rafał topolnicki, university of wrocław, elwira borawska, university of białystok dynamic...

Rafał Topolnicki, University of Wrocław,

Elwira Borawska, University of Białystok

Dynamic properties of molecules study using inelastic incoherent neutron spectroscopy and

computational quantum chemistry methods

Frank Laboratory of Neutron Physics JINR Supervisor: Dorota Nowak, Ph.D. July 2011

Pentabromophenol

Uses:Chemical intermediate

Acta Crystallographica, Sec. E. Struct. Rep. Online 64 (2008) 1921

Molecular Formula

C6HBr

5O

Melting point 223-228 ºC

Boiling point 352 ºC

Water solubility Insoluble

Appearance Light brown powder

LD50

(rat) 200mg/kg

Pentachlorophenol

Acta Crystallographica 15 (1962) 1164

Pentachlorophenol is an organochlorine compound used as a pesticide and a disinfectant.

Molecular Formula

C6HCl

5O

Melting point 190-191 ºC

Boiling point 309-310 ºC

Water solubility 0.020 g/L at 30 °C

Appearance White crystalline solid

Time of flight

t – time of flightt0 – time when neutrons leavemoderatorL1 – path from reactor to sampleL2 – path from sample to detectorw – factor (scaling neutrons'energy to velocity)E0 – initial energyE1 – final energy

Application of IINS and QC calculations in studies of properties of selected lutidines, Sylwia Dobkowska, Katarzyna Kilan, Adam Kowalczyk, Kamil Kuźma

Types of internal vibration modes

In general for any molecule containing N atoms we have 3N-6 possible vibration modes (or 3N-5 for linear molecule like CO

2)

For each mode we can assign characteristic frequency.

Our goal is to connect frequencies visible on experimental spectrum with certain types of internal vibration in molecule

C-Br Bending C-ring Torsion C-Br Stretching

Calculated Intensiv ATOMS MODE

43.4 0.006 Br-C Out of plane48.6 0.002 Br-C Out of plane91.7 0.001 OH-C Out of plane

141.6 0.092 Br-C bending146.0 0.170 Br-C bending150.1 0.125 Br-C bending158.5 0.015 Br-C bending169.5 0.459 ring Out of plane210.8 0.049 Br-C stretching222.5 0.038 Br-C stretching237.3 0.000 Br-C stretching322.5 6.032 O-C bending332.6 2.198 ring Out of plane365.6 0.030 ring Out of plane387.2 1.042 C-O stretching459.7 90.984 O-H Out of plane557.4 25.326 ring torsion

Calculations

Obtain CIF file which contain informations about loactions of all atoms in molecule and molecules in Wigner–Seitz cell,

Build izolated molecule (or dimmer) and write positions of atoms in Z-matrix form,

Execute DFT calculation using Gaussian09 programme Choose B3LYP correlation-exchange potential, Select proper functional base - 6-31G* Optimalize atoms placements, Calculate vibrations

Analysis and visualization of resultsAll calculations were preformed in ICM in Warsaw

318,78 cm-1

O-H Out of Plane

316,26 cm-1

365,94 cm-1

O-H Out of Plane in both molecues

474,01 cm-1

CC ring deformation

Pentabromophenol

318,78 cm -1

1088,11 cm -1

33,26 cm -1

275,41 cm -1

Dynamika molekularna kryształów z rodziny polifenyli, J. W. Wąsicki, Wydawnictwa UAM, 1991 Molecular dynamics of eithisterone studied by 1H NMR, IINS and quantum mechanical calculations, Chemical Physics 317 (2005) 178-187 Fizyka chemiczna, J. M. Janik, PWN 1989

References

Thank you for your attention!