Showing papers by "James Alexis Platts published in 2008"

Experimental and theoretical charge density study of chemical bonding in a Co dimer complex.

Abstract: The charge density of Co2(CO)6(HC⋮CC6H10OH) (1) in the crystalline state has been determined using multipolar refinement of single-crystal X-ray diffraction data collected (i) with a synchrotron source at very low temperatures (15 K) and (ii) using a conventional source with the crystal at intermediate temperature (100 K). The X-ray charge density model is augmented by complete active space and density functional theory calculations. Topological analyses of the different charge distributions show that the two Co atoms are not bonded to each other in the quantum theory of atoms in molecules (QTAIM) sense of the word. However, the behavior of the source function and the total energy density indicate that there is some bond-like character in the Co−Co interaction. The bridging alkyne fragment provides an unusual bonding situation, with extremely small electron density differences between the two Co−C bond critical points and the “CoC2” ring critical point. Thus, the structure is close to a topological catast...

Calculation of lipophilicity for Pt(II) complexes: experimental comparison of several methods

Abstract: Platinum containing compounds are promising antitumor agents, but must enter cells before reaching their main biological target, namely DNA. Their distribution within the body, and hence their activity is to a large extent determined by their lipophilicity, thus there is a strong interest to develop computational methods to predict this important property. This study analyses accuracy of five methods, namely ALOGPS, KOWWIN, CLOGP and two quantum chemical approaches, to predict octanol/water partition coefficients (log P) for sets of 43 and 12 Pt(II) complexes, collected from the literature and measured by the authors, respectively. All methods gave generally poor results with mean absolute error (MAE) of between 0.8 and 3 log units for prediction of new compounds. Extension of the ALOGPS program with data from the literature set resulted in the best prediction ability, MAE = 0.46, for the measured molecules. The program was also able to correctly predict errors in calculated log P values. It is freely available for interactive use at http://www.vcclab.org.

Auxiliary basis sets for density fitting-MP2 calculations: Nonrelativistic triple-ζ all-electron correlation consistent basis sets for the 3d elements Sc-Zn

Abstract: Auxiliary basis sets for density fitting second-order Moller-Plesset perturbation theory (DF-MP2) have been optimized for use with the triple-ζ nonrelativistic all-electron correlation consistent orbital basis sets, cc-pVTZ-NR and aug-cc-pVTZ-NR, for the 3d elements Sc–Zn. The relative error in using these auxiliary basis sets is found to be around four orders of magnitude smaller than that from utilizing triple-ζ orbital basis sets rather than corresponding quadruple-ζ basis sets, in calculation of the correlation energy for a test set of 54 small to medium sized transition metal complexes.

Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Møller-Plesset perturbation theory.

Abstract: Stacking interaction energies for ten B-DNA base-pair steps are computed with density fitted local second-order Moller–Plesset perturbation theory (DF-LMP2), and with the spin-component scaled (SCS) and spin-component scaled for nucleobases (SCSN) variants of DF-LMP2. Comparison with existing CBS(T) reference data indicates larger than expected energy differences for both SCS variants. After an analysis of the errors involved, an alternative method of producing reference data is proposed where DF-LMP2/aug-cc-pVTZ and DF-LMP2/aug-cc-pVQZ energies for the whole complex are extrapolated to produce interaction energies that do not require many-body correction and show reduced error in estimation of the basis set limit. A literature correction term from coupled cluster theory with perturbative triples is then added to the DF-LMP2 estimated basis set limit. These new reference data are consistently around 1 kcal mol−1 less than previous literature data. DF-SCSN-LMP2/aug-cc-pVTZ is found to reproduce the new reference interaction energies with a root mean square error (RMSE) of 0.71 kcal mol−1, while SCS consistently underestimates the binding energy.

Kinetics of Iminium Ion Catalysis

Abstract: Identifying the bottleneck: Kinetic and computational data for the key steps of the iminium ion catalyzed Diels–Alder reaction show that the cycloaddition (step II in scheme) is the rate-determining step of the catalytic cycle and provide a rationale for developing more-active catalyst architectures.

Insights into DNA binding of ruthenium arene complexes: Role of hydrogen bonding and π stacking

Abstract: Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol−1 difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene−base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and π-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N−H···X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.

Calculating interaction energies in transition metal complexes with local electron correlation methods

Abstract: The results of density fitting and local approximations applied to the calculation of transition metal–ligand binding energies using second order Moller–Plesset perturbation theory are reported. This procedure accurately reproduces counterpoise corrected binding energies from the canonical method for a range of test complexes. While counterpoise corrections for basis set superposition error are generally small, this procedure can be time consuming, and in some cases gives rise to unphysical dissociation of complexes. In circumventing this correction, a local treatment of electron correlation offers major efficiency savings with little loss of accuracy. The use of density fitting for the underlying Hartree–Fock calculations is also tested for sample Ru complexes, leading to further efficiency gains but essentially no loss in accuracy.