Elangannan Arunan

Bio: Elangannan Arunan is an academic researcher from Indian Institute of Science. The author has contributed to research in topics: Hydrogen bond & Molecule. The author has an hindex of 29, co-authored 133 publications receiving 4714 citations. Previous affiliations of Elangannan Arunan include Kansas State University & Urbana University.

Definition of the hydrogen bond (IUPAC Recommendations 2011)

Abstract: A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This def- inition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.

Defining the hydrogen bond: An account (IUPAC Technical Report)

Abstract: The term "hydrogen bond" has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material sci- entists, there has been a continual debate about what this term means. This debate has inten- sified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X-HY hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some char- acteristics that are observed in typical hydrogen-bonding environments.

The rotational spectrum, structure and dynamics of a benzene dimer

Abstract: The low J (2 to 7) rotational spectrum of a symmetric‐top benzene dimer has been obtained with a Balle/Flygare Fourier transform microwave spectrometer. Each transition is a symmetrical quartet with two J‐ and K‐dependent tunneling splittings of 30 to 400 kHz. Rotational constants B, DJ, and DJK were determined to be 427.76(2) MHz, 7.2(3) kHz, and 0.869(5) MHz. The dimer is T‐shaped with a benzene c.m. to c.m. distance of 4.96 A.

The X–C⋯Y (X = O/F, Y = O/S/F/Cl/Br/N/P) ‘carbon bond’ and hydrophobic interactions

Abstract: While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as –F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C⋯Y interaction, which could be called ‘carbon bonding’. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the ‘hydrophobic interactions’.

Low-J rotational spectra, internal rotation, and structures of several benzene-water dimers

Abstract: Low J (0–4) rotational transitions have been observed for the benzene–water dimer of which high J (≥4) transitions were reported recently by Blake [Science 257, 942 (1992)]. Our experiments used a modified Balle/Flygare Fourier transform microwave spectrometer, with a pulsed supersonic nozzle as the sample source, and examined a variety of isotopic species in the ground and first excited internal rotor states (m=0 and 1). The dimers of the parent C6H6 benzene with H2O, HDO, D2O, and H218O have symmetric top spectra characteristic of two coaxial rotors with a symmetric top frame and a very low effective V6 barrier. The dimers of H2O and D2O with the 13C and D monosubstituted benzenes have asymmetric top spectra of which only the m=0 state was assigned. However, doublets in the m=1, J=0→1 transitions show that there is a V2 term of ∼0.5 MHz in their barriers. A substitution analysis was made of the rotational constants found for the m=0 state of the dimers with H218O, D2O, and the 13C and D monosubstituted ...

Accurate description of van der Waals complexes by density functional theory including empirical corrections

Abstract: An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R−6. The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The “double counting” of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene · H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1463–1473, 2004

The Halogen Bond

Abstract: The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg