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The transition-metal complex

The copper hydroxide ion, CuOH

Chemical activation of water by a single chlorine atom was examined computationally for clusters of chlorine radicals and water in a size regime just prior to internal hydration of water/ions, Cl

The partial chemical activation of water by reactive radicals was examined computationally for small clusters of chlorine and water, Cl

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

The isomers of a hydrated Cu(I) ion with n = 1-10 water molecules were investigated by using ab initio quantum chemistry and an automated isomer-search algorithm. The electronic structure and vibrational spectra of the hundreds of resulting isomers were used to analyze the source of the observed bonding patterns. A structural evolution from dominantly two-coordinate structures (n = 1-4) toward a mixture of two- and three-coordinate structures was observed at n = 5-6, where the stability provided by expanded hydrogen-bonding was competitive with the dominantly electrostatic interaction between the water ligand and remaining binding sites of the metal ion. Further hydration (n = 7-10) led to a mixture of three- and four-coordinate structures. The metal ion was found, through spectroscopic signatures, to appreciably perturb the O-H bonds of even third-shell water molecules, which highlighted the ability of this nominally simple ion to partially activate the surrounding water network.

Because of both experimental and computational challenges, protonated tryptophan has remained the last aromatic amino acid for which the intrinsic structures of low-energy conformers have not been unambiguously solved. The IR-IR-UV hole-burning spectroscopy technique has been applied to overcome the limitations of the commonly used IR-UV double resonance technique and to measure conformer-specific vibrational spectra of TrpH(+), cooled to T = 10 K. Anharmonic ab initio vibrational spectroscopy simulations unambiguously assign the dominant conformers to the two lowest-energy geometries from benchmark coupled-cluster structure computations. The match between experimental and ab initio spectra provides an unbiased validation of the calculated structures of the two experimentally observed conformers of this benchmark ion. Furthermore, the vibrational spectra provide conformer-specific signatures of the stabilizing interactions, including hydrogen bonding and an intramolecular cation-π interaction.

On-the-fly, ab initio classical molecular dynamics are demonstrated with an underlying dual basis set potential energy surface. Dual-basis self-consistent field (Hartree-Fock and density functional theory) and resolution-of-the-identity second-order Moller-Plesset perturbation theory (RI-MP2) dynamics are tested for small systems, including the water dimer. The resulting dynamics are shown to be faithful representations of their single-basis analogues for individual trajectories, as well as vibrational spectra. Computational cost savings of 58% are demonstrated for SCF methods, even relative to Fock-extrapolated dynamics, and savings are further increased to 71% with RI-MP2. Notably, these timings outperform an idealized estimate of extended-Lagrangian molecular dynamics. The method is subsequently demonstrated on the vibrational absorption spectrum of two NO(+)(H₂O)₃ isomers and is shown to recover the significant width of the shared-proton bands observed experimentally.

Accurate potential energy surfaces for benzene.M complexes (M = Li+, Na+, K+, and NH4+) are obtained using coupled-cluster theory through perturbative triple excitations, CCSD(T). Our computations show that off-axis cation-pi interactions, where the cation is not directly above the aromatic ring, can be favorable and may influence molecular recognition. Even perpendicular, side-on interactions retain 18-32% of their pi-face interaction energy in the gas phase, making their bond strengths comparable to hydrogen bonds in the gas phase. Solvent effects have been explored for each complex using the polarizable continuum model.