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Kotov AA, Kozhedub YS, Glazov DA, Iliaš M, Pershina V, Shabaev VM. Relativistic Coupled-Cluster Calculations of Spectroscopic Properties of Copernicium and Flerovium Monoxides. Chemphyschem 2023; 24:e202200680. [PMID: 36383485 DOI: 10.1002/cphc.202200680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022]
Abstract
Calculations of spectroscopic properties of the CnO and FlO molecules are performed using ab initio all-electron 4c- and 2c-relativistic coupled-cluster approaches with single, double, and perturbative triple excitations. The corresponding calculation for HgO is also accomplished for comparison with the published data. The dependence of the results on the parameters of the basis set and approximations used is investigated in detail. The overall relative uncertainties of the recommended values on the level of 1-2 % are reached. The calculated spectroscopic constants are indicative of the following trend in the reactivity of the oxides HgO>FlO>CnO. This is confirmed by the trend in the adsorption energies, Eads , of these molecules on the surfaces of gold, quartz, and Teflon. The predicted rather low Eads values for the latter case should guarantee their delivery from the recoil chamber to the chemistry set up in gas-phase experiments.
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Affiliation(s)
- Artem A Kotov
- Department of Physics, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Yury S Kozhedub
- Department of Physics, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Dmitry A Glazov
- Department of Physics, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Miroslav Iliaš
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 97401, Banská Bystrica, Slovakia.,Helmholtz-Institut Mainz, Johannes Gutenberg-Universität, 55099, Mainz, Germany.,GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291, Darmstadt, Germany
| | - Valeria Pershina
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291, Darmstadt, Germany
| | - Vladimir M Shabaev
- Department of Physics, St. Petersburg State University, 199034, St. Petersburg, Russia
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Scotti L, Patel JS, Hassanzadeh M, Scotti MT. Editorial: Hot trends in computer-aided drug design techniques. Front Cell Infect Microbiol 2023; 13:1149994. [PMID: 37139493 PMCID: PMC10150331 DOI: 10.3389/fcimb.2023.1149994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/04/2023] [Indexed: 05/05/2023] Open
Affiliation(s)
- Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, Brazil
- University Hospital, Federal University of Paraíba, João Pessoa, Brazil
- *Correspondence: Luciana Scotti,
| | | | - Malihe Hassanzadeh
- Department of Pharmacology and Physiology in Université de Sherbrooke, QC, Sherbrooke, Canada
| | - Marcus T. Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, Brazil
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3
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Palm AA, Esbjörnsson J, Kvist A, Månsson F, Biague A, Norrgren H, Jansson M, Medstrand P. Intra-Patient Evolution of HIV-2 Molecular Properties. Viruses 2022; 14:v14112447. [PMID: 36366545 PMCID: PMC9698092 DOI: 10.3390/v14112447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/24/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Limited data are available on the pathogenesis of HIV-2, and the evolution of Env molecular properties during disease progression is not fully elucidated. We investigated the intra-patient evolution of molecular properties of HIV-2 Env regions (V1-C3) during the asymptomatic, treatment-naïve phase of the infection in 16 study participants, stratified into faster or slower progressors. Most notably, the rate of change in the number of potential N-linked glycosylation sites (PNGS) within the Env (V1-C3) regions differed between progressor groups. With declining CD4+ T-cell levels, slower progressors showed, on average, a decrease in the number of PNGSs, while faster progressors showed no significant change. Furthermore, diversity increased significantly with time in faster progressors, whereas no such change was observed in slower progressors. No differences were identified between the progressor groups in the evolution of length or charge of the analyzed Env regions. Predicted virus CXCR4 use was rare and did not emerge as a dominating viral population during the studied disease course (median 7.9 years, interquartile range [IQR]: 5.2-14.0) in either progressor groups. Further work building on our observations may explain molecular hallmarks of HIV-2 disease progression and differences in pathogenesis between HIV-1 and HIV-2.
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Affiliation(s)
- Angelica A. Palm
- Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Department of Translational Medicine, Lund University, 20502 Lund, Sweden
- Correspondence:
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 20502 Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Anders Kvist
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden
| | - Fredrik Månsson
- Department of Translational Medicine, Lund University, 20502 Lund, Sweden
| | - Antonio Biague
- National Public Health Laboratory, Bissau 1041, Guinea-Bissau
| | - Hans Norrgren
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden
| | - Marianne Jansson
- Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, 20502 Lund, Sweden
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Chen W, Yang X, Bao J, Lin Z, Li T, Wang Y, Zhang A, Hu J, Jin J. A Pilot Study on the Concentration, Distribution and Bioaccumulation of Polybrominated Diphenyl Ethers (PBDEs) in Tissues and Organs of Grassland Sheep. Int J Environ Res Public Health 2022; 19:12170. [PMID: 36231471 PMCID: PMC9566259 DOI: 10.3390/ijerph191912170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Polybrominated diphenyl ether (PBDE) concentrations in various tissues and organs of grassland sheep from Inner Mongolia, China, were determined. The abilities of PBDEs binding to ovine serum albumin (OSA) and Cytochrome P450 enzyme (CYP3A24) were assessed by fluorescence spectroscopy and molecular docking simulations. The PBDE concentrations in the sheep tissue and organ samples were 33.4-167 pg/g dw. The distribution of PBDEs in sheep organs and tissues is affected not only by the function of organs and tissues, but also by the characteristics of PBDEs. Adipose tissue tends to bioaccumulate more-brominated BDEs (BDE-154, -153, and -183), but muscle tissues and visceral organs mainly bioaccumulate less-brominated BDEs. The distribution of PBDEs in visceral organs is mainly affected by the transport of ovine serum albumin (OSA) and the metabolism of CYP3A24 enzyme. The distribution of PBDEs in adipose tissue and brain is mainly affected by their logKOW.
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Affiliation(s)
- Wenming Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xinrui Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Junsong Bao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ziyi Lin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tianwei Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ying Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Aiqin Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jicheng Hu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jun Jin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Beijing Food and Environmental Health Engineering Center, Beijing 100081, China
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Delahaije RJBM, Wierenga PA. Hydrophobicity Enhances the Formation of Protein-Stabilized Foams. Molecules 2022; 27:2358. [PMID: 35408752 PMCID: PMC9000900 DOI: 10.3390/molecules27072358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Screening proteins for their potential use in foam applications is very laborious and time consuming. It would be beneficial if the foam properties could be predicted based on their molecular properties, but this is currently not possible. For protein-stabilized emulsions, a model was recently introduced to predict the emulsion properties from the protein molecular properties. Since the fundamental mechanisms for foam and emulsion formation are very similar, it is of interest to determine whether the link to molecular properties defined in that model is also applicable to foams. This study aims to link the exposed hydrophobicity with the foam ability and foam stability, using lysozyme variants with altered hydrophobicity, obtained from controlled heat treatment (77 °C for 0-120 min). To establish this link, the molecular characteristics, interfacial properties, and foam ability and stability (at different concentrations) were analysed. The increasing hydrophobicity resulted in an increased adsorption rate constant, and for concentrations in the protein-poor regime, the increasing hydrophobicity enhanced foam ability (i.e., interfacial area created). At higher relative exposed hydrophobicity (i.e., ~2-5 times higher than native lysozyme), the adsorption rate constant and foam ability became independent of hydrophobicity. The foam stability (i.e., foam collapse) was affected by the initial foam structure. In the protein-rich regime-with nearly identical foam structure-the hydrophobicity did not affect the foam stability. The link between exposed hydrophobicity and foam ability confirms the similarity between protein-stabilized foams and emulsions, and thereby indicates that the model proposed for emulsions can be used to predict foam properties in the future.
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Affiliation(s)
| | - Peter A. Wierenga
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands;
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6
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Simkó I, Chordiya K, Császár AG, Kahaly MU, Szidarovszky T. A quantum-chemical perspective on the laser-induced alignment and orientation dynamics of the CH 3 X (X = F, Cl, Br, I) molecules. J Comput Chem 2022; 43:519-538. [PMID: 35084047 PMCID: PMC9303447 DOI: 10.1002/jcc.26811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/08/2022]
Abstract
Motivated by recent experiments, the laser-induced alignment-and-orientation (A&O) dynamics of the prolate symmetric top CH3 X (X = F, Cl, Br, I) molecules is investigated, with particular emphasis on the effect of halogen substitution on the rotational constants, dipole moments, and polarizabilities of these species, as these quantities determine the A&O dynamics. Insight into possible control schemes for preferred A&O dynamics of halogenated molecules and best practices for A&O simulations are provided, as well. It is shown that for accurate A&O -dynamics simulations it is necessary to employ large basis sets and high levels of electron correlation when computing the rotational constants, dipole moments, and polarizabilities. The benchmark-quality values of these molecular parameters, corresponding to the equilibrium, as well as the vibrationally averaged structures are obtained with the help of the focal-point analysis (FPA) technique and explicit electronic-structure computations utilizing the gold-standard CCSD(T) approach, basis sets up to quintuple-zeta quality, core-correlation contributions and, in particular, relativistic effects for CH3 Br and CH3 I. It is shown that the different A&O behavior of the CH3 X molecules in the optical regime is mostly caused by the differences in their polarizability anisotropy, in other terms, the size of the halogen atom. In contrast, the A&O dynamics of the CH3 X series induced by an intense few-cycle THz pulse is mostly governed by changes in the rotational constants, due to the similar dipole moments of the CH3 X molecules. The A&O dynamics is most sensitive to the B rotational constant: even the difference between its equilibrium and vibrationally-averaged values results in noticeably different A&O dynamics. The contribution of rotational states having different symmetry, weighted by nuclear-spin statistics, to the A&O dynamics is also studied.
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Affiliation(s)
- Irén Simkó
- Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,ELKH-ELTE Complex Chemical Systems Research Group, Budapest, Hungary
| | - Kalyani Chordiya
- ELI-ALPS, ELI-HU Non-Profit Ltd. and University of Szeged, Szeged, Hungary
| | - Attila G Császár
- Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,ELKH-ELTE Complex Chemical Systems Research Group, Budapest, Hungary
| | | | - Tamás Szidarovszky
- Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,ELKH-ELTE Complex Chemical Systems Research Group, Budapest, Hungary
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7
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Goloshchapov D, Kashkarov V, Nikitkov K, Seredin P. Investigation of the Effect of Nanocrystalline Calcium Carbonate-Substituted Hydroxyapatite and L-Lysine and L-Arginine Surface Interactions on the Molecular Properties of Dental Biomimetic Composites. Biomimetics (Basel) 2021; 6:70. [PMID: 34940013 PMCID: PMC8698581 DOI: 10.3390/biomimetics6040070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/06/2023] Open
Abstract
Differences in the surface interactions of non-stoichiometric nanocrystalline B-type carbonate-substituted hydroxyapatite (n-cHAp) with the amino acids L-Lysine hydrochloride (L-LysHCl) and L-Arginine hydrochloride (L-ArgHCl) in acidic and alkaline media were determined using structural and spectroscopic analysis methods. The obtained data confirm that hydroxyapatite synthesized using our technique, which was used to develop the n-cHAp/L-LysHCl and n-cHAp/L-ArgHCl composites, is nanocrystalline. Studies of molecular composition of the samples by Fourier transform infrared spectroscopy under the change in the charge state of L-Lysine in environments with different alkalinity are consistent with the results of X-ray diffraction analysis, as evidenced by the redistribution of the modes' intensities in the spectra that is correlated with the side chains, i.e., amide and carboxyl groups, of the amino acid. During the formation of a biomimetic composite containing L-Lysine hydrochloride and n-cHAp, the interaction occurred through bonding of the L-Lysine side chain and the hydroxyl groups of hydroxyapatite, which created an anionic form of L-Lysine at pH ≤ 5. In contrast, in biocomposites based on L-Arginine and n-cHAp, the interaction only slightly depends on pH value, and it proceeds by molecular orientation mechanisms. The X-ray diffraction and infrared spectroscopy results confirm that changes in the molecular composition of n-cHAp/L-ArgHCl biomimetic composites are caused by the electrostatic interaction between the L-ArgHCl molecule and the carbonate-substituted calcium hydroxyapatite. In this case, the bond formation was detected by Fourier transform infrared (FTIR) spectroscopy; the vibrational modes attributed to the main carbon chain and the guanidine group of L-Arginine are shifted during the interaction. The discovered interaction mechanisms between nanocrystalline carbonate-substituted hydroxyapatite that has physicochemical properties characteristic of the apatite in human dental enamel and specific amino acids are important for selecting the formation conditions of biomimetic composites and their integration with the natural dental tissue.
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Affiliation(s)
- Dmitry Goloshchapov
- Solid State Physics and Nanostructures Department, Voronezh State University, University Sq. 1, 394018 Voronezh, Russia; (D.G.); (V.K.); (K.N.)
| | - Vladimir Kashkarov
- Solid State Physics and Nanostructures Department, Voronezh State University, University Sq. 1, 394018 Voronezh, Russia; (D.G.); (V.K.); (K.N.)
| | - Kirill Nikitkov
- Solid State Physics and Nanostructures Department, Voronezh State University, University Sq. 1, 394018 Voronezh, Russia; (D.G.); (V.K.); (K.N.)
| | - Pavel Seredin
- Solid State Physics and Nanostructures Department, Voronezh State University, University Sq. 1, 394018 Voronezh, Russia; (D.G.); (V.K.); (K.N.)
- Scientific and Educational Center “Nanomaterials and Nanotechnologies”, Ural Federal, Mir Av., 620002 Yekaterinburg, Russia
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8
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Chen D, Huang X, Fan Y. Thermodynamics-Based Model Construction for the Accurate Prediction of Molecular Properties From Partition Coefficients. Front Chem 2021; 9:737579. [PMID: 34589468 PMCID: PMC8473701 DOI: 10.3389/fchem.2021.737579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Developing models for predicting molecular properties of organic compounds is imperative for drug development and environmental safety; however, development of such models that have high predictive power and are independent of the compounds used is challenging. To overcome the challenges, we used a thermodynamics-based theoretical derivation to construct models for accurately predicting molecular properties. The free energy change that determines a property equals the sum of the free energy changes (ΔGFs) caused by the factors affecting the property. By developing or selecting molecular descriptors that are directly proportional to ΔGFs, we built a general linear free energy relationship (LFER) for predicting the property with the molecular descriptors as predictive variables. The LFER can be used to construct models for predicting various specific properties from partition coefficients. Validations show that the models constructed according to the LFER have high predictive power and their performance is independent of the compounds used, including the models for the properties having little correlation with partition coefficients. The findings in this study are highly useful for applications in drug development and environmental safety.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Xiaoqing Huang
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Yulan Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
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9
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P SS, K NB, Rekha T, Padmaja A, Padmavathi V. Molecular properties prediction, synthesis, and antimicrobial activity of bis(azolyl)sulfonamidoacetamides. Arch Pharm (Weinheim) 2021; 354:e2000483. [PMID: 33977563 DOI: 10.1002/ardp.202000483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 11/07/2022]
Abstract
A library of bis(azolyl)sulfonamidoacetamides was prepared by the reaction of azolylsulfonylamines with azolylchloroacetamides in the presence of pyridine/4-(dimethylamino)pyridine (DMAP) under ultrasonication. The reaction proceeded well with DMAP, resulting in a higher yield of the products. The antimicrobial activity of the compounds indicated that N-{5-[N-(2-{[4-(4-chloro-1H-pyrrol-2-yl)-1H-imidazol-2-yl)amino}-2-oxoethyl)sulfamoyl]-4-phenylthiazol-2-yl}benzamide (22a), N-{5-[N-(2-{[4-(4-chloro-1H-pyrrol-2-yl)-1H-imidazol-2-yl]amino}-2-oxoethyl)sulfamoyl]-4-(4-chlorophenyl)thiazol-2-yl}benzamide (22c), and N-{5-[N-(2-{[4-(4-chloro-1H-pyrrol-2-yl)-1H-imidazol-2-yl]amino}-2-oxoethyl)sulfamoyl]-4-(4-chloro-phenyl)-1H-imidazol-2-yl}benzamide (24c) exhibited a low minimal inhibitory concentration (MIC) against Bacillus subtilis, equal to the standard drug, chloramphenicol. Compounds 22c and 24c also showed low MICs against Aspergillus niger, equal to the standard drug, ketoconazole. The molecular properties of the synthesized molecules were studied to identify druglikeness properties of the target compounds. On the basis of molecular properties prediction, 19a, 19b, 20b, 20c, 21a-c, 22b, 22c, and 23a-c can be treated as drug candidates.
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Affiliation(s)
- Siva Sankar P
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Narendra Babu K
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Tamatam Rekha
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Adivireddy Padmaja
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
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Wang L, Chi Y, Shu D, Weiss-Hortala E, Nzihou A, Choi S. Experimental studies of hydrothermal liquefaction of kitchen waste with H +, OH - and Fe 3+ additives for bio-oil upgrading. Waste Manag Res 2021; 39:165-173. [PMID: 32951533 DOI: 10.1177/0734242x20957408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Kitchen waste (KW) has gradually become a prominent problem in municipal solid waste treatment. Hydrothermal liquefaction (HTL) is a promising method used to make fuel oil from food and KW. However, the upgrading of bio-oil is particularly important for the sake of industrial reuse. In this study, the KW from university restaurants was subjected to HTL experiments in order to study theoretical feasibility. With the change of conversion temperature and residence time, the optimal conversion working conditions in this study were determined according to the quality and yield of the bio-oil. Moreover, the bio-oil upgrading effects of different additives (hydrogen chloride, sodium hydroxide, and iron(III) chloride) on the HTL of KW were studied. Alkaline additives have an inhibitory effect on the bio-oil yield and positive effect on coke yield. Acidic additives and iron (Fe)-containing additives can promote bio-oil yield. As an important aspect of upgrading, the effect on the nitrogen content of bio-oil with additives was revealed. The alkaline and Fe-containing additives have little effect on reducing the viscosity of the bio-oil while with the appropriate ratio (2.5 mol•kg-1) of acidic additives to the raw material, the static and dynamic fluidity of the oil phase products are reduced to about 0.1 Pa•s.
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Affiliation(s)
- Lixian Wang
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, People's Republic of China
| | - Yong Chi
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, People's Republic of China
| | - Di Shu
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, People's Republic of China
| | - Elsa Weiss-Hortala
- IMT Mines Albi, RAPSODEE CNRS UMR-5302, Université de Toulouse, Albi, Midi-Pyrénées, France
| | - Ange Nzihou
- IMT Mines Albi, RAPSODEE CNRS UMR-5302, Université de Toulouse, Albi, Midi-Pyrénées, France
| | - Sangmin Choi
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, People's Republic of China
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11
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Abstract
Voltage-gated calcium channels are the principal conduits for depolarization-mediated Ca2+ entry into excitable cells. In this review, the biophysical properties of the relevant members of this family of channels, those that are present in presynaptic terminals, will be discussed in relation to their function in mediating neurotransmitter release. Voltage-gated calcium channels have properties that ensure they are specialized for particular roles, for example, differences in their activation voltage threshold, their various kinetic properties, and their voltage-dependence of inactivation. All these attributes play into the ability of the various voltage-gated calcium channels to participate in different patterns of presynaptic vesicular release. These include synaptic transmission resulting from single action potentials, and longer-term changes mediated by bursts or trains of action potentials, as well as release resulting from graded changes in membrane potential in specialized sensory synapses.
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Affiliation(s)
- Annette C Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, WC1E 6BT, UK,Address correspondence to A.C.D. (e-mail: )
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12
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Bekalu ZE, Dionisio G, Brinch-Pedersen H. Molecular Properties and New Potentials of Plant Nepenthesins. Plants (Basel) 2020; 9:E570. [PMID: 32365700 PMCID: PMC7284499 DOI: 10.3390/plants9050570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022]
Abstract
Nepenthesins are aspartic proteases (APs) categorized under the A1B subfamily. Due to nepenthesin-specific sequence features, the A1B subfamily is also named nepenthesin-type aspartic proteases (NEPs). Nepenthesins are mostly known from the pitcher fluid of the carnivorous plant Nepenthes, where they are availed for the hydrolyzation of insect protein required for the assimilation of insect nitrogen resources. However, nepenthesins are widely distributed within the plant kingdom and play significant roles in plant species other than Nepenthes. Although they have received limited attention when compared to other members of the subfamily, current data indicates that they have exceptional molecular and biochemical properties and new potentials as fungal-resistance genes. In the current review, we provide insights into the current knowledge on the molecular and biochemical properties of plant nepenthesins and highlights that future focus on them may have strong potentials for industrial applications and crop trait improvement.
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Affiliation(s)
- Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, DK-4200 Slagelse, Denmark; (G.D.); (H.B.-P.)
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13
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Campbell A, Mohl JE, Gutierrez DA, Varela-Ramirez A, Boland T. Thermal Bioprinting Causes Ample Alterations of Expression of LUCAT1, IL6, CCL26, and NRN1L Genes and Massive Phosphorylation of Critical Oncogenic Drug Resistance Pathways in Breast Cancer Cells. Front Bioeng Biotechnol 2020; 8:82. [PMID: 32154227 PMCID: PMC7047130 DOI: 10.3389/fbioe.2020.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
Bioprinting technology merges engineering and biological fields and together, they possess a great translational potential, which can tremendously impact the future of regenerative medicine and drug discovery. However, the molecular effects elicited by thermal inkjet bioprinting in breast cancer cells remains elusive. Previous studies have suggested that bioprinting can be used to model tissues for drug discovery and pharmacology. We report viability, apoptosis, phosphorylation, and RNA sequence analysis of bioprinted MCF7 breast cancer cells at separate timepoints post-bioprinting. An Annexin A5-FITC apoptosis stain was used in combination with flow cytometry at 2 and 24 h post-bioprinting. Antibody arrays using a Human phospho-MAPK array kit was performed 24 h post-bioprinting. RNA sequence analysis was conducted in samples collected at 2, 7, and 24 h post-bioprinting. The post-bioprinting cell viability averages were 77 and 76% at 24 h and 48 h, with 31 and 64% apoptotic cells at 2 and 24 h after bioprinting. A total of 21 kinases were phosphorylated in the bioprinted cells and 9 were phosphorylated in the manually seeded controls. The RNA seq analysis in the bioprinted cells identified a total of 12,235 genes, of which 9.7% were significantly differentially expressed. Using a ±2-fold change as the cutoff, 266 upregulated and 206 downregulated genes were observed in the bioprinted cells, with the following 5 genes uniquely expressed NRN1L, LUCAT1, IL6, CCL26, and LOC401585. This suggests that thermal inkjet bioprinting is stimulating large scale gene alterations that could potentially be utilized for drug discovery. Moreover, bioprinting activates key pathways implicated in drug resistance, cell motility, proliferation, survival, and differentiation.
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Affiliation(s)
- Aleli Campbell
- Metallurgical, Materials and Biomedical Engineering, University of Texas at El Paso, El Paso, TX, United States
| | - Jonathon E Mohl
- Department of Mathematical Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Denisse A Gutierrez
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Armando Varela-Ramirez
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Thomas Boland
- Metallurgical, Materials and Biomedical Engineering, University of Texas at El Paso, El Paso, TX, United States
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14
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Abstract
Clostridium perfringens is an important human and animal pathogen that is the primary causative agent of necrotizing enteritis and enterotoxemia in many types of animals; it causes traumatic gas gangrene in humans and animals and is associated with cases of food poisoning in humans. C. perfringens produces a variety of toxins as well as many enzymes, including three sialidases, NanH, NanI, and NanJ. Sialidases could be important virulence factors that promote the pathogenesis of C. perfringens. Among them, NanI promotes the colonization of C. perfringens in the intestinal tract and enhances the cytotoxic activity and association of several major C. perfringens toxins with host cells. In recent years, studies on the structure and functions of sialidases have yielded interesting results, and the functions of sialic acid and sialidases in bacterial pathogenesis have become a hot research topic. An in-depth understanding and additional studies of sialidases will further elucidate mechanisms of C. perfringens pathogenesis and could promote the development and clinical applications of sialidase inhibitors. This article reviews the structural characteristics, expression regulation, roles of sialidases in C. perfringens pathogenesis, and effects of their inhibitors.
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Affiliation(s)
- Yan-Hua Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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15
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Peng H, Wu C, Li J, Li C, Chen Z, Pei Z, Tao L, Gong Y, Pan Y, Bai H, Ma C, Feng S. Detection and genomic characterization of Bovine papillomavirus isolated from Chinese native cattle. Transbound Emerg Dis 2019; 66:2197-2203. [PMID: 31269541 DOI: 10.1111/tbed.13285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Abstract
Bovine papillomaviruses (BPV) are small circular DNA viruses which can be widely spread in herd, inducing cattle tumours, therefore, leading economic losses in dairy and beef production industries. BPV-leads symptoms include cutaneous papillomas, fibropapillomas, urinary bladder and oesophageal carcinoma. As one of the most important producers of beef in the world, China has not provided systematic research to prevent the harm of BPV, particularly in papillomavirus molecular characterization which presents among Chinese native cattle which was known to have higher disease resistance. In this study, skin papilloma was observed and samples were collected following by histopathological analysis. We analysed all neoplasms samples and reviewed their degrees in acanthosis and/or hyperkeratosis. Full-length genomic sequencing was applied for all four isolated strains (JX180408, LA150909, HX160815, and BS160810) to exploring the molecular reason why BPV currently prevalent in Chinese native cattle. As a result, we identified that these four isolates were classified as BPV-1 and clustered into the Deltapapillomavirus genera. Our study also identified that BPV 1 isolates from Chinese indigenous cattle breeds belong to subtypes A which has a closer genetic background compare with their common ancestor and suggest it can be a more ancestral species. European isolates more recently diverged group (group B) contained almost exclusively European samples. In this study, we analysed the similarity of ORF between Chinese isolated BPV 1 and BPV 1 reference strains and listed results. This study provides the complete genomic characterization of BPVs circulating in Chinese native cattle breeds for the first time, which provide a detailed description of how diverse strains may cause skin tumour among Chinese local breed cattle therefore critical for further epidemiological study of relevant diseases.
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Affiliation(s)
- Hao Peng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Cuilan Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Jun Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Changting Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China.,Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhongwei Chen
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Zhe Pei
- The City College of New York, New York, NY, USA
| | - Li Tao
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Yu Gong
- Animal Science and Technology Station of Guizhou, Guiyang, China
| | - Yan Pan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Huili Bai
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chunxia Ma
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Shiwen Feng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
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16
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Richter MF, Hergenrother PJ. The challenge of converting Gram-positive-only compounds into broad-spectrum antibiotics. Ann N Y Acad Sci 2018; 1435:18-38. [PMID: 29446459 DOI: 10.1111/nyas.13598] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/07/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Multidrug resistant Gram-negative bacterial infections are on the rise, and there is a lack of new classes of drugs to treat these pathogens. This drug shortage is largely due to the challenge of finding antibiotics that can permeate and persist inside Gram-negative species. Efforts to understand the molecular properties that enable certain compounds to accumulate in Gram-negative bacteria based on retrospective studies of known antibiotics have not been generally actionable in the development of new antibiotics. A recent assessment of the ability of >180 diverse small molecules to accumulate in Escherichia coli led to predictive guidelines for compound accumulation in E. coli. These "eNTRy rules" state that compounds are most likely to accumulate if they contain a nonsterically encumbered ionizable Nitrogen (primary amines are the best), have low Three-dimensionality (globularity ≤ 0.25), and are relatively Rigid (rotatable bonds ≤ 5). In this review, we look back through 50+ years of antibacterial research and 1000s of derivatives and assess this historical data set through the lens of these predictive guidelines. The results are consistent with the eNTRy rules, suggesting that the eNTRy rules may provide an actionable and general roadmap for the conversion of Gram-positive-only compounds into broad-spectrum antibiotics.
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Affiliation(s)
- Michelle F Richter
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
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17
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Abstract
Chloride channel 2 (ClC-2) is one of the nine mammalian members of the ClC family. The present review discusses the molecular properties of ClC‑2, including CLCN2, ClC‑2 promoter and the structural properties of ClC‑2 protein; physiological properties; functional properties, including the regulation of cell volume. The effects of ClC‑2 on the digestive, respiratory, circulatory, nervous and optical systems are also discussed, in addition to the mechanisms involved in the regulation of ClC‑2. The review then discusses the diseases associated with ClC‑2, including degeneration of the retina, Sjögren's syndrome, age‑related cataracts, degeneration of the testes, azoospermia, lung cancer, constipation, repair of impaired intestinal mucosa barrier, leukemia, cystic fibrosis, leukoencephalopathy, epilepsy and diabetes mellitus. It was concluded that future investigations of ClC‑2 are likely to be focused on developing specific drugs, activators and inhibitors regulating the expression of ClC‑2 to treat diseases associated with ClC‑2. The determination of CLCN2 is required to prevent and treat several diseases associated with ClC‑2.
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Affiliation(s)
- Hongwei Wang
- Department of Ophthalmology, People's Hospital of Jingjiang, Jingjiang, Jiangsu 214500, P.R. China
| | - Minghui Xu
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Qingjie Kong
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Peng Sun
- Department of Ophthalmology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154000, P.R. China
| | - Fengyun Yan
- Assets Division, Harbin University of Science and Technology, Harbin, Heilongjiang 150080, P.R. China
| | - Wenying Tian
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Xin Wang
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
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18
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Sadovoy VV, Shchedrina TV, Selimov MA. [Biologically active composition for regulation of lipolysis process in the organism under obesity]. Vopr Pitan 2017; 86:74-83. [PMID: 30592856 DOI: 10.24411/0042-8833-2017-00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/07/2017] [Indexed: 11/20/2022]
Abstract
The aim of the research was to study the mechanism of intermolecular interaction of allicin and lecithin with pancreatic lipase, and developing the composition, contributing to the inactivation process of lipolysis, and reduce the absorption of fats in the organism. Methods of computer chemistry have been used for modeling spatial structures of allicin and lecithin. Geometric optimization was carried out, quantum chemical characteristics and the distribution of charge density of the molecules of the studied biologically active substances and pancreatic lipase were studied. In the study of the molecular properties of the lipase of pancreatic juice before and after molecular docking, it was found that one molecule of lecithin didn't fully block the active site of the enzyme. For complete inactivation of lipase, two molecules of lecithin or one molecule of allicin were required (Epot. = -412.36 and -159.4 kcal, respectively). An optimal composition of supplement to blocking pancreatic lipase has been set: allicin containing additive - 95% (75% sunflower oil, 25% chopped garlic), lecithin - 5%. The efficacy of lipase inactivation by supplement stored at 2-4 °C in fat-water mixture has been studied. It was found that after storage for three days the developed composition retained its properties. Acid number of fat, subjected to enzymatic treatment varies slightly (0.1 to 0.25 mg KOH/g). Peroxide value and microbiological characteristics of the investigated fraction also did not exceed the permissible norms. When evaluating the biological value of the developed composition in the experiment on white BALB/c mice (with initial body weight of 20-30 g), it was found that its administration on the background of high fat (19%) diet at a dose of 6% of the diet fat from the 15th to the 40th day was accompanied by 1.5 fold reduce in body weight increasing in comparison with animals which received no additives. Their blood levels of total lipids, cholesterol, triglycerides and glucose reduced while the level of total protein and urea increased to the level of the control group (without obesity).
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Affiliation(s)
- V V Sadovoy
- North-Caucasian Federal University, Branch in Pyatigorsk.,Stavropol Institute of Cooperation, Branch of Belgorod University of Cooperation, Economics and Law
| | - T V Shchedrina
- North-Caucasian Federal University, Branch in Pyatigorsk
| | - M A Selimov
- North-Caucasian Federal University, Branch in Pyatigorsk
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19
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Foley DJ, Nelson A, Marsden SP. Evaluating New Chemistry to Drive Molecular Discovery: Fit for Purpose? Angew Chem Int Ed Engl 2016; 55:13650-13657. [PMID: 27573303 PMCID: PMC5113762 DOI: 10.1002/anie.201604193] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/01/2016] [Indexed: 12/12/2022]
Abstract
As our understanding of the impact of specific molecular properties on applications in discovery-based disciplines improves, the extent to which published synthetic methods meet (or do not meet) desirable criteria is ever clearer. Herein, we show how the application of simple (and in many cases freely available) computational tools can be used to develop a semiquantitative understanding of the potential of new methods to support molecular discovery. This analysis can, among other things, inform the design of improved substrate scoping studies; direct the prioritization of specific exemplar structures for synthesis; and substantiate claims of potential future applications for new methods.
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Affiliation(s)
- Daniel J Foley
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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20
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Shanley TW, Bonnie F, Scott J, Toth M. Role of Gas Molecule Complexity in Environmental Electron Microscopy and Photoelectron Yield Spectroscopy. ACS Appl Mater Interfaces 2016; 8:27305-27310. [PMID: 27649062 DOI: 10.1021/acsami.6b08681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Environmental scanning electron microscopy (ESEM) and environmental photoelectron yield spectroscopy (EPYS) enable electron imaging and spectroscopy of surfaces and interfaces in low-vacuum gaseous environments. The techniques are both appealing and limited by the range of gases that can be used to amplify electrons emitted from a sample and used to form images/spectra. However, to date only H2O and NH3 gases have been identified as highly favorable electron amplification media. Here we demonstrate that ethanol vapor (CH3CH2OH) is superior to both of these and attribute its performance to its molecular complexity and valence orbital structure. Our findings improve the present understanding of what constitutes a favorable electron amplification gas and will help expand the applicability and usefulness of the ESEM and EPYS techniques.
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Affiliation(s)
- Toby W Shanley
- School of Physics and Advanced Materials, University of Technology Sydney , Ultimo, NSW 2007, Australia
| | - Fadi Bonnie
- School of Physics and Advanced Materials, University of Technology Sydney , Ultimo, NSW 2007, Australia
| | - John Scott
- School of Physics and Advanced Materials, University of Technology Sydney , Ultimo, NSW 2007, Australia
| | - Milos Toth
- School of Physics and Advanced Materials, University of Technology Sydney , Ultimo, NSW 2007, Australia
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21
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Yelithao K, Surayot U, Lee JH, You S. RAW264.7 Cell Activating Glucomannans Extracted from Rhizome of Polygonatum sibiricum. Prev Nutr Food Sci 2016; 21:245-254. [PMID: 27752501 PMCID: PMC5063210 DOI: 10.3746/pnf.2016.21.3.245] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/21/2016] [Indexed: 12/23/2022] Open
Abstract
Water-soluble polysaccharides isolated from the rhizome of Polygonatum sibiricum and fractionated using ion-exchange chromatography were investigated to determine their structure and immunostimulating activity. Crude and fractions (F1 and F2) consisted of carbohydrates (85.1~88.3%) with proteins (4.51~11.9%) and uronic acid (1.79~7.47%), and included different levels of mannose (62.3~76.3%), glucose (15.2~20.3%), galactose (4.35~15.3%), and arabinose (4.00~7.65%). The crude contained two peaks with molecular weights (Mw) of 151×103 and 31.8×103, but F1 and F2 exhibited one major peak with Mw of 103×103 and 628×103, respectively. Little immunostimulatory activity was observed by the crude; however, F1 and F2 significantly activated RAW264.7 cells to release nitric oxide and various cytokines, suggesting they were potent immunostimulators. The backbone of the most immunostimulating fraction (F1) was (1→4)-manno- and (1→4)-gluco-pyranosyl residues with galactose and glucose attached to O-6 of manno-pyranoside.
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Affiliation(s)
- Khamphone Yelithao
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangwon 25457, Korea
| | - Utoomporn Surayot
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangwon 25457, Korea
| | - Ju Hun Lee
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangwon 25457, Korea
| | - SangGuan You
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangwon 25457, Korea
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22
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Priya R, Sumitha R, Doss CGP, Rajasekaran C, Babu S, Seenivasan R, Siva R. Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica. Pharmacogn Mag 2016; 11:S414-22. [PMID: 26929575 PMCID: PMC4745211 DOI: 10.4103/0973-1296.168947] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: Acquired immunodeficiency syndrome caused by human immunodeficiency virus (HIV) is an immunosuppressive disease. Over the past decades, it has plagued human health due to the grave consequences in its harness. Objective: For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. Materials and Methods: In this investigation we have performed molecular docking, molecular property prediction, drug-likeness score, and molecular dynamics (MD) simulation to develop a novel anti-HIV drug. We have screened 12 alkaloids from a medicinal plant Toddalia asiatica for its probabilistic binding with the active site of the HIV-1-reverse transcriptase (HIV-1-RT) domain (the major contributor to the onset of the disease). Results: The docking results were evaluated based on free energies of binding (ΔG), and the results suggested toddanol, toddanone, and toddalenone to be potent inhibitors of HIV-1-RT. In addition, the alkaloids were subjected to molecular property prediction analysis. Toddanol and toddanone with more rotatable bonds were found to have a drug-likeness score of 0.23 and 0.11, respectively. These scores were comparable with the standard anti-HIV drug zidovudine with a model score 0.28. Finally, two characteristic protein-ligand complexes were exposed to MD simulation to determine the stability of the predicted conformations. Conclusion: The toddanol-RT complex showed higher stability and stronger H-bonds than toddanone-RT complex. Based on these observations, we firmly believe that the alkaloid toddanol could aid in efficient HIV-1 drug discovery. SUMMARY In the present study, the molecular docking and MD simulations are performed to explore the possible binding mode of HIV 1 RT with 12 alkaloids of T. asiatica. Molecular docking by AutoDock4 revealed three alkaloids toddanol, toddanone, and toddalenone with highest binding affinity towards HIV 1 RT. The drug likeness model score revealed a positive score for toddanol and toddanone which is comparable to the drug likeness score of the standard anti HIV drug zidovudine. Results from simulation analysis revealed that toddanol RT complex is more stable than toddanone RT complex inferring toddanol as a potential anti HIV drug molecule.
Abbreviations used: HIV: Human immunodeficiency virus, HIV 1 RT: HIV 1 reverse transcriptase, RNase H: Ribonuclease H, MD: Molecular dynamics, PDB: Protein databank, RMSD: Root mean square deviation, RMSF: Root mean square fluctuation.
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Affiliation(s)
- R Priya
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Rajendrarao Sumitha
- Department of Neurophysiology, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - C George Priya Doss
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - C Rajasekaran
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - S Babu
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - R Seenivasan
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - R Siva
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
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Abstract
![]()
Identification
of the usefulness of lipid-based formulations (LBFs)
for delivery of poorly water-soluble drugs is at date mainly experimentally
based. In this work we used a diverse drug data set, and more than
2,000 solubility measurements to develop experimental and computational
tools to predict the loading capacity of LBFs. Computational models
were developed to enable in silico prediction of
solubility, and hence drug loading capacity, in the LBFs. Drug solubility
in mixed mono-, di-, triglycerides (Maisine 35-1 and Capmul MCM EP)
correlated (R2 0.89) as well as the drug
solubility in Carbitol and other ethoxylated excipients (PEG400, R2 0.85; Polysorbate 80, R2 0.90; Cremophor EL, R2 0.93).
A melting point below 150 °C was observed to result in a reasonable
solubility in the glycerides. The loading capacity in LBFs was accurately
calculated from solubility data in single excipients (R2 0.91). In silico models, without the
demand of experimentally determined solubility, also gave good predictions
of the loading capacity in these complex formulations (R2 0.79). The framework established here gives a better
understanding of drug solubility in single excipients and of LBF loading
capacity. The large data set studied revealed that experimental screening
efforts can be rationalized by solubility measurements in key excipients
or from solid state information. For the first time it was shown that
loading capacity in complex formulations can be accurately predicted
using molecular information extracted from calculated descriptors
and thermal properties of the crystalline drug.
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Affiliation(s)
- Linda C Alskär
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University , Uppsala Biomedical Center P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Christopher J H Porter
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christel A S Bergström
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy, Uppsala University , Uppsala Biomedical Center P.O. Box 580, SE-751 23 Uppsala, Sweden.,Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Parade, Parkville, Victoria 3052, Australia
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24
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Murugan K, Sangeetha S, Ranjitha S, Vimala A, Al-Sohaibani S, Rameshkumar G. HDACiDB: a database for histone deacetylase inhibitors. Drug Des Devel Ther 2015; 9:2257-64. [PMID: 25945037 PMCID: PMC4408954 DOI: 10.2147/dddt.s78276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/website.
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Affiliation(s)
- Kasi Murugan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shanmugasamy Sangeetha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Shanmugasamy Ranjitha
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Antony Vimala
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
| | - Saleh Al-Sohaibani
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gopal Rameshkumar
- Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, India
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25
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Persson LC, Porter CJH, Charman WN, Bergström CAS. Computational prediction of drug solubility in lipid based formulation excipients. Pharm Res 2013; 30:3225-37. [PMID: 23771564 PMCID: PMC3841656 DOI: 10.1007/s11095-013-1083-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/12/2013] [Indexed: 11/25/2022]
Abstract
PURPOSE To investigate if drug solubility in pharmaceutical excipients used in lipid based formulations (LBFs) can be predicted from physicochemical properties. METHODS Solubility was measured for 30 structurally diverse drug molecules in soybean oil (SBO, long-chain triglyceride; TGLC), Captex355 (medium-chain triglyceride; TGMC), polysorbate 80 (PS80; surfactant) and PEG400 co-solvent and used as responses during PLS model development. Melting point and calculated molecular descriptors were used as variables and the PLS models were validated with test sets and permutation tests. RESULTS Solvation capacity of SBO and Captex355 was equal on a mol per mol scale (R (2) = 0.98). A strong correlation was also found between PS80 and PEG400 (R (2) = 0.85), identifying the significant contribution of the ethoxylation for the solvation capacity of PS80. In silico models based on calculated descriptors were successfully developed for drug solubility in SBO (R (2) = 0.81, Q (2) = 0.76) and Captex355 (R (2) = 0.84, Q (2) = 0.80). However, solubility in PS80 and PEG400 were not possible to quantitatively predict from molecular structure. CONCLUSION Solubility measured in one excipient can be used to predict solubility in another, herein exemplified with TGMC versus TGLC, and PS80 versus PEG400. We also show, for the first time, that solubility in TGMC and TGLC can be predicted from rapidly calculated molecular descriptors.
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Affiliation(s)
- Linda C. Persson
- Department of Pharmacy, Drug Optimization and Pharmaceutical Profiling Platform Uppsala University, Uppsala Biomedical Center, P.O. Box 580, 751 23 Uppsala, Sweden
| | - Christopher J. H. Porter
- Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052 Australia
| | - William N. Charman
- Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052 Australia
| | - Christel A. S. Bergström
- Department of Pharmacy, Drug Optimization and Pharmaceutical Profiling Platform Uppsala University, Uppsala Biomedical Center, P.O. Box 580, 751 23 Uppsala, Sweden
- Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052 Australia
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Maton C, Brooks NR, Van Meervelt L, Binnemans K, Schaltin S, Fransaer J, Stevens CV. Synthesis and properties of alkoxy- and alkenyl-substituted peralkylated imidazolium ionic liquids. Chemphyschem 2013; 14:3503-16. [PMID: 24115685 DOI: 10.1002/cphc.201300611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/09/2022]
Abstract
Novel peralkylated imidazolium ionic liquids bearing alkoxy and/or alkenyl side chains have been synthesized and studied. Different synthetic routes towards the imidazoles and the ionic liquids comprising bromide, iodide, methanesulfonate, bis(trifluoromethylsulfonyl)imide ([NTf2](-)), and dicyanamide {[N(CN)2](-)} as the anion were evaluated, and this led to a library of analogues, for which the melting points, viscosities, and electrochemical windows were determined. Incorporation of alkenyl moieties hindered solidification, except for cations with high symmetry. The alkoxy-derivatized ionic liquids are often crystalline; however, room-temperature ionic liquids (RTILs) were obtained with the weakly coordinating anions [NTf2](-) and [N(CN)2](-). For the viscosities of the peralkylated RTILs, an opposite trend was found, that is, the alkoxy derivatives are less viscous than their alkenyl-substituted analogues. Of the crystalline compounds, X-ray diffraction data were recorded and related to their molecular properties. Upon alkoxy substitution, the electrochemical cathodic limit potential was found to be more positive, whereas the complete electrochemical window of the alkenyl-substituted imidazolium salts was shifted to somewhat more positive potentials.
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Affiliation(s)
- Cedric Maton
- Department of Sustainable Chemistry and Technology, SynBioC Research Group, Ghent University, Coupure Links 653, 9000 Ghent (Belgium), Fax: (+32) (9) 264 59 57
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Petit J, Meurice N, Kaiser C, Maggiora G. Softening the Rule of Five--where to draw the line? Bioorg Med Chem 2012; 20:5343-51. [PMID: 22222160 PMCID: PMC4209914 DOI: 10.1016/j.bmc.2011.11.064] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/17/2011] [Accepted: 11/23/2011] [Indexed: 11/27/2022]
Abstract
In order to improve the discovery and development of new drugs, a broad effort is being made to assess the 'drug-like' properties of molecules in early stages of the discovery-research process. Although there are numerous approaches to this problem, perhaps the simplest and most widespread one is that developed by Chris Lipinski and his co-workers at Pfizer, which is generally referred either as the Lipinski Rules or the Rule of Five (ROF). The ROF is based on four properties of molecules, namely, molecular weight (MW), log P, number of hydrogen bond donors (HBD), and the number of hydrogen bond acceptors (HBA). A 'flag' is set if the value of a given property exceeds the chosen threshold value for that property-MW 500 Da, log P 5, the number of HBDs 5, and the number of HBAs 10. Each flag corresponds to an ROF violation. The total number of violations is the ROF-Score, which lies between '0' and '4'. Molecules with ROF-Scores greater than one are considered to be marginal for further development. The difficulty with this approach is that two molecules with nearly identical property values can, nonetheless, possess ROF-Scores that can differ by two or more. Thus, one molecule could be considered for further studies while the other, nearly identical molecule (in terms of its four ROF properties), would most likely not be. This problem arises because of the sharp thresholds imposed by the present formulation of the ROF, which is based upon classical sets. In the current work an alternative approach based on the use of utility functions, within the framework of the analytic hierarchy process (AHP), are employed to 'soften' the sharp boundaries inherent in classical sets. This provides a more realistic assessment of compounds in terms of their potential suitability in drug-discovery research programs.
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Affiliation(s)
- Joachim Petit
- Translational Genomics Research Institute, 445 N 5th Street, Suite 600, Phoenix, AZ 85004, United States
| | - Nathalie Meurice
- Translational Genomics Research Institute, 445 N 5th Street, Suite 600, Phoenix, AZ 85004, United States
| | - Christine Kaiser
- Translational Genomics Research Institute, 445 N 5th Street, Suite 600, Phoenix, AZ 85004, United States
- Department of Pharmacology and Toxicology, University of Arizona College of Pharmacy, Tucson, AZ 85721, United States
| | - Gerald Maggiora
- Translational Genomics Research Institute, 445 N 5th Street, Suite 600, Phoenix, AZ 85004, United States
- Department of Pharmacology and Toxicology, University of Arizona College of Pharmacy, Tucson, AZ 85721, United States
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Zhang Y. Ionocovalency and applications 1. Ionocovalency model and orbital hybrid scales. Int J Mol Sci 2010; 11:4381-406. [PMID: 21151444 PMCID: PMC3000088 DOI: 10.3390/ijms11114381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/19/2010] [Accepted: 10/21/2010] [Indexed: 11/28/2022] Open
Abstract
Ionocovalency (IC), a quantitative dual nature of the atom, is defined and correlated with quantum-mechanical potential to describe quantitatively the dual properties of the bond. Orbiotal hybrid IC model scale, IC, and IC electronegativity scale, XIC, are proposed, wherein the ionicity and the covalent radius are determined by spectroscopy. Being composed of the ionic function I and the covalent function C, the model describes quantitatively the dual properties of bond strengths, charge density and ionic potential. Based on the atomic electron configuration and the various quantum-mechanical built-up dual parameters, the model formed a Dual Method of the multiple-functional prediction, which has much more versatile and exceptional applications than traditional electronegativity scales and molecular properties. Hydrogen has unconventional values of IC and XIC, lower than that of boron. The IC model can agree fairly well with the data of bond properties and satisfactorily explain chemical observations of elements throughout the Periodic Table.
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Affiliation(s)
- Yonghe Zhang
- American Huilin Institute, 13810 Franklin Ave, Queens, NY 11355, USA; E-Mail:
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