I am investigating two molecules, both of which are isomers to each other, however one isomer has higher basicity in the gas-phase (experimental and theoretical).
Using ab initio methods I have carried out a conformational search and found the lowest energy geometries using DFT. Internal hydrogen bond distances and charge distribution are comparable to each other and don't give much insight into why one isomer is more basic than the other.
My one last intuition involves the molecule's conformation. One isomer adopts a visually more "compact" structure (smaller surface area). I am looking for a method or tool to calculate the "size" of each isomer that I can quantitatively compare.
At my disposal I have Spartan '14 and Gaussian 09 but am open to other tools useful in this calculation.
The Volume option from g09 (http://www.gaussian.com/g_tech/g_ur/k_volume.htm) is one way to do it and to express different "sizes" of two isomers.
Size defined in a most natural way would be, however, just the longest distance between any two atom in the molecule. See e.g. http://openmopac.net/manual/molecule_size.html , mopac (free) can do it easily.
If you want a geometry-inspired quantity, you may want to take a look at the solvent-excluded-area (Connolly surface). It can be computed using many of the standard molecular visualization programs (molekel, gOpenmol, etc)
@Bartosz Trzaskowski - Thank you for your response. I've carried out Volume calculations using g09 and have extracted the "Molar volume" values. What exactly does this value mean, the volume of space occupied by 1 mole of a specific molecule?
@Felipe Valencia - I don't know if Spartan '14 can calculate the Connolly surface specifically but it can calculate electrostatic potential map and various quantities based off the CPK model. I'll give it a try and ping back with any questions.
What about the difference in the electrostatic potential around your isomers? One can calculate this molecular property with the gaussian programm. See also:
http://link.springer.com/article/10.1007/s00214-002-0363-9
http://pubs.rsc.org/en/Content/ArticleLanding/2008/CE/b715227b#!divAbstract
Partick: yes, the molar volume given by Gaussian is the volume occupied by 1 mole of the solute.
One line below it you will find, however, a line that reads something like:
" Recommended a0 for SCRF calculation = x.xx angstrom"
The a0 is the estimate of the solute radius, which also may be a good descriptor of molecule size - you can read more about it at http://www.cup.uni-muenchen.de/oc/zipse/onsager-reaction-field-theory.html
opensource tool java/c++ / fortran available for computing surface area?
what is the keyword used in G09?
hello my dear
for calculated molecular surface area , you can used Chem3D software
Hyperchem does the molecular dynamic illustration and can give you useful information about it
http://paros.princeton.edu/cbe422/hcmd.htm
Assume all atom radii are equal to their corresponding van der waals radius. Adapt this formula for surface area
http://mathworld.wolfram.com/Sphere-SphereIntersection.html
- Badges
- Science topic
- Similar topics
- Instrumentation Engineering
- Instruments