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We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise ͑CP͒ method. This method is applied to the H-bonding complexes HF/HCN, HF/H 2 O, and HCCH/H 2 O using the 6-31G͑d,p͒ and D95ϩϩ͑d,p͒ basis sets(More)
We report completely optimized ONIOM DFT/AM1 molecular orbital calculations on several collagen-like triple helices based upon the repeating triad, ProProGly. The requirement of Gly as every third amino acid in collagen can be attributed to its enantiomorphic nature, as it behaves as a Damino acid in collagen. We, therefore, explored related collagen-like(More)
A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal. For the(More)
Zirconium-89 is an effective radionuclide for antibody-based positron emission tomography (PET) imaging because its physical half-life (78.41 h) matches the biological half-life of IgG antibodies. Desferrioxamine (DFO) is currently the preferred chelator for (89)Zr(4+); however, accumulation of (89)Zr in the bones of mice suggests that (89)Zr(4+) is(More)
Five peptides, each containing 17 amino acids, have been completely geometrically optimized in their alpha-helical and beta-strand forms using a mixed DFT/AM1 procedure. B3LYP/D95** was used for the entire helical structures, while AM1 was initially used to optimize the side chains, followed by reoptimization at the DFT level. The energetic and structural(More)
We compare the structures and energies of beta-strands, alpha-helices, and 3(10)-helices for capped polyalanines, acetyl(ala)(N)()NH(2), for values of N from 2 to 18, using completely optimized mixed DFT/AM1 calculations. Non-pairwise additive cooperativity is manifest from the variation of the relative energies, helical strain, dipole moments, and H-bond(More)
Five pentapeptides, GGGGG, GAGGG, GVGGG, GLGGG, and GIGGG, have been completely optimized in the 3(10)-helical and open beta-strand conformations at the B3LYP/D95 level. The energies of the helices relative to the beta-strands vary from -2.1 to -3.6 kcal and depend on the amino acid residue sequence. The energies of substituting A, V, L, or I for G in the(More)
The N-H...O H-bonding enthalpy between 4-pyridones connected in a chain of H-bonds can achieve 23 kcal/mol for the most central H-bonds, while that between two 4-pyridones is 9.90 kcal/mol based upon DFT calculations on the counterpoise-corrected potential energy surfaces. That the range of enthalpies for N-H...O H-bonds can vary from as little as 2 to as(More)
We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of(More)
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly(More)