The 3rd IUPAP International Conference on Women in Physics 2008, Seoul, KOREA

Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii

Raji Heyrovska* and Saraswathi Narayan#
*Institute of Biophysics, Academy of Sciences of the Czech Republic, Czech Republic; Email: * rheyrovs@hotmail.com #Stevenson University, Stevenson, MD 21153; Email: # f-naraya@stevenson.edu
ABSTRACT
Bond lengths as sums of atomic and or ionic radii: Work in recent years [1] has shown for the first time 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. Many examples are provided, where the experimental bond lengths agree with the radii sums. The examples here include inorganic compounds like alkali halides and graphene, organic like methane and benzene and biological like nucleic acids, amino acids, vitamin B2 & its reduced form and caffeine related molecules. This has enabled presenting the structures at the atomic level of these molecules for the first time. The ATOMIC STRUCTURES and the radii used are shown in Figs. 1 7.
Conventional formulae of 20 essential amino acids:

INTRODUCTION
1) THE COVALENT [2a] OR BONDING ATOMIC RADIUS [2b], d(A) and the covalent bond length, d(AB): d(A) = d(AA)/2 and d(AB) = d(A) + d(B) (for examples: see Figs. 3-7 here) (1a,b)

2) GOLDEN RATIO BASED ANIONIC AND CATIONIC RADII, [1a]: The Golden ratio ( = 1.618), also known as The Divine ratio, appears in the geometry of a variety of Natures creations [3]. It was shown [1a,b] that, in fact, arises right in the core of the H-atom due to the two opposite charges of the proton and electron, p+ and e-, respectively. The ionization potential, IH as the sum of Ip (= e/ap) and Ie (= -e/ae), where aB = ap + ae is he ground state Bohr radius, gives: IH = e/aB = Ip + Ie = (e/)[(1/ap) (1/ae)]; (1/aB) = (1/ap) (1/ae); aB = ap + ae (2a-c)

Eqs. 2b,c, give ae/ap = = (1 + 51/2)/2 = 1.618.. and ap = (aB/2) < ae = (aB/), the Golden sections of aB. The covalent bond length, d(HH) = 2d(H) (= 0.74 ) is the diagonal of a square with aB as a side. d(HH) = 2d(H) = 21/2aB = 21/2( ap + ap) = d(HH)/2 + d(HH)/ = d(H+) + d(H-) (3)

where the ionic radii, d(H+) = d(HH)/2 (= 0.28 ) and d(H-) = d(HH)/ (= 0.46 ). The empirical radius (= 0.28 ) for H suggested [2a] in the partially ionic bonds in hydrogen halides (HX), is thus actually d(H+). Also, note that H+, H- are the resonance forms [2a] of H in the H2 molecule. 3) PARTIALLY AND COMPLETELY IONIC BONDS: On subtracting d(H+) = 0.28 , from the bond lengths d(HX)expt and d(MH)expt one obtains [1a,b] the successive Eqs. (4a-c): d(HX)expt - d(H+) = d(XX)expt/2 = d(X); (for HX, hydrogen halides) (for MH, alkali hydrides) (for MX, alkali halides, see Fig. 1) (4a) (4b) (4c)
0.77 0.71 0.67 0.70 0.62 0.37 0.67 0.60 0.92 1.04

Cs.b.

Cg.b.

Cd.b.

Ns.b. Nd.b. Hs.b. Os.b. Od.b.

Ss.b.

d(MH)expt - d(H+) = d(MM)expt/2 = d(M+); d(MX)expt - d(M+) = d(XX)expt/ = d(X-); 4) IN GENERAL,

Fig. 4. Atomic structures of 20 AMINO ACIDS: COMPLETELY

COVALENT BONDS: All bond lengths = sums of covalent radii of adjacent atoms, [6] (see the box above from Fig. 2).

d(AA) = 2d(A) = d(AA)/2 + d(AA)/ = d(A+) + d(A-); (for any atom A) 5) ADDITIVITY OF RADII IN AQUEOUS SOLUTIONS AND THE HYDROGEN BONDS [1b,4] (see Fig. 3): d(--H) = md(H) + nd(H+) (where n = 1 or 2 and m = 0, 1, 2 or 3; see p.349 below from [4b])

(5)

(6)
Conventional Structures

d(M+X-) = R(M+) + R(X-); R(M+) = d(MM)/2 and R(X-) = d(XX)/

Nature Precedings : doi:10.1038/npre.2009.3292.1 : Posted 28 May 2009

Li+ R(M+): 1.33

Na+ 1.61

K+ 1.96

Rb+ 2.09

Cs+ 2.31 Na+ Cl-

All alkali halides Example:

SODIUM CHLORIDE
(shown below: an fcc plane) d(Na+Cl-) = R(Na+) + R(Cl-) 2.83 = 1.61 + 1.22

R(X-): F0.88

Cl1.22

Br1.37

I1.58

Fig. 1. Completely ionic bonds: Alkali halides, [1]: Heyrovska R., a) Mol. Phys. 2005; 103: 877- 882.
Cs.b. Cg.b. Cd.b. Ns.b. Nd.b. Hs.b. Os.b. Od.b. P Ss.b.

Fig. 5. RIBOFLAVIN (VITAMIN B2) & ITS REDUCED FORM: COMPLETELY COVALENT BONDS, [7]

Fig. 6. METHANE, BENZENE, GRAPHENE: All Bond lengths = sum of the radii of the adjacent atoms, [8]

0.77

0.71

0.67

0.70

0.62

0.37

0.67

0.60

0.92

1.04

Fig. 2. The radii (Rcov) of the six atoms, C, N, H, O, P and S, that build the molecules of life.
C (quadrivalent), N (trivalent), H (monovalent), O (divalent), P (pentavalent) & S (hexa/bivalent), which constitute the atomic structures of THE LIFE GIVING MOLECULES [1c, 6, 7, 9]. [Subscripts: s.b: single bond, g.b. : graphite/graphene bond, d.b: double bond.]

Fig. 3. COMPLETELY COVALENT BONDS: Atomic structures of MOLECULES IN DNA (17 : 20 section) All bond lengths = sums of the covalent radii of adjacent atoms, [1c]. In the 17 section, there are 5P atoms. This is half the 34 : 20 section per turn of the helix with ten P atoms, and each P atom is 10 from the central axis: Franklin R.E., Gosling R.G., [5]. Note: RNA has U and ribose in place of T and deoxyribose, [1c]. Lengths of the NHO and NHN hydrogen bonds in the AT and CG pairs: see [4b] and p. 349 in the box below: RH: CPL, 2006.

Fig. 7. COMPLETELY COVALENT BONDS Atomic structures of CAFFEINE AND RELATED MOLECULES All bond lengths = sums of covalent radii of adjacent atoms, [9].

ACKNOWLEDGEMENTS: R. H. is grateful to the IBP for support by institutional research plans Nos. AV0Z50040507 and AV0Z50040702 grants of the Academy of Sciences of the Czech Republic (ASCR) and thanks ASCR and the Organizers of ICWIP2008 for the financial support to participate in this conference. S. N. thanks Stevenson University, for the partial financial support to attend this conference. REFERENCES [1] Heyrovska R., a) Golden ratio, Bohr radius, ionic radii, additivity of radii in bond lengths etc: Mol. Phys. 2005; 103: 877, and the literature therein, b) Golden ratio, ionic radii, aqueous solutions, etc: Chapter 12 in Innovations in Chemical Biology, ed: B. Sener, Springer, October 2008 c) Atomic structures of nucleic acids etc: Open Structural Biology J., 2 (2008) 1 7. [2] a) Pauling L., The Nature of the Chemical Bond (Cornell Univ. Press, NY, 1960) and b) http://wps.prenhall.com/wps/media/objects/3311/3390919/blb0702.html [3] The Golden ratio: http://www.goldennumber.net/ (and the literature therein). [4] Heyrovska R., a) Golden ratio and additivity of radii in ionic and hydration distances Chem. Phys. Lett. 2006; 429: 600-605 and b) Golden ratio and additivity of radii in the lengths of hydrogen bonds Chem. Phys. Lett. 2006; 432: 348-351. [5]: Franklin R.E., Gosling R.G., 34:21 aspect ratio in DNA: Nature, 1953; 171: 740-741; see for full texts of this and other papers: http://www.nature.com/nature/dna50/archive.html [6]: Heyrovska R., The 20 essential amino acids: http://arxiv.org/ftp/arxiv/papers/0804/0804.2488.pdf [7]: Heyrovska R., Riboflavin and its reduced form: http://arxiv.org/ftp/arxiv/papers/0806/0806.3462.pdf [8]: Heyrovska R., Methane, Benzene and graphene: http://arxiv.org/ftp/arxiv/papers/0804/0804.4086.pdf [9]: Heyrovska R. and Narayan S., Caffeine and related molecules: http://arxiv.org/ftp/arxiv/papers/0801/0801.4261.pdf