Cheol Ho Choi

Rapid and stable determination of rotation matrices between spherical harmonics by direct recursion

Recurrence relations are derived for constructing rotation matrices between complex spherical harmonics directly as polynomials of the elements of the generating 3×3 rotation matrix, bypassing the intermediary of any parameters such as Euler angles. The connection to the rotation matrices for real spherical harmonics is made explicit. The recurrence formulas furnish a simple, efficient, and numerically stable evaluation procedure for the real and complex representations of the rotation group. The advantages over the Wigner formulas are documented. The results are relevant for directing atomic orbitals as well as multipoles.

The effects of electron correlation on the degree of bond alternation and electronic structure of oligomers of polyacetylene

Full geometry optimizations on oligoenes have been performed with Hartree–Fock and density functional theory in combination with double zeta and triple zeta quality basis sets with primary focus on the degree of bond length alternation and on the energy gap. Monitoring the dependence of the computed properties on the oligomer size provides new insights into the reliability of the calculations, which are analyzed in terms of dynamical and nondynamical electron correlation. Our theoretical bond length alternation values for the oligomers of polyacetylene extrapolate to significantly smaller values than what has been established by experiments and earlier theoretical predictions. The exact exchange mixing to the exchange-correlation functional not only improves the agreement of the theoretical gap of oligoenes with experimental excitation energies but also increases the computed bond length alternations. Based on a newly proposed one parameter functional of Becke, the effect of the exact exchange mixing has ...

Bond length alternation and aromaticity in large annulenes

Properties of [4n] and [4n+2]annulenes were studied as a function of n for up to [66]annulene using Hartree–Fock and density functional theory in the generalized gradient approximation (DFT-GGA). In the 4n+2 series a “transition” from delocalized to localized structures occurs at 4n+2=30. Various indices of aromaticity, including NMR chemical shifts, bond localization, and aromatic stabilization energy (ASE) were monitored. π-bond localization occurs not due to a dramatic decrease of ASE as n increases, but rather as a result of a pseudo-Jahn–Teller (PJT) effect that sets in as the HOMO-LUMO gap decreases with increasing size. The NMR measures of aromaticity (difference between inner and outer 1H chemical shielding constants and the nucleus-independent chemical shifts, NICS) are reduced in the localized structures in comparison to the delocalized ones. The gradual nature of this “transition” is also implied by the relatively large values of the NMR measures of aromaticity that approach zero only gradually...

Limitations of current density functional theories for the description of partial π-bond breaking

Abstract It is shown on the example of the torsional potential of butadiene, that several density functionals including gradient corrected non-local functionals exhibit an intrinsic error that leads to the overestimation of rotational barriers due to partial π-bond breaking. This problem occurs for all functionals investigated including SVWN, BLYP, B3LYP, BPL and BP86 and is independent of the basis set. The hybrid exchange functional (B3) is slightly better than the others. These errors are absent for torsional potentials around single bonds, such as in 1-butene and indicates that the problem may be related to the overestimation of conjugation energy.

Direct absolute pKa predictions and proton transfer mechanisms of small molecules in aqueous solution by QM/MM-MD.

The pKa values of HF, HCOOH, CH3COOH, CH3CH2COOH, H2CO3, HOCl, NH4(+), CH3NH3(+), H2O2, and CH3CH2OH in aqueous solution were predicted by QM/MM-MD in combination with umbrella samplings adopting the flexible asymmetric coordinate (FAC). This unique combination yielded remarkably accurate values with the maximum and root-mean-square errors of 0.45 and 0.22 in pKa units, respectively, without any numerical or experimental adjustments. The stability of the initially formed Coulomb pair rather than the proton transfer stage turned out to be the rate-determining step, implying that the stabilizations of the created ions require a large free energy increase. A remarkable correlation between DWR (degree of water rearrangements) and pKa was observed. As such, the large pKa of ethanol can be, in part, attributed to the large water rearrangement, strongly suggesting that proper samplings of water dynamics at dissociated regions are critical for accurate predictions of pKa. Current results exhibit a promising protocol for direct and accurate predictions of pKa. The significant variations in the gas phase deprotonation energies with level of theory appear to be mostly canceled by the similar changes in the averaged solute-solvent interactions, yielding accurate results.

Hydrophobic and Hydrophilic Associations of a Methanol Pair in Aqueous Solution

The association dynamics of a methanol pair in aqueous solution were theoretically studied with QM/EFP-MD and quantum mechanical methods. Stable contact pairs and solvent separated configurations (SS) were found from simulations with a free energy barrier of 2 kcal/mol, revealing the strong tendency of methanol association. The stable contact pairs were further identified as the hydrophobic (CP(A)) and hydrophilic (CP(B)) species, with the CP(A) having a larger population. Although the free energy difference between the CP(A) and CP(B) is negligible with virtually no associated free energy barrier, the slow isomerization dynamics of intermolecular rotations ensures their individual identity. Further mechanistic analysis revealed that only the CP(A) has a direct path to the SS, showing that hydrophobic attraction initiates the association process. A subsequent intermolecular hydrophilic attraction isomerizes CP(A) and CP(B). Therefore, our results show that both the hydrophobic and hydrophilic attractions between methanol molecules play important roles in the association dynamics. The former operates on the longer intermolecular distance, while the latter is effective in contact pairs.

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Is a 1.90 Å C–C bond length in polymeric fullerides possible?

Abstract The very long C–C intrafullerene bond distance of r long =1.90(15) A in RbC 60 polymeric fulleride observed by Stephens et al. is unprecedented. Large scale full geometry optimizations using non-local density functional theory on C 120 , C 120 2− , C 120 6− , as well as on the model dinaphthalene dimer were performed in exploring the potential energy surface along the long C–C bond in question. For neutral C 120 , r long should be close to 1.61 A, a value that is in agreement with the experimental value for the C 120 buckyball dimer and is close to the lower limit of the Stephens C–C value.

Conformational information from vibrational spectra of polyaniline

Abstract Vibrational (IR and Raman) spectra contain information about local conformations in materials. Their extraction, however, is possible only through accurate modeling of the vibrational spectra and by comparing various predicted spectra with experiment. We have established a Scaled Quantum Mechanical Oligomer Force Field for oligomers of leucoemeraldine base and for one oligomer of the imine form of polyaniline (pemigraniline base). We conclude, that while the shorter oligomers of LB are far from planarity, the longer oligomers and LB itself are nearly planar. This result is confirmed by energy band structure calculations. There is no doubt, that an isolated LB polymer would energetically favor a non-planar structure. Planarity is probably a consequence of interchain interactions in the material. The vibrational analysis of the PNB form is not yet complete, but optical and energy band structure data suggest, that the samples contain the non-planar form.

Asymmetric Transport Mechanisms of Hydronium and Hydroxide Ions in Amorphous Solid Water: Hydroxide Goes Brownian while Hydronium Hops

The diffusion of hydronium (H3O(+)) and hydroxide (OH(-)) ions is one of the most intriguing topics in aqueous chemistry. It is considered that these ions in aqueous solutions move via sequential proton transfer events, known as the Grotthuss mechanisms. Here, we present an experimental study of the diffusion and H/D exchange of hydronium and hydroxide ions in amorphous solid water (ASW) at 140-180 K by using low-energy sputtering (LES) and temperature-programmed desorption (TPD) measurements. The study shows that the two species transport in ASW via fundamentally different molecular mechanisms. Whereas hydronium ions migrate via efficient proton transfer, hydroxide ions move via Brownian molecular diffusion without proton transfer. The molecular hydroxide diffusion in ASW is in stark contrast to the current view of the hydroxide diffusion mechanism in aqueous solution, which involves proton transfer.