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ABSTRACT: The infrared spectra of Histidine molecule have been recorded in the Nujoll mull as well as in aqueous solution in the range
400–4000 cm−1. The Raman spectrum of the same molecule has also been measured. The different protonated/deprotonated forms of imidazole
ring which contains different forms of Histidine1, Histidine2, Histidine3 and Histidine4 have been studied with DFT and RHF
methods using several basis sets. A comparison of energies of the two neutral tautomers (Histidine1 and Histidine2) indicates
that Histidine1 is more stable as compared to Histidine2 while Histidine3 (imidazolium cation) is the most stable in gas phase.
The selected geometrical parameters and theoretically calculated frequencies for the above-mentioned form of Histidine were
also proposed. The observed IR and Raman bands of Histidine molecule are assigned to different modes on the basis of calculated
frequencies, their intensities and available literature values.
KeywordsInfrared spectra-Raman spectrum-Histidine-protonated Histidine-DFT calculation
Indian Journal of Physics and Proceedings of the Indian Association for the Cultivation of Science -New Series- 04/2012; 84(5):563-573. · 0.38 Impact Factor
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ABSTRACT: Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of
canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined.
The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We
find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly
and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent
model shows that bare zwitterionic form is more stable than bare canonical form by 1.1kcal/mol. This energy separation is
increased to 2.2 and 3.4kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed
that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred
over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the
atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine
tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted
due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed
in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with
the experiments.
Theoretical Chemistry Accounts 04/2012; 124(1):37-47. · 2.16 Impact Factor
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ABSTRACT: An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.
Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 10/2009; 73(5):865-70. · 2.10 Impact Factor
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ABSTRACT: The molecular geometry of L and D-forms of alanine and serine in gas phase have been studied by using ab-initio quantum chemical calculations at the restricted Hartree-Fock (RHF) level by employing 6-31G and 6-311++G** basis sets. Subsequently, for considering the electron correlations, Density functional Calculations at the Becke3LYP (B3LYP) and Moller-Plesset second order (MP2) level of calculations have been carried out with the same basis sets for these optimized geometries. Effect of solvation in water on the optimized geometries was studied using the polarized continuum model of the self-consistent reaction field (SCRF) theory. The dipole moment, energy, polarizabilities and vibrational frequencies have been calculated in all cases. Frequency analysis was carried out to ensure that optimized geometry corresponds to a total energy minimum.
Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 05/2007; 66(4-5):909-18. · 2.10 Impact Factor
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ABSTRACT: The infrared spectrum of bilirubin has been recorded in the spectral region 200-4000 cm(-1). The Raman spectrum has also been recorded using the second harmonic (530 nm) radiation of a 200 mW Nd-YAG laser. In order to confirm the vibrational assignment of the bands obtained from experimental observation, a normal coordinate analysis has been carried out using the semi-empirical AM1 method through MOPAC 5.1 computer program. Electronic absorption spectrum of bilirubin dissolved in CHCl3 has been recorded in the spectral region 300-600 nm. A broad spectrum is observed with peak maxima at 454.2 nm. The photoacoustic spectrum of this molecule (in the powder form) has also been recorded for the first time which shows certain discrete features.
Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 09/2002; 58(10):2145-52. · 2.10 Impact Factor
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ABSTRACT: The infrared, Raman and electronic spectra of alanine molecule have been studied in solid as well as in aqueous solution. The vibrational frequencies for the fundamental modes and the energies of low lying electronic states of alanine in neutral and its zwitterionic form have been calculated using AM1, RHF and DFT method with different basis sets. RHF/6-31G, DFT/6-31G, 6-31+G* and 6-311++G** calculations for vibrational frequencies of both l and d-alanine and zwitterionic alanine(zala) have been performed in both gas phase and in aqueous solution. It is concluded that while there is no significant difference between the corresponding frequencies of l- and d-alanine in gas phase but frequencies are changed for zala and alanine in water. A solvation model(PCM) for neutral alanine and zala at DFT/6-31+G* and 6-311++G** level has also been performed. Gas phase and solvation (PCM) model calculations for alanine and zala reveal that neutral alanine is more stable in gas phase while the reverse is true in aqueous medium. A comparison between the experimentally observed IR spectra of alanine in solid and water solution does not show much variation in corresponding frequencies but theoretically some changes are predicted. The rotational constants and dipole moments have also been calculated.
Journal of Molecular Structure. 791:23-29.
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ABSTRACT: The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.
Vibrational Spectroscopy 56(1):74-81. · 1.65 Impact Factor
