Predicting manoid molecules, a novel class of compounds

Transcription

1 Indian Journal of Chemistry Vol. 53A, October 2014, pp Predicting manoid molecules, a novel class of compounds B M Deb a, *, Debasish Mondal b & S P Bhattacharyya b, a Visva-Bharati University, Publishing Department, 6 A J C Bose Road, Kolkata , India bmdeb@yahoo.co.in b Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata , India Received 22 July 2014; revised and accepted 22 August 2014 Seven stable new molecules in the form of human beings, are predicted to be stable. The geometries of these manoid molecules have been optimized using a combination of semi-empirical and ab initio quantum chemical methods. The relative dimensions of these molecules conform by and large to those of human beings, belonging to the C 1 point group, with one kind of molecule resembling a player heading a soccer ball. A possible route is suggested for synthesizing the torso of such molecules of considerable potential interest. Keywords: Theoretical chemistry, Computational chemistry, Ab initio calculations, Manoid molecules, Molecule prediction In spite of a decades-old conjecture 1 on the possible stable existence of molecules which would look like human beings (hereafter called manoid molecules ) and therefore might possess interesting linear/nonlinear chemical, physical and biological properties, a deliberate attempt to synthesize and study such manoid molecules does not appear to have been made so far. Nor has there been any quantum mechanical attempt to predict the existence of such molecules. A carbon monoxide man has, however, been observed by chance by Zeppenfeld and Eigler 2 in their STM study of adsorption of CO nanotubes on palladium (111 plane). We report here seven such theoretically stable manoid molecules (I VII, Figs 1 & 2) for the first time, designed in their theoretical optimized geometries (point group C 1, like humans) by a combination of ab initio and semi-empirical quantum chemical methods. For each molecule, the design criteria used are: (i) the molecule should be organic ; (ii) as few atoms as possible should be used in order to achieve a human-like structure; (iii) heteroatoms, if any, should not exceed two in a ring system (we have used only one here) and should not go beyond the third row of the Periodic Table; (iv) the molecule s total charge, if any, should not be high (we have only + 1 or 1 here); (v) one should maximize π-electron conjugation in the molecule; Present address: DAE Raja Ramanna Fellow, Department of Chemistry, Indian Institute of Technology, Mumbai , India. (vi) functional groups, if any, may be attached at the hands and/or feet, to in-build supramolecular capabilities and to increase the possibility of these molecules having non-linear chemical/physical/ biological properties (not discussed in this paper); and (vi) the relative ratios of various limbs of the molecules should by and large conform to those of human beings (such anthropomorphic data on 25 Indian males in their 20 s were gathered by one of the authors). A possible route to the synthesis of the torso of these molecules has been suggested later. Method of Calculation The geometries of all the molecules reported here have been optimized by ab initio calculations using Hartree-Fock (RHF), DFT-BHHLYP and DFT-B3LYP methods, with the 6-31G (2d, 1p) basis set. Together, these constitute an optimum set of computational methods for calculating the equilibrium geometries and properties of polyatomic molecules (see Refs 3, 4 for computational chemistry). In order to reduce computer time, for every molecule, preliminary optimization was done with the semi-empirical AM1 method, using the same basis set, followed by final optimization with each of the ab initio methods. The electronic structures of the molecules in their optimized geometries were then calculated. Since these optimizations required considerable computer time, MP2 geometry optimizations were done for only three of the seven molecules. The MP2 results were found to be consistent with the other methods and therefore were not deemed necessary to be repeated

2 1318 INDIAN J CHEM, SEC A, OCTOBER 2014 Fig. 1 (a) Stick-and-ball and (b) space-filling visuals for seven manoid molecules, I VII, in their optimized geometries, according to the DFT/BHHLYP method. for the other molecules. For the same reasons, CCSD(T) geometry optimizations, which require much larger computer time, and sometimes do not converge, were not performed. However, for small polyatomic molecules where CCSD(T) geometry optimizations are possible, results are known to be close to MP2 and DFT optimized geometries. All the calculations were performed with the GAMESS software package 5-7. The formulas for the seven molecules are as follows: I, C 22 H 16 S, neutral; II, [C 22 H 16 P] + ; III, [C 26 H 22 N 2 O 4 P] + ; IV, [C 28 H 24 N 2 O 4 P]; V, [C 26 H 22 N 2 O 4 P] Li, i.e. anion IV combines with Li + (Na +, K + and Cs + have also been employed); VI, C 24 H 23 N 2 O 4 P, neutral; VII, C 23 H 22 N 3 O 4 P, neutral. II was also interacted with F -, Cl -, Br -, I -. Except I and II, the other molecules had two amino-carboxylic

3 DEB et al.: PREDICTING MANOID MOLECULES, A NOVEL CLASS OF COMPOUNDS 1319 Fig. 2 Bonding patterns with atom numberings, starting from the torso and the hand atoms, for manoid molecules I IV, VI and VII. [ A and B show atoms and their numberings respectively. The numbering focuses attention on the torso atoms. Molecule V is not shown because it is obtained by interacting molecule IV and Li + (see Fig. 1). The following may be noted: I: Atom no. 15 is sulfur atom; atom nos. 1 14, 16 21, 32, 33 are carbon atoms; the rest are hydrogen atoms; II: Atom no. 16 is phosphorus atom; atom nos. 1 15, 17, are carbon atoms; the rest are hydrogen atoms; III: Atom no. 12 is phosphorus atom; atom nos are oxygen atoms; atom nos. 25, 40 are nitrogen atoms; atom nos. 1 11, 13, 16, 17, 19 24, 34, 35, are carbon atoms; the rest are hydrogen atoms; IV: Atom nos. 11 is phosphorus atom; atom nos. 43, 44, 54, 55 are oxygen atoms; atom nos. 41, 42 are nitrogen atoms; atom nos. 1 10, 12, 15 19, 26 28, 30 35, 39, 40, 53 are carbon atoms; the rest are hydrogen atoms; VI: Atom no. 12 is phosphorus atom; atom nos are oxygen atoms; atom nos. 23, 25 are nitrogen atoms; atom nos. 1 11, 13, 16 22, 24, 34, 35, 50, 51 are carbon atoms; the rest are hydrogen atoms; VII: obtained from VI by replacing CH 3 head group with NH 2 ].

4 1320 INDIAN J CHEM, SEC A, OCTOBER 2014 functional groups at the hands, with the possibility of polypeptide linkages with other molecules. No functional groups were placed on the feet Results and Discussion For all the molecules in their optimized geometries according to the various methods, the virial ratios (-<V>/<T> = 2, exact value) were in the range which is a satisfactory indicator for the validity of the calculated results reported in Table 1 on all the seven molecules. The optimized geometries vary somewhat from method to method, but all the methods yield the molecules in a manoid form. As expected, the Hartree-Fock method yields shorter bond lengths due to its neglect of electron correlation. The main general conclusion from Table 1 is that all the seven manoid molecules are quite stable with binding energies between ev with respect to the isolated atoms and between ev with respect to the molecular fragments depicted in Fig. 3. The construction of each molecule by using the fragments is shown in Table 2. The calculated energies of these fragments according to H-F, DFT-BHHLYP, DFT-B3LYP and MP2 methods are listed in Table 3. As discussed later, these fragments might be involved in a retro-synthesis of these species. The heats of formation (Table 1), obtained by the AM1 method with the same basis set, show that molecules I V are endothermic, while molecules VI and VII are exothermic. Both the positive and negative H f values may be compared with the experimental and AM1 calculated values for H 2 O, NH 3, CH 4 and C 6 H 6, given in Table 4. As indicated by benzene, endothermic compounds can have quite stable molecules. From columns 4 and 6 in Table 1, molecule V is the most stable of all the reported molecules. Table 5 shows that the dimensions of these molecules are in broad conformity with the anthropomorphic data gathered by us on a set of humans. The following points may be noted about these molecules: (i) All the reported molecules are strained. (ii) Heteroatom: Since the P atom works better than the corresponding S atom in maintaining conjugation, Table 1 Results on molecules I VII in their optimized geometries. For each method, the geometries were optimized separately. For the fragments (except Li +, F ), see Fig. 3 and Table 3. In each of the columns 2-6, the top value comes from RHF, the second value from DFT/BHHLYP and the lowest value from DFT/B3LYP. For all calculations, the basis set used was 6-31G(2d, 1p) Molecule Total energy (a) Total energy of free atoms (b) Binding energy (a b) Total energy of fragments (c) Stabilization energy (a c) H f c (kj mol -1 ) I a ( ) II a ( ) III a ( ) IV V b VI VII ( ) ( ) ( ) (-8.498) (-8.702) ( ) ( ) (-1.093) a For molecules I, II and III, the values in parentheses are from MP2. b Molecule V is the molecule IV + Li + compound. For molecule II + F compound, column 6 results from top to bottom are , and a.u. respectively, while the heat of formation ( H f ) is kj mol -1 (1 kcal mol -1 = kj mol -1 ). c Heats of formation are obtained by the AM1 method with the same basis set.

5 DEB et al.: PREDICTING MANOID MOLECULES, A NOVEL CLASS OF COMPOUNDS 1321 Fig. 3 DFT/BHHLYP optimized fragments of the seven manoid molecules, representing head, torso, hands and feet. [(a) Cyclopropelenic cation radical, [C 3 H 2 + ] ; (b) Cyclopentadienyl anion radical, [C 5 H 4 - ] ; (c) Methyl radical, [CH 3 ] ; (d) Amino radical, [NH 2 ] ; (e) Bi-cyclopentadienyl phosphorus radical, [C 7 H 2 P] 5 ; (f) Bi-cyclopentadienyl sulfur radical, [C 7 H 2 S] 4 ; (g) Propelene radical, [C 3 H 3 ] ; (h) an amino-acid radical, [C 5 H 6 O 2 N] ; (i) a structural isomer of (h); (j) Cyclopropelenic radical, [C 3 H 2 ]. Formulas in (e) and (f) show 5 and 4 unpaired electrons, with spin multiplicities 6 and 5 respectively. Each of the other radicals has only one unpaired electron, with spin multiplicity 2, as indicated by a dot as a superscript after square brackets]. Table 2 Schemes of formation of seven manoid molecules from optimum-geometry fragments depicted in Fig. 4 Molecule I Radical f + 4 Radical g + Radical j Molecule II Radical a + Radical e + 4 Radical g Molecule III Radical a + Radical e + 2 Radical g + 2 Radical i Molecule IV Radical b + Radical e + 2 Radical g + 2 Radical h Molecule V Molecule IV + Li + Molecule VI Radical c + Radical e + 2 Radical g + 2 Radical i Molecule VII Radical d + Radical e + 2 Radical g + 2 Radical i it confers greater stability to these molecules (see molecules I and II in Table 1). Therefore, P was generally used, except molecule I where S was used. The heteroatom occurs in the torso made of two fused 5-membered rings. (iii) Functionalization: Supramolecular capability was attempted to be incorporated through amino acid functionalization of only the hands while the feet are methyl groups. The hands thus become longer, coming down to the knees (like mythical heroes). Table 3 Calculated energies of fragment radicals in their optimized geometries. [MP2 results did not converge for radicals h, i, j. See Fig. 3] Radical HF MP2 DFT/BHHLYP DFT/B3LYP a b c d e f g h i j Table 4 Calculated and experimental 8 heats of formation ( H f ) of four reference molecules, using the 6-31G (2d, 1p) basis set Molecule H f (kj mol -1 ) a AM1 Expt. 8 CH 4 (g) NH 3 (g) H 2 O (g) C 6 H 6 (g) a 1 kcal mol -1 = kj mol -1

6 1322 INDIAN J CHEM, SEC A, OCTOBER 2014 Table 5 Comparison of relative sizes of limbs of manoid molecules with anthropomorphic data on a set of human beings (gathered by one of the authors). The average ranges of parameters (a f) are obtained from a sample of 25 Indian males in their 20 s. For molecules, optimized DFT/BHHLYP values are chosen a Molecule a b c d e f I II III IV VI VII Human range a The parameters are: a = (Length of head+neck)/(total height); b = (Length of torso)/(total height); c = (Length of hand with fingers)/(total height); d = (Length of leg with foot)/(total height); e = (Width of chest)/(total wingspan); f = (Width of waist)/(total wingspan). These have the potential in forming polypeptide linkages with other molecules. (iv) All molecules are athletic with relatively broad chests and slim waists (Table 5). (v) The head group is very slightly out-of-plane with the torso, by only a fraction of a degree. A 3-member cationic head group gives greater head-torso binding, by about 0.01 a.u. (0.27 ev), compared with a 5-member anionic head group. Replacing CH 3 head group by the NH 2 group reduces the overall molecular binding energy but increases the magnitude of H f (negative). (vi) Bond lengths: As expected, wherever conjugation is present, single and double bonds (in Figs 2 and 3) are intermediate between the corresponding known single and double bonds. Triple bonds occur only in hands and legs. (vii) Non-bonded interaction: In molecule V, obtained by interacting molecule IV with a Li + ion, as well as molecule II interacting with an F - ion, the ion always attaches itself to the head group, much like a soccer player heading the ball, rather than to a single atom of the head group. This indicates that in the appropriately charged manoid molecules, the site of the positive or negative charge is the head group as a whole. Due to higher surface density of charge, Li + gives greater interaction energy with molecule IV than Na +, K + and Cs + while, for the same reason, F - gives greater interaction energy with molecule II than Cl -, Br - and I -. Conclusions Since the findings in this paper are unlikely to change even if larger basis sets and other quantum chemical software are used, we feel that the molecules presented herein are capable of real existence. Indeed, it is surprising that so far no attempt seems to have been made to synthesize these novel molecules and

7 DEB et al.: PREDICTING MANOID MOLECULES, A NOVEL CLASS OF COMPOUNDS 1323 study their chemical, physical as well as biological properties. This should open up a new area of chemistry. Possible retro-synthetic routes to these molecules are indicated by the assembly and dissociation patterns listed in Table 2 out of the various molecular fragments in Fig 3. The most crucial fragment is the torso, a strained system consisting of two fused 5-membered rings, one of them being heterocyclic, involving either S or P atom. Similar, though not the same, systems are known A plausible synthetic route 12 for preparing the torso, with P as the heterocyclic atom, is as follows (Scheme 1): A Diels-Alder reaction of diene (1) with the phosphonium cyclic olefin (2) 13 may give the cycloadduct (3). The adduct (3) can be subjected to mild oxidation to give the corresponding diketone. The cleavage of the diketone would give the compound (4) 9. The ester groups can be hydrolyzed and amide coupling can be carried out to incorporate functionality. Base-mediated dehalogenation may form the compound (6). Organometallic reactions (Grignard, zinc, etc.) can be selectively done at the carbonyl group of (7) to give compounds like (8). It may also be noted that a completely ab initio molecular dynamics simulation at an appropriate temperature might yield the lifetimes of these molecules. This, however, is beyond the scope of the present study. Acknowledgement BMD thanks the Indian National Science Academy, New Delhi, India, for financial support and Prof. Sushanta Dattagupta for hospitality at Visva-Bharati University. DM thanks IACS, Kolkata, India, while SPB thanks DAE, Mumbai, India for financial support. Helpful discussions with Dr Surajit Sinha and Dr Jyotirmayee Dash from IACS are acknowledged. Dr Dash suggested the possible synthetic route given above. The authors are grateful to Dr M W Schmidt, Iowa State University, USA, for permission to use the GAMESS software and his help with it. References 1 Deb B M, (unpublished). 2 (see Atomilism ) 3 Schleyer P v R, Encyclopedia of Computational Chemistry, (John Wiley, New York) Jensen F, Introduction to Computational Chemistry, (John Wiley, New York) Schmidt M W, Baldridge K K, Boatz J A, Elbert S T, Gordon M S, Jensen J H, Koseki S, Matsunaga N, Nguyen K A, Su S, Windus T L, Dupuis M & Montgomery Jr J A, J Comput Chem, 14 (1993) Theory and Applications of Computational Chemistry: The First Forty Years, edited by C E Dykstra, G Frenking, K S Kim & G E Scuseria, (Elsevier, Amsterdam) Atkins P W & de Paula J, Physical Chemistry, 8 th Edn, (Oxford University Press, Oxford) 2006, pp. 993, 994, 997, Khan F A, Prabhudas B, Dash J & Sahu N, J Am Chem Soc 122 (2000) Khan F A & Dash J, J Am Chem Soc 124 (2002) Das S & Zade S S, Chem Commun 46 (2010) Dash J, (personal communication). 13 Bond A, Green M & Pearson S C, J Chem Soc B (1968) 929.