Overview of the use of theory to understand infrared and Raman spectra and images of biomolecules: Colorectal cancer as an example

Theoretical Chemistry Accounts

Volumn 130, Issue 4-6, 2011, Pages 1261-1273

  Piva, J A A C ^a   Silva, J L R ^a   Raniero, L ^a   Martin, A A ^a   Bohr, H G ^b   Jalkanen, K J ^a,b,c  

^a INSTITUTO DE PESQUISA E DESENVOLVIMENTO   (Brazil)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Cluster analysis; Colorectal cancer diagnosis; First principles; Image generation; Infrared; Infrared imaging; Linear discriminant analysis; Molecular mechanics; Principal component analysis; Raman; Raman imaging; Statistical methods

Indexed keywords

EID: 81955164155     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-011-1063-0     Document Type: Article

References (42)

1. Spotlight 400 Series User's Guide (2008) PerkinElmer Ltd, Bucks HP9 2FX, United Kingdom.
2. Karsa LV, Lignini TA, Patnick J, Lambert R, Sauvaget C (2010) The dimensions of the CRC problem. Best Pract Res Clin Gastroenterol 24: 381-396.
3. Cancer Facts & Figures 2010 (2010) American Cancer Society, Los Angeles, CA. http://www. cancer. org/Research/CancerFactsFigures/CancerFactsFigures/cancer-facts-figures- 2010-rev, Accessed 28 May 2011.
4. Colorectal Cancer (2011) American Cancer Society, Los Angeles, CA. http://www. cancer. org/Cancer/ColonandRectumCancer/DetailedGuide/colorectal-cancer-pdf12, Accessed 28 May 2011.
5. Winawer SJ (2007) Colorectal cancer screening. Best Pract Res Clin Gastroenterol 21: 1031-1048.
6. Bird B, Miljkovic M, Romeo MJ, Smith J, Stone N, George MW, Diem M (2008) Infrared micro-spectral imaging: distinction of tissue types in axillary lymph node histology. BMC Clin Pathol 8: 8.
7. Fernandez D, Bhargava R, Hewitt SM, Levin IW (2005) Infrared spectroscopic imaging for histopathologic recognition. Nat Biotechnol 23: 469-474.
8. Andrade PO, Bitar RA, Yassoyama K, Martinho H, Santo AM, Bruno PM, Martin AA (2007) Study of normal colorectal tissue by FT-Raman spectroscopy. Anal Bioanal Chem 387: 1643-1648.
9. Steiner G, Koch E (2009) Trends in Fourier transform infrared spectroscopic imaging. Anal Bioanal Chem 394: 671-678.
10. Petibois C, Déléris G (2006) Chemical mapping of tumor progression by FTIR imaging: towards molecular histopathology. Trends Biotechnol 24: 455-462.
11. Lasch P, Diem M, Hansch W, Naumann D (2006) Artificial neural networks as supervised techniques for FT-IR microspectroscopic imaging. J Chemom 20: 209-220.
12. Krafft C, Codrich D, Pelizzo G, Sergo V (2008) Raman and FTIR microscopic imaging of colon tissue: a comparative study. J Biophotonics 1: 154-169.
13. Hedegaard M, Matthaus C, Hassing S, Krafft C, Diem M, Popp J (2011) Spectral imaging and clustering algorithms for assessment of single cells by Raman microscopic imaging. Theor Chem Acc. doi: 10. 1007/s00214-011-0957-1.
14. Hertz JA, Krogh AS, Palmer RG (1991) Introduction to the theory of neural computation. Addison-Wesley, Redwood City.
15. Rommelhardt DE, Hinton GE, Williams RJ (1986) Learning representations by back-propagating errors. Nature 323: 533-536.
16. Bohr H, Bohr J, Brunak S, Cotterill RM, Lautrup B, Nørskov L, Olsen OH, Petersen SB (1988) Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. FEBS Lett 241: 223-238.
17. Onsager L (1936) Electric moments of molecules in liquids. J Am Chem Soc 58: 1486-1493.
18. Nemzkin VN, Hadt RG, Belosludov RV, Mizuseki H, Kawazoe Y (2007) Influence of molecular geometry, exchange-correlation functional, and solvent effects in the modeling of vertical excitation energies in phthalocyanines using time-dependent density functional theory (TDDFT) and polarized continuum model TDDFT methods: can modern computational chemistry methods explain experimental controversies? J Phys Chem A 111: 12901-12913.
19. Tomasi J, Pérsico M (1994) Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem Rev 94: 2027-2094.
20. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105: 2999-3093.
21. Cramer C, Truhlar DG (1995) Continuum solvation models: classical and quantum mechanical implementations. In: Lipkowitz KB, Boyd DB (eds) Rev Comput Chem 6: 1-72. doi: 10. 1002/9780470125830. ch1.
22. Tajkhorshid E, Jalkanen KJ, Suhai S (1998) Structure and vibrational spectra of the zwitterion l-alanine in the presence of explicit water molecules: a density functional analysis. J Phys Chem B 102: 5899-5913.
23. Jalkanen KJ, Degtyarenko IM, Nieminen RM, Cao X, Nafie LA, Zhu F, Barron LD (2008) Role of hydration in determining the structure and vibrational spectra of l-alanine and N-acetyl l-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach. Theor Chem Acc 119: 191-210.
24. Jalkanen KJ, Suhai S (1996) N-acetyl-l-alanine N'-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra. Chem Phys 208: 81-116.
25. Deplazes E, van Bronswijk W, Zhu F, Barron LD, Ma S, Nafie LA, Jalkanen KJ (2008) A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the l-histidine zwitterion. Theor Chem Acc 119: 155-176.
26. Jalkanen KJ, Jürgensen VW, Claussen A, Jensen GM, Rahim A, Wade RC, Nardi F, Jung C, Nieminen RM, Degtyarenko IM, Herrmann F, Knapp-Mohammady M, Niehaus T, Frimand K, Suhai S (2006) The use of vibrational spectra to study protein and DNA structures, hydration, and binding of biomolecules: a combined theoretical and experimental approach. Int J Quantum Chem 106: 1160-1198.
27. Jalkanen KJ, Knapp-Mohammady M, Jensen KBS, Ma S, Nafie LA, Zhu F, Barron LD, Aoki Y, Mannfors B, Bohr J, Nieminen RM, Rodarte A, Pomogaev V, Alves RS, Carvalho CS, JACC Piva, Martin AA (2011). (in preparation).
28. Talbot I, Price A, Tellez M (2007) Biopsy pathology in colorectal disease, 2nd edn. Oxford University Press, Oxford.
29. Lasch P, Pacifico A, Diem M (2002) Spatially resolved IR microspectroscopy of single cells. Biopolym Biospectrosc 67: 335-338.
30. Walsh MJ, Hammiche A, Fellous TG, Nicholson JM, Cotte M, Susini J, Fullwood NJ, Martin-Hirsch PL, Alison MR, Martin FL (2009) Tracking the cell hierarchy in the human intestine using biochemical signatures derives by mid-infrared microespectroscopy. Stem Cell Res 3: 15-27.
31. Ramesh J, Salman A, Mordechai S, Argov S, Goldstein J, Sinelnikov I, Walfisch S, Guterman H (2001) FTIR microscopic studies on normal, polyp, and malignant human colonic tissues. Subsurfac Sens Tech Appl 2: 99-117.
32. Conti C, Ferraris P, Giorgini E, Rubini C, Sabbatini S, Tosi G, Anastassopoulou J, Arapantoni P, Boukaki E, Konstadoudakis S, Theophanidesc T, Valavanis C (2008) FT-IR microimaging spectroscopy: a comparison between healthy and neoplastic human colon tissues. J Mol Struct 881: 46-51.
33. Lasch P, Haensch W, Naumann D, Diem M (2004) Imaging of colorectal adenocarcinoma using FT-IR microspectroscopy and cluster analysis. Biochim Biophys Acta 1688: 176-186.
34. Pomogaev V, Gu FL, Pomogaeva A, Aoki Y (2009) Elongation method for calculating excited states of aromatic molecules embedded in polymers. Int J Quantum Chem 109: 1328-1340.
35. Cusasi T, Granucci G, Persico M (2011) Photodynamics and time-resolved fluorescence of azobenzene in solution: a mixed quantum-classical simulation. J Am Chem Soc 133: 5109-5123.
36. Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S (2011) Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum mechanical methods. Theor Chem Acc. doi: 10. 1007/s00214-011-0936-6.
37. Imamura A, Aoki Y, Maekawa K (1990) A theoretical synthesis of polymers by using uniform localization of molecular orbitals: proposal of an elongation method. J Chem Phys 95: 5419-5431.
38. Makowski M, Korchowiec J, Gu FL, Aoki Y (2006) Efficiency and accuracy of the elongation method as applied to electronic structures of large systems. J Comput Chem 27: 1603-1619.
39. Tawada Y, Tsuneda T, Yanagisawa S, Yanai T, Hirao K (2004) A long-range-corrected time-dependent density functional theory. J Chem Phys 120: 8425-8433.
40. Yanai T, Tew DP, Handy NC (2004) A new hybrid exchange-correlation functional using the coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett 393: 51-57.
41. Peach MJG, Helgaker T, Sałek P, Keal TW, Lutnæ OB, Tozer DJ, Handy NC (2004) Assessment of a coulomb-attenuated exchange-correlation energy functional. Phys Chem Chem Phys 8: 558-562.
42. Song J-W, Tsuneda T, Sato T, Hirao K (2011) An examination of density functional theories on isomerization energy calculations of organic molecules. Theor Chem Acc. doi: 10. 1007/s00214-011-0997-6.