Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

Stable Hydrogen-Bonded Spherical Capsules Formed from Self-Assembly of Pyrogallol[4]arenes

The self-assemblies of two pyrogallol[4]arenes held together by 48 intermolecular hydrogen bonds stably associate in the form of spherical hexameric capsules. The molecular structures of two hexameric capsules with large interior space were analyzed by single crystal X-ray crystallography.     

"Volatilizable" supports for high-throughput organic synthesis

The concepts and use of "volatilizable" solid supports are presented. Such supports, which are completely removed by volatilization following decomposition, improve the efficiency of the solid-phase synthesis of both individual and mixtures of low-molecular weight acyclic and heterocyclic compounds as well as peptides, peptidomimetics, and protected peptide fragments. The "volatilizable" silica-based solid supports and linkers used to illustrate this concept were found to be completely removed by their decomposition and ultimate "volatilization" during the final cleavage step of synthetic process to yield solely the desired synthetic product(s) in the final reaction vessel.     

Unusual reactivity of tris(pyrazolyl)borate zirconium benzyl complexes

The synthesis and reactivity of [Tp*Zr(CH2Ph)2][B(C6F5)4] (2, Tp* = HB(3,5-Me2pz)3, pz = pyrazolyl) have been explored to probe the possible role of Tp'MR2+ species in group 4 metal Tp'MCl3/MAO olefin polymerization catalysts (Tp' = generic tris(pyrazolyl)borate). The reaction of Tp*Zr(CH2Ph)3 (1) with [Ph3C][B(C6F5)4] in CD2Cl2 at -60 degrees C yields 2. 2 rearranges rapidly to [{(PhCH2)(H)B(mu-Me2pz)2}Zr(eta2-Me2pz)(CH2Ph)][B(C6F5)4] (3) at 0 degrees C. Both 2 and 3 are highly active for ethylene polymerization and alkyne insertion. Reaction of 2 with excess 2-butyne yields the double insertion product [Tp*Zr(CH2Ph)(CMe=CMeCMe=CMeCH2Ph)][B(C6F5)4] (4). Reaction of 3 with excess 2-butyne yields [{(PhCH2)(H)B(mu-Me2pz)2}Zr(Cp*)(eta2-Me2pz)][B(C6F5)4] (6, Cp* = C5Me5) via three successive 2-butyne insertions, intramolecular insertion, chain walking, and beta-Cp* elimination.     

Salvinicins A and B, new neoclerodane diterpenes from Salvia divinorum

[reaction: see text] Two new neoclerodane diterpenes, salvinicins A (4) and B (5), were isolated from the dried leaves of Salvia divinorum. The structures of these compounds were elucidated by spectroscopic techniques, including (1)H and (13)C NMR, NOESY, HMQC, and HMBC. The absolute stereochemistry of these compounds was assigned on the basis of single-crystal X-ray crystallographic analysis of salvinicin A (4) and a 3,4-dichlorobenzoate derivative of salvinorin B.     

(+)-Sorangicin A synthetic studies. Construction of the C(1-15) and C(16-29) subtargets

[structure: see text] Effective stereocontrolled syntheses of subtargets (-)-2 and (-)-4, comprising respectively the C(16-29) and C(1-15) tetrahydropyran and dihydropyran moieties of the potent antibiotic (+)-sorangicin A (1), have been achieved. The cornerstone for the synthesis of (-)-2 involved an aldol tactic exploiting 1,4-induction, followed in turn by an acid-mediated cyclization/ketalization and hydrosilane reduction promoted by TMSOTf, while construction of (-)-4 entailed a stereoselective conjugate addition/alpha-oxygenation sequence.     

Eu8(NCN)5-deltaI6+2delta (delta= 0.05): a novel rare-earth carbodiimide iodide containing oligomeric tritetrahedral Eu8 clusters

Eu8(NCN)4.95I6.10 is the first compound with discrete tritetrahedral Eu8 clusters which are interconnected by coordinating NCN2- carbodiimide anions on their triangular faces to form separated layers, the latter being bridged by iodide and carbodiimide anions.     

Rapid detection of an anthrax biomarker by surface-enhanced Raman spectroscopy

A rapid detection protocol suitable for use by first-responders to detect anthrax spores using a low-cost, battery-powered, portable Raman spectrometer has been developed. Bacillus subtilis spores, harmless simulants for Bacillus anthracis, were studied using surface-enhanced Raman spectroscopy (SERS) on silver film over nanosphere (AgFON) substrates. Calcium dipicolinate (CaDPA), a biomarker for bacillus spores, was efficiently extracted by sonication in nitric acid and rapidly detected by SERS. AgFON surfaces optimized for 750 nm laser excitation have been fabricated and characterized by UV-vis diffuse reflectance spectroscopy and SERS. The SERS signal from extracted CaDPA was measured over the spore concentration range of 10(-14)-10(-12) M to determine the saturation binding capacity of the AgFON surface and to calculate the adsorption constant (Kspore=1.7 x 10(13) M(-1)). At present, an 11 min procedure is capable of achieving a limit of detection (LOD) of approximately 2.6 x 10(3) spores, below the anthrax infectious dose of 10(4) spores. The data presented herein also demonstrate that the shelf life of prefabricated AgFON substrates can be as long as 40 days prior to use. Finally, these sensing capabilities have been successfully transitioned from a laboratory spectrometer to a field-portable instrument. Using this technology, 10(4) bacillus spores were detected with a 5 s data acquisition period on a 1 month old AgFON substrate. The speed and sensitivity of this SERS sensor indicate that this technology can be used as a viable option for the field analysis of potentially harmful environmental samples.     

Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture

Bacterial expression of beta-lactamases is the most widespread resistance mechanism to beta-lactam antibiotics, such as penicillins and cephalosporins. There is a pressing need for novel, non-beta-lactam inhibitors of these enzymes. One previously discovered novel inhibitor of the beta-lactamase AmpC, compound 1, has several favorable properties: it is chemically dissimilar to beta-lactams and is a noncovalent, competitive inhibitor of the enzyme. However, at 26 microM its activity is modest. Using the X-ray structure of the AmpC/1 complex as a template, 14 analogues were designed and synthesized. The most active of these, compound 10, had a K(i) of 1 microM, 26-fold better than the lead. To understand the origins of this improved activity, the structures of AmpC in complex with compound 10 and an analogue, compound 11, were determined by X-ray crystallography to 1.97 and 1.96 A, respectively. Compound 10 was active in cell culture, reversing resistance to the third generation cephalosporin ceftazidime in bacterial pathogens expressing AmpC. In contrast to beta-lactam-based inhibitors clavulanate and cefoxitin, compound 10 did not up-regulate beta-lactamase expression in cell culture but simply inhibited the enzyme expressed by the resistant bacteria. Its escape from this resistance mechanism derives from its dissimilarity to beta-lactam antibiotics.