ORIGINAL_ARTICLE
Lab-in-Silico Insights
Recent developments in computer hardware and software, in addition to modern algorithms, have led to new era of scientific laboratories; called Lab-in-Silico. The simulation protocols have been evaluated for several types of chemical matters and reactions to simulate the real systems in the computers. There is no doubt in the importance of efforts in the experimental chemical laboratories to yield novel materials, but the simulation processes could push ideas into products at the higher accuracy. Knowledge about what happens during the reactions and the corresponding mechanisms is always an important task for those scientists working on the mystery of chemistry.
https://www.ajchem-b.com/article_104824_b9898bdc605827be802af23c0482b463.pdf
2020-03-01
1
2
10.33945/SAMI/AJCB.2020.1.1
computational
Simulation
Lab-in-Silico
Mahmoud
Mirzaei
mirzaeimch@gmail.com
1
Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
LEAD_AUTHOR
Haack S. Trial and error: the Supreme Court’s philosophy of science. Am. J. Pub. Health 2005;95:66–73.
1
Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to ‘Crops in silico. J. Exp. Bot. 2019;70:2403–2418.
2
Poroikov VV. Computer–aided drug design: from discovery of novel pharmaceutical agents to systems pharmacology. Biomed. Khimi. 2020;66:30–41.
3
Mirzaei M, Hadipour NL, Ahmadi K. Investigation of C–H…O=C and N–H…O=C hydrogen–bonding interactions in crystalline thymine by DFT calculations of O–17, N–14 and H–2 NQR parameters. Biophys. Chem. 2007;125:411–415.
4
Soleimani M, Mirzaei M, Mofid MR, Khodarahmi G, Rahimpour SF. Lactoperoxidase inhibition by tautomeric propylthiouracils. Asian J. Green Chem. 2020;4:1–10.
5
Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α–glycine. Biophys. Chem. 2007;125:179–183.
6
Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (O=C–NH) in crystalline acetamide. J. Mol. Graph. Model. 2008;26:977–981.
7
Nouri A, Mirzaei M. DFT calculations of B–11 and N–15 NMR parameters in BN nanocone. J. Mol. Struct. THEOCHEM. 2009;913:207–209.
8
Mirzaei M. The NMR parameters of the SiC–doped BN nanotubes: a DFT study. Physica E 2010;42:1954–1957.
9
Mirzaei M, Mirzaei M. The C–doped AlP nanotubes: A computational study. Solid State Sci. 2011;13:244–250.
10
Nazemi H, Mirzaei M, Jafari E. Antidepressant activity of curcumin by monoamine oxidase–A inhibition. J. Adv. Chem. B 2019;1:3-9.
11
ORIGINAL_ARTICLE
Aflavinines: History, Biology and Total Synthesis
This review aims to provide overall aspects of the history, biology, chemistry and the total synthesis of Aflavinines. The origin of this molecule traced back from the isolation and structural elucidation by Clardy and co–workers in 1980 [Tetrahed. Lett. 1980;21:243–246]. Most of the previously published total syntheses were covered in a brief summary and the key points of each work are highlighted. Moreover, various antiinsectant and antiviral Aflavinines congener are presented. This review is almost the first in Aflavinine topics covering all aspects in brief, to the best of our knowledge.
https://www.ajchem-b.com/article_104845_a0ff981f3119876031970b47740b97f9.pdf
2020-03-13
3
9
10.33945/SAMI/AJCB.2020.1.2
Aflavinine
Antiinsectant
Epoxyeujindole–A
Aflavazole
HydroxyAflavinine
Tubingensin–A
Dirgha
Joshi
djmeropaila121@gmail.com
1
College of Pharmacy,Yonsei University, Yeonsu-gu,Incheon, Republic of Korea
LEAD_AUTHOR
Nisha
Adhikari
nepalaama.na@gmail.com
2
College of Pharmacy, Gachon University, Yeonsu–gu,Incheon, Republic of Korea
AUTHOR
Gallagher RT, McCabe T, Hirotsu K, Clardy J, Nicholson J, Wilson BJ. Aflavinine, a novel indole–mevalonate metabolite from tremorgen–producing aspergillusflavus species. Tetrahed. Lett. 1980;21:243–246.
1
Wicklow DT. Role of fungal sclerotia in the epidemiology of aspergillus flavus in maize. JSM Mycotox. 1988;1988:155–158.
2
Gloer JB, TePaske MR, Sima JS, Wicklow DT, Dowd PF. Antiinsectan aflavinine derivatives from the sclerotia of aspergillus flavus. J. Org. Chem. 1988;53:5457–5460.
3
TePaske MR, Gloer JB, Wicklow DT, Dowd PF. Aflavazole: a new antiinsectan carbazole metabolite from the sclerotia of aspergillus flavus. J. Org. Chem. 1990;55:5299–5301.
4
Gloer JB. Antiinsectan natural products from fungal sclerotia. Acc. Chem. Res. 1995;28:343–350.
5
TePaske MR, Gloer JB, Wicklow DT, Dowd PF. Aflavarin and β–Aflatrem: new anti–insectan metabolites from the sclerotia of aspergillus flavus. J. Nat. Prod. 1992;55:1080–1086.
6
Wang H–J, Gloer JB, Wicklow DT, Dowd PF. Aflavinine s and other antiinsectan metabolites from the ascostromata of eupenicillium crustaceum and related species. Appl. Environ. Microbiol. 1995;61:4429–4435.
7
Gloer JB, Rinderknecht BL, Wicklow DT, Dowd PF. Nominine: a new insecticidal indole diterpene from the sclerotia of aspergillus nomius. J. Org. Chem. 1989;54:2530–2532.
8
TePaske MR, Gloer JB, Wicklow DT, Dowd PF. Tubingensin A: an antiviral carbazole alkaloid from the sclerotia of aspergillus tubingensis. J. Org. Chem. 1989;54:4743–4746.
9
TePaske MR, Gloer JB, Wicklow DT, Dowd PF. Three new aflavinines from the sclerotia of Aspergillus tubingensis. Tetrahed. 1989;45:4961–4968.
10
Nakadate S, Nozawa K, Horie H. New type indole diterpene, eujindoles, from eupenicillium javanicum. Heterocycl. 2011;83:351–356.
11
Nakadate S, Nozawa K, Yaguchi T. Two new eujindoles from Eupenicillium javanicum. Nat. Prod. Update. 2011;83:1867–1871.
12
Nozawa K, Sekita S, Harada M, Udagawa S, Kawai K. Isolation and structures of two new indoloditerpenes related to aflavinine from a microsclerotium–producing strain of aspergillus flavus. Chem. Pharm. Bull. 1989;37:626–630.
13
TePaske MR, Gloer JB, Wicklow DT, Dowd PF. The structure of tubingensin B: A cytotoxic carbazole alkaloid from the sclerotia of aspergillustubingensis. Tetrahed. Lett. 1989;30:5965–5968.
14
Wicklow D, Dowd P, Gloer J. Antiinsectan effects of aspergillus metabolites. The genus Aspergillus. Springer; 1994. p. 93–114.
15
Laakso JA, TePaske MR, Dowd PF, Gloer JB, Wicklow DT, Staub GM. Indole antiinsectan metabolites. Google Patents; 1993.
16
Brase S, Encinas A, Keck J, Nising CF. Chemistry and biology of mycotoxins and related fungal metabolites. Chem. Rev. 2009;109:3903–3990.
17
Rank C, Klejnstrup ML, Petersen LM, Kildgaard S, Frisvad JC, Held Gotfredsen C, et al. Comparative chemistry of aspergillus oryzae (RIB40) and A. flavus (NRRL 3357). Metabol. 2012;2:39–56.
18
Abu El–Souod S, Awadalla OA, Assawah SMW, Mahmoud YA–G, El–Debaiky SAE–K. Studies on the sclerotia of some species in the genus aspergillus. Egypt. J. Botan. 2017;57:395–404.
19
Cary JW, Gilbert MK, Lebar MD, Majumdar R, Calvo AM. Aspergillus flavus secondary metabolites: More than just aflatoxins. Food Safety 2018;6:7–32.
20
Uka V, Moore GG, Arroyo–Manzanares N, Nebija D, De
21
Saeger SMDG, Diana Di Mavungu J. Secondary metabolite dereplication and phylogenetic analysis identify various emerging mycotoxins and reveal the high intra–species diversity in aspergillus flavus. Front. Microbiol. 2019;10:667.
22
Danishefsky S, Chackalamannil S, Harrison P, Silvestri M. Synthetic studies toward Aflavinine : a synthesis of 3–demethylAflavinine via a [2+ 2+ 2] annulation. J. Am. Chem. Soc. 1985;107:2474–2484.
23
Danishefsky S, Harrison P, Silvestri M, Segmuller B. A notable stereochemical variation in the 2+ 2+ 2 annulation reaction. J. Org. Chem. 1984;49:1319–1321.
24
Danishefsky S, Chackalamannil S, Silvestri M, Springer J. Stereospecific 2+ 2+ 2 annulation. J. Org. Chem. 1983;48:3615–3616.
25
Lu Z, Li H, Bian M, Li A. Total synthesis of epoxyeujindole A. J. Am. Chem. Soc. 2015;137:13764–13767.
26
Li H, Chen Q, Lu Z, Li A. Total syntheses of aflavazole and 14–hydroxyAflavinine. J. Am. Chem. Soc. 2016;138(48):15555–8.
27
Lodge EP. Experimental and theoretical studies in 1,2–asymmetric induction: feasibility of a proposed synthesis of aflavinine. University of California, Berkeley; 1988.
28
Herrmann P. Synthetic studies directed toward nitropolyzonamine, aflavinine, and a rigid HMG CoA reductase inhibitor. 1995; url: https://elibrary.ru/item.asp?id=5691740
29
Bradshaw B, Etxebarria–Jardí G, Bonjoch J. Total synthesis of (−)–anominine. J. Am. Chem. Soc. 2010;132:5966–5967.
30
Bian M, Wang Z, Xiong X, Sun Y, Matera C, Nicolaou K, et al. Total syntheses of anominine and tubingensin A. J. Am. Chem. Soc. 2012;134:8078–8081.
31
Goldberg DR, Hansen JA, Giguere RJ. The tandem intramolecular Diels–Alder reaction. Tetrahed. Lett. 1993;34:8003–8006.
32
Jo M, Lee D, Kwak YS. Rapid access to the structural core of aflavinines via stereoselective tandem intramolecular Diels–Alder cycloaddition controlled by the allylic 1,3–strain. Org. Lett. 2019;21:6529–6533.
33
ORIGINAL_ARTICLE
Determination of Selenium in Biological Samples by Flame Atomic Absorption Spectrometry after Preconcentration on Modified Polyurethane Foam
An analytical method has been proposed based on the separation and determination of selenium(IV) ion using polyurethane foam as a solid sorbent coated with ammonium pyrrolidine dithiocarbamate (APDC). Different factors including the pH of sample solution, time of extraction, volume of sample, and amount of the loaded and unloaded polyurethane foam were examined and a preconcentration factor of 5 was obtained. The interference effects of some additional salts in the solution such as NaCl, FeCl3, BaCl2, CH3COONa and Na2SO4 have been investigated. The improved limit of detection (LOD) for the method is 0.064 mg/L. The improved LOD is much lower than the LOD of FAAS and approaching the LOD of GFAAS. The new developed procedure SPE-FAAS has been Found to be successful in separating the complex matrices (human hair, bovine liver, pork liver, bovine muscle) and pre-concentrating selenium ion from real blood sample. The developed method for solid-liquid extraction is convenient, simple, sensitive and of low costs.
https://www.ajchem-b.com/article_104892_8bba2d2f1bd2c8d3f9557c7d9195deb0.pdf
2020-03-01
10
17
10.33945/SAMI/AJCB.2020.1.3
Preconcentration
Solid phase extraction
Polyurethane Foam
Mariam
Ambarak
mariam.ambarak@uob.edu.ly
1
Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
LEAD_AUTHOR
Abdelsalam
Asweisi
abdelsalam.asweisi@uob.edu.ly
2
Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
AUTHOR
House H, J.E. Inorganic chemistry. Academic Press; 2008. p: 524.
1
Lide DR. Magnetic susceptibility of the elements and inorganic compounds. Handbook of Chemistry and Physics. CRC Press; 2005. pp.:365-370.
2
Camel V. Solid phase extraction of trace elements. Spectrochim. Acta. B 2003;58:1177-1233.
3
Raukema A. Dynamics of chemisorptions. PhD Thesis. University of Amsterdam; 1995.
4
Slejko FL. Adsorption technology: a step-by-step approach to process evaluation and application. M. Dekker; 1985.
5
Wedler G. Chemisorption: an experimental approach. Butterworth-Heinemann; 1976.7. Anderson MA, Rubin AJ. Adsorption of inorganics at solid-liquid interfaces. Ann Arbor Science; 1981. p 161.
6
8 Webb PA. Introduction to chemical adsorption analytical techniques and their applications to catalysis. Micromeritics Instrument Corp. Technical Publications. 2003.
7
9 Bueno M, Potin-Gautier M. Solid-phase extraction for the simultaneous preconcentration of organic (selenocystine) and inorganic [Se (IV), Se (VI)] selenium in natural waters. J. Chromatograp. A. 2002;963:185-193.
8
Gomez-Ariza JL, Giraldez I, Morales E, Pozas JA. Use of solid phase extraction for speciation of selenium compounds in aqueous environmental samples. Analyst. 1999;124:75-78.
9
Simpson NJ. Solid-phase extraction: principles, techniques, and applications. CRC press; 2000.p: 2.
10
Alfassi Z, Wai CM. Preconcentration techniques for trace elements. CRC press; 1991. p: 363.
11
Lemos VA, Santos MS, Santos ES, Santos MJ, Dos Santos WN, Souza AS, De Jesus DS, Das Virgens CF, Carvalho MS, Oleszczuk N, Vale MG. Application of polyurethane foam as a sorbent for trace metal pre-concentration—A review. Spectrochim. Acta B 2007;62:4-12.
12
Szycher M. Basic concepts in polyurethane chemistry and technology. Szycher’s Handbook of Polyurethanes, CRC: Boca Raton, FL, USA; 1999.
13
Randall D, Lee S. The polyurethanes book. Wiley; 2002.
14
Braun T, Navratil JD, Farag AB. Polyurethane foam sorbents in separation science. 1985.
15
Moody GJ, Thomas JD. Chromatographic separation and extraction with foamed plastics and rubbers. M. Dekker; 1982.
16
Campbell AD. Determination of selenium in biological materials water. Pure Appl. Chem. 1984;56:645-651.
17
Welz B, Wolynetz MS, Verlinden M. Interlaboratory trial on the determination of selenium in lyophilized human serum, blood and urine using hydride generation atomic absorption spectrometry. Pure Appl. Chem. 1987;59:927-936.
18
Gomez-Ariza JL, Giraldez I, Morales E, Pozas JA. Use of solid phase extraction for speciation of selenium compounds in aqueous environmental samples. Analyst. 1999;124:75-78.
19
Hansson L, Pettersson J, Eriksson L, Olin A. Atomic absorption spectrometric determination of selenium in human blood components. Clin. Chem. 1989;35:537-540.
20
ORIGINAL_ARTICLE
Selective Adsorption Function of B16C16 Nano-Cage for H2O, CO, CH4 and NO2
The interactions between boron carbide (BC) nanocluster of B16C16 and H2O, NO2, CO, and CH4 small molecules were investigated by using density functional theory (DFT) computations to exploit the structural and electronic properties of the adsorbate/cluster complexes. The calculated adsorption energies of the most stable states are -16.6, -0.17, -1.28, -0.18 eV for NO2, CO, H2O, and CH4 molecules, respectively. Meanwhile, the interactions between CO and CH4 molecules and the cluster induce dramatic changes to the cluster electronic properties so that the molecular orbital (HOMO/LUMO) gap of cluster decreased its original value. It was shown that the phenomenon leads to an increment in the electrical conductivity of the cluster at a definite temperature. Furthermore, it is revealed that the adsorptions of NO2 and H2O molecules have no significant effects on the electronic properties of the cluster. Thus, this work suggests that the investigated B16C16 nano-cage could work as a selective gas sensor device towards CO, CH4, NO2 and H2O molecules.
https://www.ajchem-b.com/article_104947_24149c5bd2eb7adf299489052c360db5.pdf
2020-03-16
18
25
10.33945/SAMI/AJCB.2020.1.4
Ab initio
Adsorption
Boron carbide
Sensors
Charge transfer
Shaghayegh
Ariaei
shaghayeghariaei9595@gmail.com
1
Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
LEAD_AUTHOR
Hossein
Basiri
h.basiri90@yahoo.com
2
Young Researchers and Elite Club, Touyserkan Branch, Islamic Azad University, Touyserkan, Iran
AUTHOR
Mojtaba
Ramezani
ramezani.m1364@gmail.com
3
Department of Chemical Engineering, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
AUTHOR
Ghamsari PA, Nouraliei M, Gorgani SS. DFT simulation towards evaluation the molecular structure and properties of the heterogeneous C16Mg8O8 nano–cage as selective nano–sensor for H2 and N2 gases. J. Mol. Graph. Model. 2016;70:163-169.
1
Fallahpour F, Gorgani SS, Nouraliei M. Boron carbide nanoclusters as H 2 and N 2 gases nanosensors: theoretical investigation. Ind. J. Phys. 2016;90:931-936.
2
Mirzaei M, Yousefi M, Meskinfam M. Density functional studies of oxygen-terminations versus hydrogen-terminations in carbon and silicon nanotubes. Solid State Sci. 2012;14:874-879.
3
Golberg D, Bando Y, Stephan O, Kurashima K. Octahedral boron nitride fullerenes formed by electron beam irradiation. Appl. Phys. Lett. 1998;73:2441-2443.
4
Omidvar H, Goodarzi S, Seif A, Azadmehr AR. Influence of anodization parameters on the morphology of TiO2 nanotube arrays. Superlat. Microstruct. 2011;50:26-39.
5
Jain SK, Srivastava P. Electronic and optical properties of ultrathin single walled boron nanotubes-An ab initio study. Comput. Mater. Sci. 2011;50:3038-3042.
6
Mirzaei M, Meskinfam M. Computational NMR studies of silicon nanotubes. Comput. Theor. Chem. 2011;978:123-125.
7
Mirzaei M, Mirzaei M. The B-doped SiC nanotubes: A computational study. J. Mol. Struct. THEOCHEM 2010;953:134-138.
8
Mirzaei M. Calculation of chemical shielding in C-doped zigzag BN nanotubes. Monatsh. Chem. 2009;140:1275-1278.
9
Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Z. Naturforsch. A 2007;62:56-60.
10
Beheshtian J, Bagheri Z, Kamfiroozi M, Ahmadi A. A comparative study on the B12N12, Al12N12, B12P12 and Al12P12 fullerene-like cages. J. Mol. Model. 2012;18:2653-2658.
11
Seifert G, Hernández E. Theoretical prediction of phosphorus nanotubes. Chem. Phys. Lett. 2000;318:355-360.
12
Mirzaei M. Carbon doped boron phosphide nanotubes: a computational study. J. Mol. Model. 2011;17:89-96.
13
Mirzaei M, Meskinfam M. Computational studies of effects of tubular lengths on the NMR properties of pristine and carbon decorated boron phosphide nanotubes. Solid State Sci. 2011;13:1926-1930.
14
Feldman Y, Wasserman E, Srolovitz DJ, Tenne R. High-rate, gas-phase growth of MoS2 nested inorganic fullerenes and nanotubes. Science 1995;267:222-225.
15
Balasubramanian C, Bellucci S, Castrucci P, De Crescenzi M, Bhoraskar SV. Scanning tunneling microscopy observation of coiled aluminum nitride nanotubes. Chem. Phys. Lett. 2004;383:188-1891.
16
Bourgeois L, Bando Y, Han WQ, Sato T. Structure of boron nitride nanoscale cones: ordered stacking of 240 and 300 disclinations. Phys. Rev. B 2000;61:7686.
17
Mirzaei M, Hadipour NL, Seif A, Giahi M. Density functional study of zigzag BN nanotubes with equivalent ends. Physica E 2008;40:3060-3063.
18
Mirzaei M, Mirzaei M. The C-doped AlP nanotubes: A computational study. Solid State Sci. 2011;13:244-250.
19
Mirzaei M. A computational NMR study of boron phosphide nanotubes. Z. Naturforsch. A 2010;65:844-848.
20
Paine RT, Narula CK. Synthetic routes to boron nitride. Chem. Rev. 1990;90:73-91.
21
Deepak FL, Tenne R. Gas-phase synthesis of inorganic fullerene-like structures and inorganic nanotubes. Cent. Eur. J. Chem. 2008;6:373-389.
22
Ozkendir, O., Gunaydin, S., Mirzaei, M. Electronic structure study of the LiBC3 borocarbide graphene material. Adv. J. Chem. B 2019;1:37-41.
23
Zhuiykov S, Wlodarski W, Li Y. Nanocrystalline V2O5–TiO2 thin-films for oxygen sensing prepared by sol–gel process. Sens. Actuat. B 2001;77:484-890.
24
Chang H, Lee JD, Lee SM, Lee YH. Adsorption of NH 3 and NO2 molecules on carbon nanotubes. Appl. Phys. Lett. 2001;79:3863-3865.
25
Lu J, Nagase S, Maeda Y, Wakahara T, Nakahodo T, Akasaka T, Yu D, Gao Z, Han R, Ye H. Adsorption configuration of NH3 on single-wall carbon nanotubes. Chem. Phys. Lett. 2005;405:90-92.
26
Rostami Z, Maskanati M, Khanahmadzadeh S, Dodangi M, Nouraliei M. Interaction of nitrotyrosine with aluminum nitride nanostructures: A density functional
27
approach. Physica E 2020;116:113735.
28
Santucci S, Picozzi S, Di Gregorio F, Lozzi L, Cantalini C, Valentini L, Kenny JM, Delley B. NO 2 and CO gas adsorption on carbon nanotubes: experiment and theory. J. Chem. Phys. 2003;119:10904-10910.
29
Byl O, Liu JC, Wang Y, Yim WL, Johnson JK, Yates JT. Unusual hydrogen bonding in water-filled carbon nanotubes. J. Am. Chem. Soc. 2006;128:12090-12097.
30
Maniwa Y, Matsuda K, Kyakuno H, Ogasawara S, Hibi T, Kadowaki H, Suzuki S, Achiba Y, Kataura H. Water-filled single-wall carbon nanotubes as molecular nanovalves. Nature Mater. 2007;6:135-141.
31
Takaiwa D, Hatano I, Koga K, Tanaka H. Phase diagram of water in carbon nanotubes. Proc. Nat. Acad. Sci. 2008;105:39-43.
32
Ariaei, S. Adsorptions of diatomic gaseous molecules (H2, N2 and CO) on the surface of Li+@C16B8P8 fullerene-like nanostructure: computational studies. Adv. J. Chem. B 2019;1:29-36.
33
Ellison MD, Good AP, Kinnaman CS, Padgett NE. Interaction of water with single-walled carbon nanotubes: Reaction and adsorption. J. Phys. Chem. B 2005;109:10640-10646.
34
Zangi R. Water confined to a slab geometry: a review of recent computer simulation studies. J. Phys. 2004;16:5371-5381.
35
Gelb LD, Gubbins KE, Radhakrishnan R, Sliwinska-Bartkowiak M. Phase separation in confined systems. Rep. Prog. Phys. 1999;62:1573-1659.
36
Müller-Dethlefs K, Hobza P. Noncovalent interactions: a challenge for experiment and theory. Chem. Rev. 2000;100:143-168.
37
Ugalde JM, Alkorta I, Elguero J. Water clusters: Towards an understanding based on first principles of their static and dynamic properties. Angew. Chem. 2000;39:717-721.
38
O'boyle NM, Tenderholt AL, Langner KM. Cclib: a library for package‐independent computational chemistry algorithms. J. Comput. Chem. 2008;29:839-845.
39
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H. Gaussian09 Revision D. 01, Gaussian Inc. Wallingford CT.; 2009.
40
Bodaghi A, Mirzaei M, Seif A, Giahi M. A computational NMR study on zigzag aluminum nitride nanotubes. Physica E 2008;41:209-212.
41
Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. Int. J. Nano Dimen. 2013;3:175-179.
42
Mirzaei M. The NMR parameters of the SiC-doped BN nanotubes: a DFT study. Physica E 2010;42:1954-1957.
43
Nouri A, Mirzaei M. DFT calculations of B-11 and N-15 NMR parameters in BN nanocone. J. Mol. Struct. THEOCHEM 2009;913:207-209.
44
Mirzaei M, Mirzaei M. An electronic structure study of O-terminated zigzag BN nanotubes: Density functional calculations of the quadrupole coupling constants. Solid State Commun. 2010;150:1238-1240.
45
Ozkendir, O., Mirzaei, M. Alkali Metal Chelation by 3–Hydroxy–4–Pyridinone. Adv. J. Chem. B 2019;1:10-16.
46
Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlat. Microstruct. 2012;52:612-617.
47
Bagheri Z, Mirzaei M, Hadipour NL, Abolhassani MR. Density functional theory study of boron nitride nanotubes: calculations of the N-14 and B-11 nuclear quadrupole resonance parameters. J. Comput. Theor. Nanosci. 2008;5:614-618.
48
Mirzaei M, Yousefi M, Meskinfam M. Studying (n, 0) and (m, m) GaP nanotubes (n= 3–10 and m= 2–6) through DFT calculations of Ga-69 quadrupole coupling constants. Solid State Sci. 2012;14:801-804.
49
Reed AE, Curtiss LA, Weinhold F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev. 1988;88:899-926.
50
Li SS. Semiconductor physical electronics. Springer Science & Business Media; 2012.
51
ORIGINAL_ARTICLE
Withaferin A (WIT) Interaction with beta–Tubulin to Promote Tubulin Degradation: In Silico Study
The main purpose of present study is evaluation of structural and medicinal properties for Withaferin A (WIT) using density functional theory (DFT) method. All studies are done via computational chemistry methods using Gaussian 03 and Molegro Virtual Docker (MVD) software packages and SwissADME web-based tool. Molecular structure of WIT was optimized at the B3LYP/6-311++G(d,p) theoretical level of DFT. The reactivity and stability properties of the optimized molecule were explored via global reactivity indices. Calculating the reactivity indices using energies of frontier molecular orbitals (FMOs) showed that WIT is stable against the oxidizing agents in the cell and has low reactivity against the biomolecules. On the other hand, the docking analysis data indicated the steric interactions play important role in WIT binding to beta-Tubulin via the residues Tyr224, Cys12, Gln11, Asn101, Gly143, Gln15, Gly144, Asn206, Gly142, and Asp179.
https://www.ajchem-b.com/article_104915_278f8cb9849c1661b1b336b47d733fba.pdf
2020-03-01
26
32
10.33945/SAMI/AJCB.2020.1.5
In Silico
Molecular docking
Molecular Simulation
Tubulin
Withaferin A
Mehdi
Nabati
mnabati@ymail.com
1
Research and Development Department, Shari Pharmaceutical Company, Tehran, Iran
LEAD_AUTHOR
Elham
Pournamdari
epournamdar@yahoo.com
2
Department of Science, Islamshahr Branch, Islamic Azad University, Islamshahr, Iran
AUTHOR
Yahya
Dashti-Rahmatabadi
yahyadashti1@gmail.com
3
Science and Research Branch, Islamic Azad University, Tehran, Iran
AUTHOR
Saman
Sarshar
sarshar.saman@yahoo.com
4
LorestanPhysics Department, Faculty of Science, Lorestan University, Khorramabad, Iran
AUTHOR
Balaguer FD, Mühlethaler T, Estévez-Gallego J, Calvo E, Giménez-Abián JF, Risinger AL, Sorensen EJ, Vanderwal CD, Altmann KH, Mooberry SL, Steinmetz MO. Crystal structure of the cyclostreptin-tubulin adduct: implications for tubulin activation by taxane-site ligands. Int. J. Mol. Sci. 2019;20:1392.
1
Bargagna-Mohan P, Hamza A, Kim YE, Ho YK, Mor-Vaknin N, Wendschlag N, Liu J, Evans RM, Markovitz DM, Zhan CG, Kim KB. The tumor inhibitor and antiangiogenic agent withaferin A targets the intermediate filament protein vimentin. Chem. Biol. 2007;14:623-634.
2
Buey RM, Calvo E, Barasoain I, Pineda O, Edler MC, Matesanz R, Cerezo G, Vanderwal CD, Day BW, Sorensen EJ, López JA. Cyclostreptin binds covalently to microtubule pores and lumenal taxoid binding sites. Nature Chem. Biol. 2007;3:117-125.
3
Drahl C, Cravatt BF, Sorensen EJ. Protein‐reactive natural products. Angew. Chem. 2005;44:5788-5809.
4
Dumontet C, Jordan MA. Microtubule-binding agents: a dynamic field of cancer therapeutics. Nature Rev. Drug Discover. 2010;9:790-803.
5
Hamel E. An overview of compounds that interact with tubulin and their effects on microtubule assembly. In The Role of Microtubules in Cell Biology, Neurobiology, and Oncology. Humana Press; 2008. pp. 1-19.
6
Falsey RR, Marron MT, Gunaherath GK, Shirahatti N, Mahadevan D, Gunatilaka AL, Whitesell L. Actin microfilament aggregation induced by withaferin A is mediated annexin II. Nature Chem. Biol. 2006;2:33-38.
7
Fortin S, Lacroix J, Côté MF, Moreau E, Petitclerc É, René C. Quick and simple detection technique to assess the binding of antimicrotubule agents to the colchicine-binding site. Biol. Proc. Online 2010;12:113-117.
8
Gambhir L, Checker R, Sharma D, Thoh M, Patil A, Degani M, Gota V, Sandur SK. Thiol dependent NF-κB suppression and inhibition of T-cell mediated adaptive immune responses by a naturally occurring steroidal lactone Withaferin A. Toxicol. Appl. Pharmacol. 2015;289:297-312.
9
Gigant B, Wang C, Ravelli RB, Roussi F, Steinmetz MO, Curmi PA, Sobel A, Knossow M. Structural basis for the regulation of tubulin by vinblastine. Nature 2005;435:519-522.
10
Gu M, Yu Y, Gunaherath GK, Gunatilaka AL, Li D, Sun D. Structure-activity relationship (SAR) of withanolides to inhibit Hsp90 for its activity in pancreatic cancer cells. Invest. New Drugs 2014;32:68-74.
11
Heyninck K, Lahtela-Kakkonen M, Van der Veken P, Haegeman G, Berghe WV. Withaferin A inhibits NF-kappaB activation by targeting cysteine 179 in IKKβ. Biochemical pharmacology. 2014;91:501-509.
12
Antony ML, Lee J, Hahm ER, Kim SH, Marcus AI, Kumari V, Ji X, Yang Z, Vowell CL, Wipf P, Uechi GT. Growth arrest by the antitumor steroidal lactone withaferin A in human breast cancer cells is associated with down-regulation and covalent binding at cysteine 303 of β-tubulin. J. Biol. Chem. 2014;289:1852-1865.
13
Yang J, Yan W, Li Y, Niu L, Ye H, Chen L. The natural compound Withaferin A covalently binds to Cys239 of β-tubulin to promote tubulin degradation. Mol. Pharmacol. 2019;96:711-719.
14
Nabati M, Bodaghi-Namileh V. Molecular modeling of 3-(1,3-dioxoisoindolin-2-yl) benzyl nitrate and its molecular docking study with phosphodiesterase-5 (PDE5). Adv. J. Chem. A 2020;3:58-69.
15
Nabati M, Lohrasbi E, Sabahnoo H, Bodaghi-Namileh V, Mazidi M, Mohammadnejad-Mehrabani H, Tavakkoli A, Gervand A. In silico study of metoclopramide as a small molecule of dopamine D2 receptor. Chem. Method. 2020;4:19-33.
16
Nabati M. Exploring molecular docking and electronic studies of [11C] LY2795050 as a novel antagonist tracer for positron emission tomography (PET) scan of the kappa (κ) and mu (µ) opioid receptors (KOR and MOR). J. Med. Chem. Sci. 2020;3:22-34.
17
Nabati M, Bodaghi-Namileh V. In silico study of the active components (17α-ethinyl estradiol and segesterone acetate) of annovera as a novel vaginal contraceptive system by docking of their binding to estrogen and progesterone receptors. Iran. Chem. Commun. 2020;8:73-85.
18
Nazemi H, Mirzaei M, Jafari E. Antidepressant Activity of Curcumin by Monoamine Oxidase–A Inhibition. Adv. J. Chem. B 2019;1:3-9.
19
Ozkendir O, Mirzaei M. Alkali metal chelation by 3–hydroxy–4–pyridinone. Adv. J. Chem. B 2019;1:10-16.
20
Esfahani, A., Mirzaei, M. Flavonoid derivatives for monoamine oxidase–A inhibition. Adv. J. Chem. B 2019;1:17-22.
21
Alidoosti Z, Mirzaei M. Comparative examination of moclobemide, tranylcypromine, phenelzine and isocarboxazid for monoamine oxidase–A inhibition. Adv. J. Chem. B 2019;1:23-28.
22
Ariaei S. Adsorptions of diatomic gaseous molecules (H2, N2 and CO) on the surface of Li+@C16B8P8 fullerene-like nanostructure: computational studies. Adv. J. Chem. B 2019;1:29-36.
23
Soleimani M, Mirzaei M, Mofid MR, Khodarahmi G, Rahimpour SF. Lactoperoxidase inhibition by tautomeric propylthiouracils. Asian J. Green Chem. 2020;4:1-10.
24
Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (O=C–NH) in crystalline acetamide. J. Mol. Graph. Model. 2008;26:977-981.
25
Davarpanah M, Abbasi H, Nabati M, Sabahnoo H, Bodaghi-Namileh V, Mazidi M, Movahhed-Tazehkand H, Mohammadnejad-Mehrabani H. Kit formulation of active pharmaceutical ingredient d, l-HMPAO as a brain perfusion diagnostic system. Prog. Chem. Biochem. Res. 2019;2:185-191.
26
Nabati M, Bodaghi-Namileh V, Sarshar S. Molecular modeling of the antagonist compound esketamine and its molecular docking study with non-competitive N-methyl-D-aspartate (NMDA) receptors NR1, NR2A, NR2B and NR2D. Prog. Chem. Biochem. Res. 2019;2:108-119.
27
Nabati M, Bodaghi-Namileh V. Non-competitive N-methyl-D-aspartate (NMDA) receptor (NR2B) structure in complex with antidepressant arketamine. Iran. J. Org. Chem. 2019;11:2591-2598.
28
Nabati M, Bodaghi-Namileh V. Design of novel drugs (P3TZ, H2P3TZ, M2P3TZ, H4P3TZ and M4P3TZ) based on zonisamide for autism treatment by binding to potassium voltage-gated channel subfamily D member 2 (Kv4. 2). Int. J. New Chem. 2019;6:254-276.
29
Nabati M, Sabahnoo H. Spectroscopic (FT-IR and UV-Vis), electronic and docking studies on the red clover isoflavone irilone as a progesterone receptor (PR) effect supporter in endometrial and ovarian cancer cell lines. J. Med. Chem. Sci. 2019;2:118-125.
30
Nabati M. Modeling and interactions analysis of the novel antagonist agent flibanserin with 5-hydroxytryptamine 2A (5-HT2A) serotonin receptor as a HSDD treatment in premenopausal women. Iran. Chem. Commun. 2019;7:324-334.
31
Nabati M, Sabahnoo H, Lohrasbi E, Mazidi M. Structural Properties Study and Spectroscopic (FT-IR and UV-Vis) Profiling of the Novel Antagonist LY2157299 as a Transforming Growth Factor-β (TGF-β) Receptor I Kinase Inhibitor by Quantum-mechanical (QM) and molecular docking techniques. Chem. Method. 2019;3:377-391.
32
Nabati M. Insight into the structural and spectral (IR and UV-Vis) properties of the salts of alkali (Li, Na and K) and alkaline earth (Be, Mg and Ca) metals with pertechnetate oxoanion (99mTcO4-) as the convenient water-soluble sources of the radioactive element technetium. Chem. Method. 2019;3:258-270.
33
Nabati M, Bodaghi-Namileh V. Physicochemical properties analysis and dopamine D2 receptor (D2R) docking of zotepine as an atypical antipsychotic antagonist. J. Phys. Theor. Chem. 2018;15:149-157.
34
Nabati M, Bodaghi-Namileh V, Mazidi M. Evaluation of [18F] FPTT molecular structure and its binding to progesterone receptor (PR) for PET scan of breast cancer. J. Phys. Theor. Chem. 2018;15:159-171.
35
ORIGINAL_ARTICLE
Computational Studies of Furanone and its 5Methyl/5Phenyl Derivatives
The properties for 2(5H)-furanone and 2(5Methyl)- and 2(5Phenyl)-furanone derivatives have been explored by computational chemistry approach. The subatomic unit calculations have been done to optimize the models and to evaluate their corresponding properties, in which several achievements have been seen for the investigated models. The energy levels of molecular orbitals indicated the importance of structural modifications for obtaining better electronic properties. To this aim, total energy, energy levels of the highest occupied and the lowest unoccupied molecular orbitals, energy gap, ionization positional, electron affinity, hardness, softness and dipole moment have been evaluated in addition to the original molecular weight and LogP parameters. The results revealed better reactivity and antioxidativity for 2(5Phenyl)-furanone in comparison with two other models proposing it for various possible applications in biological systems. Moreover, hardness and softness properties were also seen more favorable for this model. As a conclusion, the importance of furanone could be very much increased regarding structural modification, which could be very well investigated by the computational chemistry approach.
https://www.ajchem-b.com/article_104932_3a92909defe4f15768b5657d13cb3479.pdf
2020-03-01
33
38
10.33945/SAMI/AJCB.2020.1.6
Furanone
Structural modification
Antioxidativity
Computational chemistry
Nikoo
Ghanbari
nikooghanbari@gmal.com
1
Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
AUTHOR
Homa
Azizian
azizian.h@iums.ac.ir
2
Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
AUTHOR
Mahmoud
Mirzaei
mirzaeimch@gmail.com
3
Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
LEAD_AUTHOR
Luo SH, Yang K, Lin JY, Gao JJ, Wu XY, Wang ZY. Synthesis of amino acid derivatives of 5-alkoxy-3, 4-dihalo-2 (5H)-furanones and their preliminary bioactivity investigation as linkers. Org. Biomol. Chem. 2019;17:5138-5147.
1
Schwab W. Natural 4-hydroxy-2, 5-dimethyl-3(2H)-furanone (Furaneol®). Molecules 2013;18:6936-6951.
2
Kozminykh VO, Igidov NM, Kozminykh EN, Konshina LO, Semenova ZN, Lyadova NV, Plaksina AN, Andreichikov YS. Synthesis and antimicrobial activity of 2-substituted-5-aryl-2,3-dihydro-3-furanones and 1,6-diaryl-3,4dihydroxy-2,4-hexadien-1,6-diones. Pharm. Chem. J. 1991;25:891-897.
3
Cannon GW, Breedveld FC. Efficacy of cyclooxygenase-2 specific inhibitors. Am. J. Med. 2001;3: 6-12.
4
Ogara JP, Humphreys H, Staphylococcus epidermidis biofilms importance and implications, J. Med. Microbiol. 2001;50:582-587.
5
Futaki N, Yoshikawa K, Hamasaka Y, Arai I, Higuchi S, Iizuka H, Otomo S. A novel non-steroidal anti-inflammatory drug with potent analgesic and antipyretic effects, which causes minimal stomach lesions. Gen. Pharmacol. 1997;24:105-110.
6
Razet R, Thomet U, Furtmuller R, Chiaroni A, Sigel E, Sieghart W, Dodd RH. 5-[1-(2-N-arylsulfonyl-1,2,3,4-tetrahydroisoquinolyl)]-4,5dihydro-2(3H)-furanones: positive allosteric modulators of the GABA receptor with a new mode of action. J. Med. Chem. 2000;43:4363-4366.
7
Abou-Elmagd WSI, Hashem AI. Synthesis and antitumor activity evaluation of some novel fused and spiro heterocycles derived from a 2(3H)-furanone derivative, J. Heterocycl. Chem. 2016;53: 202-208.
8
Akhter M, Saha R, Tanwar O, Alam MM, Zaman MS. Synthesis and antimalarial activity of quinoline-substituted furanone derivatives and their identification as selective falcipain-2 inhibitors. Med. Chem. Res. 2015;24:879-890.
9
Wang Y, Gloer JB, Scott JA, Malloch D, Appenolides AC. Three new antifungal furanones from the coprophilous fungus Podospora appendiculata. J. Nat. Prod. 1993;56:341-344.
10
Husain A, Khan SA, Iram F, Iqbal MA, Asif M. Insights into the chemistry and therapeutic potential of furanones: A versatile pharmacophore. Eur. J. Med. Chem. 2019;171:66-92.
11
Mardirossian N, Head-Gordon M. Thirty years of density functional theory in computational chemistry. Mol. Phy. 2017;115:2315-2372.
12
Mirzaei M, Hadipour NL. Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters. J. Iran. Chem. Soc. 2009;6:195-199.
13
Mirzaei M, Mirzaei M. The C-doped AlP nanotubes: A computational study. Solid State Sci. 2011;13:244-250.
14
Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophys. Chem. 2007;125:179-183.
15
Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlat. Microstruct. 2012;52:612-617.
16
Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide. J. Mol. Graph. Model. 2008;26:977-981.
17
Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. Int. J. Nano Dimens. 2013;3:175-179.
18
Partovi T, Mirzaei M, Hadipour NL. The C–H···O hydrogen bonding effects on the 17O electric field gradient and chemical shielding tensors in crystalline 1-methyluracil: A DFT study. Z. Naturforsch. A. 2006;61:383-388.
19
Harismah K, Sadeghi M, Baniasadi R, Mirzaei M. Adsorption of vitamin C on a fullerene surface: DFT studies. J. Nanoanal. 2017;4:1-7.
20
Mokhtari A, Harismah K, Mirzaei M. Covalent addition of chitosan to graphene sheets: Density functional theory explorations of quadrupole coupling constants. Superlat. Microstruct. 2015;88:56-61.
21
Harismah K, Ozkendir OM, Mirzaei M. Explorations of crystalline effects on 4-(benzyloxy) benzaldehyde properties. Z. Naturforsch. A. 2015;70:1013-1018.
22
Mirzaei M, Harismah K, Jafari E, Gülseren O, Rad AS. Functionalization of (n, 0) CNTs (n= 3–16) by uracil: DFT studies. Eur. Phys. J. B. 2018;91:14.
23
Harismah K, Mirzaei M, Sahebi H, Gülseren O, Rad AS. Chemically uracil–functionalized carbon and silicon carbide nanotubes: Computational studies. Mater. Chem. Phys. 2018;205:164-170.
24
Harismah K, Mirzaei M, Ghasemi N, Nejati M. Non-covalent functionalisation of C30 fullerene by pyrrole-n-carboxylic acid (n= 2, 3): Density functional theory studies. Z. Naturforsch. A. 2017;73:51-56.
25
Pence HE, Williams A. ChemSpider: An online chemical information resource. J. Chem. Edu. 2010;87:1123-1124.
26
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery Jr JA, Stratmann RE, Burant JC, Dapprich S, et al. Gaussian 98, Revision A. 7. Pittsburgh, PA: Gaussian. Inc. Computer Program. 1998.
27
Aramideh M, Mirzaei M, Khodarahmi G, Gülseren O. DFT Studies of Graphene-Functionalised Derivatives of Capecitabine. Z. Naturforsch. A. 2017;72:1131-1138.
28
Aghazadeh M, Mirzaei M. Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors. Chem. Phys. 2008;351:159-162.
29
Soleimani M, Mirzaei M, Mofid MR, Khodarahmi G, Rahimpour SF. Lactoperoxidase inhibition by tautomeric propylthiouracils. Asian J. Green Chem. 2020;4:1-0.
30
Alidoosti ZS, Mirzaei M. Comparative examination of moclobemide, tranylcypromine, phenelzine and isocarboxazid for monoamine oxidase–A inhibition. Adv. J. Chem. B. 2019;1:23-28.
31
Esfahani AN, Mirzaei M. Flavonoid derivatives for monoamine oxidase–A inhibition. Adv. J. Chem. B. 2019;1:17-22.
32
Ozkendir OM, Mirzaei M. Alkali metal chelation by 3–hydroxy–4–pyridinone. Adv. J. Chem. B. 2019;1:10-6.
33
Nazemi H, Mirzaei M, Jafari E. Antidepressant activity of curcumin by monoamine oxidase–A inhibition. J. Adv. Chem. B. 2019;1:3-9.
34
Mirzaei M, Meskinfam M. Computational studies of effects of tubular lengths on the NMR properties of pristine and carbon decorated boron phosphide nanotubes. Solid State Sci. 2011;13:1926-1930.
35
Mirzaei M. Calculation of chemical shielding in C-doped zigzag BN nanotubes. Monatsh. Chem. 2009;140:1275-1278.
36
Bagheri Z, Mirzaei M, Hadipour NL, Abolhassani MR. Density functional theory study of boron nitride nanotubes: calculations of the N-14 and B-11 nuclear quadrupole resonance parameters. J. Comput. Theor. Nanosci. 2008;5:614-618.
37
Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Z. Naturforsch. A 2007;62:56-60.
38
Mirzaei M, Mirzaei M. The B-doped SiC nanotubes: A computational study. J. Mol. Struct. THEOCHEM 2010;953:134-138.
39
Mirzaei M, Hadipour NL, Ahmadi K. Investigation of C–H… O=C and N–H… O=C hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters. Biophys. Chem. 2007;125:411-415.
40
Acharya C, Coop A, E Polli J, D MacKerell A. Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Cur. Comput. Aided Drug Design. 2011;7:10-22.
41
Mirzaei M, Hadipour NL. A computational NQR study on the hydrogen‐bonded lattice of cytosine‐5‐acetic acid. J. Comput. Chem. 2008;29:832-838.
42
Mirzaei M, Hadipour NL, Seif A, Giahi M. Density functional study of zigzag BN nanotubes with equivalent ends. Physica E 2008;40:3060-3063.
43
Mirzaei M. Density functional study of defects in boron nitride nanotubes. Z. Phys. Chem. 2009;223:815-823.
44
Mirzaei M. A computational NMR study of boron phosphide nanotubes. Z. Naturforsch. A 2010;65:844-848.
45
Harismah K, Mirzaei M, Moradi R. DFT studies of single lithium adsorption on coronene. Z. Naturforsch. A 2018;73:685-691.
46
Mirzaei M, Hadipour NL. Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts. Chem. Phys. Lett. 2007;438:304-307.
47
Harismah K, Mirzaei M, Samadizadeh M, Rad AS. DFT studies of stabilities and properties for X3Y6Z9 borazine–like structures (X= B/Al, Y= N/P, Z= H/Me). Superlat. Microstruct. 2017;109:360-365.
48
ORIGINAL_ARTICLE
Non-Covalent Interactions of N-(4-CarboxyPhenyl)Phthalimide with CNTs
Non-covalent interactions of N-(4-carboxyphenyl)phthalimide (CPP) with carbon nanotubes (CNTs) have been investigated to see the effects of interactions on the properties of CPP, which is a medicinal compound. Two models of (3,3) armchair and (6,0) zigzag CNTs have been considered in this work. All structures have been optimized by density functional theory (DFT) calculations to evaluate the corresponding properties. Moreover, quadrupole coupling constants (CQ) have been evaluated at the atomic scale for the optimized structures. The results yielded stabilized CPP@CNT hybrids by effects of hybridization on the properties of both of CPP and CNT counterparts. The CQ parameters also indicate that the carbon atoms are very much important to detect the type of CNT whereas other atoms showed almost the same effects at the same situations. As a result, the CPP could be very well hybridized with the CNT through non-covalent interacting system.
https://www.ajchem-b.com/article_104956_d8c676d0d7b17d11f88522ddfc6c2833.pdf
2020-03-16
39
45
10.33945/SAMI/AJCB.2020.1.7
N-(4-carboxyphenyl)phthalimide
CNT
Interaction
Hybrid
Density functional theory
Mehrnoush
Molaeian
mehrnoushmolaeian@yahoo.com
1
Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Tehran Islamic Azad Medical Sciences University, Tehran, Iran
AUTHOR
Asghar
Davood
adavood2001@yahoo.com
2
Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Tehran Islamic Azad Medical Sciences University, Tehran, Iran
AUTHOR
Mahmoud
Mirzaei
mirzaeimch@gmail.com
3
Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
LEAD_AUTHOR
Iijima S. Helical microtubules of graphitic carbon. Nature 1991;354:56-58.
1
Yang Z, Tian J, Yin Z, Cui C, Qian W, Wei F. Carbon nanotube-and graphene-based nanomaterials and applications: A review. Carbon 2019;141:467-480.
2
Barnard AW, Zhang M, Wiederhecker GS, Lipson M, McEuen PL. Real-time vibrations of a carbon nanotube. Nature 2019;566:89-93.
3
Mirzaei M. Calculation of chemical shielding in C-doped zigzag BN nanotubes. Monatsh. Chem. 2009;140:1275-1278.
4
Mirzaei M, Mirzaei M. The B-doped SiC nanotubes: A computational study. J. Mol. Struct. THEOCHEM 2010;953:134-138.
5
Mirzaei M. Carbon doped boron phosphide nanotubes: a computational study. J. Mol. Model. 2011;17:89-96.
6
Mirzaei M. Density functional study of defects in boron nitride nanotubes. Z. Phys. Chem. 2009;223:815-823.
7
Mirzaei M, Hadipour NL, Seif A, Giahi M. Density functional study of zigzag BN nanotubes with equivalent ends. Physica E 2008;40:3060-3063.
8
Mirzaei M, Mirzaei M. The C-doped AlP nanotubes: A computational study. Solid State Sci. 2011;13:244-250.
9
Mirzaei M. A computational NMR study of boron phosphide nanotubes. Z. Naturforsch. A 2010;65:844-848.
10
Mirzaei M. The NMR parameters of the SiC-doped BN nanotubes: a DFT study. Physica E 2010;42:1954-1957.
11
Ebrahim-Habibi MB, Ghobeh M, Mahyari FA, Rafii-Tabar H, Sasanpour P. An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G: A combined experimental and molecular dynamics study. Sci. Rep. 2019;9:1-8.
12
Park M, Lee H, Jang JU, Park JH, Kim CH, Kim SY, Kim J. Phenyl glycidyl ether as an effective noncovalent functionalization agent for multiwalled carbon nanotube. Compos. Sci. Technol. 2019;177:96-102.
13
Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. J. Mol. Model. 2011;17:695-699.
14
Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlat. Microstruct. 2012;52:612-617.
15
Kumar RM, Rajesh K, Haldar S, Gupta P, Murali K, Roy P, Lahiri D. Surface modification of CNT reinforced UHMWPE composite for sustained drug delivery. J. Drug Delivery Sci. Technol. 2019;52:748-759.
16
Sheikhi M, Shahab S, Khaleghian M, Ahmadianarog M, Azarakhshi F, Kumar R. Investigation of the adsorption rubraca anticancer drug on the CNT (4, 4-8) nanotube as a factor of drug delivery. Cur. Mol. Med. 2019;19:473-486.
17
Li H, Sun X, Li Y, Li B, Liang C, Wang H. Preparation and properties of carbon nanotube (Fe)/hydroxyapatite composite as magnetic targeted drug delivery carrier. Mater. Sci. Engin. C 2019;97:222-229.
18
Dong P, Rakesh KP, Manukumar HM, Mohammed YH, Karthik CS, Sumathi S, Mallu P, Qin HL. Innovative nano-carriers in anticancer drug delivery-a comprehensive review. Bioorg. Chem. 2019;85:325-336.
19
Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. Int. J. Nano Dimens. 2013;3:175-179.
20
Panwar N, Soehartono AM, Chan KK, Zeng S, Xu G, Qu J, Coquet P, Yong KT, Chen X. Nanocarbons for biology and medicine: sensing, imaging, and drug delivery. Chem. Rev. 2019;119:9559-9656.
21
Srivastava D, Menon M, Cho K. Computational nanotechnology with carbon nanotubes and fullerenes. Comput. Sci. Engin. 2001;3:42-55.
22
Belin T, Epron F. Characterization methods of carbon nanotubes: a review. Mater. Sci. Engin. B 2005;119:105-118.
23
Kumar V, Banker GS. Incompatibility of polyvinyl acetate phthalate with benzocaine: Isolation and characterization of 4-phthalimidobenzoic acid ethyl ester. Int. J. Pharm. 1992;79:61-65.
24
Liang ZP, Li J, Huang BY. 4-Phthalimidobenzoic acid N, N-dimethylformamide solvate. Acta Cryst. E 2006;62:4761-4762.
25
Iman M, Fakhari S, Jahanpanah M, Naderi N, Davood A. Design and synthesis of 4-flurophthalimides as potential anticonvulsant agents. Iran. J. Pharm. Res. 2018;17:896-905.
26
Vamecq J, Bac P, Herrenknecht C, Maurois P, Delcourt P, Stables JP. Synthesis and anticonvulsant and neurotoxic properties of substituted N-phenyl derivatives of the phthalimide pharmacophore. J. Med. Chem. 2000;43:1311-1319.
27
Lovitt JI, Hawes CS, Gunnlaugsson T. Crystallographic studies of 2-picolyl substituted naphthalene diimide and bis-phthalimide ligands and their supramolecular coordination chemistry. CrystEngComm. 2019;21:207-217.
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Singh RB, Singh GK, Chaturvedi K, Kumar D, Singh SK, Zaman MK. Design, synthesis, characterization, and molecular modeling studies of novel oxadiazole derivatives of nipecotic acid. Med. Chem. Res. 2018;27:137-152.
29
Patel N, Viguera AC, Baldessarini RJ. Mood-stabilizing anticonvulsants, spina bifida, and folate supplementation: commentary. J. Clin. Psychopharm. 2018;38:7-10.
30
Soleimani M, Mirzaei M, Mofid MR, Khodarahmi G, Rahimpour SF. Lactoperoxidase inhibition by tautomeric propylthiouracils. Asian J. Green Chem. 2020;4:1-0.
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Alidoosti ZS, Mirzaei M. Comparative examination of moclobemide, tranylcypromine, phenelzine and isocarboxazid for monoamine oxidase-A inhibition. Adv. J. Chem. B 2019;1:23-28.
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Esfahani AN, Mirzaei M. Flavonoid derivatives for monoamine oxidase-A inhibition. Adv. J. Chem. B 2019;1:17-22.
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Ozkendir OM, Mirzaei M. Alkali metal chelation by 3-hydroxy-4-pyridinone. Adv. J. Chem. B 2019;1:10-6.
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Nazemi H, Mirzaei M, Jafari E. Antidepressant activity of curcumin by monoamine oxidase-A inhibition. J. Adv. Chem. B 2019;1:3-9.
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Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery Jr JA, Stratmann RE, Burant JC, Dapprich S, et al. Gaussian 98, Revision A. 7. Pittsburgh, PA: Gaussian. Inc. Computer Program. 1998.
36
Bodaghi A, Mirzaei M, Seif A, Giahi M. A computational NMR study on zigzag aluminum nitride nanotubes. Physica E 2008;41:209-212.
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Mirzaei M, Meskinfam M. Computational studies of effects of tubular lengths on the NMR properties of pristine and carbon decorated boron phosphide nanotubes. Solid State Sci. 2011;13:1926-1930.
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Wu G. Recent developments in solid-state nuclear magnetic resonance of quadrupolar nuclei. Biochem. Cell Biol. 1998;76:429-442.
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Shen J, Terskikh V, Wang X, Hung I, Gan Z, Wu G. A quadrupole-central-transition 17O NMR study of nicotinamide. J. Phys. Chem. B 2018;122:4813-4820.
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Mirzaei M, Hadipour NL. Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts. Chem. Phys. Lett 2007;438:304-307.
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Mirzaei M, Elmi F, Hadipour NL. A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: a density functional theory study. J. Phys. Chem. B 2006;110:10991-10996.
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Bagheri Z, Mirzaei M, Hadipour NL, Abolhassani MR. Density functional theory study of boron nitride nanotubes: calculations of the N-14 and B-11 nuclear quadrupole resonance parameters. J. Comput. Theor. Nanosci. 2008;5:614-618.
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Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Z. Naturforsch. A 2007;62:56-60.
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Mirzaei M, Hadipour NL. A computational NQR study on the hydrogen‐bonded lattice of cytosine‐5‐acetic acid. J. Comput. Chemi. 2008;29:832-838.
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Mirzaei M, Hadipour NL, Ahmadi K. Investigation of C-H…O=C and N-H…O=C hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters. Biophys. Chem. 2007;125:411-415.
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Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophys. Chem. 2007;125:179-183.
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Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (O=C-NH) in crystalline acetamide. J. Mol. Graph. Model. 2008;26:977-981.
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Harismah K, Mirzaei M, Moradi R. DFT studies of single lithium adsorption on coronene. Z. Naturforsch. A 2018;73:685-691.
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Partovi T, Mirzaei M, Hadipour NL. The C-H···O hydrogen bonding effects on the 17O electric field gradient and chemical shielding tensors in crystalline 1-methyluracil: A DFT study. Z. Naturforsch. A 2006;61:383-388.
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