Classical molecular dynamics (MD) simulations are useful for characterizing the structure and dynamics of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field is widely used and has well-defined bond length, bond angle, partial charge, and van der Waals parameters for all the common amino acids and nucleotides, but it lacks parameters for many of the modifications found in nucleic acids and proteins. Presently there are 107 known naturally occurring modifications that play important roles in RNA stability, folding, and other functions. Modified nucleotides are found in almost all transfer RNAs, ribosomal RNAs of both the small and large subunits, and in many other functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known to be present in RNA. The methodology used for deriving the modified nucleotide parameters is consistent with the methods used to develop the Cornell et al. force field. These parameters will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.

The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14-0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH(+•)/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X(•),H(+)/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1-0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between guanine and 8-oxoguanine is in good agreement with the measured values.

Vibrational sum frequency generation (SFG) spectroscopy has been utilized to study the spatial orientation and alignment of Re(CO) 3 Cl(dcbpy) (dcbpy = 4,4′-dicarboxy-2,2′-bipyridine) (or ReC0A) on the (001) and ( 110) surfaces of rutile single-crystalline TiO 2 . The SFG intensity of the CO stretching modes shows an isotropic distribution on the (001) surface and an anisotropic distribution on the (110) surfaces with respect to the in-plane rotation of the crystal relative to the surface normal (or the incident laser beam plane). By combining these results with ab initio SFG simulations and with modeling of ReC0A−TiO 2 cluster binding structures at the density functional theory level, we reveal that the origin of the optical anisotropy for ReC0A on the TiO 2 (110) surface is associated with the binding preference of ReC0A along the [−110] axis. Along this direction, the binding structure is energetically favorable, because of the formation of proper hydrogen bonding between the carboxylate group and passivating water molecules adsorbed on the TiO 2 (110) surface. Simulations of dimers of ReC0A molecules binding close together with full nearest-neighbor effects give a structure that reproduces the experimental SFG polar plot. The tilt angle, defined by the bpy ring angle relative to the surface normal, of the catalyst is found to be 26°for one monomer and 18°for the other, which corresponds to an aggregate at high surface coverage.

Sum frequency generation spectroscopy (SFG) and calculations of SFG spectra based on density functional theory are combined to elucidate the orientation of two Re­(R-2,2′-bipyridine)­(CO)3Cl (R = 4-cyano or 4,4′-dicyano) electrocatalysts when adsorbed on conductive gold surfaces. We find that the electrocatalysts lean on the Au surface to orient the plane of the bipyridine ligand at 63° relative to the surface normal. While the weak binding of the complexes to the gold surface precluded the ability to perform surface immobilized catalysis, homogeneous electrochemical experiments show that the molecular catalysts are active toward the reduction of CO2 to CO and carbonate in the triply reduced state (TOF of 13.3 and 7.2 s–1 for the doubly and singly substituted complexes, respectively). These findings demonstrate the capabilities of the approach of including rigorous spectroscopic and theoretical methods for revealing the conformation and orientation of CO2 reduction catalysts bound to electrode surfaces, which are critical considerations for redox state transitions and catalytic turnover.

Despite the importance of terpenes in biology, the environment, and catalysis, their vibrational spectra remain unassigned. Here, we present subwavenumber high-resolution broad-band sum frequency generation (HR-BB-SFG) spectra of the common terpene (+)-α-pinene that reveal 10 peaks in the C-H stretching region at room temperature. The high spectral resolution resulted in spectra with more and better resolved spectral features than those of the Fourier transform infrared, femtosecond stimulated Raman spectra in the bulk condensed phase and those of the conventional BB-SFG and scanning SFG spectroscopy of the same molecule on a surface. Experiment and simulation show the spectral line shapes with HR-BB-SFG to be accurate. Homogeneous vibrational decoherence lifetimes of up to 1.7 ps are assigned to specific oscillators and compare favorably to lifetimes computed from density functional tight binding molecular dynamics calculations. Phase-resolved spectra provided their orientational information. We propose the new spectroscopy as an attractive alternative to time domain vibrational spectroscopy or heterodyne detection schemes for studying vibrational energy relaxation and vibrational coherences in molecules at molecular surfaces or interfaces.