Advanced Modeling Techniques

molecules
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TEXT DISCUSSION

PDB search query refinement
PDB entry description
GaussView PDB file warning
MolProbity output

TUTORIAL: PREPARING A GAUSSIAN INPUT FILE FOR GFP

green fluoroscent protein (GFP)
comparing water placement: PDB file vs. dowser
terminating the HIS residue

EXAMPLE 9.1: THE GEOMETRY OF METAL HEXAFLUORIDE COMPOUNDS

iridium hexafluoride
platinum hexafluoride
tungsten hexafluoride

EXAMPLE 9.2: 17O NMR CHEMICAL SHIFTS IN TRANSITION METAL OXO COMPLEXES

chromium tetraoxide dianion
molybdenum tetraoxide dianion
tungsten tetraoxide dianion

EXAMPLE 9.3: MODELING METHANE DIMER

methane dimer
methane dimer PES

EXAMPLE 9.4: MODELING PHENOL DIMER

phenol dimer

EXAMPLE 9.5: NITROGEN MOLECULE AND NITROGEN DIANION

nitrogen dianion
nitrogen molecule

EXAMPLE 9.6: A REACTION INVOLVING RADICAL SPECIES

ethylene
methyl radical
propyl radical

EXAMPLE 9.7: MODELING ANTIFERROMAGNETISM IN FERREDOXINS

FeS(SCH₃)₂ anion dimer (ferredoxin model)

EXAMPLE 9.8: SCANNING THE POTENTIAL ENERGY SURFACE OF 2,6-PYRIDYNE

didehydropyridine

EXERCISE 9.1: M-F BOND LENGTHS IN METAL HEXAFLUORIDE COMPOUNDS

iridium hexafluoride
platinum hexafluoride
tungsten hexafluoride

EXERCISE 9.2: 17O NMR CHEMICAL SHIFTS IN TRANSITION METAL OXO COMPLEXES

iron tetraoxide
osmium tetraoxide
permanganate
rhenate
ruthenium tetraoxide
technetate

EXERCISE 9.3: COUNTERPOISE CORRECTIONS: METHANE DIMER

methane dimer
methane dimer PES: considering counterpoise corrections

EXERCISE 9.4: STUDYING PHENOL DIMER WITH 6–311+G(2d,p)

phenol dimer

EXERCISE 9.5: OXYGEN MOLECULE AND OXYGEN DICATION

oxygen molecule

EXERCISE 9.6: METHYL RADICAL ADDITION TO CYANOETHENE

cyanobutane radical
cyanoethene
methyl radical

EXERCISE 9.8: MODELING THE BIRADICAL 2,6-PYRIDYNE

didehydropyridine
2,6-pyridyne active space
2,6-pyridyne PES scans
CAS orbitals for 2,6-pyridyne