Charles C. Kirkpatrick

Face-to-Face Arene−Arene Binding Energies: Dominated by Dispersion but Predicted by Electrostatic and Dispersion/Polarizability Substituent Constants

Parallel face-to-face arene-arene complexes between benzene and substituted benzenes have been investigated at the MP2(full)/6-311G** and M05-2X/6-311G** levels of theory. A reasonably good correlation was found between the binding energies and the ∑|σ(m)| values of the substituted aromatics. It is proposed that a substituent |σ(m)| value informs on both the aromatic substituent dispersion/polarizability and the effect the substituent has on the aromatic electrostatics. Supporting this hypothesis, a combination of electrostatic (∑σ(m)) and dispersion/polarizability (∑M(r)) substituent constant terms gives an excellent, and statistically significant, correlation with the benzene-substituted benzene binding energy. Symmetry adapted perturbation theory energy decomposition calculations show the dominant attractive force is dispersion; however, the sum of all nonelectrostatic forces is essentially a constant, while the electrostatic component varies significantly. This explains the importance of including an electrostatic term when predicting benzene-substituted benzene binding energies.

RNA CoSSMos: Characterization of Secondary Structure Motifs—a searchable database of secondary structure motifs in RNA three-dimensional structures

RNA secondary structure is important for designing therapeutics, understanding protein–RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database is a freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loops structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is automatically updated weekly and is available at http://cossmos.slu.edu.

Relating ion/neutral reaction rate coefficients and cross-sections by accessing a database for ion transport properties

Abstract A database is described that allows access to gaseous ion transport coefficients that have been calculated over wide ranges of reduced electric field strength and at several gas temperatures. Comparison of the computed transport coefficients with measured values allows an assessment to be made of the accuracy of the ion/buffer interaction potential assumed in the calculation. The database can also be used to compute rate coefficients for trace ions reacting with small amounts of a neutral reactant that is immersed in a larger amount of a nonreactive buffer gas. Comparison of the computed rate coefficients with values measured in drift tubes allows an assessment to be made of the accuracy of the ion/reactant cross-section assumed in the calculations. Application is made to Ar+ ions drifting through He gas and reacting with small amounts of CO.

Test of interaction potentials for rare gas-halide systems

Abstract Ab initio, model and empirical potentials for the interaction of rare gas atoms and halide ions are tested by their ability to reproduce gaseous ion transport data. The ab initio potentials are in poor agreement with the data. The model potentials give good agreement with experiment for some systems, moderate agreement for others, and very poor agreement for Br − in Ar, Kr and Xe. The potentials that were directly determined in 1985 from gaseous ion transport data more closely match those data and newer transport data than do any of the potentials proposed subsequently, with the exception of potentials inferred from zero electron kinetic energy spectroscopy.

Structural characterization of naturally occurring RNA single mismatches

RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence–structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.

Theoretical study of Cl−RG (rare gas) complexes and transport of Cl− through RG (RG = He–Rn)

We present a systematic investigation of the accuracy of the various theories and basis sets that can be applied to study the interaction of Cl(-) ions with Ar atoms. It is conclusively shown that gaseous ion mobility can distinguish among theoretical ion-neutral interaction potentials. Based on the conclusions, high-level ab initio potential energy curves are obtained for all of the Cl(-)-RG (RG = He-Rn) complexes. Spectroscopic constants have been derived from these potentials and are compared to a range of theoretical and experimental data, to which they generally show good agreement. General trends are discussed in comparison to other halogen-rare gas complexes previously studied. The potentials also have been tested by using them to calculate transport coefficients for Cl(-) moving through a bath of RG atoms.

d‐electron count, ion‐pairing and diagonal twist angles in metallo‐bis(dithiolene) complexes

Electronic structure calculations for late transition metals coordinated by two dithiolene ligands are found to be consistent with existing structures and also predict the geometries of Ni(I) species for which no solid state structures have been reported. Of particular interest are the compounds [M(mnt)2]n− (M = Ni, Pd, and Pt with n = 1, 2, 3; M = Cu with n = 2). Calculations have been performed with and without ion‐paring with M(diglyme)+ (M = Li, Na, K) and R4N+ (R = Me, Bu). The diagonal twist angle between two NiS2 planes is found to depend on (i) the metals d‐electron count, spanning from 0° (planar d7 and d8), to 42° (d9), to 90° (pseudo‐tetrahedral d10), and (ii) the identity of the ion‐paired cations. Calculated ion‐pairing energies are functions of the cation size and charge‐density, being larger for alkali‐metal coordinated diglyme and smaller for tetra‐alkyl ammonium cations.

Predicting the cation–π binding of substituted benzenes: energy decomposition calculations and the development of a cation–π substituent constant

This work proposes a new substituent constant, termed Π+, to describe cation–π binding using computational methods at the MP2(full)/6-311++G** level of theory with Symmetry Adapted Perturbation Theory (SAPT) calculations on selected cation–π complexes. The correlations between binding strength (Ebind or ΔH298) and common parameters for describing cation–π binding (∑σm, ∑σp, ∑(σm + σp), or Θzz) are decent (r2 between 0.79 and 0.90). SAPT calculations show that variations in the electrostatic (Eele), exchange (Eexch), induction (Eind), and dispersion (Edisp) component energies to the overall binding are almost entirely due to differences in arene–cation distances (dAr–cat). Eele varies most with dAr–cat; however, Eind seems to be the primary term responsible for the ∑σm, ∑σp, ∑(σm + σp) and Θzz parameters not accurately predicting the cation–π Ebind and ΔH298 values. The Π+ parameter largely reflects electrostatics, but it also includes the impact of exchange, induction, and dispersion on cation–π binding of aromatics, and the resulting correlation between ΔH298 or Ebind and Π+ is excellent (r2 of 0.97 and 0.98, respectively). Importantly, the Π+ parameter is general to cation–π systems other than those reported here, and to studies where the cation–π binding strength is determined using computational levels different from those employed in this study.