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Zheng Y, Kan CH, Tsang TF, Liu Y, Liu T, Tsang MW, Lam LY, Yang X, Ma C. Discovery of Inhibitors Targeting Protein-Protein Interaction between Bacterial RNA Polymerase and NusG as Novel Antimicrobials. J Med Chem 2024; 67:16556-16575. [PMID: 39196895 DOI: 10.1021/acs.jmedchem.4c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Bacterial RNA polymerase (RNAP), the core enzyme responsible for bacterial transcription, requires the NusG factor for efficient transcription elongation and termination. As the primary binding site for NusG, the RNAP clamp-helix (CH) domain represents a potential protein-protein interaction (PPI) target for novel antimicrobial agent design and discovery. In this study, we designed a pharmacophore model based on the essential amino acids of the CH for binding to NusG, such as R270, R278, and R281 (Escherichia coli numbering), and identified a hit compound with mild antimicrobial activity. Subsequent rational design and synthesis of this hit compound led to improved antimicrobial activity against Streptococcus pneumoniae, with the minimum inhibitory concentration (MIC) reduced from 128 to 1 μg/mL. Additional characterization of the antimicrobial activity, inhibitory activity against RNAP-NusG interaction, and cell-based transcription and fluorescent assays of the optimized compounds demonstrated their potential for further lead optimization.
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Affiliation(s)
- Yingbo Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Yanpeng Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Tiankuang Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Man Wai Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Long Yin Lam
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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2
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Wang M, Garrison N, Nguyen PM, Prasad A, Wang Y, Kwon HK, Kim G, Siegler MA, Lectka T. Can the -CF 3 Group Act as a Tight, Well-Defined Hydrogen Bond Acceptor? A Clear Crystallographic CF 2-F···H-N + Interaction Says Yes. J Org Chem 2024; 89:9681-9685. [PMID: 38965938 DOI: 10.1021/acs.joc.4c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The CF3 group is well noted for being noninteractive with other functional groups. In this Note, we present a highly rigid model system containing a significant hydrogen bonding interaction between a charged N-H donor and a CF3 acceptor that challenges this accepted wisdom. Spectroscopic and single crystal X-ray crystallography data characterize this interaction, consistent with a weak to moderate hydrogen bond that would be difficult to observe in an intermolecular system.
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Affiliation(s)
- Muyuan Wang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Nathaniel Garrison
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Phuong Minh Nguyen
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Aarush Prasad
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Yuang Wang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Hyeok-Kyu Kwon
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Gina Kim
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
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3
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Dong S, Zhao Z, Tang H, Li G, Pan J, Gu X, Jiang J, Xiao L, Scapin G, Hunter DN, Yang D, Huang Y, Bennett F, Yang SW, Mandal M, Tang H, Su J, Tudge C, deJesus RK, Ding FX, Lombardo M, Hicks JD, Fischmann T, Mirza A, Dayananth P, Painter RE, Villafania A, Garlisi CG, Zhang R, Mayhood TW, Si Q, Li N, Amin RP, Bhatt B, Chen F, Regan CP, Regan H, Lin X, Wu J, Leithead A, Pollack SR, Scott JD, Nargund RP, Therien AG, Black T, Young K, Pasternak A. Structure Guided Discovery of Novel Pan Metallo-β-Lactamase Inhibitors with Improved Gram-Negative Bacterial Cell Penetration. J Med Chem 2024; 67:3400-3418. [PMID: 38387069 DOI: 10.1021/acs.jmedchem.3c01614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The use of β-lactam (BL) and β-lactamase inhibitor combination to overcome BL antibiotic resistance has been validated through clinically approved drug products. However, unmet medical needs still exist for the treatment of infections caused by Gram-negative (GN) bacteria expressing metallo-β-lactamases. Previously, we reported our effort to discover pan inhibitors of three main families in this class: IMP, VIM, and NDM. Herein, we describe our work to improve the GN coverage spectrum in combination with imipenem and relebactam. This was achieved through structure- and property-based optimization to tackle the GN cell penetration and efflux challenges. A significant discovery was made that inhibition of both VIM alleles, VIM-1 and VIM-2, is essential for broad GN coverage, especially against VIM-producing P. aeruginosa. In addition, pharmacokinetics and nonclinical safety profiles were investigated for select compounds. Key findings from this drug discovery campaign laid the foundation for further lead optimization toward identification of preclinical candidates.
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Affiliation(s)
- Shuzhi Dong
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhiqiang Zhao
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haiqun Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Guoqing Li
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jianping Pan
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xin Gu
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jinlong Jiang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Giovanna Scapin
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David N Hunter
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dexi Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuhua Huang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Frank Bennett
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shu-Wei Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mihirbaran Mandal
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haifeng Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Su
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Clare Tudge
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Fa-Xiang Ding
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew Lombardo
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jacqueline D Hicks
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Asra Mirza
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Priya Dayananth
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Ronald E Painter
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Artjohn Villafania
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Charles G Garlisi
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rumin Zhang
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Qian Si
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nianyu Li
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rupesh P Amin
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Bhavana Bhatt
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Feifei Chen
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Christopher P Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Hillary Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Xinjie Lin
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jin Wu
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew Leithead
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Scott R Pollack
- Discovery Process Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jack D Scott
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ravi P Nargund
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Alex G Therien
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02139, United States
| | - Todd Black
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Katherine Young
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Alexander Pasternak
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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4
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Fanfrlík J, Brynda J, Kugler M, Lepšík M, Pospíšilová K, Holub J, Hnyk D, Nekvinda J, Grüner B, Řezáčová P. B-H⋯π and C-H⋯π interactions in protein-ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides. Phys Chem Chem Phys 2023; 25:1728-1733. [PMID: 36594655 DOI: 10.1039/d2cp04673c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Among non-covalent interactions, B-H⋯π and C-H⋯π hydrogen bonding is rather weak and less studied. Nevertheless, since both can affect the energetics of protein-ligand binding, their understanding is an important prerequisite for reliable predictions of affinities. Through a combination of high-resolution X-ray crystallography and quantum-chemical calculations on carbonic anhydrase II/carborane-based inhibitor systems, this paper provides the first example of B-H⋯π hydrogen bonding in a protein-ligand complex. It shows that the B-H⋯π interaction is stabilized by dispersion, followed by electrostatics. Furthermore, it demonstrates that the similar C-H⋯π interaction is twice as strong, with a slightly smaller contribution of dispersion and a slightly higher contribution of electrostatics. Such a detailed insight will facilitate the rational design of future protein ligands, controlling these types of non-covalent interactions.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Klára Pospíšilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jan Nekvinda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
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5
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Clark T. How deeply should we analyze non-covalent interactions? J Mol Model 2023; 29:66. [PMID: 36757533 PMCID: PMC9911493 DOI: 10.1007/s00894-023-05460-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
CONTEXT Just how much effort and detail should we invest in analyzing interactions of the order of 5 kcal mol-1? This comment attempts to provide a conciliatory overview of what is often a contentious field and to pose some questions that I hope will eventually lead at least to some consensus. METHODS This is an opinion article without calculations or data.
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Affiliation(s)
- Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstrasse 25, 91052, Erlangen, Germany.
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6
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Effect of hydrophobic modification of block copolymers on the self-assembly, drug encapsulation and release behavior. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Conjugates of Methylene Blue with Cycloalkaneindoles as New Multifunctional Agents for Potential Treatment of Neurodegenerative Disease. Int J Mol Sci 2022; 23:ijms232213925. [PMID: 36430413 PMCID: PMC9697446 DOI: 10.3390/ijms232213925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
The development of multi-target-directed ligands (MTDLs) would provide effective therapy of neurodegenerative diseases (ND) with complex and nonclear pathogenesis. A promising method to create such potential drugs is combining neuroactive pharmacophoric groups acting on different biotargets involved in the pathogenesis of ND. We developed a synthetic algorithm for the conjugation of indole derivatives and methylene blue (MB), which are pharmacophoric ligands that act on the key stages of pathogenesis. We synthesized hybrid structures and performed a comprehensive screening for a specific set of biotargets participating in the pathogenesis of ND (i.e., cholinesterases, NMDA receptor, mitochondria, and microtubules assembly). The results of the screening study enabled us to find two lead compounds (4h and 4i) which effectively inhibited cholinesterases and bound to the AChE PAS, possessed antioxidant activity, and stimulated the assembly of microtubules. One of them (4i) exhibited activity as a ligand for the ifenprodil-specific site of the NMDA receptor. In addition, this lead compound was able to bypass the inhibition of complex I and prevent calcium-induced mitochondrial depolarization, suggesting a neuroprotective property that was confirmed using a cellular calcium overload model of neurodegeneration. Thus, these new MB-cycloalkaneindole conjugates constitute a promising class of compounds for the development of multitarget neuroprotective drugs which simultaneously act on several targets, thereby providing cognitive stimulating, neuroprotective, and disease-modifying effects.
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8
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FDA-Approved Trifluoromethyl Group-Containing Drugs: A Review of 20 Years. Processes (Basel) 2022. [DOI: 10.3390/pr10102054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
As people around the world regard 2020 as the year of COVID-19, the medical community considers this year to be the second-best year, shared with the year 1996, with respect to the number of drug molecules approved by the US Food and Drug Administration (FDA). Both years, 2020 and 1996, had a record of 53 new drug molecules approved by the FDA. In the year 2020, 53 new chemical entities and 13 biological medicines were approved, including 10 monoclonal antibodies, 2 antibody-drug conjugates, 3 peptides, and 2 oligonucleotides. Among them, most of the compounds were found to have fluorine or fluorine-containing functional groups exhibiting numerous pharmacological activities. Herein, we summarized the trifluoromethyl (TFM, -CF3)-group-containing FDA-approved drugs for the last 20 years. This article specially features and details the previous 20-year literature data, covering CF3-incorporated potential drug molecules, including their syntheses and uses for various diseases and disorders. The review covers the detailed chemistry of 19 FDA-approved drugs in the past 20 years, which contains the TFM group as one of the pharmacophores.
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9
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Tokuhiro Y, Yoshikawa K, Murayama S, Nanjo T, Takemoto Y. Highly Stereoselective, Organocatalytic Mannich-type Addition of Glyoxylate Cyanohydrin: A Versatile Building Block for the Asymmetric Synthesis of β-Amino-α-ketoacids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Tokuhiro
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Kosuke Yoshikawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Sei Murayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Takeshi Nanjo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
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10
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Li J, Dinh T, Phillips R. The crystal structure of the S154Y mutant carbonyl reductase from Leifsonia xyli explains enhanced activity for 3,5-Bis(trifluoromethyl)acetophenone reduction. Arch Biochem Biophys 2022; 720:109158. [PMID: 35247363 DOI: 10.1016/j.abb.2022.109158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022]
Abstract
Carbonyl reductase from Leifsonia xyli (LXCAR, UniProtKB - T2FLN4) can stereoselectively catalyze the reduction of 3,5-bis(trifluoromethyl)acetophenone (BTAP) to its corresponding alcohol, (R)-[3,5-bis(trifluoromethyl)phenyl]ethanol ((R)-BTPE), which is a valuable chiral intermediate for the synthesis of antiemetic drugs, Aprepitant and Fosaprepitant. Moreover, this protein was found to have a broad spectrum of substrate specificity and can asymmetrically catalyze the reduction of a variety of ketones and keto esters. Even though molecular modelling of this protein was done by Wang et al. (2014), a crystal structure has not yet obtained. In this study, a single mutant, S154Y, which was shown to have higher catalytic activity toward BTAP than that of the wild type, was overexpressed in Escherichia coli BL21 (DE3), purified, and crystallized. The crystal structure of LXCAR-S154Y explains how the mutant enzyme can work with BTAP more efficiently than wild type carbonyl reductase. Furthermore, the structure explains why LXCAR-S154Y can use either NADH or NADPH efficiently as a cofactor, as well as elucidates a proton relay system present in the enzyme.
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Affiliation(s)
- Jun Li
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, PR China.
| | - Tung Dinh
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
| | - Robert Phillips
- Department of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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11
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Pismataro MC, Horenstein NA, Stokes C, Dallanoce C, Thakur GA, Papke RL. Stable desensitization of α 7 nicotinic acetylcholine receptors by NS6740 requires interaction with S36 in the orthosteric agonist binding site. Eur J Pharmacol 2021; 905:174179. [PMID: 34004208 DOI: 10.1016/j.ejphar.2021.174179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 01/09/2023]
Abstract
NS6740 is an α7 nicotinic acetylcholine receptor-selective partial agonist with low efficacy for channel activation, capable of promoting the stable conversion of the receptors to nonconducting (desensitized) states that can be reactivated with the application of positive allosteric modulators (PAMs). In spite of its low efficacy for channel activation, NS6740 is an effective activator of the cholinergic anti-inflammatory pathway. We observed that the concentration-response relationships for channel activation, both when applied alone and when co-applied with the PAM PNU-120596 are inverted-U shaped with inhibitory/desensitizing activities dominant at high concentrations. We evaluated the potential importance of recently identified binding sites for allosteric activators and tested the hypotheses that the stable desensitization produced by NS6740 may be due to binding to these sites. Our experiments were guided by molecular modeling of NS6740 binding to both the allosteric and orthosteric activation sites on the receptor. Our results indicate that with α7C190A mutants, which have compromised orthosteric activation sites, NS6740 may work at the allosteric activation sites to promote transient PAM-dependent currents but not the stable desensitization seen with wild-type α7 receptors. Modeling NS6740 in the orthosteric binding sites identified S36 as an important residue for NS6740 binding and predicted that an S36V mutation would limit NS6740 activity. The efficacy of NS6740 for α7S36V receptors was reduced to zero, and applications of the compound to α7S36V receptors failed to induce the desensitization observed with wild-type receptors. The results indicate that the unique properties of NS6740 are due primarily to binding at the sites for orthosteric agonists.
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Affiliation(s)
- Maria Chiara Pismataro
- Department of Pharmaceutical Sciences, Medicinal Chemistry Section "Pietro Pratesi", University of Milan, Via L. Mangiagalli 25, 20133, Milan, Italy; Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Nicole A Horenstein
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Clare Stokes
- Department of Pharmacology and Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL, 32610-0267, USA
| | - Clelia Dallanoce
- Department of Pharmaceutical Sciences, Medicinal Chemistry Section "Pietro Pratesi", University of Milan, Via L. Mangiagalli 25, 20133, Milan, Italy.
| | - Ganesh A Thakur
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Roger L Papke
- Department of Pharmacology and Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL, 32610-0267, USA
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12
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Mooibroek TJ. DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering. Chemphyschem 2021; 22:141-153. [PMID: 33241585 PMCID: PMC7898519 DOI: 10.1002/cphc.202000927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/25/2020] [Indexed: 11/25/2022]
Abstract
The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.
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Affiliation(s)
- Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van Amsterdam, Science Park 9041098 XHAmsterdamThe Netherlands
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13
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Zhang X, Yao C, Zhao J, Ali MU, Li A, Shen CKF, Yan C, He Y, Miao J, Meng H. Molecular tailoring of trifluoromethyl-substituted conjugated polymers for efficient organic solar cells. Polym Chem 2021. [DOI: 10.1039/d1py00177a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports a series of novel trifluoromethylated polymers as efficient donor materials for high-performance OSCs.
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Affiliation(s)
- Xueqiao Zhang
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Chao Yao
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Jiajun Zhao
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Muhammad Umair Ali
- Tsinghua-Berkeley Shenzhen Institute (TBSI)
- Tsinghua University
- Shenzhen 518055
- China
| | - Aiyuan Li
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | | | - Chaoyi Yan
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Yaowu He
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Jingsheng Miao
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
| | - Hong Meng
- School of Advanced Materials
- Peking University Shenzhen Graduate School
- Shenzhen 518055
- China
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14
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Espitia Cogollo E, Jios E, Hidalgo A, Ulic SE, Echeverría GA, Piro OE, Jios JL. The Bonding Interactions in Fluorinated Vinylogous Amides: A CF
3
‐Substituted Carbonyl‐β‐Aminoenone as a Case Study. CRYSTAL RESEARCH AND TECHNOLOGY 2020. [DOI: 10.1002/crat.202000162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Edeimis Espitia Cogollo
- CEQUINOR (CONICET‐UNLP), Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
| | - Eliana Jios
- CEQUINOR (CONICET‐UNLP), Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
| | - Alejandra Hidalgo
- CEQUINOR (CONICET‐UNLP), Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
| | - Sonia Elizabeth Ulic
- CEQUINOR (CONICET‐UNLP), Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
- Departamento de Ciencias Básicas Universidad Nacional de Luján Rutas 5 y 7, 6700 Luján Buenos Aires Argentina
| | - Gustavo Alberto Echeverría
- Departamento de Física, Facultad de Ciencias Exactas Universidad Nacional de La Plata e IFLP (CONICET, CCT‐La Plata) C. C. 67 La Plata 1900 Argentina
| | - Oscar Enrique Piro
- Departamento de Física, Facultad de Ciencias Exactas Universidad Nacional de La Plata e IFLP (CONICET, CCT‐La Plata) C. C. 67 La Plata 1900 Argentina
| | - Jorge Luis Jios
- Laboratorio UPL (UNLP‐CIC) Camino Centenario e/505 y 508, M.B. Gonnet Buenos Aires 1897 Argentina
- Departamento de Química, Facultad de Ciencias Exactas Universidad Nacional de La Plata 47 esq. 115 La Plata 1900 Argentina
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15
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Lü L, Liu J, Wang H, Jin WJ. π–ring–hole bond around difluoroethyne: stabilization of hydrogen bonding cyclohexamer and dicyclohexamer of ammonia molecules. J Mol Model 2020; 26:259. [DOI: 10.1007/s00894-020-04515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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16
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Schwabedissen J, Trapp PC, Stammler H, Mitzel NW, Wu Z, Chu X, Zeng X. Spectroscopic Properties, Conformation and Structure of Difluorothiophosphoryl Isocyanate in the Gaseous and Solid Phase. ChemistryOpen 2020; 9:913-920. [PMID: 32908813 PMCID: PMC7466015 DOI: 10.1002/open.202000167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Indexed: 01/02/2023] Open
Abstract
Difluorothiophosphoryl isocyanate, F2P(S)NCO was characterized with UV/vis, NMR, IR (gas and Ar-matrix), and Raman (liquid) spectroscopy. Its molecular structure was also established by means of gas electron diffraction (GED) and single crystal X-ray diffraction (XRD) in the gas phase and solid state, respectively. The analysis of the spectroscopic data and molecular structures is complemented by extensive quantum-chemical calculations. Theoretically, the Cs symmetric syn-conformer is predicted to be the most stable conformation. Rotation about the P-N bond requires about 9 kJ mol-1 and the predicted existence of an anti-conformer is dependent on the quantum-chemical method used. This syn-orientation of the isocyanate group is the only one found in the gas phase and contained likewise in the crystal. The overall molecular structure is very similar in gas and solid, despite in the solid state the molecules arrange through intramolecular O⋅⋅⋅F contacts into layers, which are further interconnected by S⋅⋅⋅N, S⋅⋅⋅C and C⋅⋅⋅F contacts. Additionally, the photodecomposition of F2P(S)NCO to form CO, F2P(S)N, and F2PNCO is observed in the solid Ar-matrix.
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Affiliation(s)
- Jan Schwabedissen
- Fakultät für ChemieLehrstuhl für Anorganische Chemie und StrukturchemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
| | - Pia C. Trapp
- Fakultät für ChemieLehrstuhl für Anorganische Chemie und StrukturchemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
| | - Hans‐Georg Stammler
- Fakultät für ChemieLehrstuhl für Anorganische Chemie und StrukturchemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
| | - Norbert W. Mitzel
- Fakultät für ChemieLehrstuhl für Anorganische Chemie und StrukturchemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
| | - Zhuang Wu
- College of ChemistryChemical Engineering and Materials ScienceSoochow UniversitySuzhou215123China
| | - Xianxu Chu
- College of ChemistryChemical Engineering and Materials ScienceSoochow UniversitySuzhou215123China
| | - Xiaoqing Zeng
- College of ChemistryChemical Engineering and Materials ScienceSoochow UniversitySuzhou215123China
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17
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Campetella M, De Mitri N, Prampolini G. Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase. J Chem Phys 2020; 153:044106. [PMID: 32752684 DOI: 10.1063/5.0014280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.
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Affiliation(s)
- Marco Campetella
- Institut des Nanosciences de Paris, Sorbonne Université, CNRS, UMR7588, F-75252 Paris, France
| | - Nicola De Mitri
- Enthought Ltd., Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, United Kingdom
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM), CNR Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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18
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Fik-Jaskółka MA, Mkrtchyan AF, Saghyan AS, Palumbo R, Belter A, Hayriyan LA, Simonyan H, Roviello V, Roviello GN. Spectroscopic and SEM evidences for G4-DNA binding by a synthetic alkyne-containing amino acid with anticancer activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117884. [PMID: 31927477 DOI: 10.1016/j.saa.2019.117884] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/26/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Herein, we present a spectroscopic (CD and UV) and SEM study of a phenylalanine derivative carrying a terminal alkyne moiety and indicated by us CF3IIIPhe, with particular attention to its interaction with Cu(II) cation and some biological macromolecules, as well as a preliminary evaluation of its effect on cancerous cells. CD spectroscopy evidenced the ability of CF3IIIPhe to interact with tel26 and c-myc, two quadruplex DNA (G4 DNA) models explored in this study. Other CD and UV studies revealed the ability of the unnatural amino acid to form aggregates in aqueous solution, to bind Cu(II) cation, and to interact with bovine serum albumin (BSA). Cellular studies demonstrated CF3IIIPhe antiproliferative activity on PC3 cells. Its ability to bind telomeric DNA was verified with tel26 by CD investigation and SEM analysis, that revealed a noteworthy change in DNA morphology (mainly based on nanosphere structures) by CF3IIIPhe, confirming its G4-DNA binding ability already evidenced by spectroscopy.
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Affiliation(s)
- Marta A Fik-Jaskółka
- Department of Bioinorganic Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 8, 61-614 Poznan, Poland; Centre for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 10, 61-614 Poznań, Poland; Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Anna F Mkrtchyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Ashot S Saghyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Rosanna Palumbo
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Liana A Hayriyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Hayarpi Simonyan
- Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Valentina Roviello
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
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19
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Liu ZF, Chen X, Wu WX, Zhang GQ, Li X, Li ZZ, Jin WJ. 1,3,5-Trifluoro-2,4,6-triiodobenzene: A neglected NIR phosphor with prolonged lifetime by σ-hole and π-hole capture. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117428. [PMID: 31376727 DOI: 10.1016/j.saa.2019.117428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Room temperature phosphorescence (RTP) materials have become a hot topic in fields of organic light-emitting dioes, biological sensing and imaging. The present work reports firstly that 1,3,5-trifluoro-2,4,6-triiodobenzene (TITFB) can act as a simple pure organic NIR phosphor due to its novel function in promoting n-π∗ transition. Also, TITFB crystal has longer phosphorescence lifetime than other ordinary multiiodoluminophors and TITFB powder. Based on the TITFB crystal structure, σ-hole and π-hole capture mechanism of n-electron is proposed, i.e., the excited state energy is decreased and n-electrons are stabilized to cause slower radiative decay rate due to the restriction of σ-hole and π-hole bond. Both computational and experimental studies support the mechanism. The new electron-capture mode is more conducive to understanding pure organic ultralong lifetime RTP.
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Affiliation(s)
- Zheng Fei Liu
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Xue Chen
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Wen Xin Wu
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Gui Qi Zhang
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Xin Li
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Zhen Zhen Li
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China
| | - Wei Jun Jin
- College of Chemistry, Beijing Normal University, Beijing, Beijing, 100875, China.
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20
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Synthesis and biological evaluation of novel pyrazolo[1,5-a]pyrimidines: Discovery of a selective inhibitor of JAK1 JH2 pseudokinase and VPS34. Bioorg Med Chem Lett 2020; 30:126813. [DOI: 10.1016/j.bmcl.2019.126813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022]
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21
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Camacho-Hernandez GA, Stokes C, Duggan BM, Kaczanowska K, Brandao-Araiza S, Doan L, Papke RL, Taylor P. Synthesis, Pharmacological Characterization, and Structure-Activity Relationships of Noncanonical Selective Agonists for α7 nAChRs. J Med Chem 2019; 62:10376-10390. [PMID: 31675224 DOI: 10.1021/acs.jmedchem.9b01467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A lack of selectivity of classical agonists for the nicotinic acetylcholine receptors (nAChR) has prompted us to identify and develop a distinct scaffold of α7 nAChR-selective ligands. Noncanonical 2,4,6-substituted pyrimidine analogues were framed around compound 40 for a structure-activity relationship study. The new lead compounds activate selectively the α7 nAChRs with EC50's between 30 and 140 nM in a PNU-120596-dependent, cell-based calcium influx assay. After characterizing the expanded lead landscape, we ranked the compounds for rapid activation using Xenopus oocytes expressing human α7 nAChR with a two-electrode voltage clamp. This approach enabled us to define the molecular determinants governing rapid activation, agonist potency, and desensitization of α7 nAChRs after exposure to pyrimidine analogues, thereby distinguishing this subclass of noncanonical agonists from previously defined types of agonists (agonists, partial agonists, silent agonists, and ago-PAMs). By NMR, we analyzed pKa values for ionization of lead candidates, demonstrating distinctive modes of interaction for this landscape of ligands.
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Affiliation(s)
- Gisela Andrea Camacho-Hernandez
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California-San Diego , La Jolla , California 92093-0751 , United States
| | - Clare Stokes
- Department of Pharmacology & Therapeutics , University of Florida , P.O. Box 100267, Gainesville , Florida 32610-0267 , United States
| | - Brendan M Duggan
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California-San Diego , La Jolla , California 92093-0751 , United States
| | - Katarzyna Kaczanowska
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California-San Diego , La Jolla , California 92093-0751 , United States
| | - Stefania Brandao-Araiza
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California-San Diego , La Jolla , California 92093-0751 , United States
| | - Lisa Doan
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California-San Diego , La Jolla , California 92093-0751 , United States
| | - Roger L Papke
- Department of Pharmacology & Therapeutics , University of Florida , P.O. Box 100267, Gainesville , Florida 32610-0267 , United States
| | - Palmer Taylor
- Department of Pharmacology & Therapeutics , University of Florida , P.O. Box 100267, Gainesville , Florida 32610-0267 , United States
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22
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Chalcogen Bonding due to the Exo-Substitution of Icosahedral Dicarbaborane. Molecules 2019; 24:molecules24142657. [PMID: 31340435 PMCID: PMC6680755 DOI: 10.3390/molecules24142657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022] Open
Abstract
Chalcogen atoms are a class of substituents capable of generating inner and outer derivatives of boron clusters. It is well known that chalcogenated boron clusters can form strong σ-hole interactions when a chalcogen atom is a part of an icosahedron. This paper studies σ-hole interactions of dicarbaboranes with two exopolyhedral chalcogen atoms bonded to carbon vertices. Specifically, a computational investigation has been carried out on the co-crystal of (1,2-C2B10H10)2Se4•toluene and a single crystal of (1,2-C2B10H10)2Te4.
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23
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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24
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Kriebel M, Heßelmann A, Hennemann M, Clark T. The Feynman dispersion correction for MNDO extended to F, Cl, Br and I. J Mol Model 2019; 25:156. [DOI: 10.1007/s00894-019-4038-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/15/2019] [Indexed: 11/25/2022]
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25
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26
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Brinck T, Borrfors AN. Electrostatics and polarization determine the strength of the halogen bond: a red card for charge transfer. J Mol Model 2019; 25:125. [DOI: 10.1007/s00894-019-4014-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
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27
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Varadwaj A, Marques HM, Varadwaj PR. Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype. J Comput Chem 2019; 40:1836-1860. [PMID: 31017721 DOI: 10.1002/jcc.25836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/10/2019] [Accepted: 03/22/2019] [Indexed: 12/14/2022]
Abstract
The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C3 F6 ), upon its interaction with another same molecule to form (C3 F6 )2 dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C3 F6 itself and the (C3 F6 )2 dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C3 F6 )2 dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C3 F6 )2 dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki Prefecture, 305-8560, Japan
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki Prefecture, 305-8560, Japan
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28
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Affiliation(s)
- Timothy Clark
- Computer-Chemistry Center, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany
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29
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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30
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Bakardjiev M, Růžička A, Růžičková Z, Tok OL, Holub J, Hnyk D, Fanfrlík J, Štíbr B. Synthesis of closo-1,2-H 2C 2B 8Me 8 and 1,2-H 2C 2B 8Me 7X (X = I and OTf) Dicarbaboranes and Their Rearrangement Reactions. Inorg Chem 2019; 58:2865-2871. [PMID: 30730720 DOI: 10.1021/acs.inorgchem.8b03550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl-camouflaged dicarbaboranes closo-1,2- and 1,10-H2C2B8Me8 have been prepared in high yields either from nido-5,6-H2C2B8H10 or closo-1,2-H2C2B8H8 via electrophilic methylation reactions and cluster-rearrangement methods. Prepared were also monosubstituted derivatives of general formulation closo-H2C2B8Me7-X (X = I or OTf). The permethylated compounds exhibit extreme air stability in comparison to unprotected counterparts as a consequence of rigid, egg-shaped hydrocarbon structures incorporating inner C2B8 carborane scaffolding. The structures of all compounds isolated were confirmed unambiguously by multinuclear (11B, 1H, 13C, and 19F) NMR measurements, supported by X-ray diffraction analyses and geometry optimization methods on several compounds.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemisty , of the Czech Academy of Sciences , Flemingovo nám, 5 , Prague 6 , Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
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31
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Abstract
The models behind simple bonding theory and the origins of some components often proposed to be involved in weak intermolecular bonds are described with special reference to σ-hole bonding, of which halogen bonds are a subset. A protocol for the analysis of weak intermolecular interactions is proposed on the basis of sound physical principles. This protocol uses three different levels of interaction; "permanent" Coulomb interactions between unperturbed monomers, relaxed Coulomb interactions and dispersion. Of the three, only dispersion is not a real, measurable quantity. It is, however, included in order to describe interactions that cannot be treated entirely by the first two levels.
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Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany.
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32
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Varadwaj A, Marques HM, Varadwaj PR. Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:E379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
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33
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Bakardjiev M, Tok OL, Růžička A, Růžičková Z, Holub J, Hnyk D, Fanfrlík J, Štíbr B. Quantitative syntheses of permethylated closo-1,10-R 2C 2B 8Me 8 (R = H, Me) carboranes. Egg-shaped hydrocarbons on the Frontier between inorganic and organic chemistry. RSC Adv 2018; 8:38238-38244. [PMID: 35559069 PMCID: PMC9090134 DOI: 10.1039/c8ra06640j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/31/2018] [Indexed: 11/25/2022] Open
Abstract
Electrophilic methylation of the closo-1,10-R2C2B8H8 (1) (R = H or Me) dicarbaboranes at higher temperatures or thermal rearrangement of the 1,6-R2C2B8Me8 (3) compounds at 400-500 °C generated the B-permethylated derivatives closo-1,10-R2C2B8Me8 (2) in quantitative (>95%) yields. The compounds exhibit extreme air stability as a consequence of a rigid, egg shaped hydrocarbon structures incorporating inner 1,10-C2B8 carborane core.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice Studentská 573 532 10 Pardubice Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice Studentská 573 532 10 Pardubice Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
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34
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Can Combined Electrostatic and Polarization Effects Alone Explain the F···F Negative-Negative Bonding in Simple Fluoro-Substituted Benzene Derivatives? A First-Principles Perspective. COMPUTATION 2018. [DOI: 10.3390/computation6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry in molecular assemblies are presented in a brief review of the field. Emphasis has been placed to show that type-I and -II halogen-centered F···F long-ranged intermolecular distances viable between the entirely negative fluorine atoms in some fluoro-substituted dimers of C6H6 can be regarded as the consequence of significant non-covalent attractive interactions. Such attractive interactions observed in the solid-state structures of C6F6 and other similar fluorine-substituted aromatic compounds have frequently been underappreciated. While these are often ascribed to crystal packing effects, we show using first-principles level calculations that these are much more fundamental in nature. The stability and reliability of these interactions are supported by their negative binding energies that emerge from a supermolecular procedure using MP2 (second-order Møller-Plesset perturbation theory), and from the Symmetry Adapted Perturbation Theory, in which the latter does not determine the interaction energy by computing the total energy of the monomers or dimer. Quantum Theory of Atoms in Molecules and Reduced Density Gradient Non-Covalent Index charge-density-based approaches confirm the F···F contacts are a consequence of attraction by their unified bond path (and bond critical point) and isosurface charge density topologies, respectively. These interactions can be explained neither by the so-called molecular electrostatic surface potential (MESP) model approach that often demonstrates attraction between sites of opposite electrostatic surface potential by means of Coulomb’s law of electrostatics, nor purely by the effect of electrostatic polarization. We provide evidence against the standalone use of this approach and the overlooking of other approaches, as the former does not allow for the calculation of the electrostatic potential on the surfaces of the overlapping atoms on the monomers as in the equilibrium geometry of a complex. This study thus provides unequivocal evidence of the limitation of the MESP approach for its use in gaining insight into the nature of reactivity of overlapped interacting atoms and the intermolecular interactions involved.
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35
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Clark T, Murray JS, Politzer P. The σ-Hole Coulombic Interpretation of Trihalide Anion Formation. Chemphyschem 2018; 19:3044-3049. [DOI: 10.1002/cphc.201800750] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum Department of Chemistry and Pharmacy; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
| | - Jane S. Murray
- Department of Chemistry; University of New Orleans; New Orleans, LA 70148 USA
| | - Peter Politzer
- Department of Chemistry; University of New Orleans; New Orleans, LA 70148 USA
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36
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Dimbarre Lao Guimarães I, Garcia JR, Wohnrath K, Boeré RT. Chemical and Electrochemical Oxidation of Tris
(3,5-di-tert
-butylphenyl)phosphine - High Z′
Crystal Structures and Conformational Effects Associated with Bulky meta
Substituents. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Jarem Raul Garcia
- Departamento de Química; Universidade Estadual de Ponta Grossa; 84030-900 Ponta Grossa Paraná Brazil
| | - Karen Wohnrath
- Departamento de Química; Universidade Estadual de Ponta Grossa; 84030-900 Ponta Grossa Paraná Brazil
| | - René T. Boeré
- Department of Chemistry and Biochemistry; University of Lethbridge; Lethbridge Alberta T1K 3M4 Canada
- Canadian Centre for Advanced Fluorine Technologies; University of Lethbridge; Lethbridge Alberta T1K 3M4Canada
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37
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Bakardjiev M, Tok OL, RůŽička A, RůŽičková Z, Holub J, Hnyk D, Špalt Z, Fanfrlík J, Štíbr B. Methyl camouflage in the ten-vertex closo-dicarbaborane(10) series. Isolation of closo-1,6-R 2C 2B 8Me 8 (R = H and Me) and their monosubstituted analogues. Dalton Trans 2018; 47:11070-11076. [PMID: 30033463 DOI: 10.1039/c8dt02586j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Reported are procedures leading to the first types of methyl camouflaged dicarbadecaboranes with fewer than eleven vertices. The compounds contain the closo-1,6-C2B8 scaffolding inside the egg-shaped hepta - decamethyl sheath, which imparts unusually high air and solvolytic stability to all of these compounds.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Aleš RůŽička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Zdeňka RůŽičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Zbyněk Špalt
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
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38
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Wick CR, Clark T. On bond-critical points in QTAIM and weak interactions. J Mol Model 2018; 24:142. [DOI: 10.1007/s00894-018-3684-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/21/2018] [Indexed: 11/29/2022]
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39
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies. Chemphyschem 2018; 19:1486-1499. [PMID: 29569853 DOI: 10.1002/cphc.201800023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/13/2023]
Abstract
We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
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40
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Clark T, Heßelmann A. The coulombic σ-hole model describes bonding in CX3I⋯Y− complexes completely. Phys Chem Chem Phys 2018; 20:22849-22855. [DOI: 10.1039/c8cp03079k] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Contrary to recent reports, the σ-hole interaction energies of complexes between the carbon tetrahalides CX3I (X = F, Cl, Br, I) and halide anions Y− (Y = F, Cl, Br, I) are described very well by the simple Coulombic σ-hole concept if it is applied properly.
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Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum
- Department of Chemistry and Pharmacy
- Friedrich-Alexander-Universität Erlangen-Nürnberg
- 91052 Erlangen
- Germany
| | - Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie
- Department of Chemistry and Pharmacy
- Friedrich-Alexander-Universität Erlangen-Nürnberg
- Erlangen
- Germany
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41
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Shirkov L, Sladek V. Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT. J Chem Phys 2017; 147:174103. [DOI: 10.1063/1.4997569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leonid Shirkov
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Vladimir Sladek
- Institute of Chemistry–Centre for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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42
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Meitei OR, Heßelmann A. Intramolecular interactions in sterically crowded hydrocarbon molecules. J Comput Chem 2017; 38:2500-2508. [PMID: 28782828 DOI: 10.1002/jcc.24908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022]
Abstract
A molecular fragmentation method has been used to analyze the intramolecular interactions in the three molecules coupled diamantane, hexaphenylethane, and all-meta-tert-butyl substituted hexaphenylethane. The significance of these systems lies in the fact, that steric crowding effects enable a stabilization of the central carbon bond that possesses an extended length (1.6 to 1.7 Å) beyond conventional carbon-carbon bonds due to the steric repulsion of the attached hydrocarbon groups. The total stability of these molecules therefore depends on a delicate balance between attractive interaction forces on the one hand and on repulsive forces on the other hand. We have quantified the different interaction energy contributions using symmetry-adapted perturbation theory based on a density functional theory description of the monomers. It has been found that the attractive dispersion interactions increase more strongly with the level of crowding in the systems than the counteracting exchange interactions. This shows that steric crowding effects can have a significant impact on the structure and stability of large and branched molecules. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Oinam Romesh Meitei
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, Erlangen, D-91058, Germany
| | - Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, Erlangen, D-91058, Germany
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43
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Taylor R. The hydrogen bond between N—H or O—H and organic fluorine: favourable yes, competitive no. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:474-488. [DOI: 10.1107/s2052520617005923] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/19/2017] [Indexed: 12/26/2022]
Abstract
A study was made ofX—H...F—C interactions (X= N or O) in small-molecule crystal structures. It was primarily based on 6728 structures containingX—H and C—F and no atom heavier than chlorine. Of the 28 451 C—F moieties in these structures, 1051 interact withX—H groups. However, over three-quarters of these interactions are either the weaker components of bifurcated hydrogen bonds (so likely to be incidental contacts) or occur in structures where there is a clear insufficiency of good hydrogen-bond acceptors such as oxygen, nitrogen or halide. In structures where good acceptors are entirely absent, there is about a 2 in 3 chance that a givenX—H group will donate to fluorine. Viable alternatives areX—H...π hydrogen bonds (especially to electron-rich aromatics) and dihydrogen bonds. The average H...F distances ofX—H...F—C interactions are significantly shorter for CR3F (R= C or H) and Csp2—F acceptors than for CRF3. TheX—H...F angle distribution is consistent with a weak energetic preference for linearity, but that of H...F—C suggests a flat energy profile in the range 100–180°.X—H...F—C interactions are more likely when the acceptor is Csp2—F or CR3F, and when the donor is C—NH2. They also occur significantly more often in structures containing tertiary alcohols or solvent molecules, or withZ′ > 1,i.e.when there may be unusual packing problems. It is extremely rare to findX—H...F—C interactions in structures where there are several unused good acceptors. When it does happen, there is often a clear reason,e.g.awkwardly shaped molecules whose packing isolates a donor group from the good acceptors.
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44
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Fanfrlík J, Pecina A, Řezáč J, Sedlak R, Hnyk D, Lepšík M, Hobza P. B–H⋯π: a nonclassical hydrogen bond or dispersion contact? Phys Chem Chem Phys 2017; 19:18194-18200. [DOI: 10.1039/c7cp02762a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum mechanical calculations disprove the attractive electrostatic nature of B–H⋯π motif and define it as dispersion-driven contact.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Robert Sedlak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i., 250 68 Husinec-Řež
- Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials
- Department of Physical Chemistry
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