Summary of information
Bulky Alcohols


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


General information about the Project

Molecule keywords

Alcohol Organic Molecule Hydrogen bond Complex Redshift


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

No Name Download Wikipedia 3D Display 1 3D Display 2
1 2-propanol Wiki_Logo Jmol_Logo JSmol_Logo
2 tert-butyl alcohol Wiki_Logo Jmol_Logo JSmol_Logo
3 3-pentanol Wiki_Logo Jmol_Logo JSmol_Logo
4 1-octanol Wiki_Logo Jmol_Logo JSmol_Logo
5 tert-butyldimethylcarbinol Wiki_Logo Jmol_Logo JSmol_Logo
6 1-adamantanol Wiki_Logo Jmol_Logo JSmol_Logo
7 2-adamantanol Wiki_Logo Jmol_Logo JSmol_Logo

Number of molecule(s) used in the charge derivation procedure 7

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 2-Propanol 2 QM Reorient Algo GAMESS-US 1 Wiki_Logo
2 tert-butyl alcohol 1 QM Reorient Algo GAMESS-US 1 Wiki_Logo
3 3-Pentanol 2 QM Reorient Algo GAMESS-US 1 Wiki_Logo
4 1-Octanol 1 QM Reorient Algo GAMESS-US 1 Wiki_Logo
5 tert-butyldimethylcarbinol 2 QM Reorient Algo GAMESS-US 1 Wiki_Logo
6 1-Adamantanol 1 QM Reorient Algo GAMESS-US 1 Wiki_Logo
7 2-Adamantanol 2 QM Reorient Algo GAMESS-US 1 Wiki_Logo

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*


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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