Structures of Molecules at the Atomic Level: Caffeine and Related Compounds
Raji Heyrovska and Saraswathi Narayan
1Institute of Biophysics, Academy of Sciences of the Czech Republic,
Královopolská 135, 612 65 Brno, Czech Republic
2Stevenson University, 1525 Greenspring Valley Rd., Stevenson, MD 21153
corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it./snarayan@stevenson.edu
ABSTRACT
Recent researches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. An investigation of the bond length data for the molecular components of nucleic acids, showed (for the first time) that all were effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O, and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.
INTRODUCTION
It was shown in recent years (Heyrovska 2005, 2006, 2009) that bond lengths of completely or partially covalent or ionic bonds are sums of the radii of the adjacent atoms and or ions. The atomic radii are the covalent radii (Pauling 1960) or the bonding atomic radii (www.prenhall.com) d(A) defined as,
d(A) = d(AA)/2 (1)
where d(AA) is the interatomic distance. The ionic radii are the Golden sections of d(AA), based on the Golden ratio φ, (Heyrovska 2005, 2006). The Golden ratio (φ = 1.618), also known as The Divine ratio, appears in the geometry of a variety of Nature’s creations, as described e.g. in (www.goldennumber.net). It is the ratio a/b of a larger segment (a) to a smaller segment (b) of a line which are such that a/b = (a + b)/a. From the latter, one obtains the Golden quadratic equation, a/b = (a/b)2 – 1 whose positive root is (a/b) = (1 + 51/2)/2 = φ (= 1.618..). The segments a = c/φ and b = c/φ2 are called the Golden sections . . . . . . . . . .
REFERENCES
EGAWA T, KAMIYA A, TAKEUCHI H, KONAKA S. 2006. Molecular structure of caffeine as determined by gas electron diffraction aided by theoretical calculations. J Mol Struc 825: 151-157.
FRANKLIN RE, GOSLING RG. 1953. Molecular configuration in sodium thymonucleate. Nature 171: 740-741. Accessed from http://www.nature.com/ nature/dna50/archive.html
GUNASEKARAN S, SANKARI G, PONNUSAMY S. 2005. Vibrational spectral investigation on xanthine and its derivatives - theophylline, caffeine and theobromine. Spectrochim Acta Part A 61: 117-127.
HEYROVSKA R. 2005. The Golden ratio, ionic and atomic radii and bond lengths. Mol Phys 103: 877-882.
HEYROVSKA R. 2009. The Golden ratio in the creations of Nature arises in the architecture of atoms and ions. Chapter 12 In: Innovations in Chemical Biology. Bilgesenar (ed). Proceedings of the 9th Eurasia Conference on Chemical Sciences: Jan 2009; Antalya, Turkey: Springer.
HEYROVSKA R. 2008. Structures of the Molecular Components in DNA and RNA with Bond Lengths Interpreted as Sums of Atomic Covalent Radii. The Open Structural Biology Journal 2: 1-7; arXiv:0708.1271v4.
HEYROVSKA R. 2006. Dependence of ion-water distances on covalent radii, ionic radii in water and distances of oxygen and hydrogen of water from ion/ water boundaries. Chem. Phys. Lett. 429: 600-605; doi:10.1016/j.cplett.2006.08.073
HEYROVSKA R. 2006. Dependence of the length of the hydrogen bond on the covalent and cationic radii of hydrogen, and additivity of bonding distances. Chem. Phys. Lett. 432: 348-351; doi:10.1016/j. cplett.2006.10.037
PAULING L. 1960. The Nature of the Chemical Bond. Ithaca, New York: Cornell University Press. 644p.
UCUN F, SAGLAM A, GUCLU V. 2007. Molecular structures and vibrational frequencies of xanthine and its mehtyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations. Spectrochim Acta Part A 67: 342-349.
ZAJAC MA, ZAKRZEWSKI AG, KOWAL MG, NARAYAN S. 2003. A novel method of caffeine synthesis from uracil. Synthetic Communs. 33: 3291-97.
http://wps.prenhall.com/wps/media/objects/3311/3390919/blb0702.html
http://www.goldennumber.net/ (and the literature therein).
http://en.wikipedia.org/wiki/User:Icey/Gallery#Chemical structures (pages was last modified on 29 July 2009 at 20.23)
