Spectroscopy and Dipole Moment of the Molecule C₁₃H₂₀BeLi₂SeSi Via Quantum Chemistry using Ab Initio, Hartree-Fock Method in the Base Set CC-Pvtz and 6-311G**(3df, 3pd) Volume 3 - Issue 5

Ricardo Gobato¹*, Marcia Regina Risso Gobato², Alireza Heidari³ and Abhijit Mitra⁴

• ¹ Laboratory of Biophysics and Molecular Modeling Genesis, State Secretariat for Education of Parana, Bela Vista do Paraiso, Parana, Brazil
• ² Seedling Growth Laboratory, Green Land Landscaping and Gardening, Bela Vista do Paraiso, Parana, Brazil
• ³ Faculty of Chemistry, California South University, 14731 Comet St. Irvine, CA 92604, USA
• ⁴Department of Marine Science, University of Calcutta, West Bengal, India

Received: September 03, 2018;   Published: September 24, 2018

*Corresponding author:Ricardo Gobato, Laboratory of Biophysics and Molecular Modeling Genesis, State Secretariat for Education of Parana, Bela Vista do Paraiso, Parana, Brazil

DOI: 10.32474/AOICS.2018.03.000171

Abstract PDF

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Abstract

The work characterizes the electric dipole moment and the infrared spectrum of the molecule C₁₃H₂₀BeLi₂SeSi. Calculations obtained in the ab initio RHF (Restrict Hartree-Fock) method, on the set of bases used indicate that the simulated molecule C₁₃H₂₀BeLi₂SeSi features the structure polar-apolar-polar predominant. The set of bases used that have are CC-pVTZ and 6-311G** (3df, 3pd). In the CC-pVTZ base set, the charge density in relation to 6-311G** (3df, 3pd) is 50% lower. The length of the molecule C₁₃H₂₀BeLi₂SeSi is of 15.799Å. The magnitude of the electric dipole moment || total obtained was p = 4.9771 Debye and p = 4.7936 Debye, perpendicular to the main axis of the molecule, for sets basis CC-pVTZ and 6-311**(3df, 3pd), respectively. The infrared spectra for absorbance and transmittance and their wavenumber (cm^-1) were obtained in the set of bases used. The infrared spectrum for Standard CC-pVTZ shows peaks in transmittance with Intensity (I), at wavenumber 1,125.44cm^-1, 1,940.70cm^-1, 2,094.82cm^-1, 2,178.43cm^-1, 2,613.99cm^-1 and transmittance 433.399km/mol, 399.425km/mol, 361.825km/mol, 378.993km/ mol, 433.774km/mol, respectively. While the infrared spectrum for Standard 6-311G** (3df,3pd), shows peaks in transmittance, at wavelengths 1,114.83cm^-1, 1,936.81cm^-1, 2,081.49cm^-1, 2,163.23 cm^-1, 2,595.24cm^-1 and transmittance 434.556 km/mol, 394.430 km/mol, 345.287 km/mol, 375.381 km/mol, 409.232 km/mol, respectively. It presents “fingerprint” between the intervals (680cm- 1 and 1,500 cm^-1) and (3,250cm^-1 and 3,500cm^-1). The dipole moments CC-pTZV are 3.69% bigger than 6-311G (3df, 3pd). As the bioinorganic molecule C₁₃H₂₀BeLi₂SeSi is the basis for a new creation of a bio-membrane, later calculations that challenge the current concepts of biomembrane should advance to such a purpose.

Introduction

The work characterizes the electric dipole moment and the infrared spectrum of the molecule C₁₃H₂₀BeLi₂SeSi [1]. Using a computational simulation using ab initio methods, RHF (Restrict Hartree-Fock), [2-9] set of basis CC-pVTZ [10-14] and 6-311G (3df, 3pd) [7,5-21]. Preliminary bibliographic studies did not reveal any works with characteristics studied here. There is an absence of a referential of the theme, finding only one work in [1]. To construct such a molecule, which was called a seed molecule, quantum chemistry was used by ab initio methods [2,3,15]. The equipment used was of the Biophysics laboratory built specifically for this task. The results were satisfactory. The ab initio calculations, by RHF [2-9] in the CC-pVTZ [10-14] and 6-311G (3df, 3pd) [7,15- 21], sets basis was shown to be stable by changing its covalent cyclic chain linkages, which was expected. The set of basis used was that of Ahlrichs and coworkers the TZVP keywords refer to the initial formations of the split valence and triple zeta basis sets from this group [22,23]. The structure of the C₁₃H₂₀BeLi₂SeSi is a Bio-inorganic seed molecule for a biomembrane genesis that defies the current concepts of a protective mantle structure of a cell such as biomenbrane to date is promising, challenging. Leaving to the Biochemists their experimental synthesis. The quantum calculations must continue to obtain the structure of the bioinorganic biomenbrane. The following calculations, which are the computational simulation via Mm+, QM/MM, should indicate what type of structure should form. Structures of a liquid crystal such as a new membrane may occur, micelles [1,24-62].

Methods

Hartree-Fock Methods

Hartree-Fock theory is one the simplest approximate theories for solving the many-body Hamiltonian [2-9]. The full Hartree-Fock equations are given by

The vast literature associated with these methods suggests that the following is a plausible hierarchy:

The extremes of ‘best’, FCI, and ‘worst’, HF, are irrefutable, but the intermediate methods are less clear and depend on the type of chemical problem being addressed. [63,64] The use of HF in the case of FCI was due to the computational cost [1, 24-62].

Hardware and Software

For Calculations A Computer Models was Used: Intel® CoreTM i3-3220 CPU@3.3 GHz x 4 processors [65], Memory DDR3 4 GB, HD SATA WDC WD7500 AZEK-00RKKA0 750.1 GB and DVDRAM SATA GH24NS9 ATAPI, Graphics Intel® Ivy Bridge [66]. The ab initio calculations have been performed to study the equilibrium configuration of C₁₃H₂₀BeLi₂SeSi molecule using the GAMESS [15,20]. The set of programs Gauss View 5.0.8 [67], Mercury 3.8 [68], Avogadro [69,70] are the advanced semantic chemical editor, visualization, and analysis platform and GAMESS [15,20] is a computational chemistry software program and stands for General Atomic and Molecular Electronic Structure System [15,20] set of programs. For calculations of computational dynamics, the Ubuntu Linux version 16.10 system was used [71].

Result

(Figures 1-5) and (Tables 1-3).

Selects Stuttgart potentials for Z > 2. MC-311G is a synonym for 6-311G [7]. The elemental charge e (e = ±1,607 x 10-19 C) [1,24-62].

Discussion

The Figure 1 shows the final stable structure of the bioinorganic C₁₃H₂₀BeLi₂SeSi molecule obtained by an ab initio calculation with the method RHF (Restrict Hatrree-Fock), in sets of bases such as: 6-311G**(3df,3pd) and CC-pVTZ. As an example of analysis the set of bases CC-pVTV, with the charge distribution (Δδ) through it, whose charge variation is Δδ = 0.680 a.u. of elemental charge. In green color the intensity of positive charge displacement. In red color the negative charge displacement intensity. Variable, therefore, of δ- = 0.340 a.u. negative charge, passing through the absence of charge displacement, represented in the absence of black - for the green color of δ+ = 0.340 a.u. positive charge. The magnitude of the electric dipole moment || total obtained was p =4.9771 Debye, perpendicular to the main axis of the molecule, for sets basis CC-pVTZ. By the distribution of charge through the bioinorganic molecule it is clear that the molecule has a polar-apolarpolar structure, Figure 2 and Table 1. An analysis of the individual charge value of each atom of the molecule could be made, but here it was presented only according to Figure 2, due to the objective being to determine the polar-apolar-polar, the polar characteristic of the molecule, whose moment of dipole is practically perpendicular to the central axis of the molecule. In Figure 2 the dipole moment is visualized 6-311G**(3df,3pd) and CC-pVTZ in base sets, being represented by an arrow in dark blue color, with their respective values in Debye. This also presents the orientation axes x, y and z and the distribution of electric charges through the molecule.

In the set of bases used the CC-pTZV and 6-311**(3df, 3pd) present the same characteristic for the distribution of charges to the polar end with Carbon atom (negative charge) bound to the -SiH3 radical and the two Lithium atoms. It is seen that Δδ =0.680 a.u. of CC-pTZV and Δδ =1.366 a.u. of 6-311 (3df, 3pd), this latter has a twice greater Δδ, Figure 2, although the dipole moments CC-pTZV are 3.69% larger, (Table 1). The main chain (backbone of the molecule) for the CC-pTZV base set has a small negative charge displacement for the Carbon atoms from the Hydrogen atoms attached to them. Therefore, with positive charge the Hydrogen atoms connected to the Carbon of the central chain. For the set of bases 6-311**(3df, 3pd) the carbon atoms of the main chain are presented with very small distribution of negative charge, coming from the Hydrogen linked to these neutrals, Figure 2. At the other polar end for the base set 6-311**(3df, 3pd) the cyclic chain shows the characteristics as the Beryllium atom with strong charge displacement positive, these charges shift to the Carbon atoms attached to it, Figure 2. The cyclic chain with a strong negative charge, displaced from the Beryllium atom. The two carbon atoms bonded in double bonds, present a slight positive charge, with their neutral Hydrogen, Figure 2. The Selenium atom connected to two Carbon atoms of the cyclic chain presents a slight negative charge, originating from the Carbon atom connected to the main chain with a slight positive charge, and the other Carbon atom connected to the cyclic chain presents a neutral charge, Figure 2. The magnitude of the electric dipole moment || total obtained was p = 4.7936 Debye for 6-311**(3df, 3pd), (Table 1). Figures 3 & 4 represent the normalized infrared spectrum for the base set RHF / 6-311G ** (3df, 3pd) and CC-pVTZ for Absorbance and Transmittance. Figures 5 represent the normalized infrared spectrum for the base set RHF/6-311G** (3df, 3pd and CC-pVTZ for absorbance, making a comparison between the two sets of base. The infrared spectrum for Standard RHF/CC-pVTZ shows peaks in transmittance, at wavelengths 1,125.44cm^-1, 1,940.70cm- 1, 2,094.82cm^-1, 2,178.43cm^-1, 2,613.99cm^-1 and transmittance 433.399km/mol, 399.425km/mol, 361.825km/mol, 378.993km/ mol, 433.774km/mol, respectively, Figure 3 and Table 2. The infrared spectrum for Standard RHF/6-311G**(3df,3pd) shows peaks in transmittance, at wavelengths 1,114.83cm^-1, 1,936.81cm- 1, 2,081.49cm^-1, 2,163.23 cm^-1, 2,595.24cm^-1 and transmittance 434.556km/mol, 394.430 km/mol, 345.287 km/mol, 375.381 km/ mol, 409.232 km/mol, respectively, Figure 4 and Table 3. It presents “fingerprint” between the intervals (680cm^-1 and 1,500cm^-1) and (3,250cm^-1 and 3,500cm^-1), Figures 3-5.

Conclusion

Calculations obtained in the ab initio RHF method, on the set of bases used, indicate that the simulated molecule, C₁₃H₂₀BeLi₂SeSi, is acceptable by quantum chemistry. Its structure has polarity at its ends, having the characteristic polar-apolar-polar. The 6-311G (3df, 3pd) set of basis exhibits the characteristic of the central chain, with a small density of negative charges, near the ends of the Carbons of this. In the CC-pVTZ base set, the charge density in relation to 6-311G (3df, 3pd) is 50% lower. It is characterized infrared spectrum of the molecule C₁₃H₂₀BeLi₂SeSi, for absorbance and transmittance, in Hartree method in the set of bases CC-pVTZ and 6-311G (3df, 3pd). The infrared spectrum for Standard RHF/ CC-pVTZ shows peaks in transmittance, at wavelengths 1,125.44cm- 1, 1,940.70cm^-1, 2,094.82cm^-1, 2,178.43cm^-1, 2,613.99cm^-1 and transmittance 433.399 km/mol, 399.425km/mol, 361.825km/ mol, 378.993km/mol, 433.774km/mol, respectively. The infrared spectrum for Standard RHF/6-311G**(3df,3pd) [7,30,60,71,72] shows peaks in transmittance, at wavelengths 1,114.83cm- 1, 1,936.81cm^-1, 2,081.49cm^-1, 2,163.23cm^-1, 2,595.24cm^-1 and transmittance 434.556km/mol, 394.430km/mol, 345.287km/ mol, 375.381km/mol, 409.232km/mol, respectively. It presents “fingerprint” between the intervals (680cm^-1 and 1,500cm^-1) and (3,250cm^-1 and 3,500cm^-1). The dipole moments CC-pTZV are 3.69% bigger than 6-311G (3df, 3pd). As the bio-inorganic molecule C₁₃H₂₀BeLi₂SeSi is the basis for a new creation of a biomembrane, later calculations that challenge the current concepts of biomembrane should advance to such a purpose.

Acknowledgement

To the doctors: Prof. Ph.D. Tolga Yarman, Okan University, Akfirat, Istanbul, Turkey & Savronik, Organize Sanayi Bolgesi, Eskisehir, Turkey, and Prof. Ph.D. Ozan Yarman, Istanbul University, Rihtim Nr:1, 81300 Kadikoy, Istanbul, Turkey, for their valuable contributions to the work.

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