1
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Chen X, Zhang X, Chen J, Wang M, Yang Y, An L, Liu Z, Song X, Yao L. Quantification of CH and NH/π-Stacking Interactions in Cells Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2024. [PMID: 39177663 DOI: 10.1021/acs.analchem.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
π-Stacking, a type of noncovalent interactions involving aromatic residues, plays an important role in protein folding and function. In this work, an attempt has been made to measure CH/π and NH/π stacking interactions in a protein in Escherichia coli cells using a combined double-mutant cycle and nuclear magnetic resonance spectroscopy method. The results show that the CH/π and NH/π stacking interactions are generally weaker in cells than those in the buffer. The transient intermolecular noncovalent interactions between the protein and the complex cellular environment may compete with and thus weaken the stacking interactions in the protein. The weakening of stacking interactions can enhance the local conformational opening of proteins in E. coli cells. This is evident from the faster rates of amide hydrogen/deuterium exchange observed in cells than in the buffer, for residues that undergo local conformational opening. This study highlights the influence of the cellular environment on π-stacking and the conformational dynamics of proteins.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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2
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Chen Z, Yuan P, Chen C, Wang X, Wang J, Jia J, Davaasuren B, Lai Z, Khashab NM, Huang KW, Bakr OM, Yin J, Salama KN. Balancing Pd-H Interactions: Thiolate-Protected Palladium Nanoclusters for Robust and Rapid Hydrogen Gas Sensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404291. [PMID: 38975670 DOI: 10.1002/adma.202404291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/20/2024] [Indexed: 07/09/2024]
Abstract
The transition toward hydrogen gas (H2) as an eco-friendly and renewable energy source necessitates advanced safety technologies, particularly robust sensors for H2 leak detection and concentration monitoring. Although palladium (Pd)-based materials are preferred for their strong H2 affinity, intense palladium-hydrogen (Pd-H) interactions lead to phase transitions to palladium hydride (PdHx), compromising sensors' durability and detection speeds after multiple uses. In response, this study introduces a high-performance H2 sensor designed from thiolate-protected Pd nanoclusters (Pd8SR16), which leverages the synergistic effect between the metal and protective ligands to form an intermediate palladium-hydrogen-sulfur (Pd-H-S) state during H2 adsorption. Striking a balance, it preserves Pd-H binding affinity while preventing excessive interaction, thus lowering the energy required for H2 desorption. The dynamic adsorption-dissociation-recombination-desorption process is efficiently and highly reversible with Pd8SR16, ensuring robust and rapid H2 sensing at parts per million (ppm). The Pd8SR16-based sensor demonstrates exceptional stability (50 cycles; 0.11% standard deviation in response), prompt response/recovery (t90 = 0.95 s/6 s), low limit of detection (LoD, 1 ppm), and ambient temperature operability, ranking it among the most sensitive Pd-based H2 sensors. Furthermore, a multifunctional prototype demonstrates the practicality of real-world gas sensing using ligand-protected metal nanoclusters.
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Affiliation(s)
- Zhuo Chen
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Peng Yuan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Cailing Chen
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Xinhuilan Wang
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jinrong Wang
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jiaqi Jia
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Bambar Davaasuren
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhiping Lai
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Niveen M Khashab
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kuo-Wei Huang
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Osman M Bakr
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jun Yin
- Department of Applied Physics, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Khaled N Salama
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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3
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Amonov A, Scheiner S. Halogen Bonding to the π-Systems of Polycyclic Aromatics. Chemphyschem 2024:e202400482. [PMID: 38923736 DOI: 10.1002/cphc.202400482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University, University blv. 15, 140104, Samarkand, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA
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4
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Britt LH, Eradeh R, Leung C, Zhao Y. DFT investigations of phenyldithiafulvene dimers at different oxidation states. Phys Chem Chem Phys 2023. [PMID: 38047908 DOI: 10.1039/d3cp04122k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Oxidative dimerization of aryl-substituted dithiafulvenes (Ar-DTFs) presents an efficient C-C bond forming method for the preparation of diverse redox-active π-conjugated molecules and conductive polymers. Previous experimental data indicated a reaction pathway in which direct combination of two Ar-DTF radical cations is a key step. However, mechanistic details about how Ar-DTF dimers are formed under different oxidation states have not yet been clearly established prior to this work. The assembly of two Ar-DTF molecules generates a vast conformational and configurational landscape, which is quite complex but fundamentally important for understanding the dimerization mechanism. To cast a deep insight into this aspect, we have performed density functional theory (DFT) calculations at the M06-2X/Def2-SVP level of theory to thoroughly investigate the potential energy surfaces (PESs) of various dimers of a phenyl-substituted dithiafulvene (Ph-DTF) in the mixed-valence radical cation and dication states. Key stationary points in these PESs, including minimum-energy conformers (π-dimers and σ-dimers) as well as the transition states connected to them, were examined and compared. We have also calculated the binding energies of these dimers to evaluate the energetic driving forces for their formation. Based on our computational results, the roles that various Ph-DTF dimers play in different pathways of oxidative dimerization have been clarified.
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Affiliation(s)
- Liam H Britt
- Department of Chemistry, Memorial University of Newfoundland, Core Science Facility, 45 Arctic Avenue, St. John's, NL, A1C 5S7, Canada.
| | - Ramin Eradeh
- Department of Chemistry, Memorial University of Newfoundland, Core Science Facility, 45 Arctic Avenue, St. John's, NL, A1C 5S7, Canada.
| | - Chris Leung
- Department of Chemistry, Memorial University of Newfoundland, Core Science Facility, 45 Arctic Avenue, St. John's, NL, A1C 5S7, Canada.
| | - Yuming Zhao
- Department of Chemistry, Memorial University of Newfoundland, Core Science Facility, 45 Arctic Avenue, St. John's, NL, A1C 5S7, Canada.
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5
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Özcan E, Vagolu SK, Gündüz MG, Stevanovic M, Kökbudak Z, Tønjum T, Nikodinovic-Runic J, Çetinkaya Y, Doğan ŞD. Novel Quinoline-Based Thiosemicarbazide Derivatives: Synthesis, DFT Calculations, and Investigation of Antitubercular, Antibacterial, and Antifungal Activities. ACS OMEGA 2023; 8:40140-40152. [PMID: 37929089 PMCID: PMC10620885 DOI: 10.1021/acsomega.3c03018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023]
Abstract
The discovery of new antimicrobial agents as a means of treating drug-resistant microbial pathogens is of utmost significance to overcome their immense risk to human well-being. The current investigation involves the development, synthesis, and assessment of the antimicrobial efficacy of novel quinoline derivatives incorporating a thiosemicarbazide functionality. To design the target compounds (QST1-QST14), we applied the molecular hybridization approach to link various thiosemicarbazides to the quinoline core with a sulfonyl group. Upon the synthesis and completion of structural characterization via spectroscopic techniques (1H NMR, 13C NMR, 15N NMR, IR, and HRMS), the title molecules were extensively evaluated for their potential antitubercular, antibacterial, and antifungal activities. N-(3-Chlorophenyl)-2-(quinolin-8-ylsulfonyl)hydrazine-1-carbothioamide (QST4), the most effective compound against Mycobacterium tuberculosis H37Rv, was also tested on isoniazid-resistant clinical isolates with katG and inhA promoter mutations. Based on molecular docking studies, QST4 was also likely to demonstrate its antimycobacterial activity through inhibition of the InhA enzyme. Furthermore, three derivatives (QST3, QST4, and QST10) with preferable antimicrobial and drug-like profiles were also shown to be nontoxic against human embryonic kidney (HEK) cells. All compounds were optimized by the density functional theory method using B3LYP with the 6-31+G(d,p) basis set. Structural analysis, natural bond orbital calculations of donor-acceptor interactions, molecular electrostatic potential analysis, and frontier molecular orbital analysis were carried out. Quantum chemical descriptors and charges on the atoms were determined to compare the strengths of the intramolecular hydrogen bonds formed and their stabilities. We determined that the sulfur atom forms a stronger intramolecular hydrogen bond than the nitrogen, oxygen, and fluorine atoms in these sulfonyl thiosemicarbazide derivatives.
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Affiliation(s)
- Esma Özcan
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Siva Krishna Vagolu
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Milena Stevanovic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Zülbiye Kökbudak
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
| | - Tone Tønjum
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for
Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0316 Oslo, Norway
| | - Jasmina Nikodinovic-Runic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Yasin Çetinkaya
- Department
of Chemistry, Faculty of Science, Atatürk
University, 25240 Erzurum, Turkey
| | - Şengül Dilem Doğan
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
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6
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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7
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Strom A, Shah R, Dolot R, Rogers MS, Tong CL, Wang D, Xia Y, Lipscomb JD, Wagner CR. Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides. Biochemistry 2022; 61:2648-2661. [PMID: 36398895 PMCID: PMC9854251 DOI: 10.1021/acs.biochem.2c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state kcat and Km for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that KD also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Cher-Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David Wang
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Youlin Xia
- Department of Structural Biology, St. Jude’s Research Hospital, Memphis, Tennessee 38105, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States,Address correspondence to: Carston R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 2231 6th Street S.E., Cancer & Cardiovascular Research Building, Minneapolis, Minnesota 55455, USA,
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8
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Metya S, Das A. S–H···O Hydrogen Bond Can Win over O–H···S Hydrogen Bond: Gas-Phase Spectroscopy of 2-Fluorothiophenol···H 2O Complex. J Phys Chem A 2022; 126:9178-9189. [DOI: 10.1021/acs.jpca.2c06083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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9
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Wang Z, Zhou H, Yu H, Pu Z, Xu J, Zhang H, Wu J, Yang L. Computational Redesign of the Substrate Binding Pocket of Glutamate Dehydrogenase for Efficient Synthesis of Noncanonical l-Amino Acids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ziyuan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Haisheng Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Zhongji Pu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Jinling Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Hongyu Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
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10
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Bridging H2O and H2S homomeric clusters via H2O-H2S mixed clusters: Impact of the changing ratio of H2O and H2S moieties. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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12
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Dutta J, Sahu AK, Bhadauria AS, Biswal HS. Carbon-Centered Hydrogen Bonds in Proteins. J Chem Inf Model 2022; 62:1998-2008. [PMID: 35293733 DOI: 10.1021/acs.jcim.2c00015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrogen bonding (H-bonding) without lone pair(s) of electrons and π-electrons is a concept developed 2-3 years ago. H-bonds involving less electronegative tetrahedral carbon are beyond the classical concept of H-bonds. Herein, we present the first report on H-bonds with tetravalent carbons in proteins. A special bonding arrangement is needed to increase the negative charge density around the sp3-hybridized carbon atom. Therefore, less electronegative elements such as As and Mg, when bonded to sp3-C, enable the C-atoms as H-bond acceptors. Careful protein structure analysis aided by several quantum chemical calculations suggests that these H-bonds are weak to moderate in strength. We developed an empirical equation to estimate the C-H···C H-bond energy in proteins from the distances between the C- and H-atoms. In proteins, the binding energies range from -5.4 to -14.0 kJ/mol. The C-H···C H-bonds assist the substrate binding in proteins. We also explored the potential role of these carbon-centered H-bonds in C-H bond activation through σ-bond metathesis. To our surprise, contribution from these H-bonds is almost of similar magnitude as that from C-H···π H-bonds for C-H bond activation.
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Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Abhijeet S Bhadauria
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
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13
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Azide⋅⋅⋅Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Saigusa H, Oyama A, Kitamura S, Asami H. Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase. J Phys Chem A 2021; 125:7217-7225. [PMID: 34433270 DOI: 10.1021/acs.jpca.1c05219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.
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Affiliation(s)
- Hiroyuki Saigusa
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Ayumi Oyama
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Saki Kitamura
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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15
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Sureshan KM, Madhusudhanan MC, Balan H, Werz DB. Azide···Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021; 60:22797-22803. [PMID: 34399025 DOI: 10.1002/anie.202106614] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/15/2021] [Indexed: 11/09/2022]
Abstract
We have designed, synthesized and crystallized 36 compounds, each containing an azide group and an oxygen atom separated by three bonds. Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O ··· N b contact. Geometry-optimized structures [using M06-2X/6-311G(d,p) level of theory ] also showed the syn conformation in all 36 of these cases, suggesting that this not merely a crystal packing effect. Quantum topological analysis using Bader's Atoms in Molecules (AIM) theory revealed bond paths and bond critical points (BCP) in these structures suggesting its nature and energetics to be similar to weak hydrogen bonding. The NCI-RDG plot clearly revealed the attractive interaction consisting of electrostatic or dispersive components in all the 36 systems. NBO analysis suggested a weak orbital-relaxation (charge-transfer) contribution of energy for a few (sp2) O-donor systems. Natural population analysis (NPA) and molecular electrostatic potential mapping (MESP) of these crystal structures further revealed the existence of favorable azide-oxygen interaction. A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds.
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Affiliation(s)
- Kana M Sureshan
- Indian Institute of Science Education and Research, School of Chemistry, Thiruvananthapuram, Maruthamala, 695551, Thiruvananthapuram, INDIA
| | - Mithun C Madhusudhanan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 795551, Thiruvananthapuram, INDIA
| | - Haripriya Balan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 695551, Thiruvananthapuram, INDIA
| | - Daniel B Werz
- TU Braunschweig: Technische Universitat Braunschweig, Institute fur Organic Chemie, Hagenring 30, Braunschweig, 38106, Braunschweig, GERMANY
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16
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Monu, Oram BK, Bandyopadhyay B. A unified cost-effective method for the construction of reliable potential energy surfaces for H 2S and H 2O clusters. Phys Chem Chem Phys 2021; 23:18044-18057. [PMID: 34387290 DOI: 10.1039/d1cp01544c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S-HS H-bond and SS interactions are identified in dimers, trimers and pentamers, while no SS interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are -1.66, -5.21, -8.57 and -12.54 kcal mol-1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol-1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.
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Affiliation(s)
- Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
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17
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Albanese KI, Waters ML. Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding. Chem Sci 2021; 12:8900-8908. [PMID: 34257891 PMCID: PMC8246079 DOI: 10.1039/d1sc02175c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Recognition of trimethyllysine (Kme3) by reader proteins is an important regulator of gene expression. This recognition event is mediated by an aromatic cage made up of 2-4 aromatic residues in the reader proteins that bind Kme3 via cation-π interactions. A small subset of reader proteins contain a methionine (Met) residue in place of an aromatic sidechain in the binding pocket. The unique role of sulfur in molecular recognition has been demonstrated in a number of noncovalent interactions recently, including interactions of thiols, thioethers, and sulfoxides with aromatic rings. However, the interaction of a thioether with an ammonium ion has not previously been investigated and the role of Met in binding Kme3 has not yet been explored. Herein, we systematically vary the Met in two reader proteins, DIDO1 and TAF3, and the ligand, Kme3 or its neutral analog tert-butyl norleucine (tBuNle), to determine the role of Met in the recognition of the cationic Kme3. Our studies demonstrate that Met contributes to binding via dispersion forces, with about an equal contribution to binding Kme3 and tBuNle, indicating that electrostatic interactions do not play a role. During the course of these studies, we also discovered that DIDO1 exhibits equivalent binding to tBuNle and Kme3 through a change in the mechanism of binding.
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Affiliation(s)
- Katherine I Albanese
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
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18
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Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy. Molecules 2021; 26:molecules26102928. [PMID: 34069140 PMCID: PMC8155843 DOI: 10.3390/molecules26102928] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.
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19
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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20
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Mishra KK, Borish K, Singh G, Panwaria P, Metya S, Madhusudhan MS, Das A. Observation of an Unusually Large IR Red-Shift in an Unconventional S-H···S Hydrogen-Bond. J Phys Chem Lett 2021; 12:1228-1235. [PMID: 33492971 DOI: 10.1021/acs.jpclett.0c03183] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The S-H···S non-covalent interaction is generally known as an extremely unconventional weak hydrogen-bond in the literature. The present gas-phase spectroscopic investigation shows that the S-H···S hydrogen-bond can be as strong as any conventional hydrogen-bond in terms of the IR red-shift in the stretching frequency of the hydrogen-bond donor group. Herein, the strength of the S-H···S hydrogen-bond has been determined by measuring the red-shift (∼150 cm-1) of the S-H stretching frequency in a model complex of 2-chlorothiophenol and dimethyl sulfide using isolated gas-phase IR spectroscopy coupled with quantum chemistry calculations. The observation of an unusually large IR red-shift in the S-H···S hydrogen-bond is explained in terms of the presence of a significant amount of charge-transfer interactions in addition to the usual electrostatic interactions. The existence of ∼750 S-H···S interactions between the cysteine and methionine residues in 642 protein structures determined from an extensive Protein Data Bank analysis also indicates that this interaction is important for the structures of proteins.
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Affiliation(s)
- Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Gulzar Singh
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - M S Madhusudhan
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
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21
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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22
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Choudhuri K, Pramanik M, Mal P. Noncovalent Interactions in C–S Bond Formation Reactions. J Org Chem 2020; 85:11997-12011. [DOI: 10.1021/acs.joc.0c01534] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Khokan Choudhuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. Bhimpur-Padanpur,
Via Jatni, District Khurda, Bhubaneswar, Odisha 752050, India
| | - Milan Pramanik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. Bhimpur-Padanpur,
Via Jatni, District Khurda, Bhubaneswar, Odisha 752050, India
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. Bhimpur-Padanpur,
Via Jatni, District Khurda, Bhubaneswar, Odisha 752050, India
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23
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Jena S, Tulsiyan KD, Rana A, Choudhury SS, Biswal HS. Non-conventional Hydrogen Bonding and Aromaticity: A Systematic Study on Model Nucleobases and Their Solvated Clusters. Chemphyschem 2020; 21:1826-1835. [PMID: 32506748 DOI: 10.1002/cphc.202000386] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Abstract
The conceptual development of aromaticity is essential to rationalize and understand the structure and behavior of aromatic heterocycles. This work addresses for the first time, the interconnection between aromaticity and sulfur/selenium centered hydrogen bonds (S/SeCHBs) involved in representative heterocycle models of canonical nucleobases (2-Pyridone; 2PY) and its sulfur (2-Thiopyridone; 2TPY) and selenium (2-Selenopyridone; 2SePY) analogs. The nucleus-independent chemical shift (NICS) and gauge induced magnetic current density (GIMIC) values suggested significant reduction of aromaticity upon replacement of exocyclic carbonyl oxygen with sulfur and selenium. However, we observed two-fold (57 %) and three-fold (80 %) enhancement in the aromaticity for 2TPY dimer, and 2SePY dimer, respectively which are connected through S/SeCHBs. Aromaticity enhancement was also noticed in 1 : 1 H-bonded complexes (heterodimers), micro hydrated clusters and for bulk hydration. It is expected that exocyclic S and Se incorporation into heterocycles without compromising aromatic loss would definitely reinforce to design new supramolecular building blocks via S/SeCH-bonded complexes.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Shubhranshu S Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
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24
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Chand A, Sahoo DK, Rana A, Jena S, Biswal HS. The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials. Acc Chem Res 2020; 53:1580-1592. [PMID: 32677432 DOI: 10.1021/acs.accounts.0c00289] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.
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Affiliation(s)
- Apramita Chand
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
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25
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Ghosh S, Chopra P, Wategaonkar S. C-HS interaction exhibits all the characteristics of conventional hydrogen bonds. Phys Chem Chem Phys 2020; 22:17482-17493. [PMID: 32531006 DOI: 10.1039/d0cp01508c] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.44), has not been considered as a potential HB acceptor for a long time. The C-HY (Y = HB acceptor) interaction has its own history of exhibiting omnidirectional shifts in the CH stretching frequency upon complex formation. Therefore, a systematic investigation of the C-HS interaction was the primary goal of the work presented here. Together with gas-phase vibrational spectroscopy and ab initio quantum chemical calculations, the nature and strength of the C-HS hydrogen bond (HB) have been investigated in the complexes of 1,2,4,5-tetracyanobenzene (TCNB) with various sulfur containing solvents. Despite the unconventional nature of both HB donor and HB acceptor (C-H and S, respectively), it was found that the C-HS hydrogen bond exhibits all the characteristics of the conventional hydrogen bond. The binding strength of the C-HS H-bond in these complexes was found to be comparable to that of the conventional hydrogen bonds. The unusual stabilities of these HBs have been mainly attributed to the attractive dispersion interaction.
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Affiliation(s)
- Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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Absorptive Desulfurization of Model Biogas Stream Using Choline Chloride-Based Deep Eutectic Solvents. SUSTAINABILITY 2020. [DOI: 10.3390/su12041619] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The paper presents a synthesis of deep eutectic solvents (DESs) based on choline chloride (ChCl) as hydrogen bond acceptor and phenol (Ph), glycol ethylene (EG), and levulinic acid (Lev) as hydrogen bond donors in 1:2 molar ratio. DESs were successfully used as absorption solvents for removal of dimethyl disulfide (DMDS) from model biogas steam. Several parameters affecting the absorption capacity and absorption rate have been optimized including kinds of DES, temperature, the volume of absorbent, model biogas flow rate, and initial concentration of DMDS. Furthermore, reusability and regeneration of DESs by means of adsorption and nitrogen barbotage followed by the mechanism of absorptive desulfurization by means of density functional theory (DFT) as well as FT-IR analysis were investigated. Experimental results indicate that the most promising DES for biogas purification is ChCl:Ph, due to high absorption capacity, relatively long absorption rate, and easy regeneration. The research on the absorption mechanism revealed that van der Waal interaction is the main driving force for DMDS removal from model biogas.
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Wang J, Yao L. Dissecting C-H∙∙∙π and N-H∙∙∙π Interactions in Two Proteins Using a Combined Experimental and Computational Approach. Sci Rep 2019; 9:20149. [PMID: 31882834 PMCID: PMC6934659 DOI: 10.1038/s41598-019-56607-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023] Open
Abstract
C−H∙∙∙π and N−H∙∙∙π interactions can have an important contribution for protein stability. However, direct measurements of these interactions in proteins are rarely reported. In this work, we combined the mutant cycle experiments and molecular dynamics (MD) simulations to characterize C−H∙∙∙π and N−H∙∙∙π interactions and their cooperativity in two model proteins. It is shown that the average C−H∙∙∙π interaction per residue pair is ~ −0.5 kcal/mol while the N−H∙∙∙π interaction is slightly stronger. The triple mutant box measurement indicates that N−H∙∙∙π∙∙∙C−H∙∙∙π and C−H∙∙∙π∙∙∙C−H∙∙∙π can have a positive or negative cooperativity. MD simulations suggest that the cooperativity, depending on the local environment of the interactions, mainly arises from the geometric rearrangement when the nearby interaction is perturbed.
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Affiliation(s)
- Jia Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. .,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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28
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29
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Makoś P, Boczkaj G. Deep eutectic solvents based highly efficient extractive desulfurization of fuels – Eco-friendly approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111916] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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31
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Chand A, Biswal HS. Hydrogen Bonds with Chalcogens: Looking Beyond the Second Row of the Periodic Table. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00140-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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32
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McCaslin TG, Pagba CV, Hwang H, Gumbart JC, Chi SH, Perry JW, Barry BA. Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette. Chem Commun (Camb) 2019; 55:9399-9402. [PMID: 31322154 DOI: 10.1039/c9cc04067f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tyrosine residues act as intermediates in proton coupled electron transfer reactions (PCET) in proteins. For example, in ribonucleotide reductase (RNR), a tyrosyl radical oxidizes an active site cysteine via a 35 Å pathway that contains multiple aromatic groups. When singlet tyrosine is oxidized, the radical becomes a strong acid, and proton transfer reactions, which are coupled with the redox reaction, may be used to control reaction rate. Here, we characterize a tyrosine-containing beta hairpin, Peptide O, which has a cross-strand, noncovalent interaction between its single tyrosine, Y5, and a cysteine (C14). Circular dichroism provides evidence for a thermostable beta-turn. EPR spectroscopy shows that Peptide O forms a neutral tyrosyl radical after UV photolysis at 160 K. Molecular dynamics simulations support a phenolic/SH interaction in the tyrosine singlet and radical states. Differential pulse voltammetry exhibits pH dependence consistent with the formation of a neutral tyrosyl radical and a pKa change in two other residues. A redox-coupled decrease in cysteine pKa from 9 (singlet) to 6.9 (radical) is assigned. At pD 11, picosecond transient absorption spectroscopy after UV photolysis monitors tyrosyl radical recombination via electron transfer (ET). The ET rate in Peptide O is indistinguishable from the ET rates observed in peptides containing a histidine and a cyclohexylalanine (Cha) at position 14. However, at pD 9, the tyrosyl radical decays via PCET, and the decay rate is slowed, when compared to the histidine 14 variant. Notably, the decay rate is accelerated, when compared to the Cha 14 variant. We conclude that redox coupling between tyrosine and cysteine can act as a PCET control mechanism in proteins.
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Affiliation(s)
- Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA and School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - San-Hui Chi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Center of Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph W Perry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Center of Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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33
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Wang D, Chopra P, Wategaonkar S, Fujii A. Electronic and Infrared Spectroscopy of Benzene-(H2S)n (n = 1 and 2): The Prototype of the SH-π Interaction. J Phys Chem A 2019; 123:7255-7260. [DOI: 10.1021/acs.jpca.9b02199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dandan Wang
- Department of Chemistry, Graduate school of Science, Tohoku University, Sendai 980-8578, Japan
| | - Pragya Chopra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
| | - Asuka Fujii
- Department of Chemistry, Graduate school of Science, Tohoku University, Sendai 980-8578, Japan
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34
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Liu ZY, Hu JW, Huang CH, Huang TH, Chen DG, Ho SY, Chen KY, Li EY, Chou PT. Sulfur-Based Intramolecular Hydrogen-Bond: Excited-State Hydrogen-Bond On/Off Switch with Dual Room-Temperature Phosphorescence. J Am Chem Soc 2019; 141:9885-9894. [DOI: 10.1021/jacs.9b02765] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zong-Ying Liu
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, Republic of China
| | - Jiun-Wei Hu
- Department of Chemical Engineering, Feng Chia University, Taichung, 40724 Taiwan, Republic of China
| | - Chun-Hao Huang
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677 Taiwan, Republic of China
| | - Teng-Hsing Huang
- Department of Chemical Engineering, Feng Chia University, Taichung, 40724 Taiwan, Republic of China
| | - Deng-Gao Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, Republic of China
| | - Ssu-Yu Ho
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, Republic of China
| | - Kew-Yu Chen
- Department of Chemical Engineering, Feng Chia University, Taichung, 40724 Taiwan, Republic of China
| | - Elise Y. Li
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677 Taiwan, Republic of China
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, Republic of China
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35
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Carmona-Negrón JA, Flores-Rivera MM, Santana A, Rheingold AL, Meléndez E. Synthesis, crystal structure, Hirshfeld Surface analysis, and DFT studies of 16-ferrocenylidene-17β-estra-1,3,5-triene-3,17-diol: Towards the application of ferrocene-hormone conjugates to target hormone dependent breast cancer. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
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37
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Argudo PG, Contreras-Montoya R, Álvarez de Cienfuegos L, Martín-Romero MT, Camacho L, Giner-Casares JJ. Optimization of Amino Acid Sequence of Fmoc-Dipeptides for Interaction with Lipid Membranes. J Phys Chem B 2019; 123:3721-3730. [DOI: 10.1021/acs.jpcb.9b01132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pablo G. Argudo
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Investigación en Química Fina y Nanoquímica IUIQFN, Facultad de Ciencias, Universidad de Córdoba (UCO), Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain
| | - Rafael Contreras-Montoya
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Granada (UGR), C. U. Fuentenueva, Granada E-18071, Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Granada (UGR), C. U. Fuentenueva, Granada E-18071, Spain
| | - María T. Martín-Romero
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Investigación en Química Fina y Nanoquímica IUIQFN, Facultad de Ciencias, Universidad de Córdoba (UCO), Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain
| | - Luis Camacho
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Investigación en Química Fina y Nanoquímica IUIQFN, Facultad de Ciencias, Universidad de Córdoba (UCO), Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain
| | - Juan J. Giner-Casares
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Investigación en Química Fina y Nanoquímica IUIQFN, Facultad de Ciencias, Universidad de Córdoba (UCO), Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain
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38
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Choudhuri K, Maiti S, Mal P. Iodine(III) Enabled Dehydrogenative Aryl C−S Coupling by in situ Generated Sulfenium Ion. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801510] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Khokan Choudhuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
| | - Saikat Maiti
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
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39
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Jaju K, Pal D, Chakraborty A, Chakraborty S. Electronic substituent effect on Se-H⋯N hydrogen bond: A computational study of para-substituted pyridine-SeH2 complexes. Chem Phys Lett 2019. [DOI: 10.1016/j.cpletx.2019.100031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Hwang J, Li P, Smith MD, Warden CE, Sirianni DA, Vik EC, Maier JM, Yehl CJ, Sherrill CD, Shimizu KD. Tipping the Balance between S-π and O-π Interactions. J Am Chem Soc 2018; 140:13301-13307. [PMID: 30251855 DOI: 10.1021/jacs.8b07617] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A comprehensive experimental survey consisting of 36 molecular balances was conducted to compare 18 pairs of S-π versus O-π interactions over a wide range of structural, geometric, and solvent parameters. A strong linear correlation was observed between the folding energies of the sulfur and oxygen balances across the entire library of balance pairs. The more stable interaction systematically switched from the O-π to S-π interaction. Computational studies of bimolecular PhSCH3-arene and PhOCH3-arene complexes were able to replicate the experimental trends in the molecular balances. The change in preference for the O-π to S-π interaction was due to the interplay of stabilizing (dispersion and solvophobic) and destabilizing (exchange-repulsion) terms arising from the differences in size and polarizability of the oxygen and sulfur atoms.
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Affiliation(s)
- Jungwun Hwang
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Ping Li
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Mark D Smith
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | | | | | - Erik C Vik
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Josef M Maier
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Christopher J Yehl
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | | | - Ken D Shimizu
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
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Dreux KM, Tschumper GS. Examination of the structures, energetics, and vibrational frequencies of small sulfur‐containing prototypical dimers, (H
2
S)
2
and H
2
O/H
2
S. J Comput Chem 2018; 40:229-236. [DOI: 10.1002/jcc.25578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Katelyn M. Dreux
- Department of Chemistry and Biochemistry University of Mississippi University Mississippi, 38677‐1848
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi University Mississippi, 38677‐1848
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42
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Isaev AN. syn- and anti-H Bonds in Ammonia and Phosphine Complexes with Proton Donors. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418100096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Lobo IA, Robertson PA, Villani L, Wilson DJD, Robertson EG. Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2-Phenylethanethiol Complexes. J Phys Chem A 2018; 122:7171-7180. [PMID: 30113835 DOI: 10.1021/acs.jpca.8b06649] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evidence and understanding of sulfur-centered hydrogen bonding, especially where the donor is a thiol, lags far behind that for conventional OH interactions. To help address this deficiency, conformer specific IR spectra of 2-phenylethanethiol (PET) and associated 1:1 solvent complexes have been measured in SH, OH, and CH stretch regions using resonant-two-photon-ionization (R2PI) and IR-UV ion dip spectroscopic techniques. The aromatic and aliphatic CH stretch regions show signature differences between anti and gauche conformers. Supported by ab initio calculations, a PET-water cluster with an OH···S arrangement and a PET-diethyl ether cluster expressing an SH···O interaction were identified. The SH stretch band of the SH···O complex is red-shifted and undergoes significant intensity enhancement compared to the bare molecule, which is characteristic of hydrogen bonding. These findings offer insight into the nature of the thiol functional group as a potential hydrogen bond donor and acceptor.
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Affiliation(s)
- Isabella A Lobo
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Patrick A Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Luigi Villani
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - David J D Wilson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Evan G Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
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Choudhuri K, Pramanik M, Mandal A, Mal P. S−H⋅⋅⋅π Driven Anti-Markovnikov Thiol-Yne Click Reaction. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Khokan Choudhuri
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); HBNI; Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
| | - Milan Pramanik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); HBNI; Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
| | - Arkalekha Mandal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); HBNI; Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
| | - Prasenjit Mal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); HBNI; Bhubaneswar; PO Bhimpur-Padanpur; Via Jatni, District Khurda Odisha 752050 India
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45
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Wategaonkar S, Bhattacherjee A. N–H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers. J Phys Chem A 2018; 122:4313-4321. [DOI: 10.1021/acs.jpca.8b01943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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46
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Orabi EA, English AM. Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility. J Phys Chem B 2018. [PMID: 29533644 DOI: 10.1021/acs.jpcb.8b00089] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H2S, MeSH) and Met (Me2S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-Har···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-Har···S or S-H···Oar/Nar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.
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Affiliation(s)
- Esam A Orabi
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
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Zheng D, Yuan XA, Ma H, Li X, Wang X, Liu Z, Ma J. Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171928. [PMID: 29657794 PMCID: PMC5882718 DOI: 10.1098/rsos.171928] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/09/2018] [Indexed: 06/07/2023]
Abstract
Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o-cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o-cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o-cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o-cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o-cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.
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Affiliation(s)
| | | | | | | | | | | | - Jing Ma
- Author for correspondence: Jing Ma e-mail:
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Grote J, Friedrich F, Berthold K, Hericks L, Neumann B, Stammler HG, Mitzel NW. Dithiocarboxylic Acids: An Old Theme Revisited and Augmented by New Preparative, Spectroscopic and Structural Facts. Chemistry 2018; 24:2626-2633. [PMID: 29266463 DOI: 10.1002/chem.201704235] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 11/11/2022]
Abstract
The unstable dithiocarboxylic acids dithioacetic acid, 2-methyl-dithiopropionic acid, 2,2-dimethyl-dithiopropionic acid and dithiobenzoic acid were synthesized and characterized by NMR spectroscopy and GC/MS. The stable dithiocarboxylic acids 2,4,6-trimethyl benzoic acid, 2,4,6-tri-iso-propylbenzoic acid and 2,6-dimesityl benzoic acid were synthesized, isolated and characterized by spectroscopic methods and in parts by mass spectrometry and X-ray crystallography. The new data were used to re-evaluate literature data on the synthesis, spectroscopy and structural data of dithiocarboxylic acids as a fundamental class of organic compounds in general.
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Affiliation(s)
- Johanna Grote
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Felix Friedrich
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Katarína Berthold
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Loreen Hericks
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Beate Neumann
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hans-Georg Stammler
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert W Mitzel
- Anorganische Chemie und Strukturchemie, Centrum für Molekulare Materialien CM2, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
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49
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Computational study of red- and blue-shifted C H⋯Se hydrogen bond in Q 3 C H⋯SeH 2 (Q = Cl, F, H) complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Singh A, Sahoo DK, Sethi SK, Jena S, Biswal HS. Nature and Strength of the Inner-Core H⋅⋅⋅H Interactions in Porphyrinoids. Chemphyschem 2017; 18:3625-3633. [DOI: 10.1002/cphc.201700742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ankit Singh
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Srikant Kumar Sethi
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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