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 Jagiellonian University in Krakow Poland SUMMER STUDENT PRACTICE JINR 2014

The Hydrogen bonding definition ,, 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 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

Hydrogen bonding: the experimental evidence IR .8 * .8 * .6 .6 Absorbance Absorbance .4 .4 .2 .2 0 0 3000 2000 1000 3000 2000 1000 Wavenumber (cm-1) 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 .

VIBRATIONAL SPECTROSCOPY : • IR and Raman • INS HYDROGEN BOND: EXPERIMENTAL INVESTIGATION

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

Hydrogen bonding investigation: IR and Raman Example Selection rules: Vib. states • 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 I IR 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 Selection rules: Vib. states • 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 I Raman depends on the change of polarizability a during this vibration: where q is the normal coordinate.

IINS ( I nelastic I ncoherent N eutron S cattering ): Theoretical aspects 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 • Momentum transfer : Cross sections [b]: Q = k i - k f • Energy transfer : E i , E f – energy of the incident and scattered neutrons k i , k f – wave vectors of the incident and scattered neutrons

IINS ( I nelastic I ncoherent N eutron S cattering ): 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: d Ω =2sin πθ d θ , and into the energy range: from h ω’ 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 ( I nelastic I ncoherent N eutron S cattering ): 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 ( I nelastic I ncoherent N eutron S cattering ): 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 ( I nelastic I ncoherent N eutron S cattering ): Experimental approach Energy of the unscattered neutron beam ( E i ) L f2 L f1 Change of the neutron energy upon inelastic scattering

IINS ( I nelastic I ncoherent N eutron S cattering ): Experimental approach L f2 L f1 Change of the momentum upon inelastic scattering

IINS vs IR and Raman IR and Raman INS • no selection rules connected with the symmetry of • selection rules the molecule • low intensity for the low freq modes • probability of the e.t . depends on the cross-section , (hydrogen bonding dynamics) and on the amplitude of the vibration of an • solid, liquid, gaseous samples 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

Experimental results IR and QM IINS 700 O H N CH 3 CH 3 CH 3 O H N O D N 600 C H C CH 3 C C D 3 500 IR SPECTRA (GAZ) Q( ) [a. u.] 400 300 200 1000 2000 3000 MP2/6-31G(d,p) 100 0 0 250 500 750 1000 1250 absorbance , cm -1 400 1000 2000 3000 O H N CH 3 O D N CH 3 B3LYP/6-31G(d,p) C C 300 H H Q( ) [a. u.] 200 O D N CH 3 1000 2000 3000 C H 100 IR SPECTRA (GAZ) 0 0 250 500 750 1000 1250 , cm -1 1000 2000 3000 A. Filarowski, A. Koll, G. Karpfen, P. Wolschann , Chem. Phys . 297 (2004) 323. -1 wavenumber, cm A. Filarowski* , A. Koll, P. Lipkowski, A. Pawlukojć . J. Mol. Struct . 880 (2008) 97

Why hydrogen bonding investigation is important? Antigen – antibody recognition Protein structure DNA 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

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