Research Structure and Reactivity Solvation Variable Spin Molecules Phosphorus Project Dossiers

Interests and Future Plans

Through many collaborations with experimental colleagues, we have contributed to the better understanding of a variety of issues associated with organic and inorganic structure and reactivity. The areas where we continue to have key interests include elucidating the mechanistic and stereochemical course of electrocyclic organic reactions, characterizing processes by which various classes of contaminants are degraded in the environment, and the nature of inter- and intramolecular interactions governing crystal morphology, molecular recognition, etc.

In addition, we are expanding our interests into classical simulations of macro(bio)molecular systems. Currently our focus is on tRNA structure and dynamics. One of the key steps in the biological synthesis of proteins is the translation of the genetic code, as carried by messenger ribonucleic acid (mRNA), into the correct sequence of amino acids that defines a given protein. This translation is accomplished within cellular assemblies of RNAs and proteins called ribosomes. Amino acids are delivered to the ribosome by transfer RNA (tRNA) molecules having "anticodon" regions that are complementary to the 3-base "codon" sequence of the mRNA. Thus, one key aspect of this translation involves ensuring that distinct tRNA molecules always carry their designated amino acid. Using classical simulations with explicit solvent, we are studying the process by which tRNA molecules become "charged" with the proper amino acid and in particular the mechanism by which aminoacyl-tRNA synthetases specifically recognize their substrate tRNA molecules.

Accomplishments

Our diverse efforts have:

• illustrated the importance of including dynamical effects in the calculation of ESR hyperfine couplings for simple and monofluorinated alkyl radicals. (See Publication 13.)

• characterized [4+3] cycloaddition reactions between the 2-hydroxyallyl cation and various dienes, rationalizing experimentally observed stereoselectivities. We have also proposed a new cycloaddition reaction between the (classical) cyclopropylcarbinyl cation and olefins or dienesÑthe latter reaction permits single-step construction of eight-membered carbocycles. (See Publications 41 and 105.)

• collaborated to explain the structure, and in particular the localization of unpaired spin density, in copper nitrosyl complexes (with Professor Bill Tolman of the University of Minnesota). (See Publication 29.)

• collaborated to understand the effect of silicon trigonal-bipyramidal stereochemistry on the stereoselective reduction of carbonyl compounds by dialkoxysiliconates in the gas phase (with the late Professor Bob Squires of Purdue University). (See Publication 51.)

• collaborated to correct estimated gas-phase heats of formation for enols and enol radical cations (with Professor Frank Turecek of the University of Washington). (See Publication 55.)

• collaborated to explain the crystal structures of a series of substituted o-nitrobenzonitriles in terms of incipient nucleophilic addition character between nitro group oxygen atoms and the nitrile (with Professor Doyle Britton of the University of Minnesota). (See Publication 56.)

• collaborated to characterize the dihydrogen bond between donor-acceptor complexes of Group 13 and Group 15 hydrides and its implications for the design of novel electronic materials (with Professor Wayne Gladfelter of the University of Minnesota). (See Publications 82 and 95.)

• collaborated to determine the free energies of activation for key surface reactions governing the morphology of single-crystal diamond growth (with Professor Jeff Roberts of the University of Minnesota). (See Publication 83.)

• collaborated to rationalize the function of critical elements affecting the recognition of the acceptor stem domain of Escherichia coli tRNA^Ala by alanyl-tRNA synthetase. This latter work, in collaboration with Professor Karin Musier-Forsyth of the University of Minnesota, represents the initiation of a broader effort within the group to understand protein/RNA interactions. (See Publication 124.)

  
  
  

  
  
  
• collaborated to better characterize the electronic nature of the junction between arylthiols and a single-crystal copper surface, particularly with respect to semiconductor behavior (with Professor Xiaoyang Zhu of the University of Minnesota). (Wait for it . . . )