Biomedical subjects

K K Baldridge

Publications and source records attributed to K K Baldridge.

5 recordsLinked to original sources

PubMed2001

Quantum mechanical designs toward planar delocalized cyclooctatetraene: a new target for synthesis.

Ab initio and hybrid density functional quantum mechanical computation are applied to the structure and energetics of a series of annelated cyclooctatetraenes. Tetrakis-cyclobuteno, perfluorocyclobuteno or bicyclo[2.1.1]hexeno annelations result in planar structures with distinct exo and endo valence tautomers of the double bonded cycle. The contribution of each basic annelation to the exo/endo relative energy is estimated. An additivity scheme for approximating the energy of a mixed system is developed and compared to the quantum mechanical prediction. Bis bicyclic annelation to the a and d positions creates "valence tautomeric frustration" and strongly perturbs the molecular structure. This phenomenon leads to a general design for a planar cyclooctatetraenes where the "delocalized" diradicaloid state is the minimum energy form. These compounds are seen as excellent targets for chemical synthesis.

Alkenes↗

PubMed2001

Structure/energy correlation of bowl depth and inversion barrier in corannulene derivatives: combined experimental and quantum mechanical analysis.

Synthesis of a series of corannulene derivatives with varying bowl depths has allowed for a study correlating the structure (bowl depth) and the energy of bowl inversion. Substituents placed in the peri positions are repulsive and flatten the bowl, thus causing a decrease in the bowl inversion barrier. Conversely, annelation across the peri positions causes a deepening of the bowl, thus an increase in the bowl inversion barrier. Barriers between 8.7 and 17.3 kcal/mol have been measured, and their structures have been calculated using a variety of ab initio methods. The energy profile of an individual corannulene derivative is assumed to fit a mixed quartic/quadratic function from which an empirical correlation of bowl depth and inversion barrier that follows a quartic function is derived. Structure/energy correlations of this type speak broadly of the nature of enzymatic and catalytic activation of substrates.

Chemical Phenomena↗

PubMed2000

The structure of the chromophore within DsRed, a red fluorescent protein from coral.

DsRed, a brilliantly red fluorescent protein, was recently cloned from Discosoma coral by homology to the green fluorescent protein (GFP) from the jellyfish Aequorea. A core question in the biochemistry of DsRed is the mechanism by which the GFP-like 475-nm excitation and 500-nm emission maxima of immature DsRed are red-shifted to the 558-nm excitation and 583-nm emission maxima of mature DsRed. After digestion of mature DsRed with lysyl endopeptidase, high-resolution mass spectra of the purified chromophore-bearing peptide reveal that some of the molecules have lost 2 Da relative to the peptide analogously prepared from a mutant, K83R, that stays green. Tandem mass spectrometry indicates that the bond between the alpha-carbon and nitrogen of Gln-66 has been dehydrogenated in DsRed, extending the GFP chromophore by forming C==N==C==O at the 2-position of the imidazolidinone. This acylimine substituent quantitatively accounts for the red shift according to quantum mechanical calculations. Reversible hydration of the C==N bond in the acylimine would explain why denaturation shifts mature DsRed back to a GFP-like absorbance. The C==N bond hydrolyses upon boiling, explaining why DsRed shows two fragment bands on SDS/PAGE. This assay suggests that conversion from green to red chromophores remains incomplete even after prolonged aging.

Animals↗

PubMed1997

Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth.

A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.

Acetonitriles↗

PubMed1995

QMView: a computational chemistry three-dimensional visualization tool at the interface between molecules and mankind.

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, PostScript files, slide, and/or video. These and other original features discussed in this article provide a graphic interface that is unique compared to others that are currently available. Examples of images produced by QMView are presented.

Computer Graphics↗