Analysis of spectroscopic and theoretical results of compounds with - - PowerPoint PPT Presentation

Analysis of spectroscopic and theoretical results of compounds with intermolecular hydrogen bonding

Supervisor: prof. Aleksander Filarowski

Gabriela Drabik SUMMER STUDENT PRACTICE JINR 2014

Jagiellonian University in Krakow Poland

The Hydrogen bonding definition

The hydrogen bond definition: The hydrogen bond is an attractive interaction between a hydrogen atom from a molecule or a molecular fragment X–H in which X is more electronegative than H, and an atom or a group of atoms in the same or a different molecule, in which there is evidence of bond formation.

Pure Appl. Chem., Vol. 83, No. 8, pp. 1637–1641, 2011

,,The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological”.

• T. Steiner, Angew. Chem. Int. Ed. 2002, 41, 48 - 76

Hydrogen bonding: the experimental evidence

.2 .4 .6 .8 Absorbance 3000 2000 1000 Wavenumber (cm-1) .2 .4 .6 .8 Absorbance 3000 2000 1000 Wavenumber (cm-1)

IR spectra: Left: 2,4,6-tri-Cl-phenol (no hydrogen bond); right: 2,4,6-tri-Cl-phenol + N-benzyldenomethylamine (hydrogen bonding occurence). Asterix: stretching mode of the X-H bonding.

Upon generation of a hydrogen bond a wide maximum corresponding to the stretching mode of hydrogen bond occurs.

* * IR

HYDROGEN BOND: EXPERIMENTAL INVESTIGATION

VIBRATIONAL SPECTROSCOPY:

• IR and Raman
• INS

Hydrogen bonding investigation: IR and Raman

Example

• Vib. states

Selection rules:

• Rule of mutual exclusion

In general, molecular vibrations symmetric with regard to the centre of symmetry are forbidden in the infrared spectrum, whereas molecular vibrations which are antisymmetric to the centre

• f symmetry are forbidden in the Raman
• spectrum. This is known as the rule of mutual

exclusion.

Hydrogen bonding investigation: IR and Raman

Example

• Vib. states

Selection rules:

• Infrared absorption can be detected if the

dipole momentum µ in a molecule is changed during the normal vibration. The intensity of an infrared absorption band IIR depends on the change of the dipole moment µ during this vibration where q is the normal coordinate.

Hydrogen bonding investigation: IR and Raman

Example

• Vib. states

Selection rules:

• A Raman active vibration can be detected if the

polarizability a in a molecule is changed during the normal vibration. The intensity of a Raman active band IRaman depends on the change

• f polarizability a during this vibration:

where q is the normal coordinate.

IINS (Inelastic Incoherent Neutron Scattering):

Theoretical aspects

• Momentum transfer:
• Energy transfer:

The main contribution to the incoherent neutron scattering comes from the interaction of the atom and neutron spins and from the random isotope distribution in the sample

Ei, Ef – energy of the incident and scattered neutrons ki, kf – wave vectors of the incident and scattered neutrons

Q = ki - kf

Cross sections [b]:

IINS (Inelastic Incoherent Neutron Scattering):

Theoretical aspects

Double differential crossection: describes the density of the probability, that the incident neutron with energy: is scattered by an angle: θ, within the solid angle element: dΩ=2sinπθdθ, and into the energy range: from hω’ to h(ω’+dω’). Fourier transform of the correlation function of the nuclei pairs and describes the collective motion of atoms and molecules Fourier transform of the autocorrelation function of atomic nuclei and describes individual atomic and molecular movements

IINS (Inelastic Incoherent Neutron Scattering):

Theoretical aspects

The S(Q,w) function is named the scattering law. It depends only on structural and dynamical properties of a system. Where: Mean square displacement:

IINS (Inelastic Incoherent Neutron Scattering):

Experimental approach

SAMPLE

Inverted geometry time-of-flight spectrometer NERA at the IBR-2 high flux pulsed reactor in Dubna

I.Natkaniec, S.I.Bragin, J.Brankowski and J.Mayer, in Proc. ICANS XII Meeting, Abington 1993, RAL Report 94-025, vol.I.,p.89- (1994).

IINS (Inelastic Incoherent Neutron Scattering):

Experimental approach

Energy of the unscattered neutron beam (Ei) Change of the neutron energy upon inelastic scattering

Lf1 Lf2

IINS (Inelastic Incoherent Neutron Scattering):

Experimental approach

Change of the momentum upon inelastic scattering

Lf1 Lf2

IINS vs IR and Raman

INS IR and Raman

• no selection rules connected with the symmetry of

the molecule

• probability of the e.t. depends on the cross-section,

and on the amplitude of the vibration of an particular atom

• resolution does not exeed 2-3%
• samples: solid state at low temperature
• useful for the studies of molecular vibrations of

low frequency internal modes

• selection rules
• low intensity for the low freq modes

(hydrogen bonding dynamics)

• solid, liquid, gaseous samples

• A. Filarowski, A. Koll, G. Karpfen, P. Wolschann, Chem. Phys. 297 (2004) 323.
• A. Filarowski*, A. Koll, P. Lipkowski, A. Pawlukojć. J. Mol. Struct. 880 (2008) 97

1000 2000 3000

wavenumber, cm

• 1

1000 2000 3000 1000 2000 3000

absorbance

1000 2000 3000

IR SPECTRA (GAZ) IR SPECTRA (GAZ)

B3LYP/6-31G(d,p) MP2/6-31G(d,p)

O H N C H CH3 O D N C H CH3

100 200 300 400 500 600 700 250 500 750 1000 1250 , cm-1 Q( ) [a. u.]

O H N C CH3 CH3 O D N C CD3 CH3

100 200 300 400 250 500 750 1000 1250 , cm-1 Q( ) [a. u.]

O H N C H CH3 O D N C H CH3

Experimental results

IINS IR and QM

Why hydrogen bonding investigation is important?

Antigen – antibody recognition DNA structure Protein structure

References

• Parker, S.F., Inelastic Neutron Scattering Spectroscopy, in: Handbook of Vibrational Spectroscopy

(Chalmers J., Griffiths P. R. eds), J. Wiley & Sons Ltd, 2002, Vol. 1, pp 838-852

• Natkaniec I., Bragin, S. I., Brankowski I., and Mayer, I, Proc. ICANS-XIII, Abignton, RAL Report 94-025,

1993, Vol. 1, p.89

• A. Pawlukojć, L. Sobczyk, Application of inelastic neutron scattering (INS) in studies on low frequency

molecular vibrations, Trends in Applied Spectroscopy Vol. 5 , 2004

• A. V. Belushkin, J.W. Wąsicki, Wprowadzenie do neutronowych metod badania fazy skondensowanej

materii, WN UAM 2013

• J.M. Janik, Fizyka Chemiczna, PWN 1989

Thank you for your attention!