193
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Molecular Structure, Hydrogen Bonding Interactions and Docking Simulations of Nicotinamide (Monomeric and Trimeric Models) by Using Spectroscopy and Theoretical Approach

, , , &
Pages 1537-1555 | Received 07 Nov 2022, Accepted 04 Apr 2023, Published online: 20 Apr 2023

References

  • D. B. Kennedy, “B Vitamins and the Brain: Mechanisms, Dose and Efficacy-A Review,” Nutrients 8, no. 2 (2016): 68. doi:10.3390/nu8020068
  • Y. Chi, and A. A. Sauve, “Nicotinamide Riboside, a Trace Nutrient in Foods, is a Vitamin B3 with Effects on Energy Metabolism and Neuroprotection,” Current Opinion in Clinical Nutrition and Metabolic Care 16, no. 6 (2013): 657–61. doi:10.1097/MCO.0b013e32836510c0
  • Maria Yanez, Megha Jhanji, Kendall Murphy, R. Michael Gower, Mathew Sajish, and Ehsan Jabbarzadeh, “Nicotinamide Augments the Anti-Inflammatory Properties of Resveratrol through PARP1 Activation,” Scientific Reports 9, no. 1 (2019): 1–10. doi:10.1038/s41598-019-46678-8
  • Y. C. Boo, “Mechanistic Basis and Clinical Evidence for the Applications of Nicotinamide (Niacinamide) to Control Skin Aging and Pigmentation,” Antioxidants 10, no. 8 (2021): 1315. doi:10.3390/antiox10081315
  • I P. Nikas, S A. Paschou, and H S. Ryu, “The Role of Nicotinamide in Cancer Chemoprevention and Therapy,” Biomolecules 10, no. 3 (2020): 477. doi:10.3390/biom10030477
  • K. Maiese, “Nicotinamide as a Foundation for Treating Neurodegenerative Disease and Metabolic Disorders,” Current Neurovascular Research 18, no. 1 (2021): 134–49. doi:10.2174/18755739MTEzaMDMw2
  • H. Abd-Allah, M. Nasr, O. A. Ahmed-Farid, S. A. El-Marasy, R. M. Bakeer, and R. F. Ahmed, “Biological and Pharmacological Characterization of Ascorbic Acid and Nicotinamide Chitosan Nanoparticles against Insulin-Resistance-Induced Cognitive Defects: A Comparative Study,” ACS Omega 6, no. 5 (2021): 3587–601. doi:10.1021/acsomega.0c05096
  • D. B. Conze, J. Crespo-Barreto, and C. L. Kruger, “Safety Assessment of Nicotinamide Riboside, a Form of Vitamin B3,” Human & Experimental Toxicology 35, no. 11 (2016): 1149–60. doi:10.1177/0960327115626254
  • T. Van Mourik, M. Bühl, and M. P. Gaigeot, “Density Functional Theory across Chemistry, Physics and Biology,” Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences 372, no. 2011 (2014): 20120488. doi:10.1098/rsta.2012.0488
  • P. K. Murthy, V. Suneetha, S. Armaković, S. J. Armaković, P. A. Suchetan, L. Giri, and R. S. Rao, “Synthesis, Characterization and Computational Study of the Newly Synthetized Sulfonamide Molecule,” Journal of Molecular Structure. 1153, no. 2017 (2018): 212–29. doi:10.1016/j.molstruc.2017.10.028
  • M. Muthukkumar, T. Bhuvaneswari, G. Venkatesh, C. Kamal, P. Vennila, Stevan Armaković, Sanja J. Armaković, Y. Sheena Mary, and C. Yohannan Panicker, “Synthesis, Characterization and Computational Studies of Semicarbazide Derivative,” Journal of Molecular Liquids. 272 (2018): 481–95. doi:10.1016/j.molliq.2018.09.123
  • M. Bakiler, O. Bolukbasi, and A. Yilmaz, “An Experimental and Theoretical Study of Vibrational Spectra of Picolinamide, Nicotinamide, and Isonicotinamide,” Journal of Molecular Structure. 826, no. 1 (2007): 6–16. doi:10.1016/j.molstruc.2006.04.021
  • E. Akalin, and S. Akyuz, “Vibrational Analysis of Free and Hydrogen Bonded Complexes of Nicotinamide and Picolinamide,” Vibrational Spectroscopy 42, no. 2 (2006): 333–40. doi:10.1016/j.vibspec.2006.05.015
  • T. Takeshima, H. Takeuchi, T. Egawa, and K. Shigehiro, “Gas-Phase Molecular Structure of Nicotinamide Studied by Electron Diffraction Combined with MP2 Calculations,” Journal of Molecular Structure. 644, no. 1–3 (2003): 197–205. doi:10.1016/S0022-2860(02)00482-9
  • M. Jeeva, G. Venkatesa Prabhu, and C. M. Rajesh, “Inhibition Effect of Nicotinamide and Its Mannich Base Derivatives on Mild Steel Corrosion in HCl,” Journal of Materials Science 52, no. 21 (2017): 12861–88. doi:10.1007/s10853-017-1401-2
  • Y. Miwa, T. Mizuno, K. Tsuchida, T. Taga, and Y. Iwata, “Experimental Charge Density and Electrostatic Potential in Nicotinamide,” Acta Crystallographica. Section B, Structural Science 55, no. Pt 1 (1999): 78–84. doi:10.1107/s0108768198007848
  • S. Ramalingam, S. Periandy, M. Govindarajan, and S. Mohan, “FT-IR and FT-Raman Vibrational Spectra and Molecular Structure Investigation of Nicotinamide: A Combined Experimental and Theoretical Study,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 75, no. 5 (2010): 1552–8. doi:10.1016/j.saa.2010.02.015
  • T. Misiaszek, and Ż. Czyżnikowska, “The Nature of Interactions in Nicotinamide Crystal,” Journal of Molecular Graphics & Modelling 51 (2014): 73–8. doi:10.1016/j.jmgm.2014.04.007
  • Ana Borba, Merwe Albrecht, Andrea Gómez-Zavaglia, Leszek Lapinski, Maciej J. Nowak, Martin A. Suhm, and Rui Fausto, “Dimer Formation in Nicotinamide and Picolinamide in the Gas and Condensed Phases Probed by Infrared Spectroscopy,” Physical Chemistry Chemical Physics : PCCP 10, no. 46 (2008): 7010–21. doi:10.1039/b810002k
  • S. M. Soliman, and R. A. Massoud, “Theoretical Studies of Molecular Structure and Vibrational Spectra of Free, H-Bonded and Coordinated Nicotinamide,” Computational and Theoretical Chemistry. 988 (2012): 27–33. doi:10.1016/j.comptc.2012.02.022
  • Katarzyna N. Jarzembska, Anna A. Hoser, Radosław Kamiński, Anders Ø. Madsen, Krzysztof Durka, and Krzysztof Woźniak, “Combined Experimental and Computational Studies of Pyrazinamide and Nicotinamide in the Context of Crystal Engineering and Thermodynamics,” Crystal Growth and Design. 14, no. 7 (2014): 3453–65. doi:10.1021/cg500376z
  • L. Tabrizi, T. L. A. Nguyen, and D. Q. Dao, “Experimental and Theoretical Investigation of Cyclometalated Phenylpyridine Iridium(iii) Complex Based on Flavonol and Ibuprofen Ligands as Potent Antioxidant,” RSC Advances 9, no. 30 (2019): 17220–37. doi:10.1039/c9ra02726b
  • S. Chandrakumari, M. Gopalakrishnan, D. Sivakumar, and H. Manikandan, “One Pot Synthesis, Characterization, DFT Studies and AIM Analyses of Ethyl-1-Aryl-1H-Tetrazole-5-Carboxylate,” Letters in Organic Chemistry 16, no. 3 (2019): 185–93. doi:10.2174/1570178615666180907151830
  • Mahmoud Abdellatif, Viktoria Trummer-Herbst, Franziska Koser, Sylvère Durand, Rui Adão, Francisco Vasques-Nóvoa, Johanna K. Freundt, Julia Voglhuber, Maria-Rosaria Pricolo, Michael Kasa, et al, “Nicotinamide for the Treatment of Heart Failure with Preserved Ejection Fraction,” Science Translational Medicine 13, no. 580 (2021): 7064.doi:10.1126/scitranslmed.abd7064
  • N. Matsushita, Y. Takami, M. Kimura, S. Tachiiri, M. Ishiai, T. Nakayama, and M. Takata, “Role of NAD-Dependent Deacetylases SIRT1 and SIRT2 in Radiation and Cisplatin-Induced Cell Death in Vertebrate Cells,” Genes to Cells : devoted to Molecular & Cellular Mechanisms 10, no. 4 (2005): 321–32. doi:10.1111/j.1365-2443.2005.00836.x
  • M. Fujimura, T. Tominaga, and T. Yoshimoto, “Nicotinamide Inhibits Inducible Nitric Oxide Synthase mRNA in Primary Rat Glial Cells,” Neuroscience Letters 228, no. 2 (1997): 107–10. doi:10.1016/s0304-3940(97)00373-x
  • Felipe Salech, Daniela P. Ponce, Andrea C. Paula-Lima, Carol D. SanMartin, and María I. Behrens, “Nicotinamide, a Poly [ADP-Ribose] Polymerase 1 (PARP-1) Inhibitor, as an Adjunctive Therapy for the Treatment of Alzheimer’s Disease,” Frontiers in Aging Neuroscience 12 (2020): 255. doi:10.3389/fnagi.2020.00255
  • Ritu Jakhar, Mehak Dangi, Alka Khichi, and Anil Kumar Chhillar, “Relevance of Molecular Docking Studies in Drug Designing,” Current Bioinformatics 15, no. 4 (2020): 270–8. doi:10.2174/1574893615666191219094216
  • R. Wałęsa, T. Kupka, and M. A. Broda, “Density Functional Theory (DFT) Prediction of Structural and Spectroscopic Parameters of Cytosine Using Harmonic and Anharmonic Approximations,” Structural Chemistry 26, no. 4 (2015): 1083–93. doi:10.1007/s11224-015-0573-0
  • M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, J. R. Cheeseman, M. A. Robb, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, et al, GAUSSIAN 09, Revision, Wallingford CT: Gaussian, Inc., 2009.
  • C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density,” Physical Review. B, Condensed Matter 37, no. 2 (1988): 785–9. doi:10.1103/physrevb.37.785
  • A. D. Becke, “Density‐Functional Thermochemistry. IV. A New Dynamical Correlation Functional and Implications for Exact‐Exchange Mixing,” The Journal of Chemical Physics 104, no. 3 (1996): 1040–6. doi:10.1063/1.470829
  • R. G. Parr, Horizons Quant Chem. Dordrecht: Springer, 1980. pp. 5–15.
  • M. P. Andersson, and P. Uvdal, “New Scale Factors for Harmonic Vibrational Frequencies Using the B3LYP Density Functional Method with the Triple-Zeta Basis Set 6-311 + G(d,p),” The Journal of Physical Chemistry. A 109, no. 12 (2005): 2937–41. doi:10.1021/jp045733a
  • A. Frisch, A. B. Nielson, and A. J. Holder, Gaussview User Manual, Pittsburgh, PA,: Gaussian Inc, 2000., 556.
  • J. L. M. Martin, and C. V. Alsenoy, Gar2ped, Antwerp: University of Antwerp, 1995.
  • R. F. W. Bader, and J. R. Cheeseman, AIMPAC: A Suite of Programs for the AIM Theory (Ontario, Canada: McMaster University, 2000).
  • A. D. Laurent, and D. Jacquemin, “TD-DFT Benchmarks: A Review,” International Journal of Quantum Chemistry 113, no. 17 (2013): 2019–39. doi:10.1002/qua.24438
  • S. Miertus, E. Scrocc, and J. Tomasi, “Electrostatic Interaction of a Solute with a Continuum. A Direct Utilizaion of AB Initio Molecular Potentials for the Prevision of Solvent Effects,” Chemical Physics. 55, no. 1 (1981): 117–29. doi:10.1016/0301-0104(81)85090-2
  • M. Cossi, V. Barone, R. Cammi, and J. Tomasi, “Ab Initio Study of Solvated Molecules: A New Implementation of the Polarizable Continuum Model,” Chemical Physics Letters. 255, no. 4-6 (1996): 327–35. doi:10.1016/0009-2614(96)00349-1
  • S. Miertus, and J. Tomasi, “Approximate Evaluations of the Electrostatic Free Energy and Internal Energy Changes in Solution Processes,” Chemical Physics. 65, no. 2 (1982): 239–45. doi:10.1016/0301-0104(82)85072-6
  • M. E. Casida, and D. P. Chong, Recent Developments in Density Functional Theory, vol. 1, Singapore : World Scientific.1995.
  • S. Armaković, and S. J. Armaković, “Atomistica.online – Web Application for Generating Input Files for ORCA Molecular Modelling Package Made with the Anvil Platform,” Molecular Simulation. 49, no. 1 (2023): 117–23. doi:10.1080/08927022.2022.2126865
  • Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, and Arthur J. Olson, “AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility,” Journal of Computational Chemistry 30, no. 16 (2009): 2785–91. doi:10.1002/jcc.21256
  • Discovery Studio 45 Guide, Accelrys Inc, San Diego, 2009. http://wwwaccelryscom.
  • E. Runge, and E. K. U. Gross, “Density-Functional Theory for Time-Dependent Systems,” Physical Review Letters 52, no. 12 (1984): 997–1000. doi:10.1103/PhysRevLett.52.997
  • Hiroshi Yoshida, Kumi Takeda, Junko Okamura, Akito Ehara, and Hiroatsu Matsuura, “A New Approach to Vibrational Analysis of Large Molecules by Density Functional Theory: Wavenumber-Linear Scaling Method,” The Journal of Physical Chemistry A 106, no. 14 (2002): 3580–6. doi:10.1021/jp013084m
  • G. Socrates, Infrared and Raman Characteristic Group Frequencies, Tables and Charts Germany (Germany: Wiley, 2004).
  • B. Smith, Infrared Spectral Interpretation, a Systematic Approach. Florida US: CRC press 2018.
  • R. M. Silverstein, and G. C. Bassler, “Spectrometric Identification of Organic Compounds,” Journal of Chemical Education 39, no. 11 (1962): 546. doi:10.1021/ed039p546
  • N. Sundaraganesan, S. Ilakiamani, B. Anand, H. Saleem, and B. D. Joshua, “FTIR, FT-Raman Spectra and ab Initio DFT Vibrational Analysis of 2-Amino-5-Chloropyridine,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 64, no. 3 (2006): 586–94. doi:10.1016/j.saa.2005.07.061
  • A. J. Stone, “Natural Bond Orbitals and the Nature of the Hydrogen Bond,” The Journal of Physical Chemistry. A 121, no. 7 (2017): 1531–4. doi:10.1021/acs.jpca.6b12930
  • R. P. Gangadharan, and S. S. Krishnan, “Natural Bond Orbital (NBO) Population Analysis of 1-Azanapthalene-8-ol,” Acta Physica Polonica A 125, no. 1 (2014): 18–22. doi:10.12693/APhysPolA.125.18
  • D. L. N. González, A. Saeed, G. Shabir, U. Flörk, and M. F. Erben, “Conformational and Crystal Structure of Acyl Thiourea Compounds: The Case of the Simple (2,2-Dimethyl-Propionyl) Thiourea Derivative,” Journal of Molecular Structure. 1215 (2020): 128227. doi:10.1016/j.molstruc.2020.128227
  • J. Pandey, P. Prajapati, A. Srivastava, P. Tandon, K. Sinha, A. P. Ayala, and A. K. Bansal, “Spectroscopic and Molecular Structure (Monomeric and Dimeric Model) Investigation of Febuxostat: A Combined Experimental and Theoretical Study,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 203 (2018): 1–12. doi:10.1016/j.saa.2018.05.074
  • R. F. W. Bader, Atoms in Molecules, a Quantum Theory,” Oxford, UK: Oxford University Press, 1990.
  • U. Koch, and P. L. Popelier, “Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density,” The Journal of Physical Chemistry 99, no. 24 (1995): 9747–54. doi:10.1021/j100024a016
  • I. Rozas, I. Alkorta, and J. Elguero, “Intramolecular Hydrogen Bonds in ortho -Substituted Hydroxybenzenes and in 8-Susbtituted 1-Hydroxynaphthalenes: Can a Methyl Group Be an Acceptor of Hydrogen Bonds?,” The Journal of Physical Chemistry A 105, no. 45 (2001): 10462–7. doi:10.1021/jp002808b
  • E. Espinosa, E. Molins, and C. Lecomte, “Hydrogen Bond Strengths Revealed by Topological Analyses of Experimentally Observed Electron Densities,” Chemical Physics Letters 285, no. 3–4 (1998): 170–3. doi:10.1016/S0009-2614(98)00036-0
  • G. Merino, A. Vela, and T. Heine, “Description of Electron Delocalization via the Analysis of Molecular Fields,” Chemical Reviews 105, no. 10 (2005): 3812–41. doi:10.1021/cr030086p
  • E. J. Baerends, O. V. Gritsenko, and R. Van Meer, “The Kohn-Sham Gap, the Fundamental Gap and the Optical Gap: The Physical Meaning of Occupied and Virtual Kohn-Sham Orbital Energies,” Physical Chemistry Chemical Physics : PCCP 15, no. 39 (2013): 16408–25. doi:10.1039/c3cp52547c
  • M. E. D. Lestard, D. M. Gil, O. Estevez-Hernandez, M. F. Erben, and J. Duque, “Structural, Vibrational and Electronic Characterization of 1-Benzyl-3-Furoyl-1-Phenylthiourea: An Experimental and Theoretical Study,” New Journal of Chemistry 39, no. 9 (2015): 7459–71. doi:10.1039/C5NJ01210D
  • M. Agrawal, A. Kumar, and A. Gupta, “Conformational Stability, Spectroscopic Signatures and Biological Interactions of Proton Pump Inhibitor Drug Lansoprazole Based on Structural Motifs,” RSC Advances 7, no. 66 (2017): 41573–84. doi:10.1039/C7RA00130D
  • A. K. Srivastava, A. K. Pandey, S. Jain, and N. Misra, “FT-IR Spectroscopy, Intra-Molecular C − H⋯O Interactions, HOMO, LUMO, MESP Analysis and Biological Activity of Two Natural Products, Triclisine and Rufescine: DFT and QTAIM Approaches,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 136 (2015): 682–9. doi:10.1016/j.saa.2014.09.082
  • S. K. Tripathi, and S. K. Singh, “Insights into the Structural Basis of 3,5-Diaminoindazoles as CDK2 Inhibitors: Prediction of Binding Modes and Potency by QM-MM Interaction, MESP and MD Simulation,” Molecular bioSystems 10, no. 8 (2014): 2189–201. doi:10.1039/c4mb00077c
  • S. R. Gadre, C. H. Suresh, and N. Mohan, “Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity,” Molecules 26, no. 11 (2021): 3289. doi:10.3390/molecules26113289
  • J. Frau, and D. Glossman-Mitnik, “Conceptual DFT Study of the Local Chemical Reactivity of the Colored BISARG Melanoidin and Its Protonated Derivative,” Frontiers in Chemistry 6 (2018): 136. doi:10.3389/fchem.2018.00136
  • N. Flores-Holguín, J. Frau, and D. Glossman-Mitnik, “Chemical Reactivity Properties, Drug-Likeness Features and Bioactivity Scores of the Cholecystokinin Peptide Hormone,” Computational Molecular Bioscience 09, no. 02 (2019): 41–7. doi:10.4236/cmb.2019.92004
  • P. Verma, A. Srivastava, K. Srivastava, P. Tandon, and M. R. Shimpi, “Molecular Structure, Spectral Investigations, Hydrogen Bonding Interactions and Reactivity-Property Relationship of Caffeine-Citric Acid Cocrystal by Experimental and DFT Approach,” Frontiers in Chemistry 9 (2021): 708538. doi:10.3389/fchem.2021.708538
  • G. Klopman, “Chemical Reactivity and the Concept of Charge- and Frontier-Controlled Reactions,” Journal of the American Chemical Society 90, no. 2 (1968): 223–34. doi:10.1021/ja01004a002
  • R. G. Parr, L. V. Szentpály, and S. Liu, “Electrophilicity Index,” Journal of the American Chemical Society 121, no. 9 (1999): 1922–4. doi:10.1021/ja983494x
  • L. R. Domingo, M. Ríos-Gutiérrez, and P. Pérez, “Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity,” Molecules 21, no. 6 (2016): 748. doi:10.3390/molecules21060748
  • K. Gupta, T. K. Ghanty, and S. K. Ghosh, “Polarizability, Ionization Potential, and Softness of Water and Methanol Clusters: An Interrelation,” The Journal of Physical Chemistry. A 116, no. 25 (2012): 6831–6. doi:10.1021/jp3048357
  • P. Geerlings, F. De Proft, and W. Langenaeker, “Conceptual Density Functional Theory,” Chemical Reviews 103, no. 5 (2003): 1793–873. doi:10.1021/cr990029p
  • Z. Ashraf, A. Saeed, and H. Nadeem, “Design, Synthesis and Docking Studies of Some Novel Isocoumarin Analogues as Antimicrobial Agents,” RSC Adv. 4, no. 96 (2014): 53842–53. doi:10.1039/C4RA07223E
  • L. G. Ferreira, R. N. Dos Santos, G. Oliva, and A. D. Andricopulo, “Molecular Docking and Structure-Based Drug Design Strategies,” Molecules 20, no. 7 (2015): 13384–421. doi:10.3390/molecules200713384
  • David Gfeller, Aurélien Grosdidier, Matthias Wirth, Antoine Daina, Olivier Michielin, and Vincent Zoete, “SwissTargetPrediction: A Web Server for Target Prediction of Bioactive Small Molecules,” Nucleic Acids Research 42, no. Web Server issue (2014): W32–W38. doi:10.1093/nar/gku293
  • M. Ishii, and Y. Kurachi, “Muscarinic Acetylcholine Receptors,” Current Pharmaceutical Design 12, no. 28 (2006): 3573–81. doi:10.2174/138161206778522056
  • M. Jung, R. C. Neugebauer, and W. Sippl, “Inhibitors of NAD + Dependent Histone Deacetylases (Sirtuins),” Current Pharmaceutical Design 14, no. 6 (2008): 562–73. doi:10.2174/138161208783885380
  • A. Mittal, and R. Kakkar, “Nitric Oxide Synthases and Their Inhibitors: A Review,” Letters in Drug Design & Discovery 17, no. 3 (2020): 228–52. doi:10.2174/1570180816666190222154457
  • F. Laudisi, M. Sambucci, and C. Pioli, “Poly (ADP-Ribose) Polymerase-1 (PARP-1) as Immune Regulator,” Endocrine, Metabolic & Immune Disorders Drug Targets 11, no. 4 (2011): 326–33. doi:10.2174/187153011797881184
  • K. P. S. Adinarayana, and R. K. Devi, “Protein-Ligand Interaction Studies on 2, 4, 6- Trisubstituted Triazine Derivatives as anti-Malarial DHFR Agents Using AutoDock,” Bioinformation 6, no. 2 (2011): 74–7. doi:10.6026/97320630006074

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.