S. Karthikeyan

How Different Are Aromatic π Interactions from Aliphatic π Interactions and Non-π Stacking Interactions?

We compare aromatic π interactions with aliphatic π interactions of double- and triple-bonded π systems and non-π stacking interactions of single-bonded σ systems. The model dimer systems of acetylene (C2H2)2, ethylene (C2H4)2, ethane (C2H6)2, benzene (C6H6)2, and cyclohexane (C6H12)2 are investigated. The ethylene dimer has large dispersion energy, while the acetylene dimer has strong electrostatic energy. The aromatic π interactions are strong with particularly large dispersion and electrostatic energies, which would explain why aromatic compounds are frequently found in crystal packing and molecular self-engineering. It should be noted that the difference in binding energy between the benzene dimer (aromatic-aromatic interactions) and the cyclohexane dimer (aliphatic-aliphatic interactions) is not properly described in most density functionals.

Molecular design and synthesis of ruthenium(II) sensitizers for highly efficient dye-sensitized solar cells

We synthesized hydrophobic ruthenium(II) sensitizers (SY-04 and SY-05) with high molar extinction coefficient by extending the π-conjugation of 3,4- or 3-alkylthiophene-substituted bipyridine ligands. Both dyes displayed a remarkably high molar extinction coefficient of 21.7 × 103 M−1 cm−1 arising from red-shift of their metal-to-ligand charge transfer band when compared to a commonly used N3 sensitizer. The solar-to-electrical energy conversion efficiency (η) of the SY-04 based dye-sensitized solar cell (DSC) was 7.70%, which is 27% higher than that (6.05%) of the N3-based DSC under the same cell fabrication conditions. The increased η was attributed to the increase in life time and recombination half-life measured by electrochemical impedance and transition absorption spectroscopy, respectively. Density functional theory and time-dependent density functional theory calculations of two dyes in both gas phase and solution were performed. The calculated values of the highest occupied and the lowest unoccupied molecular orbitals and absorption spectra are in good agreement with the experimental results.

Undissociated versus Dissociated Structures for Water Clusters and Ammonia−Water Clusters: (H2O)n and NH3(H2O)n−1 (n = 5, 8, 9, 21). Theoretical Study

To understand the autoionization of pure water and the solvation of ammonia in water, we investigated the undissociated and dissociated (ion-pair) structures of (H2O) n and NH3(H2O)n-1 (n = 5, 8, 9, 21) using density functional theory (DFT) and second order Moller-Plesset perturbation theory (MP2). The stability, thermodynamic properties, and infrared spectra were also studied. The dissociated (ion-pair) form of the clusters tends to favor the solvent-separated ion-pair of H3O+/NH4+ and OH-. As for the NH3(H2O)20 cluster, the undissociated structure has the internal conformation, in contrast to the surface conformation for the (H2O)21 cluster, whereas the dissociated structure of NH3(H2O)20 has the surface conformation. As the cluster size of (H2O)n/NH3(H2O)n-1 increases, the difference in standard free energy between undissociated and dissociated (ion-pair) clusters is asymptotically well corroborated with the experimental free energy change at infinite dilution of H3O+/NH4+ and OH-. The predicted NH and OH stretching frequencies of the undissociated and dissociated (ion-pair) clusters are discussed.

Structure, stability, thermodynamic properties, and infrared spectra of the protonated water octamer H(+)(H2O)8.

We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H (+)(H 2O) 8, using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Beckes three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.

Structures, energetics, vibrational spectra of NH4+(H2O)n=4,6 clusters : Ab initio calculations and first principles molecular dynamics simulations

Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

Binary complexes of tertiary amines with phenylacetylene. Dispersion wins over electrostatics

The structures of the binary complexes between phenylacetylene and several tertiary amines viz., triethylamine, 1-ethylpiperidine, 1-ethylpiperazine, 1-azabicyclo[2.2.2]octane, and 1,4-diazabicyclo[2.2.2]octane were inferred using infrared-optical double resonance spectroscopy. The IR spectra in the acetylenic C-H stretching region clearly rule out the formation of electrostatic dominated C-HN hydrogen bonded complexes. The IR spectra also point to the fact that all the five tertiary amines interact with the extended pi electron density of the phenylacetylene moiety, leading to the formation of multidentate C-Hpi hydrogen bonded complexes. Additionally a very weak electrostatic C-HN hydrogen bond enhances the stability of the complex marginally. The multidentate C-Hpi hydrogen bonded complexes are stabilized by a substantial contribution from the dispersion energy.

(R)-lipo-diaza-18-crown-6 self-assembled monolayer as a selective serotonin receptor.

A highly selective receptor for serotonin was designed using cages formed by the (R)-lipo-diaza-18-crown-6 self-assembled monolayer (SAM) on gold and experimentally verified by a variety of electrochemical experiments in solutions containing large amounts of dopamine and ascorbic acid, as well as other interferents. The molecular modeling study showed that parameters such as the H-pi interaction provided important driving forces for the cage to form a strong inclusion complex with serotonin. The charge-transfer resistance (R(CT)s) to/from redox probe ions, Fe(CN)(6)(3-/4-), was greatly enhanced because of their electrostatic attractions to ammonium ions of serotonin molecules captured by cages. The changes in R(CT)-values were shown to be remarkably selective for serotonin in the presence of many interferents.

Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

Structure, Stability, Thermodynamic Properties, and IR Spectra of the Protonated Water Decamer H+(H2O)10

Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.

Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study.

We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The -OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (ΔEe/ΔE0) interaction energies and the enthalpies/free energies (ΔHr/ΔGr at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (HmXOn where X = B/N/P/Cl/Br/I, m = 1-3, and n = 0-4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X(+)···O(-) electrostatic interactions are important.