| Date | Speaker | Title | Supplementary Reading/Material |
||
| 06/03 |
Brent Gregersen | Hybrid QM/MM calculations of phosphate
hydrolysis reactions in solution |
Phosphate hydrolysis, Gregersen et al. |
||
| 06/10 |
Jana Khandogin |
A linear-scaling smooth solvation method for electronic structure methods | COSMO, LS-COSMO, smooth COSMO |
||
| 06/17 |
Evelyn Mayaan | Non-standard CHARMM residues to model RNA catalytic structures | MacKerell et al.: 1,2,3,4 |
||
| 06/24 | Yun Liu | Development of new semi-empirical
quantum models for RNA catalysis |
MNDO/d, OM2 method, preliminary results, related work |
||
| 07/01 |
Kevin Range |
DNA Bending, Error Analysis Made Easy,
You Too Can Have Terabytes of Disk Space, and Selecting a Group
Messaging System |
RAID
levels, SCSI-to-IDE RAID, MHonArc, Mailman, phpBB |
||
| 07/08 |
Kwangho Nam |
Calculation of Dynamic Transmission
Coefficient from Molecular Dynamics Simulations of Enzyme Catalyzed
Reaction |
related work |
||
| 07/15 |
Adam Moser |
Fast Multipole Method for
Multipole-Multipole Interactions |
White
and Head-Gordon, Perez-Jorda
and Yang |
||
| 07/22 |
Olalla Nieto Faza | Electrocyclic opening of
2,3-disubstituted 1-bromocyclopropanes |
Ring-current model
for in-plane aromaticity, Torquoselectivity in cyclobutanes |
||
| 08/05 |
Carlos Silva Lopez | Sulfolene Cheletropic Reactions, from
Theory to Experiment (hopefully), towards the synthesis of protein
ligands |
New
synthetic application, Synthetic application 2, Previous work |
||
| 08/12 |
Tim Giese | Comparison of complete basis set
functional forms and procedures as applied to rare gas and alkali
halide systems in determination of complete basis extrapolated
properties |
LaTeX/Manuscripts/IntJQuantumChem_TheoBiophysSymp LaTeX/Manuscripts/AlkaliHalide Adiabatic <-> Diabatic Transformations |
||
| 08/19 |
Brent Gregersen | NAG compiler tricks, theory and an
update on qmmm sims and cutoffs |
NONE |
||
| 09/02 |
Teresa Jentzsch | Calculating pKa's for
macromolecules |
Bashford
and Karplus |
||
| 09/16 |
Jana Khandogin | Application of the smooth COSMO method
within MNDO/d: some preliminary results |
CVS/LaTeX/Manuscripts/
Khandogin_MNDO_COSMO |
||
| 09/23 |
Evelyn Mayaan | A density-functional database for RNA
catalysis III: Interactions of solvated Mg(II) ions with biological
ligands |
CVS/LaTeX/Manuscripts/PH_Database_paper3 |
||
| 09/30 |
Yun Liu | DFT calculations of phosphate
hydrolysis reactions in gas phase |
Phosphate hydrolysis, Gregersen et al. |
||
| 10/07 |
Kwangho Nam |
Open question: What is the problem of
my QM/MM simulations with small model reaction? |
none |
||
| 11/04 |
Tim Giese |
Scaling of electric response
properties with respect to system size: 1D neon chains An introduction to the York Group Linux Cluster |
A general understanding of chemical
potential equalization The YGLC homepage |
||
| 11/11 |
Brent
Gregersen |
||||
| 11/18 12/02 |
Teresa
Jentzsch |
COSMO: How does it work? |
York
and Karplus |
||
| 12/16 |
Yun Liu |
DFT study of transphosphorylation thio
effects in solution |
Gregersen et al. |
||
| 1/20 |
Evelyn
Mayaan |
The importance of Mg(II) |
CVS/LaTeX/Manuscripts/PH_Database_paper3 The biological chemistry of the elements, J.J.R. Frausto & R. J. P. Williams, 2001 Oxford Univ. Press |
||
| 1/27 |
Kwangho
Nam |
Semiempirical parameterization for
specific reaction parameters of O, H, and P atom in AM1 and AM1/d
Hamiltonian |
Lopez and York |
||
| 2/03 |
Brent
Gregersen |
Hybrid QM/MM Studies of
Transphosphorylation Reactions |
|||
| 2/10 |
Kevin
Range |
DNA Bending |
CVS/LaTeX/Manuscripts/DNA_bending CVS/Software/Programs/MC-DNA Strauss_Science_1994_v266_p1829 Williams_AnnuRevBiophysBiomolStruct_2000_v29_p497 Hardwidge_unpublished |
||
| 2/24 |
Tim Giese |
Pairwise damping of Coulomb
interactions cannot (and will not ever, no matter how hard you try)
simultaneously model the polarizability of water in vacuum and
condensed phase. It is time for "people" to give up on this
concept - it will NEVER work. I know the solution to the
problem, but I'm not telling. The talk will discuss the
problem... my next talk will give the solution. |
If you are interested in details, then
see me and I can point you to some papers. I won't present
details during the talk so as to avoid getting boged down by
questions regarding the details...which could go on-and-on like an
energizer bunny and thus obscure the otherwise relatively simple
conclusion which depends on the details in only a hand waiving,
general way. The point of the talk is to not dwell on the
details, but to try and convey a more general problem regarding the
many-body nature of the coupling between polarizability and
non-classical interactions. |
||
| 3/02 |
Teresa
Jentzsch |
Practice Oral: Semi-empirical
calculations of multiple pKa values for phosphates and phosphoranes
|
None |
||
| 3/09 |
Yun Liu |
Practice Oral: Construction of
DFT-database and development of new semiempirical quantum models for
RNA catalysis |
None |
||
| 3/23 |
Evelyn
Mayaan |
Thio effects in the hammerhead
ribozyme Rescheduled for Thurs. at 10am |
Herschlag_Biochemistry_1991_v30_p4844.pdf Almer_TetrahedronLett_1991_v32_p3723.pdf Zhou_ChemRev_1998_v98_p991.pdf(p.1003) Oivanen_ChemRev_1998_v98_p961.pdf(pp.986-7) |
||
| 4/6 |
Kwangho
Nam |
Implementaion and test of Ewald
summation with QM/MM potential |
Honestly, I will not talk about
Particle Mesh Ewald method. I will talk about regular Ewald sum: how
to implement and why we need to do that. Thus, for the intered
reader, see Darden_JChemPhys_1993_v98_p10089.pdf Sagui_AnnuRevBiophysBiomolStruct_1999_v28_p155.pdf Feller_JPhysChem_1996_v100_p17011.pdf |
||
| 4/13 |
Brent
Gregersen |
Variational Electrostatic Projection | Solvent Boundary Potentials: Im_JChemPhys_2001_v114_p2924 Banavali_JChemPhys_2002_v117_p7381 Im_JChemPhys_2001_v115_p4850 Charge Rescaling: Simonson_JPhysChemB_1997_v101_p8349 Simonson_JPhysChemB_1999_v103_p6142 |
||
| 4/20 |
Kevin
Range |
DNA Bending |
CVS/LaTeX/Manuscripts/DNA_bending2 CVS/Software/Programs/MC-DNA Strauss_Science_1994_v266_p1829 Williams_AnnuRevBiophysBiomolStruct_2000_v29_p497 Hardwidge_unpublished |
||
| 4/27 | Tim Giese |
Dispersion in semiemperical methods |
Winget_TheorChemAcc_2003_v110_p254 Elstner_JChemPhys_2001_v114_p5149 Hodges_MolPhys_2000_v98_p275 Pellenq_MolPhys_1998_v95_p549 |
||
| 5/04 | Yun Liu |
Kinetic isotope effects (KIEs)
and equilibrium isotope effects (EIEs) for monoanionic/monoprotic
transphosphorylation reactions in solution |
CVS/LaTeX/Manuscripts/Liu_2003a Marlier_AccChemRes_2001_v34_p283 Hengge_AccChemRes_2002_v35_p105 |
||
| 5/11 | Evelyn Mayaan |
New CHARMM residue for the phosphoryl transfer reaction of beta-phosphoglucomutase | CVS/Projects/Glucomutase Lahiri_Science_2003_v299_p2067.pdf |
||
| 5/25 | Kwangho
Nam |
Semiempirical quantum method | A new concept for an approximate MO
method and/or approximate density functional formalism. Kollmar_MolPhys_2002_v100_p1945.pdf Kollmar_ZNaturforsch_1999_v54_p101.pdf Weber_TheorChemAcc_2000_v103_p495.pdf |