Towards multireference equivalents of the G2 and G3 methods

The effect of replacing the standard single-determinant reference wave functions in variants of G2 and G3 theory by multireference (MR) wave functions based on a full-valence complete active space has been investigated. Twelve methods of this type have been introduced and comparisons, based on a slightly reduced G2-1 test set, are made both internally and with the equivalent single-reference methods. We use CASPT2 as the standard MR-MP2 method and MRCl+Q as the higher correlation procedure in these calculations. We find that MR-G2(MP2,SVP), MR-G2(MP2), and MR-G3(MP2) perform comparably with their single-reference analogs, G2(MP2,SVP), G2(MP2), and G3(MP2), with mean absolute deviations (MADs) from the experimental data of 1.41, 1.54, and 1.23 kcal mol−1, compared with 1.60, 1.59, and 1.19 kcal mol−1, respectively. The additivity assumptions in the MR-Gn methods have been tested by carrying out MR-G2/MRCI+Q and MR-G3/MRCI+Q calculations, which correspond to large-basis-set MRCI+Q+ZPVE+HLC calculations. These give MADs of 1.84 and 1.58 kcal mol−1, respectively, i.e., the agreement with experiment is somewhat worse than that obtained with the MR-G2(MP2) and MR-G3(MP2) methods. In a third series of calculations, we have examined pure MP2 and MR-MP2 analogs of the G2 and G3 procedures by carrying out large-basis-set MP2 and CASPT2(+ZPVE+HLC) calculations. The resultant methods, which we denote G2/MP2, G3/MP2, MR-G2/MP2, and MR-G3/MP2, give MADs of 4.19, 3.36, 2.01, and 1.66 kcal mol−1, respectively. Finally, we have examined the effect of using MCQDPT2 in place of CASPT2 in five of our MR-Gn procedures, and find that there is a small but consistent deterioration in performance. Our calculations suggest that the MR-G3(MP2) and MR-G3/MP2 procedures may be useful in situations where a multireference approach is desirable.The authors would also like to thank the National Science Foundation International Division for providing travel funds to ~M.S.G. and M.A.F.! and the National Science Foundation Chemistry Division for supporting the research

Environmental and genetic factors associated with Solanesol accumulation in potato leaves

Solanesol is a high value 45-carbon, unsaturated, all-trans-nonaprenol isoprenoid. Recently solanesol has received particular attention because of its utility, both in its own right and as a precursor in the production of numerous compounds used in the treatment of disease states. Solanesol is found mainly in solanaceous crops such as potato, tomato, tobacco and pepper where it accumulates in the foliage. There is considerable potential to explore the extraction of solanesol from these sources as a valuable co-product. In this study we have characterised the genetic variation in leaf solanesol content in a biparental, segregating diploid potato population. We demonstrate that potato leaf solanesol content is genetically controlled and identify several quantitative trait loci associated with leaf solanesol content. Transient over-expression of genes from the methylerythritol 4-phosphate (MEP) and mevalonic acid (MVA) pathways, either singly or in combination, resulted in enhanced accumulation of solanesol in leaves of Nicotiana benthamiana, providing insights for genetically engineering the pathway. We also demonstrate that in potato, leaf solanesol content is enhanced by up to six-fold on exposure to moderately elevated temperature and show corresponding changes in expression patterns of MEP and MVA genes. Our combined approaches offer new insights into solanesol accumulation and strategies for developing a bio-refinery approach to potato production

Density functional theory based effective fragment potential method

The effective fragment potential (EFP) method, is a discrete method for the treatment of solvent effects, originally formulated using Hartree–Fock (HF) theory. Here, a density functional theory(DFT) based implementation of the EFP method is presented for water as a solvent. In developing the DFT based EFP method for water, all molecular properties (multipole moments, polarizabilitytensors, screening parameters, and fitting parameters for the exchange repulsion potential) are recalculated and optimized, using the B3LYP functional. Initial tests for water dimer, small water clusters, and the glycine–water system show good agreement with ab initioand DFT calculations. Several computed properties exhibit marked improvement relative to the Hartree–Fock based method, presumably because the DFT based method includes some dynamic electron correlation through the corresponding functional.The following article appeared in Journal of Chemical Physics 118 (2003): 6725, and may be found at doi:10.1063/1.1559912.</p

Development of a Tetrameric Streptavidin Mutein with Reversible Biotin Binding Capability: Engineering a Mobile Loop as an Exit Door for Biotin

A novel form of tetrameric streptavidin has been engineered to have reversible biotin binding capability. In wild-type streptavidin, loop3–4 functions as a lid for the entry and exit of biotin. When biotin is bound, interactions between biotin and key residues in loop3–4 keep this lid in the closed state. In the engineered mutein, a second biotin exit door is created by changing the amino acid sequence of loop7–8. This door is mobile even in the presence of the bound biotin and can facilitate the release of biotin from the mutein. Since loop7–8 is involved in subunit interactions, alteration of this loop in the engineered mutein results in an 11° rotation between the two dimers in reference to wild-type streptavidin. The tetrameric state of the engineered mutein is stabilized by a H127C mutation, which leads to the formation of inter-subunit disulfide bonds. The biotin binding kinetic parameters (koff of 4.28×10−4 s−1 and Kd of 1.9×10−8 M) make this engineered mutein a superb affinity agent for the purification of biotinylated biomolecules. Affinity matrices can be regenerated using gentle procedures, and regenerated matrices can be reused at least ten times without any observable reduction in binding capacity. With the combination of both the engineered mutein and wild-type streptavidin, biotinylated biomolecules can easily be affinity purified to high purity and immobilized to desirable platforms without any leakage concerns. Other potential biotechnological applications, such as development of an automated high-throughput protein purification system, are feasible