Upload 05-10-2006 13:12 (Day-Month-Year, Paris time)
Information about the Author (who submitted the project in R.E.DD.B.)
Firstname Christine
Lastname Cezard
Institute University of Goettingen - IPC
City Goettingen
Country GERMANY
General information about the Project
Molecule keywords
Alcohol |
Organic Molecule |
Hydrogen bond |
Complex |
Redshift |
Abstract
We suggest the following simplified protocol to predict hydrogen-bond-induced redshifts of donor OH-stretching fundamentals in pure and mixed dimers of monofunctional, reasonably unstrained, aliphatic alcohols:
i) Construct a Wang et al. AMBER force field (parm99.dat) with standard settings for Lennard-Jones interactions, in which the OH hydrogen atoms carry a charge of +0.42 e and the oxygen atoms carry a charge of -0.68 e.
ii) Add -0.03 e to each oxygen for each alkyl substituent on its adjacent C atom and subtract -0.03 e if there is no such substituent (i.e. in the case of methanol).
iii) Set all other atomic charges to zero except for the C atoms adjacent to O, which carry the charge required for monomer electro-neutrality.
iv) Minimize the dimer structure and compare its harmonic donor OH stretching mode with that of the isolated donor molecule.
The result is predicted to be close to the experimental anharmonic redshift in the dimer, relative to a monomer of the same conformation. It may be used to guide and assist experimental assignments. If absolute wavenumbers are to be predicted, the Wang et al. AMBER OH force constant of the monomer may be slightly adjusted to reproduce the experimental monomer value.
Dimers tested: methanol dimer, ethanol dimer, 1-octanol dimer, 2-propanol dimer, 3-pentanol dimer, tert-butyl alcohol dimer, tert-butyldimethylcarbinol dimer, 1-adamantanol dimer, 2-adamantanol dimer, methanol-tert-butyl alcohol dimer, methanol-1-adamantanol dimer, methanol-1-octanol dimer and 2-adamantanol-1 adamantanol dimer.
Publication YES 
Author(s) C. Cezard, C. A. Rice and M. A. Suhm
Journal J. Phys. Chem. A
Year 2006
Volume 110
Page(s) 9839-9848
"Whole molecule" or "Molecule fragment" type projectWHOLE MOLECULE
Interface R.E.D. used ? NO
Charge derivation procedure
Number of Tripos mol2 file(s) provided by the author(s) 7
Contain charge values & information about molecular topology
Information regarding Quantum Calculations
Geometry optimization
Program 1 GAMESS-US
Theory level 1 HF
More information 1 -
Basis set 1 6-31G*
Molecular electrostatic potential computation
Program 2 GAMESS-US
Theory level 2 HF
More information 2 -
Basis set 2 6-31G*
Algorithm CONNOLLY SURFACE
Information about the charge fit
Program RESP
Number of stage(s) 2
input of stage 1 
input of stage 2 
Files the author of the project wishes to provide...
A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...
A file (choice made by the author) to provide more information about the project...
A file (choice made by the author) to provide more information about the project...
Download the whole project...

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