An Assessment of Computational Methods for Obtaining Structural Information of Moderately Flexible Biomolecules from Ion Mobility Spectrometry

When utilized in conjunction with modeling, the collision cross section (Ω) from ion mobility spectrometry can be used to deduce the gas phase structures of analyte ions. Gas phase conformations are determined computationally, and their Ω calculated using an approximate method, the results of which are compared with experimental data. Though prior work has focused upon rigid small molecules or large biomolecules, correlation of computational and experimental Ω has not been thoroughly examined for analytes with intermediate conformational flexibility, which constitute a large fraction of the molecules studied in the field. Here, the computational paradigm for calculating Ω has been tested for the tripeptides WGY, YGW, and YWG (Y = tyrosine, W = tryptophan, G = glycine). Experimental data indicate that Ωexp (YWG) > Ωexp (WGY) ≈ Ωexp (YGW). The energy distributions of conformations obtained from tiers of simulated annealing molecular dynamics (SAMD) were analyzed using a wide array of density functionals. These quantum mechanical energy distributions do not agree with the MD data, which leads to structural differences between the SAMD and DFT conformations. The latter structures are obtained by reoptimization of the SAMD geometries, and are the only suite of structures that reproduce the experimental trend in analyte separability. In the absence of fitting Lennard Jones potentials that reproduce experimental results for the Trajectory Method, the Exact Hard Sphere Scattering method produced numerical values that are in best agreement with the experimental cross sections obtained in He drift gas

A theoretical study of standard heat of formation of systems involving in the zinc reduction of silicon tetrachloride

The gas phase zinc reduction of silicon tetrachloride produces the silicon for solar cells. While this reaction provides a new low-cost production route for silicon materials for photovoltaic cells, little is known about the chemistry of this process. Theoretical methods, based on quantum chemistry predictions, in the gas phase, are now fully capable of providing molecular thermochemistry and kinetic parameters with sufficient accuracy for modeling purposes. This kind of kinetic information is crucial for reactor design and scale-up of reaction systems. In this spirit, we have developed two test sets, one for silicon and another for zinc compounds, for evaluating the performance of various computational methods: density functional theory (B3LYP, BH and HLYP, BMK, and M05-2X), and composite methods (G3 and CBS-QB3). The new generation of DFT methods BMK and M05-2X and the composite CBS-QB3 method allow to predict the standard heat of formation, Delta H-f(0), of the silicon compounds with MAD of, respectively, 7, 13, and 15 kJ mol(-1), whereas the previous DFT methods are less reliable. At least triple zeta, for basis set, is needed in order to predict correctly the standard heat of formation. For the zinc compounds, BMK, B3LYP, and CBS-QB3 are the best performing methods for the calculation of Delta H-f(0) with MADs of 24, 25, and 28 kJ mol(-1), respectively. We recommend BMK and CBS-QB3 methods for investigating the new solar silicon process