Chemistry collegiate section.

Gordon, James S.

* Dorn, S.M. and E.V. Patterson. Division of Science, Truman State University. Ab Initio Molecular Dynamics On The Phenylcarbene Rearrangement. The photochemical rearrangement of phenylcarbene to cycloheptataraene has been studied using ab initio density functional theory coupled with atom-centered density matrix propagation (ADMP) molecular dynamics. Previous computational work indicates that bicyclo[4.1.0]heptatriene should form as an intermediate during the course of this rearrangement. However, no experimental evidence for the existence of bicyclo[4.1.0]heptatriene has been found, despite several attempts by various research groups to isolate this molecule. The previous computational work employed the Born-Oppenheimer approximation, and nuclear kinetic energy was taken to be zero. The current calculations allow for the inclusion of nuclear kinetic energy according to Newton's classical laws of motion and thus provide a more accurate representation of the potential energy surface under experimental conditions. The dynamics calculations were started at the transition state structure previously determined to connect phenylcarbene and bicyclo [4.1.0] heptatriene. The reaction was allowed 212,482 microHartrees of kinetic energy, corresponding to experimental photolysis conditions. Two hundred random trajections were each integrated over 400 femtoseconds. Analysis of the results will provide an accurate picture of the minimum energy pathway connecting phenylcarbene and cycloheptatetraene. The results will also provide lifetime data for all involved species and will lead to a better understanding of the role bicyclo[4.1.0]heptatrie ne plays in this rearrangement.

* Kennett, K.J., Nagan, M.C. Science Division, Truman State University. Molecular Dynamics Simulations Of The Rev-Rre Complex. Translation of viral messenger RNA (mRNA) encoded by the genome of human immunodeficiency virus type-1 (HIV-1) originally produces viral regulatory proteins, such as rev. Rev protein recognition of a sequence of mRNA called the rev response element (RRE) serves as a switch for shuttling unspliced and singly spliced viral mRNA out of the nucleus and into the cytosol of the host cell. Without this protein-RNA interaction, most viral mRNA cannot be translated on host cell ribosomes. Nuclear magnetic resonance (NMR) spectroscopy structures have already characterized the structure of the rev-RRE complex. Molecular dynamics (MD) simulations of the rev-RRE complex have been acquired starting from three different NMR structures (Battiste, J.L., et al. (1996) Science, 273, 1547). The root mean square displacement (RMSD) from starting and average structures have shown that the MD simulations have reached equilibrium, thus allowing for accurate analysis of the occurrence and duration of interactions between arginine side chains of rev and the RRE. The results of this study could eventually be used to develop antiviral pharmaceuticals that would inhibit binding between rev and RRE, thus slowing or possibly arresting the HIV life cycle.

* Mengwasser, J., Lincoln University and Dr. Wimalasea, Wichita State University. "Synthesis of Phenylcyclopropylamines for Structure-Activity Studies of Monoamine Transporters." Dibenzylformamide was treated with cyclohexylmagnesium chloride in the presence of titanium tetraisopropoxide and styrene, as well as two of its derivatives, 4-flourostyrene and 3-flourostyrene. This reaction produced N, N-dibenzylcyclopropylamines. The cis and trans isomers of these compounds were isolated. Then the compounds were debenzylated by catalytic hydrogenation, giving the primary cycloproplyamines. Following debenzylation, they were converted to HC1 salts. Later, the compounds will be used for structure-activity studies of monoamine transporters.

* Menke, J.L. and E.V. Patterson. Division of Science, Truman State University. Ab Initio Density Functional Studies Of Twisted Intramolecular Charge Transfer (Tict) Characteristics Of Substituted Pyrrolylpyridines. Pyrrolylpyridines such as 2-(1-pyrrolyl)-pyridine and three of its methylated derivatives, 3-methyl-2-(1-pyrrolyl)pyridine, 2,4-dimethyl-6-(1-pyrrolyl)-pyridine, and 5-methyl-2-(1-pyrrolyl)-pyridine are known to show fluorescence behavior consistent with a low-lying twisted intramolecular charge transfer excited state. Such behavior is often revealed through dual fluorescence and a significant solvatochromic shift of the long-wavelength emission. All four pyrrolylpyridines mentioned above display these characteristics, although the various methyl substitutions affect both the intensity of emission and the magnitude of the solvatochromic shift. To better understand these differences, these molecules have been studied using quantum mechanical density functional calculations. The ground state energy surface for the rotation about the central axis between the two ring systems was obtained at the B3LYP/631G * level of theory. The corresponding excited state surface was obtained through time-dependent density functional theory (TD-DFT), also at the B3LYP/6-31G * level. The effect of polar (acetonitrile) and nonpolar (cyclohexane) solvent is accounted for through the integral equation formalism polarizable continuum model (IEF-PCM). Trends show that the excited states of each of these molecules are more stable in a twisted conformation whereas the ground states prefer planar or near-planar geometries, confirming that these are TICT molecules.

* K. Schembri, M.C. Nagan, M. Varner, and A. Combs. Science Division, Truman State University. Molecular Dynamics Simulations Of The [Trna.sup.lys,3.sub.uuu] Anticodon Stem Loop. Transfer ribonucleic acid (tRNA) anticodon recognition of messenger RNA (mRNA) codons in the context of the ribosome is critical to accurate translation of the genetic code. Nuclear magnetic resonance (NMR) structures of the third human tRNA that codes for lysine indicates that the inclusion of the posttranscriptionally modified base threonylcarbamoyladenosine at position 37 ([t.sup.6]A37) changes the anticodon stem loop structure such that uracil 34 flips around, leaving only two remaining uracil bases to interact with the messenger RNA codon. It has been proposed that the unusual C32 * [A.sup.+]38 base pair stabilizes [t.sup.6]A37. The NMR structure was obtained in acidic conditions but at physiological pH, this base pair should not form. The purpose of this study is to analyze the dynamics of [t.sup.6]A37 in the tRN[A.sup.Lys, 3.sub.UUU] structure at pH 7. Four tRN[A.sup.Lys,3] variants are being analyzed using molecular dynamics simulations. They include an unmodified tRNA molecule, one containing [t.sup.6]A37, one containing the [A.sup.+]38 modification, and one with both modifications. Trajectories for all four systems have been collected. Root mean square displacements from starting and average structures as well as helical parameters, all indicate that the systems are equilibrated.

* Soemo, A. R., M. C. Nagan. Science Division, Truman State University. Molecular Dynamics Studies Of Arginine Side-Chain Dynamics In The Hiv Rev-Rre Complex Under High And Low Salt Conditions. The human immunodeficiency virus Type 1 (HIV-1) leads to the onset of the acquired immunodeficiency syndrome (AIDS) which has resulted in the deaths of 3 million people in 2003 alone (UNAIDS). The interaction between the Rev protein and the rev response element (RRE), a sequence in messenger RNA (mRNA), is a critical step in the HIV-1 lifecycle. Rev-RRE binding allows mRNA to be transported out of the nucleus and into the cytoplasm of the cell where viral proteins can be translated. The purpose of our study is to examine Rev-RRE interactions to better understand the recognition mechanism. The Rev peptide is arginine rich with 11 arginines of 23 total amino acids. Arginine has a long chain of carbons ending with two amine groups, one of which is positively charged. We are using molecular dynamics simulations to determine how these positively charged arginine side-chains bind to RRE. Specifically, the effects of high and low salt concentrations (150 mM and 50 mM, respectively) are examined to assess the strength of arginine binding to the RRE RNA. All simulations began from a high-resolution nuclear magnetic resonance structure (Battiste et al.). It is believed that an increase in salt concentration reduces nonspecific Rev-RRE recognition. Arginine side-chain dynamics and affinity for RRE will be compared to experimentally determined side-chain mobility.

* Tiemann, S.M., Nagan, M.C. Science Division, Truman State University. The Role Of Pseudouridine At The Spliceosomal Branch Site: A Molecular Dynamics Analysis. The spliceosome, a complex which contains small nuclear RNA (snRNA) and small nuclear ribonucleoprotiens (snRNPs), is where the splicing of pre-messenger RNA (pre-mRNA) molecules occurs. The spliceosome excises or cuts the non-coding regions (introns) and splices together the coding regions (exons). In absence of snRNPs, the splicing reaction still can occur, albeit at a slower reaction rate, and is therefore known as a ribozyme. Two of the five snRNA molecules, U2 and U6, comprise the catalytic acitive site. In the splicing reaction, which occurs via two transesterification reactions, the branch site adenosine (A24) 2'-OH acts as a nucleophile and attacks at the 5'-phosphate on the intron site to form a lariat structure. Biochemical studies have shown that a nonstandard highly conserved base in U2, pseudouridine, is required for splicing activity and in general, increases thermal stability. Nuclear magnetic resonance (NMR) structures show that this pseudouridine induces a structural change in the intron:U2 snRNA helix and places the A24 in an extrahelical position. Molecular dynmamics (MD) simulations of the helix containing the pseudouridine have been acquired in the presence of water and sodium counterions. All simulations utilize the Cornell et al. forcefield and particle mesh Ewald treatment of electrostatics. Equilibration of the MD simulations is assessed with root mean square displacement plots and analysis of helical parameters.

James S. Gordon

Central Methodist College