Brian T. Psciuk

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA.

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.

Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases

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 pKas 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.

Accurate line shapes from sub-1 cm(-1) resolution sum frequency generation vibrational spectroscopy of α-pinene at room temperature.

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.

Computational prediction of one-electron reduction potentials and acid dissociation constants for guanine oxidation intermediates and products

Reduction potentials and pK(a) values were calculated for intermediates and products along three major pathways for guanine oxidation using the B3LYP and CBS-QB3 levels of theory with the SMD implicit solvation model. N-methylated nucleobases were used as models for nucleoside species. Ensemble averaged reduction potentials at pH 7 (E7) were obtained by combining calculated standard reduction potentials with calculated pKa values in addition to accounting for tautomerization energies. Calculated pK(a) values are reasonable based on experimental estimates and chemical intuition. Pathway A leads to guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp). The first step is the oxidation of 8-oxoguanine which proceeds by the loss of an electron followed by the loss of two protons and loss of another electron, yielding 8-oxopurine. The calculated E7 values for the remaining intermediates and products are at least 0.3 V higher than that of guanine, indicating that further oxidation of these species is unlikely. Pathway B leads to two formamidopyrimidine isomers (FAPyG and 2,5FAPyG). Species along this pathway have calculated reduction potentials that are much lower than the oxidation potential for guanine and would likely be very short-lived in an oxidatively stressed environment. Pathway C leads to reduced spiroiminodihydantoin and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). Similar to pathway A, the calculated reduction potentials for species along this pathway are at least 0.4 V higher than that of guanine.

Correlating Photoacidity to Hydrogen-Bond Structure by Using the Local O–H Stretching Probe in Hydrogen-Bonded Complexes of Aromatic Alcohols

To assess the potential use of O-H stretching modes of aromatic alcohols as ultrafast local probes of transient structures and photoacidity, we analyze the response of the O-H stretching mode in the 2-naphthol-acetonitrile (2N-CH3CN) 1:1 complex after UV photoexcitation. We combine femtosecond UV-infrared pump-probe spectroscopy and a theoretical treatment of vibrational solvatochromic effects based on the Pullin perturbative approach, parametrized at the density functional theory (DFT) level. We analyze the effect of hydrogen bonding on the vibrational properties of the photoacid-base complex in the S0 state, as compared to O-H stretching vibrations in a wide range of substituted phenols and naphthols covering the 3000-3650 cm(-1) frequency range. Ground state vibrational properties of these phenols and naphthols with various substituent functional groups are analyzed in solvents of different polarity and compared to the vibrational frequency shift of 2N induced by UV photoexcitation to the (1)Lb electronic excited state. We find that the O-H stretching frequency shifts follow a linear relationship with the solvent polarity function F0 = (2ε0 - 2)/(2ε0 + 1), where ε0 is the static dielectric constant of the solvent. These changes are directly correlated with photoacidity trends determined by reported pKa values and with structural changes in the O···N and O-H hydrogen-bond distances induced by solvation or photoexcitation of the hydrogen-bonded complexes.

Characterization of Parallel β-Sheets at Interfaces by Chiral Sum Frequency Generation Spectroscopy

Characterization of protein secondary structures at interfaces is still challenging due to the limitations of surface-selective optical techniques. Here, we address the challenge of characterizing parallel β-sheets by combining chiral sum frequency generation (SFG) spectroscopy and computational modeling. We focus on human islet amyloid polypeptide aggregates and a de novo designed short polypeptide at lipid/water and air/glass interfaces. We find that parallel β-sheets adopt distinct orientations at various interfaces and exhibit characteristic chiroptical responses in the amide I and N-H stretch regions. Theoretical analysis indicates that the characteristic chiroptical responses provide valuable information on the symmetry, orientation, and vibrational couplings of parallel β-sheet at interfaces.

Can Metallapyrimidines Be Aromatic? A Computational Study into a New Class of Metallacycles.

The aromaticity of a series of metallapyrimidines involving second row transition metals was examined using density functional theory. Nucleus independent chemical shifts (NICS) placed above the ring (NICS(1)zz) were used to gauge the amount of aromaticity. Natural chemical shielding analysis (NCS) was employed to decompose the chemical shifts in terms of diamagnetic and paramagnetic contributions from individual molecular orbitals. While NICS(1)zz for niobapyrimidine, [(pz)2(Nb-pyr)](0), suggested slightly aromatic character, the NCS analysis shows this is due to the diamagnetic (field-free) contribution. Instead, the positive paramagnetic (field-induced) contribution suggests that niobapyrimidine may be slightly antiaromatic. A series of d(0) metallapyrimidines, [(pz)2(M-pyr)] with M = Y(III), Zr(IV), Nb(V), Mo(VI), Tc(VII), demonstrated similar behavior. Variation of the number of metal d electrons in a series of M(V) metallapyrimidines, [(pz)2(M-pyr)] where M = Mo, Tc, Ru, and Rh, showed strong evidence for aromaticity, with NICS(1)zz values of -15.4, -36.0, -31.6, and -22.4, respectively, that are comparable to benzene (-28.7). NCS analysis of the Tc(V), Ru(V), and Rh(V) complexes shows that aromaticity is favored by an unoccupied d-π orbital that serves as an acceptor to facilitate conjugation in the metallapyrimidine ring. This unoccupied orbital is not sufficient as the d(0) series of complexes demonstrated, and we propose that the occupied d-δ orbital prevents bond localization and enables aromaticity in these metallacycles.

Ab Initio Classical Trajectory Study of the Fragmentation of C3H4 Dications on the Singlet and Triplet Surfaces

Ab initio molecular dynamics have been used to examine the fragmentation of allene, propyne, and cyclopropene dications on the singlet and triplet potential energy surfaces. Accurate energies and barrier heights were computed at the CBS-APNO level of theory. Classical trajectories were calculated at the B3LYP/6-31G(d,p) level of theory. To simulate vertical double ionizations of allene, propyne, and cyclopropene by short, intense laser pulses, the trajectories were started from the corresponding neutral geometries and were given ca. 240 kcal/mol excess kinetic energy; 200 trajectories were integrated for each case. Approximately one-third of the trajectories underwent extensive rearrangement before dissociation. Proton dissociation is the dominant pathway for all six cases, accounting for 50-75% of the trajectories. H(2)/H(2)(+) is produced in ca. 20% of the trajectories on the singlet propyne and cyclopropene dication surface. The calculated ratio of CH(+)/CH(2)(+)/CH(3)(+) compares favorably to that obtained in laser-induced Coulomb explosion of allene. The yield of CH(2)(+) is ca. 12% on the singlet and triplet allene dication surfaces compared to 6% or less in the other cases, whereas CH(+) is favored on the singlet propyne dication surface (12% vs 0-8% on the other surfaces). CH(3)(+) is formed primarily by direct dissociation on the triplet propyne dication surface (5% vs <1% on the other surfaces). The small amount of H(3)(+) seen experimentally for allene indicates that rearrangement can occur before dissociation. The dynamics simulations confirm that extensive isomerization occurs, even though the initial kinetic energy was too high to yield H(3)(+).

Assessment of DFT for Computing Sum Frequency Generation Spectra of an Epoxydiol and a Deuterated Isotopologue at Fused Silica/Vapor Interfaces

We assess the capabilities of eight popular density functional theory (DFT) functionals, in combination with several basis sets, as applied to calculations of vibrational sum frequency generation (SFG) spectra of the atmospherically relevant isoprene oxidation product trans-β-isoprene epoxydiol (IEPOX) and one of its deuterated isotopologues at the fused silica/vapor interface. We use sum of squared differences (SSD) and total absolute error (TAE) calculations to estimate the performance of each functional/basis set combination in producing SFG spectra that match experimentally obtained spectra from trans-β-IEPOX and one of its isotopologues. Our joined SSD/TAE analysis shows that while the twist angle of the methyl C3v symmetry axis of trans-β-IEPOX relative to the surface is sensitive to the choice of DFT functional, the calculated tilt angle relative to the surface normal is largely independent of the functional and basis set. Moreover, we report that hybrid functionals such as B3LYP, ωB97X-D, PBE0, and B97-1 in combination with a modest basis set, such as 6-311G(d,p), provides good agreement with experimental data and much better performance than pure functionals such as PBE and BP86. However, improving the quality of the basis set only improves agreement with experimental data for calculations based on pure functionals. A conformational analysis, based on comparisons of calculated and experimental SFG spectra, suggests that trans-β-IEPOX points all of its oxygen atoms toward the silica/vapor interface.