A Computational Study of 1-Substituted Methyl 9-Methyl-9H-Pyrido[3,4- b]indole-3-Carboxylate: Quantum Chemical Descriptors, FMO and NBO Analysis

Mustafa Elik; Goncagül Serdaroğlu

doi:10.17776/csj.356185

Research Article

A Computational Study of 1-Substituted Methyl 9-Methyl-9H-Pyrido[3,4- b]indole-3-Carboxylate: Quantum Chemical Descriptors, FMO and NBO Analysis

Year 2017, , 138 - 155, 08.12.2017

Mustafa Elik , Goncagül Serdaroğlu

https://doi.org/10.17776/csj.356185

Cited By: 19

Abstract

This work dealt with the
investigation of the methyl 9H-pyrido[3,4-b]indole-3-carboxylate (Basic
compound) and its C1-substituted derivatives to search for the best substituent
group that enhances the chemical reactivity behavior of the Basic compound. In
this context, DFT (Density Functional Theory) calculations were performed at
B3LYP level of theory at three basis sets, also
in 10 different solvents because the chemical behavior strongly depends on the
solvent media. This study revealed that the
anthracene-9-yl substitution on the C1-position of the Basic compound has
increased the chemical reactivity of the Basic compound more than those of the
other substituent groups. Also, the
results were supported by the NBO analysis: the highest electron delocalization
for the structure A was found out π C19-C20→ p_v C42-C43 with the
interaction energy of the 50.98 kcalmol-1, due to the anthracene-9-yl
substitution on the C1-position of the Basic compound makes the
electron delocalization on the substituted compound enhances, at
6-311++g**basis set in the water phase.

Keywords

Quantum chemical descriptors, substituent effect, NBO

References

[1] Martin L., Leon A., Martin M. A., Castillo B. and Menendez J.C., “Detection and characterization of cyclodextrin complexes with β-carboline derivatives by spectroscopic techniques”, Journal of Pharmaceutical and Biomedical Analysis, 2003, 32, 991-1001.
[2] Pari K., Sundari C. S, Chandani S., Balasubramanian D., “β -Carbolines That Accumulate in Human Tissues May Serve a Protective Role against Oxidative Stress”, THE JOURNAL OF BIOLOGICAL CHEMISTRY. 2000, 275(4), 2455–2462.
[3] Prinsep M. R, Blunt J.W. and Munro M.H.G, “New Cytotoxic β -Carboline Alkaloids from the Marine Bryozoan, Cribricellina Cribraria”, Journal of Natural Products. 1991, 54(4), 1068-1076.
[4] Allen M.S., Tan Y.C., Trudell M.L., Narayanan K., Schindler L.R., Martin M.J., Schultz C., Hagen T.J., Koehler K.F., Codding P.W., Skolnick P. and Cook J.M., “Synthetic and Computer-Assisted Analyses of the Pharmacophore for the Benzodiazepine Receptor Inverse Agonist Site”, J. Med. Chem.,1990, 33: 2343-2357.
[5] Allen M.S., LaLoggia A.J., Dorn L.J., Martin M.J., Costantino G., Hagen T.J., Koehler K.F., Skolnick P. and Cook J.M., “Predictive Binding of β -Carboline Inverse Agonists and Antagonists via the CoMFA/GOLPE Approach” J. Med. Chem., 1992, 35: 4001-4010.
[6] Glennon R.A., Dukat M., Grella B., Seo Hong S.S., Costantino L., Teitler M., Smith C., Egan C., Davis K. and Mattson M.V., “Binding of β -carbolines and related agents at serotonin (5-HT2 and 5-HT1A), dopamine (D2) and benzodiazepine receptors”, Drug and Alcohol Dependence, 2000, 60: 121–132.
[7] Brahmbhatt K.G., Ahmed N., Sabde S., Mitra D., Singh I.P. and Bhutani K.K., “Synthesis and evaluation of β -carboline derivatives as inhibitors of human immunodeficiency virus”, Bioorganic & Medicinal Chemistry Letters, 2010, 20: 4416- 4419.
[8] Kusurkar R.S and Goswami S.K., “Efficient one-pot synthesis of anti-HIVand anti-tumour β-carbolines”, Tetrahedron, 2004, 60: 5315–5318.
[9] Bai B., Li X.Y., Liu L., Li Y and Zhu H.J., “Syntheses of novel β-carboline derivatives and the activities against five tumor-cell lines”, Bioorganic & Medicinal Chemistry Letters, 2014, 24: 96- 98.
[10] Cao R., Fan W., Guo L., Ma Q., Zhang G., Li J., Chen X., Ren Z. and Qiu L., “Synthesis and structure-activity relationships of harmine derivatives as potential antitumor agents”, European Journal of Medicinal Chemistry, 2013, 60: 135-143.
[11] Cao R., Peng W., Chen H., Hou X., Guan H., Chen Q., Ma Y. and Xu A., “Synthesis and in vitro cytotoxic evaluation of 1,3-bisubstituted and 1,3,9-trisubstituted β-carboline derivatives”, European Journal of Medicinal Chemistry, 2005, 40: 249–257.
[12] Bai B., Li X.Y., Liu L., Li Y. and Zhu H.J., “Design, synthesis and cytotoxic activities of novel β -amino alcohol derivatives”, Bioorganic & Medicinal Chemistry Letters, 2011, 21: 2302–2304.
[13] Chen Z., Cao R., Shi B., Guo L., Sun J., Ma Q., Fan W. and Song H., “Synthesis and biological evaluation of 1,9-disubstituted β -carbolines as potent DNA intercalating and cytotoxic agents”, European Journal of Medicinal Chemistry, 2011, 46: 5127-5137.
[14] Reyman D., Tapia M.J., Carcedob C. and Vinasc M.H., “Photophysical properties of methyl β-carboline-3-carboxylate mediated by hydrogen-bonded complexes—a comparative study in different solvents”, Biophysical Chemistry, 2003, 104: 683–696.
[15] Carmona C., Balon M., Coronilla A.S. and Munoz M.A., “New Insights on the Excited-State Proton-Transfer Reactions of Betacarbolines: Cationic Exciplex Formation”, J. Phys. Chem. A., 2004, 108: 1910-1918.
[16] Tarzi O.I. and Erra-Balsells R., “Photochemistry of the alkaloids eudistomin N (6-bromo-nor-harmane) and eudistomin O (8-bromo-nor-harmane) and other bromo- β -carbolines”, Journal of Photochemistry and Photobiology B: Biology, 2005, 80: 29–45.
[17] Tarzi O.I. and Erra-Balsells R., “Effect of chlorine as substituent on the photochemistry and acid–base properties of β-carboline alkaloids”, Journal of Photochemistry and Photobiology B: Biology, 2006, 82: 79–93.
[18] Reyman D., Pardo A. and Poyato J.M.L., “Phototautomerism of β -Carboline”, J. Phys. Chem., 1994, 98: 10408-10411.
[19] Biondic M.C. and Erra-Balsells R., “Photochemical behaviour of β -carbolines. Part 4. Acid–base equilibria in the ground and excited states in organic media”, J. Chem. Soc. Perkin Trans., 1997, 2:1323-1327.
[20] Guan H., Liu X., Peng W., Cao R., Ma Y., Chen H. and Xu A., “β -Carboline derivatives: Novel photosensitizers that intercalate into DNA to cause direct DNA damage in photodynamic therapy”, Biochemical and Biophysical Research Communications, 2006, 342: 894–901.
[21] Ponce M.A. and Erra-Balsells R., “Synthesis and Isolation of Nitro- β -carbolines Obtained by Nitration of Commercial β -Carboline Alkaloids”, J. Heterocyclic Chem., 2001, 38, 1071-1082.
[22] Tapia M.J., Reyman D., Viñas M.H., Arroyo A. and Poyato J.M.L., “An experimental and theoretical approach to the acid–base and photophysical properties of 3-substituted β-carbolines in aqueous solutions”, Journal of Photochemistry and Photobiology A: Chemistry, 2003, 156: 1–7.
[23] Frisch M.J. et. al, Gaussian 09, D.01. Gaussian, Inc, 2013, Wallingford CT.
[24] Becke A.D., “A new mixing of Hartree–Fock and local density‐functional theories” J. Chem. Phys., 1993, 98: 1372- 1377.
[25] Lee C., Yang W. and Parr R.G., “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density”, Phys. Rev., 1988, B37: 785- 789.
[26] Foresman J.B., Keith T.A., Wiberg K.B., Snoonian J. and Frisch M.J., “Solvent Effects. 5. Influence of Cavity Shape, Truncation of Electrostatics, and Electron Correlation on ab Initio Reaction Field Calculations”, J. Phys. Chem., 1996, 100: 16098- 16104.
[27] Tomasi J., Mennuci B. and Cammi R., “Quantum Mechanical Continuum Solvation Models”, Chem Rev., 2005, 105: 2999- 3093.
[28] Fukui K., “Role of frontier orbitals in chemical reactions”, Science, 1982, 218(4574): 747- 754.
[29] Jensen F., “Introduction to Computational Chemistry”, John Wiley and Sons Ltd., West Sussex, Chapter 9, p. 309, p. 492, 2007.
[30] Parr R.G, Szentpaly L.V. and Liu S. “Electrophilicity Index”, J. Am. Chem. Soc., 1999, 121: 1922-1924.
[31] Codding P.W., “Structure-activity studies of β -carbolines. 1. Molecular structure and conformation of cis-3-carboxylic acid-P,2,3,4-tetrahydroharmane dihydrate”, Can. J. Chem., 1983, 61: 529-532.
[32] Dorey G., Poissonnet G., Potier M.C., Carvalho L.P., Venault P., Chapouthier G., Rossier J., Potier P. and Dodd R.H. “Synthesis and Benzodiazepine Receptor Affinities of Rigid Analogues of 3-Carboxy- β-carbolines: Demonstration That the Benzodiazepine Receptor Recognizes Preferentially the s-Cis Conformation of the 3-Carboxy Group” J. Med. Chem., 1989, 32: 1799-1804.
[33] Wiberg K.B., “Properties of Some Condensed Aromatic Systems”, J. Org. Chem., 1997, 62: 5720-5727.
[34] Weinhold F., Landis C.R. and Glendening E.D., “What is NBO analysis and how is it useful?”, International Reviews in Physical Chemistry, 2016, 35(3): 399–440.
[35] Reed A.E., Curtiss L.A., Weinhold F., “Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint”, Chem. Rev., 1988, 88: 899-926.
[36] Cramer, C. J., “Essentials of the Computational Chemistry: Theories and Models”, Second edition, John Wiley and Sons Ltd., West Sussex, Chapter 6, p.578.
[37] Suresh D.M., Amalanathan M., Sebastian S., Sajan D., Joe I.H., Jothy V.B. and Nemec I., “Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate– DFT approach”, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2013, 115: 595–602.
[38] Zhang, J., Zheng, H., Zhang, T. and Wu, M., “Theoretical Study for High-Energy-Density Compounds Derived from Cyclophosphazene. IV. DFT Studies on 1,1-Diamino-3,3,5,5,7,7-hexaazidocyclotetraphosphazene and Its Isomers”, Int. J. Mol. Sci., 2009, 10: 3502-3516.
[39] Sayın, K. , Karakaş, D., “Theoretical studies on oxovanadium(IV) complexes with sterically crowded Schiff base ligands”, Cumhuriyet Science Journal, 2017, 38 (1), 1-12.

1- Sübstitüeli Metal-9-Metil-9H-Pirido [3,4-b]indol-3-Karboksilat Üzerine Hesaplamalı Kimya Çalışması: Kuantum Kimyasal Belirleyiciler, FMO ve NBO Analizi

Year 2017, , 138 - 155, 08.12.2017

Mustafa Elik , Goncagül Serdaroğlu

https://doi.org/10.17776/csj.356185

Cited By: 19

Abstract

Bu çalışma metil 9H-pirido [3,4-b] indol-3-karboksilat
(Temel bileşik) ve bu bileşiğin C1-substitüeli türevlerinin incelenmesi ile
Temel bileşiğin kimyasal tepkime davranışını arttıran en iyi substitüe grubu
belirlemek ile ilgilenmiştir. Bu bağlamda DFT (Yoğunluk Fonksiyonel Teori)
hesaplamaları 3 temel set ve kimyasal aktivite davranışı çözücü ortamına bağlı
olduğundan dolayı 10 farklı çözücü ortamında yapılmıştır. Bu çalışma, Temel
bileşiğin C1-konumundaki antrasen-9-il substitüe grubunun, diğer sübstitüe
gruplarınınkinden daha fazla Temel bileşiğin kimyasal reaktivitesini
arttırdığını ortaya koymuştur. Ayrıca, sonuçlar NBO analizi ile
desteklenmiştir: 6-311++g(d,p)
temel seti ile su fazında, Temel bileşiğin C1 konumunda antrasen-9-il substitüe
grubu bulunduğunda elektron delokalizasyonu arttığından dolayı, A bileşiğinin
en büyük elektron delokalizasyonu π
C19-C20→ p_v C42-C43 elektronik
geçişi için 50.98 kcalmol^-1olarak bulunmuştur.

Keywords

Kuantum kimyasal tanımlayıcılar, bağlı grup etkisi, NBO, FMO analizi

References

[1] Martin L., Leon A., Martin M. A., Castillo B. and Menendez J.C., “Detection and characterization of cyclodextrin complexes with β-carboline derivatives by spectroscopic techniques”, Journal of Pharmaceutical and Biomedical Analysis, 2003, 32, 991-1001.
[2] Pari K., Sundari C. S, Chandani S., Balasubramanian D., “β -Carbolines That Accumulate in Human Tissues May Serve a Protective Role against Oxidative Stress”, THE JOURNAL OF BIOLOGICAL CHEMISTRY. 2000, 275(4), 2455–2462.
[3] Prinsep M. R, Blunt J.W. and Munro M.H.G, “New Cytotoxic β -Carboline Alkaloids from the Marine Bryozoan, Cribricellina Cribraria”, Journal of Natural Products. 1991, 54(4), 1068-1076.
[4] Allen M.S., Tan Y.C., Trudell M.L., Narayanan K., Schindler L.R., Martin M.J., Schultz C., Hagen T.J., Koehler K.F., Codding P.W., Skolnick P. and Cook J.M., “Synthetic and Computer-Assisted Analyses of the Pharmacophore for the Benzodiazepine Receptor Inverse Agonist Site”, J. Med. Chem.,1990, 33: 2343-2357.
[5] Allen M.S., LaLoggia A.J., Dorn L.J., Martin M.J., Costantino G., Hagen T.J., Koehler K.F., Skolnick P. and Cook J.M., “Predictive Binding of β -Carboline Inverse Agonists and Antagonists via the CoMFA/GOLPE Approach” J. Med. Chem., 1992, 35: 4001-4010.
[6] Glennon R.A., Dukat M., Grella B., Seo Hong S.S., Costantino L., Teitler M., Smith C., Egan C., Davis K. and Mattson M.V., “Binding of β -carbolines and related agents at serotonin (5-HT2 and 5-HT1A), dopamine (D2) and benzodiazepine receptors”, Drug and Alcohol Dependence, 2000, 60: 121–132.
[7] Brahmbhatt K.G., Ahmed N., Sabde S., Mitra D., Singh I.P. and Bhutani K.K., “Synthesis and evaluation of β -carboline derivatives as inhibitors of human immunodeficiency virus”, Bioorganic & Medicinal Chemistry Letters, 2010, 20: 4416- 4419.
[8] Kusurkar R.S and Goswami S.K., “Efficient one-pot synthesis of anti-HIVand anti-tumour β-carbolines”, Tetrahedron, 2004, 60: 5315–5318.
[9] Bai B., Li X.Y., Liu L., Li Y and Zhu H.J., “Syntheses of novel β-carboline derivatives and the activities against five tumor-cell lines”, Bioorganic & Medicinal Chemistry Letters, 2014, 24: 96- 98.
[10] Cao R., Fan W., Guo L., Ma Q., Zhang G., Li J., Chen X., Ren Z. and Qiu L., “Synthesis and structure-activity relationships of harmine derivatives as potential antitumor agents”, European Journal of Medicinal Chemistry, 2013, 60: 135-143.
[11] Cao R., Peng W., Chen H., Hou X., Guan H., Chen Q., Ma Y. and Xu A., “Synthesis and in vitro cytotoxic evaluation of 1,3-bisubstituted and 1,3,9-trisubstituted β-carboline derivatives”, European Journal of Medicinal Chemistry, 2005, 40: 249–257.
[12] Bai B., Li X.Y., Liu L., Li Y. and Zhu H.J., “Design, synthesis and cytotoxic activities of novel β -amino alcohol derivatives”, Bioorganic & Medicinal Chemistry Letters, 2011, 21: 2302–2304.
[13] Chen Z., Cao R., Shi B., Guo L., Sun J., Ma Q., Fan W. and Song H., “Synthesis and biological evaluation of 1,9-disubstituted β -carbolines as potent DNA intercalating and cytotoxic agents”, European Journal of Medicinal Chemistry, 2011, 46: 5127-5137.
[14] Reyman D., Tapia M.J., Carcedob C. and Vinasc M.H., “Photophysical properties of methyl β-carboline-3-carboxylate mediated by hydrogen-bonded complexes—a comparative study in different solvents”, Biophysical Chemistry, 2003, 104: 683–696.
[15] Carmona C., Balon M., Coronilla A.S. and Munoz M.A., “New Insights on the Excited-State Proton-Transfer Reactions of Betacarbolines: Cationic Exciplex Formation”, J. Phys. Chem. A., 2004, 108: 1910-1918.
[16] Tarzi O.I. and Erra-Balsells R., “Photochemistry of the alkaloids eudistomin N (6-bromo-nor-harmane) and eudistomin O (8-bromo-nor-harmane) and other bromo- β -carbolines”, Journal of Photochemistry and Photobiology B: Biology, 2005, 80: 29–45.
[17] Tarzi O.I. and Erra-Balsells R., “Effect of chlorine as substituent on the photochemistry and acid–base properties of β-carboline alkaloids”, Journal of Photochemistry and Photobiology B: Biology, 2006, 82: 79–93.
[18] Reyman D., Pardo A. and Poyato J.M.L., “Phototautomerism of β -Carboline”, J. Phys. Chem., 1994, 98: 10408-10411.
[19] Biondic M.C. and Erra-Balsells R., “Photochemical behaviour of β -carbolines. Part 4. Acid–base equilibria in the ground and excited states in organic media”, J. Chem. Soc. Perkin Trans., 1997, 2:1323-1327.
[20] Guan H., Liu X., Peng W., Cao R., Ma Y., Chen H. and Xu A., “β -Carboline derivatives: Novel photosensitizers that intercalate into DNA to cause direct DNA damage in photodynamic therapy”, Biochemical and Biophysical Research Communications, 2006, 342: 894–901.
[21] Ponce M.A. and Erra-Balsells R., “Synthesis and Isolation of Nitro- β -carbolines Obtained by Nitration of Commercial β -Carboline Alkaloids”, J. Heterocyclic Chem., 2001, 38, 1071-1082.
[22] Tapia M.J., Reyman D., Viñas M.H., Arroyo A. and Poyato J.M.L., “An experimental and theoretical approach to the acid–base and photophysical properties of 3-substituted β-carbolines in aqueous solutions”, Journal of Photochemistry and Photobiology A: Chemistry, 2003, 156: 1–7.
[23] Frisch M.J. et. al, Gaussian 09, D.01. Gaussian, Inc, 2013, Wallingford CT.
[24] Becke A.D., “A new mixing of Hartree–Fock and local density‐functional theories” J. Chem. Phys., 1993, 98: 1372- 1377.
[25] Lee C., Yang W. and Parr R.G., “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density”, Phys. Rev., 1988, B37: 785- 789.
[26] Foresman J.B., Keith T.A., Wiberg K.B., Snoonian J. and Frisch M.J., “Solvent Effects. 5. Influence of Cavity Shape, Truncation of Electrostatics, and Electron Correlation on ab Initio Reaction Field Calculations”, J. Phys. Chem., 1996, 100: 16098- 16104.
[27] Tomasi J., Mennuci B. and Cammi R., “Quantum Mechanical Continuum Solvation Models”, Chem Rev., 2005, 105: 2999- 3093.
[28] Fukui K., “Role of frontier orbitals in chemical reactions”, Science, 1982, 218(4574): 747- 754.
[29] Jensen F., “Introduction to Computational Chemistry”, John Wiley and Sons Ltd., West Sussex, Chapter 9, p. 309, p. 492, 2007.
[30] Parr R.G, Szentpaly L.V. and Liu S. “Electrophilicity Index”, J. Am. Chem. Soc., 1999, 121: 1922-1924.
[31] Codding P.W., “Structure-activity studies of β -carbolines. 1. Molecular structure and conformation of cis-3-carboxylic acid-P,2,3,4-tetrahydroharmane dihydrate”, Can. J. Chem., 1983, 61: 529-532.
[32] Dorey G., Poissonnet G., Potier M.C., Carvalho L.P., Venault P., Chapouthier G., Rossier J., Potier P. and Dodd R.H. “Synthesis and Benzodiazepine Receptor Affinities of Rigid Analogues of 3-Carboxy- β-carbolines: Demonstration That the Benzodiazepine Receptor Recognizes Preferentially the s-Cis Conformation of the 3-Carboxy Group” J. Med. Chem., 1989, 32: 1799-1804.
[33] Wiberg K.B., “Properties of Some Condensed Aromatic Systems”, J. Org. Chem., 1997, 62: 5720-5727.
[34] Weinhold F., Landis C.R. and Glendening E.D., “What is NBO analysis and how is it useful?”, International Reviews in Physical Chemistry, 2016, 35(3): 399–440.
[35] Reed A.E., Curtiss L.A., Weinhold F., “Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint”, Chem. Rev., 1988, 88: 899-926.
[36] Cramer, C. J., “Essentials of the Computational Chemistry: Theories and Models”, Second edition, John Wiley and Sons Ltd., West Sussex, Chapter 6, p.578.
[37] Suresh D.M., Amalanathan M., Sebastian S., Sajan D., Joe I.H., Jothy V.B. and Nemec I., “Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate– DFT approach”, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2013, 115: 595–602.
[38] Zhang, J., Zheng, H., Zhang, T. and Wu, M., “Theoretical Study for High-Energy-Density Compounds Derived from Cyclophosphazene. IV. DFT Studies on 1,1-Diamino-3,3,5,5,7,7-hexaazidocyclotetraphosphazene and Its Isomers”, Int. J. Mol. Sci., 2009, 10: 3502-3516.
[39] Sayın, K. , Karakaş, D., “Theoretical studies on oxovanadium(IV) complexes with sterically crowded Schiff base ligands”, Cumhuriyet Science Journal, 2017, 38 (1), 1-12.

There are 39 citations in total.

Details

Primary Language	English
Subjects	Pharmacology and Pharmaceutical Sciences
Journal Section	Natural Sciences
Authors	Mustafa Elik Goncagül Serdaroğlu
Publication Date	December 8, 2017
Submission Date	November 19, 2017
Acceptance Date	December 6, 2017
Published in Issue	Year 2017

Cite

APA	Elik, M., & Serdaroğlu, G. (2017). A Computational Study of 1-Substituted Methyl 9-Methyl-9H-Pyrido[3,4- b]indole-3-Carboxylate: Quantum Chemical Descriptors, FMO and NBO Analysis. Cumhuriyet Science Journal, 38(4), 138-155. https://doi.org/10.17776/csj.356185