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Exploring Ultrashort Hydrogen-Hydrogen NonBonded Contacts in Constrained Molecular Cavities Nilangshu Mandal, Saied Md Pratik, and Ayan Datta J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.6b12391 • Publication Date (Web): 05 Jan 2017 Downloaded from http://pubs.acs.org on January 6, 2017
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Exploring Ultrashort Hydrogen-Hydrogen Non-Bonded Contacts in Constrained Molecular Cavities Nilangshu Mandal, Saied Md Pratik and Ayan Datta*
Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur – 700032, Kolkata, West Bengal, India.
Abstract Confined molecular chambers like macrocycle bridged E1-H…H-E2 (E1(E2)=Si(Si), 1) exhibit rare ultrashort H…H non-bonded contacts (d(H…H)=1.56 Å). In this article, based on density functional theory (DFT) and Ab-Initio Molecular Dynamics (AIMD) simulations, we propose new molecular motifs where d(H…H) can be reduced to 1.44 Å (E1(E2)=Si (Ge), 3). Further tuning the structure of the macrocycle by replacing the bulky phenyl groups by ethylenic spacers and substitution the H-atoms by –CN groups makes the cavity more compact and furnishes even shorter d(H…H)=1.38 Å (E1(E2)=Ge (Ge), 8). These unusually close H…H non-bonded contacts originate from the strong attractive Non-Covalent Interactions between them which are evident from various computational indicators namely NCI, Wiberg bond index, relaxed force constant, QTAIM and ETS-NOCV analyses. Substantial stabilization of the in,in-configuration (exhibiting short H…H contacts) over the out,out-configuration (by ~ 5.7 kcal/mol) and statistically insignificant fluctuations in and (θ(E1(E2)-H…H=1520) at room temperature confirm that the ultra-short H…H distances in these molecules are thermodynamically stable and would be persistent under ambient experimental conditions.
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Introduction Art requires creativity and therefore, chemistry is one of the finest forms of art as chemists are in an eternal pursuit to make new molecules. Every year, thousands of new molecules are designed for immediate or far-fetched applications in the pharmaceutetical or materials sciences. Amongst them, molecules with unusual structures or bonding are most interesting as they expand our existing chemical knowledge. Synthesis of fullerenes1, aromatic/antiaromatic metal clusters2-4, quadrabonded C2 molecule5, superbases like orthodiethynylbenzene dianion6, long C-C bonds in sterically congested alkanes (dC-C ~ 1.7 Å)7-8 and unusual hydrocarbon structures likes prismane9, radialene10 and even polytwistane11-12 are few such examples. While this list would be rather long and expanding, the contribution of molecular modelling in generating new theoretically interesting molecules is particularly important. The readers are encouraged to read Bachrach’s blog, Computational Organic Chemistry for regular updates on such new molecular entities.13 One amongst such chemical curiosity which has generated substantial interest has been the question: How close can two non-bonded hydrogen atoms be squeezed? One might empirically gauge this based on the variation of the radius of H-atom in various chemical environments. The latest estimate for the radius of free H-atom (at an electron density cut-off ~ 0.001 electron/Bohr3) is 1.54 Å14 leading to a non-interacting distance of 3.08 Å between two hydrogen atoms. Of course, the presence of attractive interaction between them is expected to bring them closer. Based on the comparison of van der Waals radius of H-atoms as determined through crystallography from 1939-2005, r(van-der-Waals) ~ 1.20 Å.15 Therefore, van der Waals distance between two weakly (non-covalent, dispersion forces stabilized) interacting hydrogen atoms, d (H…H) ~ 2.40 Å. So, a 3.08 Å → 2.40Å reduction of d(H…H) can indeed be attained simply through the incorporation of dispersion interactions between them as observed in the van der Waals solids. In fact, these seemingly
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weak H…H dispersion interactions explain the high melting temperature and heat of vaporization for polyhedrons in the solid-state.16 Nevertheless, it is important to note that rvan der Waals(H…H)=1.20
Å is statistically averaged over intermolecular orientations and therefore,
at specific arrangements for molecules stabilized in crystal structures, smaller van der Waals H…H contacts are indeed possible. Even for a highly symmetric molecule like methane, the transverse van der Waals radius, rt(H)=0.886 Å is smaller than its longitudinal counterpart (rl(H)=1.01 Å).17 Also, the van der Waals radii are strongly correlated with charge density of the covalently linked atoms. For example, within the HX crystals, the longitudinal van der Waals radius for H-atom decreases along HI (rl(H)=0.92 Å)→HBr (rl(H)=0.86 Å)→HCl (rl(H)=0.75 Å) following the increased electronegativity of X.15-17 Reduction of the H…H distances beyond the sum of their van der Waals radii would additionally require specifically designed molecular architectures where the two hydrogens are constrained within close H…H proximity, notwithstanding their repulsive non-nonded nature. Crabtree and co-workers published an unconventional intermolecular three-center (NH...H2Re) hydrogen bond (~1.74 Å) in a Re-complex.18 Using neutron diffraction and other studies, Reiger and his co-workers established the molecular hydrogen tweezers, in which NH...HB short dihydrogen bond was found about 1.67 Å.19 Ermor and co-workers reported H…H non-bonded distance of 1.617 (3) Å for half-cage pentacyclododecane.20 Firouzi et al. have reported ultrashort intramolecular non-bonded H…H distances for rigid hydrocarbons like tetracyclododecanes and pentacyclododecanes and their halogenated analogues.21 Using similar logic, Baldridge and co-workers have computationally designed highly compressed molecular architectures like triply bridged triptycenes where the H…H non-bonded distance can be reduced by ~ 11% with respect to the sum of the their van der Waals radius (~ 2.4 Å),22 and subsequently they could report shorter H...H non-bonded distance by designing a 1(SiH>
