Volume 3 - Issue 6

Article Citation

  • Alireza Heidari. Neurotoxin and Alpha-Neurotoxin Time-Resolved Absorption and Resonance FT-IR and Raman Bio spectroscopy and Density Functional Theory (DFT) Investigation of Vibrionic-Mode Coupling Structure in Vibrational Spectra Analysis. Am J Biomed Sci & Res. 2019 - 3(6). AJBSR.MS.ID.000738. DOI:10.34297/AJBSR.2019.03.000738

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Research Article Biomedical Science and Research Biomedical Science and Research CC by Creative Commons, CC-BY

Neurotoxin and Alpha-Neurotoxin Time-Resolved Absorption and Resonance FT-IR and Raman Bio spectroscopy and Density Functional Theory (DFT) Investigation of Vibrionic-Mode Coupling Structure in Vibrational Spectra Analysis

*Corresponding author: Alireza Heidari, Faculty of Chemistry, California South University, 14731 Comet St. Irvine, CA 92604, USA.

Received: April 24, 2019; Published: July 11, 2019

DOI: 10.34297/AJBSR.2019.03.000738

Abstract

α-Neurotoxins are a group of neurotoxic peptides found in the venom of snakes in the families Elapidae and Hydrophiidae. They can cause paralysis, respiratory failure, and death. Members of the three-finger toxin protein family, they are antagonists of post-synaptic nicotinic acetylcholine receptors (nAChRs) in the neuromuscular synapse that bind competitively and irreversibly, preventing synaptic acetylcholine (ACh) from opening the ion channel. Over 100 α-neurotoxins have been identified and sequenced. Parameters such as FT-IR and Raman vibrational wavelengths and intensities for single crystal Neurotoxin and Alpha-Neurotoxin are calculated using density functional theory and were compared with empirical results.

The investigation about vibrational spectrum of cycle dimers in crystal with carboxyl groups from each molecule of acid was shown that it leads to create Hydrogen bounds for adjacent molecules. The current study aimed to investigate the possibility of simulating the empirical values. Analysis of vibrational spectrum of Alpha-Neurotoxin is performed based on theoretical simulation and FT- IR empirical spectrum and Raman empirical spectrum using density functional theory in levels of F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31-HEG**. Vibration modes of methylene, carboxyl acid and phenyl cycle are separately investigated. The obtained values confirm high accuracy and validity of results obtained from calculations [1-42] (Figure 1).

Biomedical Science & Research

Figure 1: Molecular structure of Neurotoxin (left) and Alpha–Neurotoxin (right).

Keywords:Vibrionic Structure; Vibrational Spectra Analysis; Density Functional Theory (DFT); Alpha-Neurotoxin; non-Focal Functions of Becke; Correlation Functions of Lee-Yang-Parr; Time-Resolved Absorption and Resonance; FT-IR and Raman Bio spectroscopy

Introduction

α-Neurotoxins are a group of neurotoxic peptides found in the venom of snakes in the families Elapidae and Hydrophiidae. They can cause paralysis, respiratory failure, and death. Members of the three-finger toxin protein family, they are antagonists of post-synaptic nicotinic acetylcholine receptors (nAChRs) in the neuromuscular synapse that bind competitively and irreversibly, preventing synaptic acetylcholine (ACh) from opening the ion channel. Over 100 α- neurotoxins have been identified and sequenced.

Density Functional Theory (DFT) is one of the most powerful calculation methods for electronic structures [5-7]. Numerous results have been previously studied and indicate successful use of these methods [8-10]. The theory is one of the most appropriate methods for simulating the vibrational wavenumbers, molecular structure as well as total energy. It may be useful to initially consider the calculated results by density functional theory using F/6-31G*, HF/6-31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6- 31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31- HEG** approach [11-16]. It should be noted that calculations are performed by considering one degree of quantum interference as well as polarization effects of 2d orbitals in interaction [17-320].

Details of Calculations

All calculations of molecular orbital in the base of ab are performed by Gaussian 09. In calculation process, the structure of Alpha-Neurotoxin molecule (Figure 2) is optimized and FT- IR and Raman wavenumbers are calculated using F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** base. All optimized structures are adjusted with minimum energy. Harmonic vibrational wavenumbers are calculated using second degree of derivation to adjust convergence on potential surface as good as possible and to evaluate vibrational energies at zero point. In optimized structures considered in the current study, virtual frequency modes are not observed which indicates that the minimum potential energy surface is correctly chosen. The optimized geometry is calculated by minimizing the energy relative to all geometrical quantities without forcing any constraint on molecular symmetry. Calculations were performed by Gaussian 09.

Biomedical Science & Research

Figure 2:Different sections of the Neurotoxin (upper) and Alpha– Neurotoxin (lower) [43–93].

The current calculation is aimed to maximize structural optimization using density functional theory. The calculations of density functional theory are performed by F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** function in which non-focal functions of Becke and correlation functions of Lee-Yang- Parr beyond the Franck-Condon approximation are used. After completion of optimization process, the second order derivation of energy is calculated as a function of core coordination and is investigated to evaluate whether the structure is accurately minimized. Vibrational frequencies used to simulate spectrums presented in the current study are derived from these second order derivatives. All calculations are performed for room temperature of 316 (K).

Vibration Analysis

Analysis of vibrational spectrum of Alpha-Neurotoxin is performed based on theoretical simulation and FT-IR empirical spectrum and Raman empirical spectrum using density functional theory in levels of F/6-31G*, HF/6-31++G**, MP2/6-31G, MP2/6- 31++G**, BLYP/6-31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31-HEG**. Vibration modes of methylene, carboxyl acid and phenyl cycle are separately investigated. C-H stretching vibrations in single replacement of benzene cycles are usually seen in band range of 3250-3650 cm-1. Weak Raman bands are at 3191 cm-1 and 3207 cm-1. C-C stretching mode is a strong Raman mode at 1211 cm-1. Raman weak band is seen at 1687 cm-1 too. Bending mode of C-H is emerged as a weak mode at 1429 cm-1 and 1205 cm-1 and a strong band at 1289 cm-1 in Raman spectrum. Raman is considerably active in the range of 1250-1650 cm-1 which 1199 cm-1 indicates this issue.

C-H skew-symmetric stretching mode of methylene group is expected at 3189 cm-1 and its symmetric mode is expected at 3000 cm-1. Skew-symmetric stretching mode of CH4 in Alpha- Neurotoxin has a mode in mid-range of Raman spectrum at 3250- 3650 cm-1. When this mode is symmetric, it is at 3099 cm-1 and is sharp. The calculated wavenumbers of higher modes are at 3073 cm-1 and 3096 cm-1 for symmetric and skew-symmetric stretching mode of methylene, respectively.

Scissoring vibrations of CH4 are usually seen at the range of 1530-1590 cm-1 which often includes mid-range bands. Weak bands at 1550 cm-1 are scissoring modes of CH4 in Raman spectrum. Moving vibrations of methylene are usually seen at 1479 cm -1. For the investigated chemical in the current study, these vibrations are at 1349 cm-1 were calculated using density functional theory. Twisting and rocking vibrations of CH4 are seen in Raman spectrum at 925 cm-1 and 1191 cm-1, respectively, which are in good accordance with the results at 907 cm-1 and 1167 cm- 1, respectively. In a non-ionized carboxyl group (COOH), stretching vibrations of carbonyl [C=O] are mainly observed at the range of 1850-1898 cm-1. If dimer is considered as an intact constituent, two stretching vibrations of carbonyl for symmetric stretching are at 1750-1795 cm-1 in Raman spectrum. In the current paper, stretching vibration of carbonyl mode is at 1799 cm-1 which is a mid-range value.

Stretching and bending bands of hydroxyl can be identified by width and band intensity which in turn is dependent on bond length of Hydrogen. In dimer form of Hydrogen bond, stretching band of O-H is of a strong Raman peak at 1377 cm-1 which is due to in-plain metamorphosis mode. Out-of-plain mode of O-H group is a very strong mode of peak at 1056 cm-1 of Raman spectrum. The stretching mode of C-O (H) emerges as a mid-band of Raman spectrum at 1263 cm-1. Lattice vibrations are usually seen at the range of 0-850 cm-1. These modes are induced by rotary and transferring vibrations of molecules and vibrations and are including Hydrogen bond. Bands with low wavenumbers of Hydrogen bond vibrations in FT-IR and Raman spectrum (Figure 3) are frequently weak, width and unsymmetrical. Rotary lattice vibrations are frequently stronger than transferring ones. Intramolecular vibrations with low wavenumbers involving two-bands O-H …O dimer at 99 cm-1, 199 cm-1 and 269 cm-1 are attributed to a rotary moving of two molecules involving in-plain rotation of molecules against each other.

Biomedical Science & Research

Figure 3:3D Simulation of (a) FT–IR spectrum and (b) Raman spectrum of Alpha–Neurotoxin.

Conclusion and Summary

Calculations of density functional theory using F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** levels were used to obtain vibrational wavenumbers and intensities in single crystal of Alpha- Neurotoxin. Investigation and consideration of vibrational spectrum confirm the formation of dimer cycles in the investigated crystal with carboxyl groups from each Hydrogen molecule of acid protected from adjacent molecules. The calculated vibrational spectrum which obtains from calculations of density functional theory is in good accordance with recorded empirical values which indicates successful simulation of the problem. The obtained results indicate that the results obtained from theoretical calculations are valid through comparing with empirical recorded results.

Acknowledgements

Authors are supported by an American International Standards Institute (AISI) Future Fellowship Grant FT1201009373493. We acknowledge Ms. Isabelle Villena for instrumental support and Dr. Michael N. Cocchi for constructing graphical abstract figure. We gratefully acknowledge Prof. Dr. Christopher Brown for proofreading the manuscript.

References

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