Friday morning, 9 July 1999: Computers in the Curriculum
Session
Session Chair: William G. Golden, Conference
Co-Chair
8:30 am Coffee and baked goods ... "Registrations",
introductions, and in general a great
time to arrive at the Department of Chemistry.
9:00 - 9:10 am Richard A. Paselk, Conference Chair
"Introduction and Greeting"
9:15 - 9:40 am Patrick E. Fleming; California State
University - Sacramento
CCS-1: "Ab initio reaction pathways for the dissociation of small radicals: An
experiment for an upper-division laboratory"
9:45 - 10:10 am Elisheva Goldstein, P. Siegel; California
State Polytechnic University - Pomona
CCS-2: "Computational Chemistry/Physics: A 400-level interactive course"
10:15 - 10:40 am Mervin P. Hanson; Humboldt State University
CCS-3: "Duplicating the work of giants with some help from Mathematica® and Gaussian®"
10:45 - 10:55 am Break for coffee.
11:00 - 11:25 am Randy M. Miller; California State University - Chico
CCS-4: "Introducing fundamental chemical principles and dynamic modeling in the
context of global warming"
11:30 - 11:55 am Richard A. Paselk; Humboldt State University
CCS-5: "Academic web-sites: Faculty design and creation"
12:00 - 12:25 pm Ray Trautman; San Francisco State University
CCS-6: "Spartan® and Chime® - Essential tools for all chemistry instructors"
Friday afternoon, 9 July 1999: Lunch
12:30 - 2:00 pm Lunch ad lib in Arcata.
Friday afternoon, 9 July 1999: Undergraduate Poster Session:
Session Chair: William G. Golden, Conference Co-Chair
2:00 - 3:00 pm Posters
Lyndsay Jacks, Dana Ray, and Randy M. Miller; California State University - Chico
UPS-1: "An integrated lab experience using molecular modeling to elucidate the synthesis and conformational properties of 2-bromo-3,3,5,5-tetramethylcyclohexanone"
John Merle and Susan M. Crawford; California State University - Sacramento
UPS-2: "Determination of the energy of activation for the ring inversion of 5,5-dimethyl-1,3-dioxane via ab initio calculations"
Byron Wanzong, Robert W. Zoellner, and William G. Golden; Humboldt State University
UPS-3: "Computationally-determined pre-adsorbate structures of simple hydrocarbon molecules and their perfluorocarbon analogs"
Terry Yen, Elisheva Goldstein; California State Polytechnic University - Pomona
UPS-4: "Theoretical study of the inhibition of HIV protease by curcumin boron
complex"
Friday evening, 9 July 1999: Dinner
7:00 pm Dinner at Hunan Plaza in Arcata
Saturday morning, 10 July 1999: Computers in Undergraduate Research Session:
Session Chair: William G. Golden, Conference Co-Chair
8:30 am Coffee and baked goods
9:00 - 9:05 am Robert W. Zoellner, Conference Secretary
"Introduction of Invited Speaker"
9:10 - 10:10 am Keynote Invited Speaker
Scot R. Mente; Central Research Division, Pfizer, Inc.
CRS-1: "Computer simulations of solvation phenomena ... or how to get a job by playing with computers for six years"
10:15 - 10:25 am Break for coffee
10:30 - 10:55 am Sergio Aragon; San Francisco State University
CRS-2: "Accurate molecular hydrodynamics"
11:00 - 11:25 am Elisheva Goldstein, K. N. Houk; California State Polytechnic University - Pomona
CRS-3: "Ab initio calculations of the concerted transition state of [6 + 4] cycloadditions"
11:30 - 11:55 am Robert W. Zoellner, Lisa A. Nader, and Claudio Bianchini; Humboldt State University
CRS-4: "Transition state structures for the interconversion between the PM3(tm)-calculated absolute configurations of [(triphos)MH(h 2-(C,S)-C20H12S)], M = Co or Rh and triphos = h 3-CH3C(CH2PPh2)3"
12:00 - 12:10 pm Richard A. Paselk, Conference Chair
"Closing remarks"
CCS-1
Patrick E. Fleming; California State University - Sacramento
"Ab initio reaction pathways for the dissociation of small radicals: An experiment for an upper-division laboratory"
Abstract unavailable.
CCS-2
Elisheva Goldstein, P. Siegel; California State Polytechnic University - Pomona
"Computational Chemistry/Physics: A 400-level interactive course"
This course is designed as an overview of computational chemistry and physics with an emphasis on using modern software packages for atomic and molecular modeling, and computer code writing. This course is not meant to be an introduction to theoretical chemistry/physics but rather to introduce experimental chemists/physicists to the available computational tools. Both IBM RISC 6000 (UNIX) and PC terminals are used locally. Time is split evenly between formal lectures and laboratory work.
The general approach is to try to understand the spectra of alkali metals (one valence electron). We use a parallel approach by solving the problem using Gaussian 94 and writing our own code. Once wavefunctions are obtained, we also calculate atomic properties: Oscillator strengths, radial extent, and spin-orbit splitting.
CCS-3
Mervin P. Hanson; Humboldt State University
"Duplicating the work of giants with some help from Mathematica® and Gaussian®"
The ground-state wave function
of the hydrogen molecule ion can be approximated with a simple
LCAO-MO composed of hydrogen atom 1s orbitals. All terms
in the expectation value of the Hamiltonian can be determined
easily using the CAS Mathematica® and the result compared
to reality.
Gaussian® can approximate the exact wavefunction (reality) for the hydrogen molecule ion using a sufficiently extensive basis set and the Hartree-Fock method. Given the exact wavefunction over a cross section of the molecule ion, the expectation values for the kinetic energy and potential energy can be evaluated using Mathematica® and some numerical approximations. Knowing the various energies allows one to see what really makes up the simplest chemical bond.
The Heitler-London and LCAO-MO (Coulson) approximations for the energy of a hydrogen molecule are explicitly coded in Mathematica® and compared to the Hartree-Fock approximation as well as the "exact" results (QCISD(T)) from Gaussian®.
CCS-4
Randy M. Miller; California
State University - Chico
"Introducing fundamental chemical principles and dynamic modeling in the context of global warming"
Global warming provides the backdrop for the introduction of some fundamental chemical principles and dynamic modeling. A lab activity has been designed in which students measure the density and specific heat capacity of water and other materials like sand or soil. The results of these measurements are incorporated into a dynamic model of the temperature of the earth's surface developed using STELLA®. The model is extremely simple, but does enable students to simulate the influence of the absorption of solar radiation and the composition of the earth's surface on surface temperature. The activity is designed so that students see the importance of some of the physical properties of substances on a bigger and perhaps more interesting problem like global warming.
CCS-5
Richard A. Paselk; Humboldt State University
"Academic web-sites: Faculty design and creation"
In this talk I will briefly describe the course-related web-sites I have created. I will focus on their value to myself as creator and to my students. The sites described are strictly supplemental: They are not intended as "distance learning" sites, nor is "distance learning" in my plans for the future. The talk will focus on my biochemistry site as it is the most highly developed. However, I will also compare the student responses to two other course sites as they reflect on the responses of students at different academic levels (sophomore vs. senior) to this kind of on-line "help".
CCS-6
Ray Trautman; San Francisco State University
"Spartan ® and Chime® - Essential tools for all chemistry instructors"
Computational chemistry and molecular visualization applications can be effective pedagogical tools to help students learn chemistry concepts at the microscopic level. In addition, they enable the presentation and learning of quantitative information in an apparently qualitative manner. The Spartan ® graphical user interface provides a simple tool for building molecules, submitting computational calculations, creating surfaces, and creating pdb and vibrational analysis output files. CHIME® enables the simple incorporation of interactive molecular structures into web pages. CHIME® can display both spectra and molecular graphics and link between the two. Examples of instructional materials for General and Organic Chemistry created with Spartan ® and CHIME® will be presented.
UPS-1
Lyndsay Jacks, Dana Ray
and Randy M. Miller; California State University - Chico
"An integrated lab experience using molecular modeling to elucidate the synthesis and conformational properties of 2-bromo-3,3,5,5-tetramethylcyclohexanone"
The Chemistry Department at CSU, Chico is exploring the potential for integrating the upper division laboratories in organic, physical, inorganic and analytical chemistry. In an effort to evaluate the effectiveness and efficiency of this integration, a synthetic organic reaction which has typically been used in an advanced organic lab has been carried out under the supervision of faculty members from organic chemistry and physical chemistry. In addition to utilizing various spectroscopic tools to characterize the reaction, classic physical chemistry experiments and molecular modeling techniques have been used to understand the reaction mechanism and the conformational properties of the products.
UPS-2
John Merle and Susan M. Crawford; California State University - Sacramento
"Determination of the energy of activation for the ring inversion of 5,5-dimethyl-1,3-dioxane via ab initio calculations"
The energy of activation for the ring inversion of 5,5-dimethyl-1,3-dioxane was determined via ab initio calculations using Gaussian 94 quantum chemical software. Initial optimizations were performed using the AM1 semiempirical method followed by restricted Hartree-Fock theory with the 6-31G* basis set. A driving technique was implemented by incrementally changing one of the ring dihedral angles to simulate ring inversion. Transition states were isolated and confirmed with frequency calculations. The resulting conformational activation barrier was compared with experimental temperature dependent proton NMR results.
UPS-3
Byron Wanzong, Robert W.
Zoellner, and William G. Golden; Humboldt State University
"Computationally-determined pre-adsorbate structures of simple hydrocarbon molecules and their perfluorocarbon analogs"
Perfluorocarbon molecules are of fundamental importance to many industrial processes, and are commonly used as lubricants under highly demanding conditions. The rigidity of a molecule can strongly affect both the surface adsorption energetics and the desorption energies. Thus, the rigidity will ultimately affect the material's lubricant properties. However, the stiffness of a molecule may not be related to the force constants of normal mode vibrations, because rearrangements occurring during adsorption are not limited by the symmetry of the isolated molecule. We report the computational comparison of the non-equilibrium, non-normal mode structures of simple hydrocarbon molecules (methane, CH4, ethane, C2H6, propane, C3H8, etc.). These structures will be compared to their perfluorocarbon analogs (tetrafluoromethane, CF4, hexafluoroethane, C2F6, octafluoropropane, C3F8, etc.) to determine the relative flexibility of these molecules during simulated adsorption. In this computational investigation, the PC Spartan Plus® program (Wavefunction, Inc.), employing the PM3 semiempirical method, has been used extensively. The molecular deformation modes expected to be important in the adsorption process will be defined, and the deformation energetics in both the hydrocarbon and perfluorocarbon series will be compared.
UPS-4
Terry Yen, Elisheva Goldstein; California State Polytechnic University - Pomona
"Theoretical study of the inhibition of HIV protease by curcumin boron complex"
There is an increasing need for non-toxic and yet potent inhibitors that will restrain resistant mutant HIV-1-protease (HIV PR) activity. This ab initio Gaussian 94 study using the STO-3G basis set was conducted on a 92-atom, positive-charged curcumin boron complex to investigate anti-HIV PR activities. Molecular modeling using Spartan® was applied for the ab initio approach, while the AM1 semiempirical, and MM3 and MacroModel force-field approaches were also used. In this study, the inhibitor examined was a curcumin boron complex. This complex is a non-toxic product isolated from Curcuma longa, and its HIV PR irreversible inhibitor properties are enhanced by the formation of an orthogonal dimer about boron. The two potential binding sites in HIV PR are not truly orthogonal, and due to their being at different distances from the aspartyl groups, can be simultaneously occupied by the boron complex. Previous studies on other curcumin analogs indicate that it is the planar network of conjugated double bonds connecting the two aromatic rings that contribute significantly to inhibitory activity, not the phenolic hydroxyls (as was first hypothesized). These planar a ,b -unsaturated carbonyl systems are thus the sites the inhibitor uses to bind to the HIV PR by the 1,4-Michael addition. Resistant strains of HIV PR produced as a result of AZT and other protease inhibitors also can now be better studies due to our additional investigation of the boron complex's bonding changes when bound to aspartic acid. Hence, from this study, it is concluded that this curcumin boron complex is a potential anti-viral agent against normal type HIV PR and its resistant mutant strains.
CRS-1
Scot R. Mente; Central Research Division, Pfizer, Inc.
"Computer simulations of solvation phenomena ... or how to get a job by playing with computers for six years"
Computer simulations of three solvated
systems are presented. The first of these studies focused on the
solvent effects upon the excited-state proton transfer reactions
which occur in 7-azaindole (7-AI) and 1-azacarbazole (1-AC). Reactions
were examined in eight polar-protic solvents: methanol, ethanol,
1-propanol, 2-propanol, t-butanol, 2,2,2-trifluoroethanol,
ethylene glycol and water. In all cases, the percentage of "cyclic
complex" thought necessary for successful reaction is small,
< 2 %. Further, dynamical studies showed that the lifetimes
of these cyclic complexes are very short, implying that the equilibrium
between non-cyclic and cyclic species, and not the solvation dynamics,
determines the observed solvent dependence in these systems. The
second study used Monte Carlo simulations to examine the microscopic
origins of solvent "polarity." Here, the Betaine-30
molecule, which forms the basis of the ET(30) solvent polarity
scale, is simulated in the same eight solvents. It was found that
the common classical potentials generally employed in solution
phase simulations reproduced the observed solvent dependence found
in steady-state absorption measurements very well. Finally, a
methodology is presented which attempts to calculate the infrared
spectrum from common classical potentials using a perturbative
expansion technique.
CRS-2
Sergio Aragon; San Francisco State University
"Accurate molecular hydrodynamics"
Bead methods
have been almost universally used to compute the transport properties
(with stick boundary conditions) of arbitrarily shaped molecules
since their introduction in the 1930's by Kirkwood. Yet, beads
methods are intrinsically approximate because the hydrodynamic
interaction tensors cannot be calculated exactly and a truncated
series expansion is typically used instead. In addition, atomistic
modeling is inhibited by the fact that it has not been possible
to obtain hydrodynamic interaction tensors for unequal sized overlapping
beads. In an atomistic representation of a molecule, the van der
Waals spheres of atoms usually overlap with those of their nearest
neighbors. Coarse-grained models that avoid the overlap difficulty
do not have sufficient accuracy to yield rotational diffusion
and translational diffusion coefficients that both agree with
experiment. Lastly, no hydrodynamic interaction tensors have been
formulated for the "slip" boundary conditions that are
appropriate for intermediate to small molecules dissolved in apolar
solvents.
A different method (proposed in 1975 by Youngren and Acrivos) is now possible for small to large molecules due to the increase in computational capacity of modern workstations. This method expresses the solution to the creeping flow equations as an exact integral over the arbitrarily shaped surface of the body. The equations are solved in practice by discretizing the surface into N surface patches and obtaining a coupled system of 3N ¥ 3N equations which are solved by matrix inversion. Either slip or stick boundary conditions are solvable with this method. There is no "overlap" problem because the focus is on the surface that the atom overlaps, as seen by the solvent, produce. Thus, in addition, the solvent size can be taken into account. Because the equations are exact, a refinement of the surface mesh produces results that are linear in 1/N, and extrapolations to N Æ · can be done based on relatively few surface patches. The computations can be done to high precision, yielding self-consistent transport properties such as rotational and translational diffusion, as well as intrinsic viscosity. The high precision obtainable should allow the elucidation of small conformational changes in proteins, a more realistic study of the solvation effects in proteins and nucleic acids, and the accurate determination of shape for small to large molecules in solution.
CRS-3
Elisheva Goldstein, K. N. Houk; California State Polytechnic University - Pomona
"Ab initio calculations of the concerted transition state of [6 + 4] cycloadditions"
Density functional theory transition structures were located for three concerted [6 + 4] cycloaddition reactions involving cis-hexatriene and butadiene, cyclopentadiene and cycloheptatriene, and cyclopentadiene and tropone. Geometries, energies, and entropies were computed at the Becke3LYP/6-31G* level. The activation energy of the concerted [6 + 4] cycloaddition of cis-hexatriene and butadiene is 33.3 kcal/mol, about 8 kcal/mol above the activation energy of the butadiene plus ethylene [4 + 2] cycloaddition. The endo concerted [6 + 4] transition state is 1.1 kcal/mol higher than the exo. The [6 + 4] reaction of cyclopentadiene and cycloheptatriene has a barrier of 25.9 kcal/mol, while the cyclopentadiene plus tropone barrier drops to 20.7 kcal/mol.
CRS-4
Robert W. Zoellner, Lisa A. Nader, and Claudio Bianchini; Humboldt State University
"Transition state structures for the interconversion between the PM3(tm)-calculated absolute configurations of [(triphos)MH(h 2-(C,S)-C20H12S)], M = Co or Rh and triphos = h 3-CH3C(CH2PPh2)3"
The absolute configurations of
the diastereomers of [(triphos)IrH(h 2(C,S)-C20H12S)]
(triphos = CH3C(CH2PPh2)3)
have been assigned by comparison to the calculated relative energies
of the structures of their cobalt and rhodium analogs. The PM3(tm)
computational method was used in this determination. Possible
transition state structures for the interconversion between the
diastereomers have also been located for derivatives of the molecules
in which the phenyl groups on the triphos ligand have been replaced
by hydrogen or methyl groups.
Last modified 11 May 2000