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D'Arminio N, Ruggiero V, Pierri G, Marabotti A, Tedesco C. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns. Protein Sci 2024; 33:e4868. [PMID: 38100281 PMCID: PMC10806932 DOI: 10.1002/pro.4868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types.
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Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Valentina Ruggiero
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
- Present address:
Department of PharmacyUniversity of SalernoFiscianoItaly
| | - Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
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Louis H, Amodu IO, Eno EA, Benjamin I, Gber TE, Unimuke TO, Isang BB, Adeyinka AS. Modeling the Interactionof F-gases on Ruthenium-Doped Boron Nitridenanotube. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00645-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Miroslaw B, Demchuk OM, Luboradzki R, Tyszczuk-Rotko K. Low-Molecular-Weight Organogelators Based on N-dodecanoyl-L-amino Acids-Energy Frameworks and Supramolecular Synthons. MATERIALS (BASEL, SWITZERLAND) 2023; 16:702. [PMID: 36676438 PMCID: PMC9867098 DOI: 10.3390/ma16020702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Lauric acid was used to synthesize the low-molecular-weight organogelators (LMOGs), derivatives of two endogenous (L)-alanine, (L)-leucine, and three exogenous (L)-valine, (L)-phenylalanine, and (L)-proline amino acids. The nature of processes responsible for the gel formation both in polar and in apolar solvents of such compounds is still under investigation. Knowing that the organization of surfactant molecules affects the properties of nano scale materials and gels, we decided to elucidate this problem using crystallographic diffraction and energy frameworks analysis. The single crystals of the mentioned compounds were produced successfully from heptane/tBuOMe mixture. The compounds form lamellar self-assemblies in crystals. The energetic landscapes of single crystals of a series of studied amphiphilic gelators have been analyzed to explore the gelling properties. The presented results may be used as model systems to understand which supramolecular interactions observed in the solid state and what energy contributions are desired in the designing of new low-molecular-weight organic gelators.
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Affiliation(s)
- Barbara Miroslaw
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, 20-031 Lublin, Poland
| | - Oleg M. Demchuk
- Faculty of Medicine, The John Paul II Catholic University of Lublin, 1h-Konstantynów St., 20-708 Lublin, Poland
| | - Roman Luboradzki
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Katarzyna Tyszczuk-Rotko
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, 20-031 Lublin, Poland
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Shin JW, Ullah I, Tokunaga R, Hayami S, Min KS. Air oxidation-induced single-crystal-to-single-crystal transformation of mixed-valence tetranuclear Fe(II)-Fe(III) complexes. Dalton Trans 2022; 51:14429-14433. [PMID: 36134441 DOI: 10.1039/d2dt02551e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mixed valence tetranuclear iron complex [(Hpmide)FeII(NCSe)2FeIII(pmide)]2·5CH3OH (1) underwent oxidation and ligand exchange in the solid state (H2pmide = N-(2-pyridylmethyl)iminodiethanol). Upon air oxidation, 1 was converted into [(pmide)FeIII(NCSe)FeIII(pmide)]2(NCSe)2·2H2O (2), which was accompanied by deprotonation and ligand exchange through a single crystal-to-single-crystal transformation.
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Affiliation(s)
- Jong Won Shin
- Department of Chemistry, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ihsan Ullah
- Department of Chemistry, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ryuya Tokunaga
- Department of Chemistry, Kumamoto University, Kumamoto 860-8555, Japan
| | - Shinya Hayami
- Department of Chemistry, Kumamoto University, Kumamoto 860-8555, Japan
| | - Kil Sik Min
- Department of Chemistry Education, Kyungpook National University, Daegu 41566, Republic of Korea.
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Pierri G, Schettini R, Summa FF, De Riccardis F, Monaco G, Izzo I, Tedesco C. Right- and left-handed PPI helices in cyclic dodecapeptoids. Chem Commun (Camb) 2022; 58:5253-5256. [PMID: 35388839 DOI: 10.1039/d2cc00682k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enantiomorphic right- and left-handed polyproline type I helices in four cyclic dodecapeptoids with methoxyethyl and propargyl side chains are observed for the first time by single crystal X-ray diffraction. The peculiar absence of NH⋯OC hydrogen bonds in peptoids unveils the role of intramolecular backbone-to-backbone CO⋯CO interactions and CH⋯OC hydrogen bonds in the stabilization of the macrocycle conformation. Moreover, intramolecular backbone-side chain C5 CH⋯OC hydrogen bonds emerge as a stabilizing factor.
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Affiliation(s)
- Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Rosaria Schettini
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco F Summa
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Guglielmo Monaco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, I-84084 Fisciano, Italy.
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Gber TE, Louis H, Owen AE, Etinwa BE, Benjamin I, Asogwa FC, Orosun MM, Eno EA. Heteroatoms (Si, B, N, and P) doped 2D monolayer MoS 2 for NH 3 gas detection. RSC Adv 2022; 12:25992-26010. [PMID: 36199611 PMCID: PMC9468912 DOI: 10.1039/d2ra04028j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022] Open
Abstract
2D transition metal dichalcogenide MoS2 monolayer quantum dots (MoS2-QD) and their doped boron (B@MoS2-QD), nitrogen (N@MoS2-QD), phosphorus (P@MoS2-QD), and silicon (Si@MoS2-QD) surfaces have been theoretically investigated using density functional theory (DFT) computation to understand their mechanistic sensing ability, such as conductivity, selectivity, and sensitivity toward NH3 gas. The results from electronic properties showed that P@MoS2-QD had the lowest energy gap, which indicated an increase in electrical conductivity and better adsorption behavior. By carrying out comparative adsorption studies using m062-X, ωB97XD, B3LYP, and PBE0 methods at the 6-311G++(d,p) level of theory, the most negative values were observed from ωB97XD for the P@MoS2-QD surface, signifying the preferred chemisorption surface for NH3 detection. The mechanistic studies provided in this study also indicate that the P@MoS2-QD dopant is a promising sensing material for monitoring ammonia gas in the real world. We hope this research work will provide informative knowledge for experimental researchers to realize the potential of MoS2 dopants, specifically the P@MoS2-QD surface, as a promising candidate for sensors to detect gas. 2D transition metal dichalcogenide MoS2 monolayer quantum dots (MoS2-QD) and their doped boron (B@MoS2-QD), nitrogen (N@MoS2-QD), phosphorus (P@MoS2-QD), and silicon (Si@MoS2-QD) counterparts are proposed as selective sensors for NH3 gas.![]()
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Affiliation(s)
- Terkumbur E. Gber
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, Akwa-Ibom State University, Uyo, Nigeria
| | - Aniekan E. Owen
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, Akwa-Ibom State University, Uyo, Nigeria
| | - Benjamin E. Etinwa
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Innocent Benjamin
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Fredrick C. Asogwa
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | | | - Ededet A. Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
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