NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions.

In order to examine the origins of the large positive cooperativity (ΔG(0)(coop) = -2.9 kcal mol(-1)) of trimethoprim (TMP) binding to a bacterial dihydrofolate reductase (DHFR) in the presence of NADPH, we have determined and compared NMR solution structures of L. casei apo DHFR and its binary and ternary complexes with TMP and NADPH and made complementary thermodynamic measurements. The DHFR structures are generally very similar except for the A-B loop region and part of helix B (residues 15-31) which could not be directly detected for L. casei apo DHFR because of line broadening from exchange between folded and unfolded forms. Thermodynamic and NMR measurements suggested that a significant contribution to the cooperativity comes from refolding of apo DHFR on binding the first ligand (up to -0.95 kcals mol(-1) if 80% of A-B loop requires refolding). Comparisons of Cα-Cα distance differences and domain rotation angles between apo DHFR and its complexes indicated that generally similar conformational changes involving domain movements accompany formation of the binary complexes with either TMP or NADPH and that the binary structures are approaching that of the ternary complex as would be expected for positive cooperativity. These favorable ligand-induced structural changes upon binding the first ligand will also contribute significantly to the cooperative binding. A further substantial contribution to cooperative binding results from the proximity of the bound ligands in the ternary complex: this reduces the solvent accessible area of the ligand and provides a favorable entropic hydrophobic contribution (up to -1.4 kcal mol(-1)).

Toward more reliable 13C and 1H chemical shift prediction: a systematic comparison of neural-network and least-squares regression based approaches.

The efficacy of neural network (NN) and partial least-squares (PLS) methods is compared for the prediction of NMR chemical shifts for both 1H and 13C nuclei using very large databases containing millions of chemical shifts. The chemical structure description scheme used in this work is based on individual atoms rather than functional groups. The performances of each of the methods were optimized in a systematic manner described in this work. Both of the methods, least-squares and neural network analyses, produce results of a very similar quality, but the least-squares algorithm is approximately 2--3 times faster.

Exceptionally facile CO addition to a saturated ruthenium complex.

Synthesis and characterization of Cp*Ru[eta3-HC(PPh2NPh)2], 1, reveals it to have a "piano stool" structure with the ligand bound to Ru(II) via two N and the unique, sp3 hybridized carbon. While the analogous (cymene) Ru[eta3-HC(PPh2NPh)2]+ does not react with CO, under the same conditions, 1 adds one CO rapidly (25 degrees C, 1 atm CO). Characterization, including an X-ray structure determination, shows that CO has displaced one chelate ligand nitrogen, which then hangs off the molecule, free of Ru. DFT calculations reveal a possible mechanism via a remarkably low energy (+9.3 kcal/mol) intermediate, pendant N, but with one phenyl on phosphorus stabilizing Ru via donation from a C(ipso)=C(ortho) bond. DFT calculations show that the electronic energy change for binding CO is over 20 kcal/mol less favorable for cymene than for C5Me5- as ligand; the reactivity difference is thus thermodynamic in origin.

Multifunctional behavior by a Bis-(phosphinimino)methanide ligand: eta 2- vs eta 3-coordination vs Bronsted basicity.

The reaction of [(Cymene)RuCl2]2 with the chelate LiHC(PPh2NPh)2 occurs to remove both chloride ligands, to furnish a cationic Ru(II) complex with the monoanionic ligand bound eta3, through two N and an sp3 carbon. This cation is also produced from the conjugate acid of the ligand H2C(PPh2NPh)2 because this molecule can serve as a Brønsted base, to deprotonate the acidic carbon of another molecule of H2C(PPh2NPh)2. DFT calculations show an energy surface where (Cymene)RuHC(PPh2NPh)2L is more stable with a Ru-CH(PPh2NPh)2 bond and with L = Cl- or MeCN not coordinated to Ru, than to an eta2-HC(PPh2NPh)2 structure with coordinated L; this is tested experimentally. The greater tendency for this ligand to be coordinated eta3 vs analogous diketiminates is discussed. The nucleophilicity of Cgamma in structure 1, vs that of donors L = Cl- or MeCN, is evaluated to understand the preference of the bis(phosphinimino)methanide to be bidentate or tridentate.