Component Crystal Formation of GABA and Gabapentin. Pharmaceutics 2023; 15:2299. [PMID: 37765268 PMCID: PMC10536459 DOI: 10.3390/pharmaceutics15092299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
This study exploits the polymorphism and multi-component crystal formation of γ-amino butanoic acid (GABA) and its pharmaceutically active derivative, gabapentin. Two polymorphs of GABA and both polymorphs of gabapentin are structurally revisited, together with gabapentin monohydrate. Hereby, GABA form II is only accessible under special conditions using additives, whereas gabapentin converts to the monohydrate even in the presence of trace amounts of water. Different accessibilities and phase stabilities of these phases are still not fully clarified. Thus, indicators of phase stability are discussed involving intermolecular interactions, molecular conformations, and crystallization environment. Calculated lattice energy differences for polymorphs reveal their similar stability. Quantification of the hydrogen bond strengths with the atoms-in-molecules (AIM) model in conjunction with non-covalent interaction (NCI) plots also shows similar hydrogen bond binding energy values for all polymorphs. We demonstrate that differences in the interacting modes, in an interplay with the intermolecular repulsion, allow the formation of the desired phase under different crystallization environments. Salts and co-crystals of GABA and gabapentin with fumaric as well as succinic acid further serve as models to highlight how strongly HBs act as the motif-directing force in the solid-phase GABA-analogs. Six novel multi-component entities were synthesized, and structural and computational analysis was performed: GABA fumarate (2:1); two gabapentin fumarates (2:1) and (1:1); two GABA succinates (2:1) and (1:1); and a gabapentin:succinic acid co-crystal. Energetically highly attractive carboxyl/carboxylate interaction overcomes other factors and dominates the multi-component phase formation. Decisive commonalities in the crystallization behavior of zwitterionic GABA-derivatives are discussed, which show how they can and should be understood as a whole for possible related future products.
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Affiliation(s)
- Daniel Komisarek
- Laboratory for Crystal Engineering, Department of Inorganic and Structural Chemistry 1, Heinrich-Heine-University Dueseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany; (D.K.)
| | - Fulya Demirbas
- Laboratory for Crystal Engineering, Department of Inorganic and Structural Chemistry 1, Heinrich-Heine-University Dueseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany; (D.K.)
| | - Takin Haj Hassani Sohi
- Laboratory for Crystal Engineering, Department of Inorganic and Structural Chemistry 1, Heinrich-Heine-University Dueseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany; (D.K.)
| | - Klaus Merz
- Inorganic Chemistry 1, Ruhr-University Bochum, Universitaetstrasse 150, 44801 Bochum, Germany
| | | | - Vera Vasylyeva
- Laboratory for Crystal Engineering, Department of Inorganic and Structural Chemistry 1, Heinrich-Heine-University Dueseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany; (D.K.)
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23
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Pinacho P, Loru D, Šumanovac T, Šekutor M, Schnell M. Increasing Complexity in Adamantyl Thioethers Characterized by Rotational Spectroscopy. Chemphyschem 2023:e202300561. [PMID: 37673788 DOI: 10.1002/cphc.202300561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
We report on the synthesis and characterization using high-resolution rotational spectroscopy of three bulky thioethers that feature an adamantyl group connected to a sulfur atom. Detailed experimental and theoretical structures are provided and compared with the 1,1'-diadamantyl ether. In addition, we expand on previous findings concerning microsolvation of adamantyl derivatives by investigating the cluster formation between these thioethers and a water molecule. The investigation of such clusters provides valuable insights into the sulfur-centered hydrogen bonding in thioethers with increasing size and steric repulsion.
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Affiliation(s)
- Pablo Pinacho
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Present address: Physical Chemistry Department, University of the Basque Country (UPV/EHU) B° Sarriena, S/N, 48940, Leioa, Spain
| | - Donatella Loru
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tatjana Šumanovac
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Christian-Albrechts-Universität zu Kiel, Institute of Physical Chemistry, Max-Eyth-Str. 1, 24118, Kiel, Germany
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24
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Baweja S, Kalal B, Kumar Mitra P, Maity S. Competing Excited-State Hydrogen and Proton-Transfer Processes in 6-Azaindole-S 3,4 and 2,6-Diazaindole-S 3,4 Clusters (S=H 2 O, NH 3 ). Chemphyschem 2023:e202300270. [PMID: 37671972 DOI: 10.1002/cphc.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/07/2023]
Abstract
Excited state hydrogen (ESHT) and proton (ESPT) transfer reaction pathways in the three and four solvent clusters of 6-azaindole (6AI-S3,4 ) and 2,6-diazaindole (26DAI-S3,4 )(S=H2 O, NH3 ) were computationally investigated to understand the fate of photo-excited biomolecules. The ESHT energy barriers in (H2 O)3 complexes (39.6-41.3 kJmol-1 ) were decreased in (H2 O)4 complexes (23.1-20.2 kJmol-1 ). Lengthening the solvent chain lowered the barrier because of the relaxed transition states geometries with reduced angular strains. Replacing the water molecule with ammonia drastically decreased the energy barriers to 21.4-21.3 kJmol-1 in (NH3 )3 complexes and 8.1-9.5 kJ mol-1 in (NH3 )4 complexes. The transition states were identified as Ha atom attached to the first solvent molecule. The formation of stronger hydrogen bonds in (NH3 )3,4 complexes resulted in facile ESHT reaction than that in the (H2 O)3,4 complexes. The ESPT energy barriers in 6AI-S3,4 and 26DAI-S3,4 were found to range between 40-73 kJmol-1 . The above values were significantly higher than that of the ESHT processes and hence are considered as a minor channel in the process. The effect of N(2) insertion was explored for the very first time in the isolated solvent clusters using local vibrational mode analysis. In DAI-S4 , the higher Ka (Ha ⋯Sa ) values depicted the increased photoacidity of the N(1)-Ha group which may facilitate the hydrogen transfer reaction. However, the increased N(6)⋯Hb bond length elevated the reaction barriers. Therefore, in the ESHT reaction channel, the co-existence of two competing factors led to a marginal/no change in the overall energy barriers due to the N(2) insertion. In the ESPT reaction pathway, the energy barriers showed notable increase upon N(2) insertion because of the increased N(6)⋯Hb bond length.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Bhavika Kalal
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Prajoy Kumar Mitra
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Surajit Maity
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
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25
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Zasedateleva OA, Surzhikov SA, Kuznetsova VE, Shershov VE, Barsky VE, Zasedatelev AS, Chudinov AV. Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency. Int J Mol Sci 2023; 24:13643. [PMID: 37686447 PMCID: PMC10487964 DOI: 10.3390/ijms241713643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase-DNA-dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease in PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity.
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Affiliation(s)
- Olga A. Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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26
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Jiang QQ, Li YJ, Wu Q, Liang RP, Wang X, Zhang R, Wang YA, Liu X, Qiu JD. Molecular Insertion: A Master Key to Unlock Smart Photoelectric Responses of Covalent Organic Frameworks. Small 2023; 19:e2302254. [PMID: 37236205 DOI: 10.1002/smll.202302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/07/2023] [Indexed: 05/28/2023]
Abstract
Covalent organic frameworks (COFs) show potentials in prominent photoelectric responses by judicious structural design. However, from the selections of monomers and condensation reactions to the synthesis procedures, the acquisition of photoelectric COFs has to meet overmuch high conditions, limiting the breakthrough and modulation in photoelectric responses. Herein, the study reports a creative "lock-key model" based on molecular insertion strategy. A COF with suitable cavity size, TP-TBDA, is used as the host to load guests. Merely through the volatilization of mixed solution, TP-TBDA and guests can be spontaneously assembled via non-covalent interactions (NCIs) to produce molecular-inserted COFs (MI-COFs). The NCIs between TP-TBDA and guests acted as a bridge to facilitate charge transfer in MI-COFs, unlocking the photoelectric responses of TP-TBDA. By exploiting the controllability of NCIs, the MI-COFs can realize the smart modulation of photoelectric responses by simply changing the guest molecule, thus avoiding the arduous selection of monomers and condensation reactions required by conventional COFs. The construction of molecular-inserted COFs circumvents complicated procedures for achieving performance improvement and modulation, providing a promising direction to construct late-model photoelectric responsive materials.
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Affiliation(s)
- Qiao-Qiao Jiang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Ya-Jie Li
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Qiong Wu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Ru-Ping Liang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Xun Wang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Rui Zhang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Ying-Ao Wang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Xin Liu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Jian-Ding Qiu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology (ECUT), Nanchang, 330013, China
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27
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Heinen T, Merzenich S, Kwill A, Vasylyeva V. Halogen Bonding in Sulphonamide Co-Crystals: X···π Preferred over X···O/N? Molecules 2023; 28:5910. [PMID: 37570880 PMCID: PMC10420850 DOI: 10.3390/molecules28155910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Sulphonamides have been one of the major pharmaceutical compound classes since their introduction in the 1930s. Co-crystallisation of sulphonamides with halogen bonding (XB) might lead to a new class of pharmaceutical-relevant co-crystals. We present the synthesis and structural analysis of seven new co-crystals of simple sulphonamides N-methylbenzenesulphonamide (NMBSA), N-phenylmethanesulphonamide (NPMSA), and N-phenylbenzenesulphonamide (BSA), as well as of an anti-diabetic agent Chlorpropamide (CPA), with the model XB-donors 1,4-diiodotetrafluorobenzene (14DITFB), 1,4-dibromotetrafluorobenzene (14DBTFB), and 1,2-diiodotetrafluorobenzene (12DITFB). In the reported co-crystals, X···O/N bonds do not represent the most common intermolecular interaction. Against our rational design expectations and the results of our statistical CSD analysis, the normally less often present X···π interaction dominates the crystal packing. Furthermore, the general interaction pattern in model sulphonamides and the CPA multicomponent crystals differ, mainly due to strong hydrogen bonds blocking possible interaction sites.
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Affiliation(s)
| | | | | | - Vera Vasylyeva
- Laboratory for Molecular Crystal Engineering, Department of Inorganic and Structural Chemistry, Heinrich-Heine University Duesseldorf, Universitaetstr. 1, 40225 Dusseldorf, Germany; (T.H.)
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28
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Russo S, Acocella MR, Mariconda A, Volpe V, Pantani R, Longo P. Mechano Chemical Compatibilization of Polyethylene with Graphite by Means of a Suitable Ester. Polymers (Basel) 2023; 15:2770. [PMID: 37447416 DOI: 10.3390/polym15132770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
An effective non-covalent compatibilization method for graphite and low-density polyethylene is reported. To obtain this result, pyren-1-yl-stearate (P1S) was synthesized, characterized and mixed with graphite to provide a better dispersion in polyethylene matrix. The P1S improves the dispersion of carbon filler in polyethylene through non-covalent compatibilization: the pyrenyl group gives π-π stacking interactions with graphite and the stearyl chain provides van der Waals interaction with the polymer chain (specifically London dispersion forces). In this study, different P1S/graphite fillers were prepared with a ratio by weight of 90/10 and 50/50, respectively, by using manual and ball-milling mixing. Their stability, interaction and morphology were evaluated through TGA, RX, and SEM. Thermogravimetric analyses showed that ball-milling mixing is more effective than manual mixing in promoting π-π stacking interactions of molecules such as P1S ester containing an alkyl chain and aromatic rings. The role of ball milling is confirmed by X-ray diffraction measurements since it was possible to observe both exfoliation and intercalation phenomena when this technique was used to mix the P1S ester with graphite. SEM analyses of polyethylene containing 1% of the carbon fillers again highlighted the importance of ball milling to promote the interaction of the ester with graphite and, simultaneously, the importance of the alkyl chain in order to achieve polyethylene-graphite compatibilization.
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Affiliation(s)
- Simona Russo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Maria Rosaria Acocella
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Annaluisa Mariconda
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Valentina Volpe
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Roberto Pantani
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Pasquale Longo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
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29
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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30
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Parra RD. Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study. Molecules 2023; 28:4812. [PMID: 37375366 DOI: 10.3390/molecules28124812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F interactions. The complex with both interactions is the most stable one, followed by the complex with only N-H⋯F interactions. Doubling the size of the former resulted in a complex with a LiF dimer sandwiched between the model tetraamides. In turn, doubling the size of the latter resulted in a more stable tetramer with bracelet-like geometry having the two LiF molecules also sandwiched but far apart from each other. Additionally, all methods show that the energy barrier to transition to the more stable tetramer is small. The self-assembly of the bracelet-like complex mediated by the interactions of adjacent LiF molecules is demonstrated by all computational methods employed.
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Affiliation(s)
- Rubén D Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
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31
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Gómez-Flores AK, López-Pérez E, Alas-Guardado SJ. Molecular Dynamics Simulations of HPr Proteins from a Thermophilic and a Mesophilic Organism: A Comparative Thermal Study. Int J Mol Sci 2023; 24:ijms24119557. [PMID: 37298508 DOI: 10.3390/ijms24119557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The histidine-containing phosphocarrier (HPr) is a monomeric protein conserved in Gram-positive bacteria, which may be of mesophilic or thermophilic nature. In particular, the HPr protein from the thermophilic organism B. stearothermophilus is a good model system for thermostability studies, since experimental data, such as crystal structure and thermal stability curves, are available. However, its unfolding mechanism at higher temperatures is yet unclear at a molecular level. Therefore, in this work, we researched the thermal stability of this protein using molecular dynamics simulations, subjecting it to five different temperatures during a time span of 1 μs. The analyses of the structural parameters and molecular interactions were compared with those of the mesophilic homologue HPr protein from B. subtilis. Each simulation was run in triplicate using identical conditions for both proteins. The results showed that the two proteins lose stability as the temperature increases, but the mesophilic structure is more affected. We found that the salt bridge network formed by the triad of Glu3-Lys62-Glu36 residues and the salt bridge made up of Asp79-Lys83 ion pair are key factors to keep stable the thermophilic protein, maintaining the hydrophobic core protected and the structure packed. In addition, these molecular interactions neutralize the negative surface charge, acting as "natural molecular staples".
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Affiliation(s)
- Ana K Gómez-Flores
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Mexico City 05300, Mexico
| | - Edgar López-Pérez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Mexico City 05300, Mexico
| | - Salomón J Alas-Guardado
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Mexico City 05300, Mexico
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32
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Magin IM, Pushkin IA, Ageeva AA, Martianova SO, Polyakov NE, Doktorov AB, Leshina TV. Impact of Non-Covalent Interactions of Chiral Linked Systems in Solution on Photoinduced Electron Transfer Efficiency. Int J Mol Sci 2023; 24:ijms24119296. [PMID: 37298248 DOI: 10.3390/ijms24119296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino acids in the association. We have recently demonstrated the unique sensitivity of chemically induced dynamic nuclear polarization (CIDNP) formed in photoinduced electron transfer (PET) in chiral donor-acceptor dyads to non-covalent interactions of its diastereomers in solutions. The present study further develops the approach for quantitatively analyzing the factors that determine the association by examples of dimerization of the diastereomers with the RS, SR, and SS optical configurations. It has been shown that, under the UV irradiation of dyads, CIDNP is formed in associates, namely, homodimers (SS-SS), (SR-SR), and heterodimers (SS-SR) of diastereomers. In particular, the efficiency of PET in homo-, heterodimers, and monomers of dyads completely determines the forms of dependences of the CIDNP enhancement coefficient ratio of SS and RS, SR configurations on the ratio of diastereomer concentrations. We expect that the use of such a correlation can be useful in identifying small-sized associates in peptides, which is still a problem.
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Affiliation(s)
- Ilya M Magin
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
| | - Ivan A Pushkin
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra A Ageeva
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sofia O Martianova
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay E Polyakov
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
| | - Alexander B Doktorov
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
| | - Tatyana V Leshina
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia
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33
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Arcudi F, Đorđević L. Supramolecular Chemistry of Carbon-Based Dots Offers Widespread Opportunities. Small 2023:e2300906. [PMID: 37078923 DOI: 10.1002/smll.202300906] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/01/2023] [Indexed: 05/03/2023]
Abstract
Carbon dots are an emerging class of nanomaterials that has recently attracted considerable attention for applications that span from biomedicine to energy. These photoluminescent carbon nanoparticles are defined by characteristic sizes of <10 nm, a carbon-based core and various functional groups at their surface. Although the surface groups are widely used to establish non-covalent bonds (through electrostatic interactions, coordinative bonds, and hydrogen bonds) with various other (bio)molecules and polymers, the carbonaceous core could also establish non-covalent bonds (ππ stacking or hydrophobic interactions) with π-extended or apolar compounds. The surface functional groups, in addition, can be modified by various post-synthetic chemical procedures to fine-tune the supramolecular interactions. Our contribution categorizes and analyzes the interactions that are commonly used to engineer carbon dots-based materials and discusses how they have allowed preparation of functional assemblies and architectures used for sensing, (bio)imaging, therapeutic applications, catalysis, and devices. Using non-covalent interactions as a bottom-up approach to prepare carbon dots-based assemblies and composites can exploit the unique features of supramolecular chemistry, which include adaptability, tunability, and stimuli-responsiveness due to the dynamic nature of the non-covalent interactions. It is expected that focusing on the various supramolecular possibilities will influence the future development of this class of nanomaterials.
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Affiliation(s)
- Francesca Arcudi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, Padova, 35131, Italy
| | - Luka Đorđević
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, Padova, 35131, Italy
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Osipova ES, Kovalenko SA, Gulyaeva ES, Kireev NV, Pavlov AA, Filippov OA, Danshina AA, Valyaev DA, Canac Y, Shubina ES, Belkova NV. The Dichotomy of Mn-H Bond Cleavage and Kinetic Hydricity of Tricarbonyl Manganese Hydride Complexes. Molecules 2023; 28:molecules28083368. [PMID: 37110601 PMCID: PMC10143952 DOI: 10.3390/molecules28083368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Acid-base characteristics (acidity, pKa, and hydricity, ΔG°H- or kH-) of metal hydride complexes could be a helpful value for forecasting their activity in various catalytic reactions. Polarity of the M-H bond may change radically at the stage of formation of a non-covalent adduct with an acidic/basic partner. This stage is responsible for subsequent hydrogen ion (hydride or proton) transfer. Here, the reaction of tricarbonyl manganese hydrides mer,trans-[L2Mn(CO)3H] (1; L = P(OPh)3, 2; L = PPh3) and fac-[(L-L')Mn(CO)3H] (3, L-L' = Ph2PCH2PPh2 (dppm); 4, L-L' = Ph2PCH2-NHC) with organic bases and Lewis acid (B(C6F5)3) was explored by spectroscopic (IR, NMR) methods to find the conditions for the Mn-H bond repolarization. Complex 1, bearing phosphite ligands, features acidic properties (pKa 21.3) but can serve also as a hydride donor (ΔG≠298K = 19.8 kcal/mol). Complex 3 with pronounced hydride character can be deprotonated with KHMDS at the CH2-bridge position in THF and at the Mn-H position in MeCN. The kinetic hydricity of manganese complexes 1-4 increases in the order mer,trans-[(P(OPh)3)2Mn(CO)3H] (1) < mer,trans-[(PPh3)2Mn(CO)3H] (2) ≈ fac-[(dppm)Mn(CO)3H] (3) < fac-[(Ph2PCH2NHC)Mn(CO)3H] (4), corresponding to the gain of the phosphorus ligand electron-donor properties.
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Affiliation(s)
- Elena S Osipova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
| | - Sergey A Kovalenko
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
| | - Ekaterina S Gulyaeva
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
- LCC-CNRS, Université de Toulouse, CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| | - Nikolay V Kireev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
| | - Alexander A Pavlov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
- Center of National Technological Initiative, Bauman Moscow State Technical University, 2nd Baumanskaya Str., 5, 105005 Moscow, Russia
| | - Oleg A Filippov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
| | - Anastasia A Danshina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy per., 9, 141700 Dolgoprudny, Russia
| | - Dmitry A Valyaev
- LCC-CNRS, Université de Toulouse, CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| | - Yves Canac
- LCC-CNRS, Université de Toulouse, CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| | - Elena S Shubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
| | - Natalia V Belkova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28, Vavilova Str., 119334 Moscow, Russia
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Wang B, Qiao C, Wang YL, Dong X, Zhang W, Lu Y, Yuan J, Zeng H, Wang H. Multifunctional Underwater Adhesive Film Enabled by a Single-Component Poly(ionic liquid). ACS Nano 2023; 17:5871-5879. [PMID: 36926859 DOI: 10.1021/acsnano.2c12767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tremendous efforts have been devoted to exploiting synthetic wet adhesives for real-life applications. However, developing low-cost, robust, and multifunctional wet adhesive materials remains a considerable challenge. Herein, a wet adhesive composed of a single-component poly(ionic liquid) (PIL) that enables fast and robust underwater adhesion is reported. The PIL adhesive film possesses excellent stretchability and flexibility, enabling its anchoring on target substrates regardless of deformation and water scouring. Surface force measurements show the PIL can achieve a maximum adhesion of 56.7 mN·m-1 on diverse substrates (both hydrophilic and hydrophobic substrates) in aqueous media, within ∼30 s after being applied. The adhesion mechanisms of the PIL were revealed via the force measurements, and its robust wet adhesive capacity was ascribed to the synergy of different non-covalent interactions, such as of hydrogen bonding, cation-π, electrostatic, and van der Waals interactions. Surprisingly, this PIL adhesive film exhibited impressive underwater sound absorption capacity. The absorption coefficient of a 0.7 mm-thick PIL film to 4-30 kHz sound waves could be as high as 0.80-0.92. This work reports a multifunctional PIL wet adhesive that has promising applications in many areas and provides deep insights into interfacial interaction mechanisms underlying the wet adhesion capability of PILs.
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Affiliation(s)
- Binmin Wang
- Key Laboratory of Functional Polymer Materials (Ministry of Education), Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Chenyu Qiao
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Yong-Lei Wang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
- Department of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Xiaoxiao Dong
- Key Laboratory of Functional Polymer Materials (Ministry of Education), Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Wangqing Zhang
- Key Laboratory of Functional Polymer Materials (Ministry of Education), Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yan Lu
- Department of Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Jiayin Yuan
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hong Wang
- Key Laboratory of Functional Polymer Materials (Ministry of Education), Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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Wojtkowiak K, Jezierska A. Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach. Pharmaceuticals (Basel) 2023; 16:ph16040479. [PMID: 37111236 PMCID: PMC10146004 DOI: 10.3390/ph16040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.
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Affiliation(s)
- Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Marques LR, Ando RA. Infrared Spectroscopy Evidence of Weak Interactions in Frustrated Lewis Pairs Formed by Tris(pentafluorophenyl)borane. Chemphyschem 2023; 24:e202200715. [PMID: 36450662 DOI: 10.1002/cphc.202200715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
Frustrated Lewis pairs (FLPs) have been widely investigated as promising catalysts due to their metal-free feature and ability to activate small molecules. Since their discovery, many works have been investigating how these Lewis pairs (intermolecular pairs) are held together in an encounter complex. This prompted several studies based on theoretical investigations, but experimental ones are limited yet. In this communication we show evidence of weak intermolecular interactions between Lewis acids and Lewis bases, distinguishing the Lewis adduct from FLPs, by probing fluorine-carbon vibrational modes using infrared spectroscopy. The main evidence is based on the band shifts occurring in FLPs due to weak hydrogen bonds between the hydrogen atoms of the Lewis base and the fluorine atoms of Lewis acid.
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Affiliation(s)
- Leandro Ramos Marques
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000, São Paulo-SP, Brazil
| | - Rômulo Augusto Ando
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000, São Paulo-SP, Brazil
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Yaragani M, Yadlapalli P, Raghavan S, Giridhar T, Mandava VBR, Singh RV, Kottapalli RP, Chinnusamy S. Electronic effect-dependent intramolecular non-covalent interactions on the activity of 4,4-dimethylimidazolidin-2-one pharmacophore-based androgen receptor antagonists. Chem Biol Drug Des 2023; 101:614-625. [PMID: 36198102 DOI: 10.1111/cbdd.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Because androgen receptor (AR) signalling is important for the development and progression of prostate cancer (PC), AR antagonists are utilized in clinical practices to treat PC and are referred to as androgen deprivation therapy (ADT). However, continued administration of AR antagonists often results in the development of resistance, known as castration-resistant prostate cancer (CRPC). Despite castration, it has been demonstrated that AR signalling continues to be fundamental to tumour growth. In this regard, a series of readily synthesizable 4,4-dimethylimidazolidine-2-one pharmacophore-based AR antagonists (FAR01-FAR11) were designed and synthesized. Androgen-dependent LNCaP PC cell line was used to test the AR-antagonist activity of these compounds in vitro and compared with the U.S. Food and Drug Administration (FDA) approved second-generation enzalutamide. In our previous work, rigid thiohydantoin pharmacophore in enzalutamide is replaced by the flexible 4,4-dimethylimidazolidin-2-one. In order to improve the flexibility further, one methylene group is introduced between the pharmacophore and one of the aromatic ring. Despite the fact that the amide functional group is a crucial characteristic for building AR antagonists, this class of molecules lacks one. FAR06 has the exact same activity as enzalutamide (IC50 : 0.782 μM) with an IC50 value of 0.801 μM among the series of compounds.
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Affiliation(s)
- Muralikrishna Yaragani
- Department of Chemistry, Koneru Lakshmaiah Education Foundation, Guntur, Andhra Pradesh, India
| | | | - Sriram Raghavan
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - Thota Giridhar
- Sigma-Aldrich Chemicals Pvt. Ltd, Bangalure, Karnataka, India
| | | | | | | | - Saravanan Chinnusamy
- Center for Advanced Organic Materials (Sona-AROMA), Department of Chemistry, Sona College of Technology, Salem, Tamil Nadu, India
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Ren H, Ji L, Jia X, Tao J, Liu R, Wei D, Wang X, Ji G. Theoretically Revealing the Response of Intermolecular Vibration Energy Transfer and Decomposition Process of the DNTF System to Electric Fields Using Two-Dimensional Infrared Spectra. Int J Mol Sci 2023; 24. [PMID: 36901784 DOI: 10.3390/ijms24054352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The external electric field (E-field), which is an important stimulus, can change the decomposition mechanism and sensitivity of energetic materials. As a result, understanding the response of energetic materials to external E-fields is critical for their safe use. Motivated by recent experiments and theories, the two-dimensional infrared (2D IR) spectra of 3,4-bis (3-nitrofurazan-4-yl) furoxan (DNTF), which has a high energy, a low melting point, and comprehensive properties, were theoretically investigated. Cross-peaks were observed in 2D IR spectra under different E-fields, which demonstrated an intermolecular vibration energy transfer; the furazan ring vibration was found to play an important role in the analysis of vibration energy distribution and was extended over several DNTF molecules. Measurements of the non-covalent interactions, with the support of the 2D IR spectra, indicated that there were obvious non-covalent interactions among different DNTF molecules, which resulted from the conjugation of the furoxan ring and the furazan ring; the direction of the E-field also had a significant influence on the strength of the weak interactions. Furthermore, the calculation of the Laplacian bond order, which characterized the C-NO2 bonds as trigger bonds, predicted that the E-fields could change the thermal decomposition process of DNTF while the positive E-field facilitates the breakdown of the C-NO2 in DNTFⅣ molecules. Our work provides new insights into the relationship between the E-field and the intermolecular vibration energy transfer and decomposition mechanism of the DNTF system.
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Smirnov AS, Mikherdov AS, Rozhkov AV, Gomila RM, Frontera A, Kukushkin VY, Bokach NA. Halogen Bond-Involving Supramolecular Assembly Utilizing Carbon as a Nucleophilic Partner of I⋅⋅⋅C Non-covalent Interaction. Chem Asian J 2023; 18:e202300037. [PMID: 36807544 DOI: 10.1002/asia.202300037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 02/21/2023]
Abstract
Co-crystallization of 180°-orienting σ-hole-accepting tectons, namely, 1,4-diisocyanobenzene (1) and 1,4-diisocyanotetramethylbenzene (2), with such homoditopic halogen bond donors as 1,4-diiodotetrafluorobenzene (1,4-FIB) and 4,4'-diiodoperfluorobiphenyl (4,4'-FIBP) afforded co-crystals 1 ⋅ 1,4-FIB, 1 ⋅ 4,4'-FIBP, and 2 ⋅ 1,4-FIB. Their solid-state structures exhibit 1D-supramolecular arrangements, which are based on poorly explored I⋅⋅⋅C halogen bonding; this study is the first in which the supramolecular assembly utilizing halogen bonding with a terminal C atom was performed. The use of the potentially tetrafunctional σ-hole accepting tetraiodoethylene (TIE) leads to supramolecular architecture of a higher dimension, 3D-framework, observed in the structure of 1 ⋅ TIE. DFT calculations, used to characterize the halogen bonding situation, revealed that the I⋅⋅⋅C non-covalent interactions are moderately strong, ranging from -4.07 in 1 ⋅ TIE to -5.45 kcal/mol in 2 ⋅ 1,4-FIB. The NBO analysis disclosed that LP(C)→σ* charge transfer effects are relevant in all co-crystals.
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Affiliation(s)
- Andrey S Smirnov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034, Saint Petersburg, Russian Federation
| | - Alexander S Mikherdov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034, Saint Petersburg, Russian Federation
| | - Anton V Rozhkov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034, Saint Petersburg, Russian Federation
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034, Saint Petersburg, Russian Federation.,Laboratory of Crystal Engineering of Functional Materials, South Ural State University, 76, Lenin Av., Chelyabinsk, 454080, Russian Federation
| | - Nadezhda A Bokach
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034, Saint Petersburg, Russian Federation
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Lavrenova LG, Ivanova AI, Glinskaya LA, Artem'ev AV, Lavrov AN, Novikov AS, Abramov PA. Halogen Bonding Channels for Magnetic Exchange in Cu(II) Complexes with 2,5-Di(methylthio)-1,3,4-thiadiazole. Chem Asian J 2023; 18:e202201200. [PMID: 36629842 DOI: 10.1002/asia.202201200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/12/2023]
Abstract
Copper(II) complexes with 2,5-bis(methylthio)-1,3,4-thiadiazole (tda) formulated as [Cu(tda)n X2 ] (n=2, X=Cl- , Br- , C2 N3 - ; n= 1, X=C2 N3 - ) have been isolated and fully characterized. The crystal structures of all compounds have been determined using single-crystal X-ray diffraction (SCXRD). A study of the magnetic susceptibility in the range 1.77-300 K has shown that magnetic properties of the [Cu(tda)2 Cl2 ] and [Cu(tda)2 Br2 ] complexes match those of 1D chains of antiferromagnetically-coupled Cu2+ ions. The intrachain interaction J in [Cu(tda)2 Cl2 ] turns out to be ∼1.2 times weaker than in its bromide analogue. In its turn, [Cu(tda)2 (C2 N3 )2 ] exhibits J being an order of magnitude smaller and of the opposite ferromagnetic sign. Halogen bonding (HB) between adjacent complexes is much stronger than the H-bonds or π-π interactions between tda ligands according to the DFT calculations.
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Affiliation(s)
- Ludmila G Lavrenova
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Alina I Ivanova
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Lyudmila A Glinskaya
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Alexander V Artem'ev
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Alexander N Lavrov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia
| | - Alexander S Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034, Saint Petersburg, Russia.,Research Institute of Chemistry, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya St., 6, 117198, Moscow, Russia
| | - Pavel A Abramov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 3 acad. Lavrentiev Ave., 630090, Novosibirsk, Russia.,Institute of Natural Sciences and Mathematics Ural Federal University named after B.N. Yeltsin, Lenin Ave, 51, Yekaterinburg, 620075, Russia
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Agarkov AS, Nefedova AA, Gabitova ER, Mingazhetdinova DO, Ovsyannikov AS, Islamov DR, Amerhanova SK, Lyubina AP, Voloshina AD, Litvinov IA, Solovieva SE, Antipin IS. (2-Hydroxy-3-Methoxybenzylidene)thiazolo[3,2-a]pyrimidines: Synthesis, Self-Assembly in the Crystalline Phase and Cytotoxic Activity. Int J Mol Sci 2023; 24. [PMID: 36768407 DOI: 10.3390/ijms24032084] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
A series of new 2-hydroxy-3-methoxybenzylidenethiazolo[3,2-a]pyrimidines with different aryl substituents at the 5 position are synthesized and characterized by 1H/ 13C NMR and IR-spectroscopy and mass-spectrometry, as well as single crystal X-ray diffraction (SCXRD). It was demonstrated that the type of hydrogen bonding can play a key role in the chiral discrimination of these compounds in the crystalline phase. The hydrogen bond of the O-H...N type leads to 1D supramolecular heterochiral chains or conglomerate crystallization in the case of the formation of homochiral chains. The hydrogen bond of O-H...O type gave racemic dimers, which are packed into 2D supramolecular layers with a parallel or angular dimers arrangement. Halogen bonding of the N...Br or O...Br type brings a new motif into supramolecular self-assembly in the crystalline phase: the formation of 1D supramolecular homochiral chains instead 2D supramolecular layers. The study of cytotoxicity against various tumor cells in vitro was carried out. It was found that 2-hydroxy-3-methoxybenzylidenethiazolo[3,2-a]pyrimidines with 3-nitrophenyl substituent at C5 carbon atom demonstrated a high efficiency against M-HeLa (cervical adenocarcinoma) and low cytotoxicity against normal liver cells.
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Sebaaly AP, Dias H, Christ L, Merzoud L, Chermette H, Hoffmann G, Morell C. Insight into the Varying Reactivity of Different Catalysts for CO(2) Cycloaddition into Styrene Oxide: An Experimental and DFT Study. Int J Mol Sci 2023; 24. [PMID: 36768447 DOI: 10.3390/ijms24032123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 01/25/2023] Open
Abstract
The cycloaddition of CO2 into epoxides to form cyclic carbonates is a highly sought-after reaction for its potential to both reduce and use CO2, which is a greenhouse gas. In this paper, we present experimental and theoretical studies and a mechanistic approach for three catalytic systems. First, as Lewis base catalysts, imidazole and its derivatives, then as a Lewis acid catalyst, ZnI2 alone, and after that, the combined system of ZnI2 and imidazole. In the former, we aimed to discover the reasons for the varied reactivities of five Lewis base catalysts. Furthermore, we succeeded in reproducing the experimental results and trends using DFT. To add, we emphasized the importance of non-covalent interactions and their role in reactivity. In our case, the presence of a hydrogen bond was a key factor in decreasing the reactivity of some catalysts, thus leading to lower conversion rates. Finally, mechanistically understanding this 100% atom economy reaction can aid experimental chemists in designing better and more efficient catalytic systems.
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Migliore R, Ferreri L, Aleo D, Leotta CG, Pitari GM, D’Antona N, Sgarlata C, Consoli GML. p-Sulfonato-Calix[4]arene Micelles Stabilize a Povidone Iodine Solution: Supramolecular Interactions, Iodine Retention, and Bactericidal Activity. Nanomaterials (Basel) 2023; 13:286. [PMID: 36678039 PMCID: PMC9865561 DOI: 10.3390/nano13020286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/24/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Povidone iodine (PVPI) is an antiseptic widely used against a broad spectrum of pathogens. However, undesired side-effects are still associated with PVPI treatment due to the irritant effect of iodine. Reducing the concentration of a PVPI formulation could provide safer and more friendly formulations, for routine use and applications in very delicate organs such as the eye. However, managing the storage of a low-concentration solution of PVPI is challenging due to the high iodine volatility. In this study, we demonstrated that an amphiphilic p-sulfonato-calix[4]arene derivative forming micelles (SC4OC6) improves the stability of a 0.1% PVPI aqueous buffered solution. UV-vis and NMR spectra as well as dynamic and electrophoretic light scattering measurements showed that SC4OC6 establishes non-covalent supramolecular interactions with PVPI, resulting in the formation of nanoaggregates with a negatively charged surface. Isothermal titration calorimetry provided the aggregation parameters and evidenced that the formation of the supramolecular assembly is an enthalpically favored process. The interaction of SC4OC6 with PVPI enhances the iodine retention and stability of the solution without affecting the rapid and effective bactericidal activity of PVPI, as demonstrated by a time-killing assay with Staphylococcus epidermidis.
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Affiliation(s)
- Rossella Migliore
- Institute of Biomolecular Chemistry—National Research Council (C.N.R.), Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Loredana Ferreri
- Institute of Biomolecular Chemistry—National Research Council (C.N.R.), Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Danilo Aleo
- MEDIVIS Srl, Via Carnazza 34C, Tremestieri Etneo, 95030 Catania, Italy
| | | | | | - Nicola D’Antona
- Institute of Biomolecular Chemistry—National Research Council (C.N.R.), Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Carmelo Sgarlata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Grazia Maria Letizia Consoli
- Institute of Biomolecular Chemistry—National Research Council (C.N.R.), Via Paolo Gaifami 18, 95126 Catania, Italy
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45
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Jana P, Samanta K, Ehlers M, Zellermann E, Bäcker S, Stauber RH, Schmuck C, Knauer SK. Impact of Peptide Sequences on Their Structure and Function: Mimicking of Virus-Like Nanoparticles for Nucleic Acid Delivery. Chembiochem 2023; 24:e202200519. [PMID: 36314419 PMCID: PMC10099937 DOI: 10.1002/cbic.202200519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/30/2022] [Indexed: 01/05/2023]
Abstract
We rationally designed a series of amphiphilic hepta-peptides enriched with a chemically conjugated guanidiniocarbonylpyrrole (GCP) unit at the lysine side chain. All peptides are composed of polar (GCP) and non-polar (cyclohexyl alanine) residues but differ in their sequence periodicity, resulting in different secondary as well as supramolecular structures. CD spectra revealed the assembly of β-sheet-, α-helical and random structures for peptides 1, 2 and 3, respectively. Consequently, this enabled the formation of distinct supramolecular assemblies such as fibres, nanorod-like or spherical aggregates. Notably, all three cationic peptides are equipped with the anion-binding GCP unit and thus possess a nucleic acid-binding centre. However, only the helical (2) and the unstructured (3) peptide were able to assemble into small virus-like DNA-polyplexes and effectively deliver DNA into cells. Notably, as both peptides (2 and 3) were also capable of siRNA-delivery, they could be utilized to downregulate expression of the caner-relevant protein Survivin.
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Affiliation(s)
- Poulami Jana
- Department of Chemistry, Kaliachak College Sultanganj, Malda, 732201-, West Bengal, India
| | - Krishnananda Samanta
- Department of Chemistry, Balurghat College Dakshin Dinajpur, 733101-, West Bengal, India
| | - Martin Ehlers
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Elio Zellermann
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Sandra Bäcker
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology, ENT Department, University Mainz Medical Center, 55131, Mainz, Germany
| | - Carsten Schmuck
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
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46
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Cohen E, Avram L, Poverenov E. Formation of Robust and Adaptive Biopolymers via Non-Covalent Supramolecular Interactions. Macromol Rapid Commun 2023; 44:e2200579. [PMID: 36153845 DOI: 10.1002/marc.202200579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/16/2022] [Indexed: 01/26/2023]
Abstract
Biomass-originated materials are the future's next-tier polymers. This work suggests improving mechanical and barrier properties of nature-sourced polymers using non-covalent supramolecular interactions. Polysaccharide chitosan is modified with amino acids via an esterification pathway using a systematic variation of hydrogen bond and aromatic domains (Degrees of substitution 12-49%). These controlled modifications improve stability due to non-covalent interactions, resulting in biopolymers with tailored thermal (decomposition temperature 232-275 °C), mechanical (Young's modulus 540-2667 MPa), and surface properties (roughness 4-40 nm). Chitosan and natural amino acids that are already manufactured at scale are purposely selected. The facile synthesis, controlled properties, stimuli-responsive potential, and inexhaustible origin of the raw materials provide the presented findings with the potential to become the method for the formation of high-performance biodegradable alternatives to petroleum-based polymers that can be used in packaging, food, agriculture, and medicine.
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Affiliation(s)
- Erez Cohen
- Agro-Nanotechnology and Advanced Materials Center, Institute of Postharvest and Food Sciences, Agriculture Research Organization, The Volcani Center, 68 HaMacabim Road, Rishon LeZion, 7505101, Israel.,Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 229 Herzl Street, Rehovot, 7610001, Israel
| | - Liat Avram
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Elena Poverenov
- Agro-Nanotechnology and Advanced Materials Center, Institute of Postharvest and Food Sciences, Agriculture Research Organization, The Volcani Center, 68 HaMacabim Road, Rishon LeZion, 7505101, Israel
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47
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Reddy CN, Sankararamakrishnan R. Molecular dynamics studies of CED-4/CED-9/EGL-1 ternary complex reveal CED-4 release mechanism in the linear apoptotic pathway of Caenorhabditis elegans. Proteins 2022; 91:679-693. [PMID: 36541866 DOI: 10.1002/prot.26457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/14/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Many steps in programmed cell death are evolutionarily conserved across different species. The Caenorhabditis elegans proteins CED-9, CED-4 and EGL-1 involved in apoptosis are respectively homologous to anti-apoptotic Bcl-2 proteins, Apaf-1 and the "BH3-only" pro-apototic proteins in mammals. In the linear apoptotic pathway of C. elegans, EGL-1 binding to CED-9 leads to the release of CED-4 from CED-9/CED-4 complex. The molecular events leading to this process are not clearly elucidated. While the structures of CED-9 apo, CED-9/EGL-1 and CED-9/CED-4 complexes are known, the CED-9/CED-4/EGL-1 ternary complex structure is not yet determined. In this work, we modeled this ternary complex and performed molecular dynamics simulations of six different systems involving CED-9. CED-9 displays differential dynamics depending upon whether it is bound to CED-4 and/or EGL-1. CED-4 exists as an asymmetric dimer (CED4a and CED4b) in CED-9/CED-4 complex. CED-4a exhibits higher conformational flexibility when simulated without CED-4b. Principal Component Analysis revealed that the direction of CED-4a's winged-helix domain motion differs in the ternary complex. Upon EGL-1 binding, majority of non-covalent interactions involving CARD domain in the CED-4a-CED-9 interface have weakened and only half of the contacts found in the crystal structure between α/β domain of CED4a and CED-9 are found to be stable. Additional stable contacts in the ternary complex and differential dynamics indicate that winged-helix domain may play a key role in CED-4a's dissociation from CED-9. This study has provided a molecular level understanding of potential intermediate states that are likely to occur when CED-4a is released from CED-9.
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Affiliation(s)
- C Narendra Reddy
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ramasubbu Sankararamakrishnan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India.,Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, India
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48
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Seitz A, Wende RC, Schreiner PR. Site-Selective Acylation of Pyranosides with Immobilized Oligopeptide Catalysts in Flow. Chemistry 2022; 29:e202203002. [PMID: 36538197 DOI: 10.1002/chem.202203002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
We report the site-selective acetylation of partially protected monosaccharides using immobilized oligopeptide catalysts, which are readily accessible via solid-phase peptide synthesis. The catalysts are able to invert the intrinsic selectivity, which was determined using N-methylimidazole, for a variety of pyranosides. We demonstrate that the catalysts are stable for multiple reaction cycles and can be easily reused after separation from the reaction solution. The catalysts can also be used in flow without loss of reactivity and selectivity.
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Affiliation(s)
- Alexander Seitz
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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49
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Wojtkowiak K, Jezierska A. Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives. Molecules 2022; 27. [PMID: 36557978 DOI: 10.3390/molecules27248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.
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50
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Gómez S, Gómez S, David J, Guerra D, Cappelli C, Restrepo A. Dissecting Bonding Interactions in Cysteine Dimers. Molecules 2022; 27:molecules27248665. [PMID: 36557799 PMCID: PMC9786917 DOI: 10.3390/molecules27248665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.
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Affiliation(s)
- Santiago Gómez
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Jorge David
- Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300, Medellín 050022, Colombia
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Correspondence: (C.C.); (A.R.)
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
- Correspondence: (C.C.); (A.R.)
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