ISSN : 0975-2927
EISSN : 0975-9166
SREEPAD H.R.1*
1Post-Graduate Department of Physics, Research Centre, Government College (Autonomous), Mandya – 571401, Karnataka State, India
* Corresponding Author : hrsreepad@gmail.com
Received : 29-09-2011 Accepted : 03-11-2011 Published : 07-11-2011
Volume : 3 Issue : 3 Pages : 108 - 111
Int J Mach Intell 3.3 (2011):108-111
DOI : http://dx.doi.org/10.9735/0975-2927.3.3.108-111
Conflict of Interest : None declared
Acknowledgements/Funding : Author is highly thankful to the University Grants
Commission, India for granting minor research project
[MRP(S)-798/10-11/KAMY022/UGC-SWRO]. Author is
also thankful to Prof. Umesh V. Waghmare, Theoretical
Sciences Unit, JNCASR, Bangalore for his guid
Structural pattern recognition in case of molecules is an important task in the field of bio-engineering. Several techniques are employed in order to get the exact structural conformation and structural parameters of molecules. Present paper discusses some of the available techniques such as Fourier Infra-Red Spectrocopy, Raman Spectroscopy and Theoretical Structure simulation which are employed in this technologically important field. An attempt has been made to look for the exact structural conformation in case of Polyformaldehyde using First-principles calculations based on Density Functional Theory.
FTIR spectroscopy, Pattern recognition, Raman spectroscopy, Structural parameters, Theoretical structure simulation.
Structural pattern recognition is a challenged task in case of several molecules. That too, it is a highly challenged task in case of bio-molecules. Usually, the structure determination is done by employing the well known X-ray diffraction technique. Protein structure determination has been done by several investigators [1,2] using this technique.
But, it has been observed that in several bio-molecules, X-rays themselves bring in changes in the structural pattern. This is because of high sensitivity of those molecules for radiation [3] . It has been observed that irradiation with X-rays and gamma rays cause for radiation induced solid state polymerization in several cyclic oligomers of Formaldehyde [4,5] .
X-ray diffraction techniques cannot be used for the study of liquids and gaseous molecules. Several organic compounds which are used for the synthesis of bio-molecules are in liquid form. Thus bio-engineering looks for other techniques which can be employed for structural pattern recognition in case of bio-molecules.
Fourier Transform Infra-Red Spectroscopy (FTIR) plays an important role in the pattern recognition in case of organic molecules. Digital signatures of the presence of different types of chemical bonds are obtained by looking at the IR frequency modes arising due to different stretching modes of chemical bonds.
FTIR spectroscopy is a measurement technique that allows one to record infrared spectra. Infrared light is guided through an interferometer present in the instrument and then through the sample (or vice versa). A moving mirror inside the apparatus alters the distribution of infrared light that passes through the interferometer. The signal is recorded directly and is called an ‘interferogram’. It represents light output as a function of the mirror position. A data-processing method called ‘Fourier transform technique’ turns this raw data into the desired result, which comes out as a spectrum with light output as a function of infrared wavelength (or wave number). The sample's spectrum is always compared to a reference [6] .
Looking at the wave numbers at which peaks are observed in the spectrum, one gets information about the presence of particular mode of vibration associated with the respective bond.
Raman Spectroscopy also plays an important role in the structural pattern recognition of molecules [7] . Polyatomic molecules can be linear or non-linear, symmetric or non-symmetric.
Consider a tri-atomic molecule AB2. The arrangement of atoms in this case can be any one as listed in [Table-1] .
For example: CO2 has Linear and symmetric conformation as shown below:
[Formula-1] N2O has Linear and non-symmetric conformation as shown below:
[Formula-2] H2O has got Non-linear and symmetric conformation as shown below;
[Formula-3] structural pattern recognition in all the above cases can be done by processing the digital signatures of the respective bonds by looking at the intensity, polarization and frequency of Raman lines [8] .
Structure simulation can be done using several programs [9] . Using those codes one can simulate different possible structures for a given molecule. Theoretically one can look at various parameters of the simulated structures. Using those parameters one can compute several other physical and chemical parameters pertaining to those structures. By looking at the computed values, one can decide whether the structure is feasible or not. Hence one can arrive at a definite conclusion regarding the possible structure without any ambiguity.
First-principles calculations based on Density Functional Theory (DFT) can be effectively used to study the internal structure and properties of the material in detail [10] .
We use plane wave self consistent field (PWSCF) [11] implementation of density functional theory (DFT), with a Local density approximation (LDA) [12] to exchange correlation energy of electrons and ultrasoft pseudopotentials [13] , to represent interaction between ionic cores and valence electrons.
Kohn-Sham wave functions were represented with a plane wave basis with an energy cutoff of 40 Ry and charge density cutoff of 240 Ry. Integration over Brillouin zone was sampled with a Monkhorst-Pack scheme [14] with appropriate k point mesh and occupation numbers were smeared using Methfessel-Paxton scheme [15] with broadening of 0.003 Ry. The structure was relaxed to minimize energy.
Polyformaldehyde is a technologically important polymer. Corrosion resistant conductive Polyformaldehyde compositions with carbon nanotube and carbon nano fibre conductive fillers have been patented [16] .
Polyformaldehyde is generally found to have hexagonal unit cell structure. But Carozzolo & Mammi [17] have discussed a new type of Polyformaldehyde having Orthorhombic unit cell with space group P212121 and lattice constants a=4.77Ã…, b=7.65 Ã…, c=3.56 Ã….
It is interesting to see that the single crystals of formaldehyde can be synthesized in the form of cyclic trimer, tetromer, pentomer and hexomers. Hence, understanding of various crystal structures and properties of Polyformaldehyde is important to its technological applications.
Different structural conformations have been considered for the Polyformaldehyde [18] (also known as Polyoxymethylene or POM) and phonon modes along X axis have been computed for all the conformations. They are tabulated in [Table-2] .
The respective simulated structures of all the non helical conformations are given below in Figs. 1(a to e):
Looking at the optical phonon modes one can decide that there are two stable conformations for the Polyformaldehyde. First-principles calculations reveal that the helical conformation with four monomers per unit cell is highly acceptable.
“SCF'†calculation was done using the final atomic positions obtained after relaxing the structure using the program 'pw.x' of Quantum espresso. Completely relaxed structure of the unit cell was visualized using the program “XCrySDen†[19] . Structure of unit cell in case of helical structure with 4 monomers per unit cell as seen along X, Y and Z axes are given in Figs. 2(a), 2(b) and 2(c) respectively.
The Polyformaldehyde under consideration has orthorhombic structure having four monomers per unit cell with lattice parameters a=4.45 Ã…, b=7.28 Ã…, c=3.51 Ã…. Volume of the unit cell is 113.8 (Ã…)3. The space group of the simulated structure has been found using the ABINIT program and is found to be P212121. Bond lengths and bond angles in the simulated structure have been tabulated in [Table-3] and [Table-4] .
Structural pattern recognition plays an important role in deciding the structural conformation of molecules. Specially, it is highly essential in case of study of bio-molecules and polymeric systems. FTIR, Raman and Structure simulation techniques have become versatile tools for the structural pattern recognition of molecules.
First-principles calculations clearly indicate that, among various possible conformations of Polyformaldehyde, the one with Orthorhombic unit cell having four monomers per unit cell showing helical structure of molecular arrangement is most stable.
Author is highly thankful to the University Grants Commission, India for granting minor research project [MRP (S) - 798 / 10 - 11 / KAMY022 / UGC - SWRO]. Author is also thankful to Prof. Umesh V. Waghmare, Theoretical Sciences Unit, JNCASR, Bangalore for his guidance.
[1] Glusker J.P., Lewis M. and Rossi M. (1994) Crystal Structure Analysis for Chemists and Biologists. New York: VCH Publishers. ISBN 0471185434.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[2] Rupp B. (2009) Biomolecular Crystallography: Principles, Practice and Application to Structural Biology. New York: Garland Science. ISBN 0815340818.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[3] Sreepad H.R., Sreeramalu V., Chandrashekara A, Ravindrachary V., Ranganathaiah C., and Gopal S. (1991) Phys. Stat. Sol (a), 124, 441-446.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[4] Okamura S., Hayashi K. and Kitanishi Y. (1962) J. Polym. Science, 58, 925-953.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[5] Chatani Y., Ohno T., Yamamuchi T. and Miyake Y. (1973) J. Polym. Sci. Polymer Physics, 11, 369-388.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[6] http://en.wikipedia.org/wiki/Fourier_transform_infrared_spectroscopy.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[7] Gardiner, D.J. (1989) Practical Raman spectroscopy. Springer-Verlag. ISBN 978-0387502540.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[8] Journal of Raman Spectroscopy, Available at: http://onlinelibrary.wiley.com/journal/10.1002.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[9] http://en.wikipedia.org/wiki/Molecular_modelling.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[10] Payne M.C., Teter M.P., Allan D.C., T.A. Arias T.A. and Joannopoulas J.D. (1992) Rev. Mod. Phys., 64 (4) 1045-1097.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[11] Baroni S, Dal Corso S.A., De Gironcoli P, and Gianozzi, Available at: http://www.pwscf.org.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[12] Perdew J.P. and Zunger A. (1981) Phys. Rev. B 23, 5048-5079.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[13] Vanderbilt D. (1990) Phys. Rev. B. 41, 7892–7895.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[14] Monkhorst H.J. and Pack J.D. (1976) Phys. Rev. B 13, 5188-5192.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[15] Methfessel M.A. and Paxton, (1989) Phys. Rev. B. 40, 3616 – 3621.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[16] David C.K., Majiid K., Wolfgang H. and Theodore Z. (2010) US Patent No. 7648653.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[17] Carazzolo G. and Mammi M.J. (1963) Polymer Sci, A1, 965.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[18] Sreepad H.R., Hembram K.P.S.S. and Waghmare U.V. (2011) AIP Conf. Proc. 1349, 871-872: doi: 10.1063/1.3606135.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[19] Kokalj A. (2003) Comp. Mater. Sci., 28, 155-168.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
 | Fig. 1a- Structural pattern of Planar POM |
 | Fig. 1b- Structural pattern of 1NPNH |
 | Fig. 1c- Structural pattern of 2NPNH |
 | Fig. 1d- Structural pattern of 3NPNH |
 | Fig. 1e- Structural pattern of 4NPNH |
 | Fig. 2a,b,c- Orthorhombic helical Polyformaldehyde viewed along X, Y and Z axes respectively |
 | Formula 1- |
 | Formula 2- |
 | Formula 3- |
 | Table 1- Arrangement of Polyatomic molecules |
 | Table 2- Simulated Structural Conformations of POM |
 | Table 3- Bond lengths in Polyformaldehyde |
 | Table 4- Bond angles in Polyformaldehyde |