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Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi 2 SeSi

Authors:
  • Secretary of State Education and Sport of Parana - Computer Lab - 86130.000

Abstract

Inorganic crystals have been used in the most diverse electronic systems since the nineteenth century, which apply to the wide variety of technological applications, which are the quartz crystals are the most used. Elements such as beryllium, lithium, silicon and selenium are widely used. The difficulty of finding such crystals from the combination of elements in nature or synthesized, suggest an advanced study of the same. In this sense, these elements were chosen because of the physical-chemical properties of each one, to simulate a seed molecule whose arrangement would be formed by the combination of these, aiming at the future development of a crystal to be used technologically. A study using computer programs with ab initio method was applied and the quantum chemistry was utilized through Molecular Mechanics, Hartree-Fock, Møller-Plesset and Density Functional Theory, on several bases. The main focus was to obtain a stable molecular structure acceptable to quantum chemistry. As a result of the likely molecular structure of the arrangement of a crystal was obtained, beyond the dipole moment, thermal energy, heat of vaporization and entropy of the molecule. The simulated molecule has a cationic molecular structure, in the atoms Selenium and Silicon. As a consequence, it has a strong electric dipole moment. Due to its geometry, it presents a probable formation structure of a crystal with a tetrahedral and hexahedral crystal structure.
American
Journal
of
Quantum
Chemistry
and
Molecular
2017; 2(3): 37-46
http://www.sciencepublishinggroup.com/j/ajqcms
doi: 10.11648/j.ajqcms.20170203.12
Calculations Using Quantum Chemistry for Inorganic
Molecule Simulation BeLi2SeSi
Ricardo Gobato1, *, Alireza Heidari2
1State Secretariat for Education of Paraná, Laboratory of Biophysics and Molecular Modeling, Bela Vista do Paraíso, Paraná, Brazil
2Faculty of Chemistry, California South University, Costa Mesa, USA
Email address:
ricardogobato@seed.pr.gov.br (R. Gobato), Scholar.Researcher.Scientist@gmail.com (A. Heidari), Alireza.Heidari@calsu.us (A. Heidari)
*Corresponding author
To cite this article:
Ricardo Gobato, Alireza Heidari. Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi2SeSi. American Journal
of Quantum Chemistry and Molecular Spectroscopy. Vol. 2, No. 3, 2017, pp. 37-46. doi: 10.11648/j.ajqcms.20170203.12
Received: June 20, 2017; Accepted: July 17, 2017; Published: August 28, 2017
Abstract: Inorganic crystals have been used in the most diverse electronic systems since the nineteenth century, which apply
to the wide variety of technological applications, which are the quartz crystals are the most used. Elements such as beryllium,
lithium, silicon and selenium are widely used. The difficulty of finding such crystals from the combination of elements in
nature or synthesized, suggest an advanced study of the same. In this sense, these elements were chosen because of the
physical-chemical properties of each one, to simulate a seed molecule whose arrangement would be formed by the
combination of these, aiming at the future development of a crystal to be used technologically. A study using computer
programs with ab initio method was applied and the quantum chemistry was utilized through Molecular Mechanics, Hartree-
Fock, Møller-Plesset and Density Functional Theory, on several bases. The main focus was to obtain a stable molecular
structure acceptable to quantum chemistry. As a result of the likely molecular structure of the arrangement of a crystal was
obtained, beyond the dipole moment, thermal energy, heat of vaporization and entropy of the molecule. The simulated
molecule has a cationic molecular structure, in the atoms Selenium and Silicon. As a consequence, it has a strong electric
dipole moment. Due to its geometry, it presents a probable formation structure of a crystal with a tetrahedral and hexahedral
crystal structure.
Keywords: Beryllium, DFT, Lithium, Molecular Geometry, Selenium, Silicon
1. Introduction
A crystal [1] oscillator is an electronic oscillator circuit
that uses the mechanical resonance of a vibrating crystal of
piezoelectric material to create an electrical signal with a
very precise frequency. This frequency is commonly used to
keep track of time (as in quartz wristwatches), to provide a
stable clock signal for digital integrated circuits, and to
stabilize frequencies for radio transmitters and receivers. The
most common type of piezoelectric resonator used is the
quartz crystal, so oscillator circuits incorporating them
became known as crystal oscillators, but other piezoelectric
materials including polycrystalline ceramics are used in
similar circuits. [2, 3]
The use of inorganic crystals technology has been widely
date. Since quartz crystals [1] for watches in the nineteenth
century, and common way radio in the early twentieth
century, to computer chips with new semiconductor
materials. [2] Chemical elements such as beryllium, lithium,
selenium and silicon, [1, 4] are widely used in technology.
The development of new crystals arising from that
arrangement can bring technological advances in several
areas of knowledge.
Within many electronics resonates a crystal that
determines a precise rhythm functioning. The clocks, timers,
computers, communications equipment and many other tiny
devices quartz crystals [1] vibrate accurately ensuring that
your circuits work completely orderly and synchronized way.
It is difficult to predict what would be electronics today
without the presence of these elements. [5]
A study using computer programs with ab initio method
was applied and the quantum chemistry was utilized through
Molecular Mechanics, Hartree-Fock, Møller-Plesset and
Density Functional Theory, on several bases. [6, 7]
38 Ricardo Gobato and Alireza Heidari: Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi2SeSi
A preliminary literature search did not indicate any
compounds of said arrangement of these chemical elements.
This fact the study can lead to getting new crystals to be used
in the materials industry. A study using computer programs
with ab initio have been applied. The calculations indicate by
the ab initio methods used that the molecular structure of the
simulated molecule can in more detailed calculations
generate a crystalline structure. [8, 9]
2. Chemical Properties of the
Compounds of Beryllium, Lithium,
Selenium and Silicon
The Beryllium, Lithium, Selenium and Silicon elements
were chosen due to their peculiar physicochemical properties
and their wide use in industry and technology.
2.1. Beryllium
Beryllium is a chemical element with symbol Be and
atomic number 4. It is created through stellar nucleosynthesis
and is a relatively rare element in the universe. It is a divalent
element which occurs naturally only in combination with
other elements in minerals. Notable gemstones which contain
beryllium include beryl (aquamarine, emerald) and
chrysoberyl. As a free element it is a steel-gray, strong,
lightweight and brittle alkaline earth metal. [2]
Beryllium improves many physical properties when added
as an alloying element to aluminium, copper (notably the
alloy beryllium copper), iron and nickel. [10] Tools made of
beryllium copper alloys are strong and hard and do not create
sparks when they strike a steel surface. In structural
applications, the combination of high flexural rigidity,
thermal stability, thermal conductivity and low density (1.85
times that of water) make beryllium metal a desirable
aerospace material for aircraft components, missiles,
spacecraft, and satellites. [10] Because of its low density and
atomic mass, beryllium is relatively transparent to X-rays and
other forms of ionizing radiation; therefore, it is the most
common window material for X-ray equipment and
components of particle physics experiments [10]. The high
thermal conductivities of beryllium and beryllium oxide have
led to their use in thermal management applications.
2.2. Lithium
Lithium (from Greek: l´ıq oc¸ lithos, “stone”) is a chemical
element with symbol Li and atomic number 3. It is a soft,
silver-white metal belonging to the alkali metal group of
chemical elements. Under standard conditions it is the
lightest metal and the least dense solid element. Like all
alkali metals, lithium is highly reactive and flammable. For
this reason, it is typically stored in mineral oil. When cut
open, it exhibits a metallic luster, but contact with moist air
corrodes the surface quickly to a dull silvery gray, then black
tarnish. Because of its high reactivity, lithium never occurs
freely in nature, and instead, only appears in compounds,
which are usually ionic. Lithium occurs in a number of
pegmatitic minerals, but due to its solubility as an ion, is
present in ocean water and is commonly obtained from brines
and clays. On a commercial scale, lithium is isolated
electrolytically from a mixture of lithium chloride and
potassium chloride. [2]
Lithium and its compounds have several industrial
applications, including heat-resistant glass and ceramics,
lithium grease lubricants, flux additives for iron, steel and
aluminum production, lithium batteries and lithium-ion
batteries. These uses consume more than three quarters of
lithium production. [2]
Figure 1. Above and to the left the representation of the molecular structure of BeLi2SeSi seed [9], obtained through computer via Molecular Mechanics Mm+
calculation, and then its geometry was optimized via PM3 [12, 13, 14, 15, 16] with distance measured in Ångstron obtained using computer programs Hyper
Chem 7.5 Evaluation [6]. Above and to the right the representation of the molecular structure of BeLi2SeSi, obtained through computer via Ab Initio
calculation method DFT, functional B3LYP in base 6-311G**(3df, 3pd), obtained using computer programs GAMESS [7, 17]. Images obtained in the software
Mercury 3.8 [18], above and to the left and the right Avogadro [19]. Represented in gray color the atom of Silicon, in the purple color Lithium, in the lemon
yellow color Beryllium, and in the pumpkin the Selenium.
American Journal of Quantum Chemistry and Molecular Spectroscopy 2017; 2(3): 37-46 39
2.3. Selenium
Selenium is a chemical element with symbol Se and
atomic number 34. It is a nonmetal with properties that are
intermediate between those of its periodic table column-
adjacent chalcogen elements sulfur and tellurium. It rarely
occurs in its elemental state in nature, or as pure ore
compounds. Selenium (Greek selene meaning “Moon”) was
discovered in 1817 by J. Jacob Berzelius. [2]
Selenium is found impurely in metal sulfide ores, copper
where it partially replaces the sulfur. The chief commercial
uses for selenium today are in glassmaking and in pigments.
Selenium is a semiconductor and is used in photocells. Uses
in electronics, once important, have been mostly supplanted
by silicon semiconductor devices. Selenium continues to be
used in a few types of DC power surge protectors and one
type of fluorescent quantum dot. [2]
2.4. Silicon
Silicon is a chemical element with symbol Si and atomic
number 14. It is a tetravalent metalloid, more reactive than
germanium, the metalloid directly below it in the table. [2] Is
the eighth most common element in the universe by mass,
but very rarely occurs as the pure free element in nature. It is
most widely distributed in dusts, sands, planetoids, and
planets as various forms of silicon dioxide (silica) or
silicates. Over 90% of the Earth’s crust is composed of
silicate minerals, making silicon the second most abundant
element in the Earth’s crust (about 28% by mass) after
oxygen. [11]
Elemental silicon also has a large impact on the modern
world economy. Although most free silicon is used in the
steel refining, aluminium-casting, and fine chemical
industries (often to make fumed silica), the relatively small
portion of very highly purified silicon that is used in
semiconductor electronics (<10%) is perhaps even more
critical. Because of wide use of silicon in integrated circuits,
the basis of most computers, a great deal of modern
technology depends on it. [2]
3. Methods
3.1. Hartree-Fock
The Hartree-Fock self–consistent method is based on the
one-electron approximation in which the motion of each
electron in the effective field of all the other electrons is
governed by a one-particle Schrodinger¨ equation. The
Hartree-Fock approximation takes into account of the
correlation arising due to the electrons of the same spin,
however, the motion of the electrons of the opposite spin
remains uncorrelated in this approximation. The methods
beyond self-consistent field methods, which treat the
phenomenon associated with the many-electron system
properly, are known as the electron correlation methods. One
of the approaches to electron correlation is the Møller-Plesset
(MP) perturbation theory in which the Hartree-Fock energy is
improved by obtaining a perturbation expansion for the
correlation energy. [20] However, MP calculations are not
variational and can produce an energy value below the true
energy. [21]
Another first principles approach to calculate the
electronic structure for many-electron systems is the Density
Functional Theory (DFT). In this theory, the exchange-
correlation energy is expressed, at least formally, as a
functional of the resulting electron density distribution, and
the electronic states are solved for self-consistently as in the
Hartree-Fock approximation. [22, 23, 24, 25] The Density
Functional Theory is, in principle, exact but, in practice, both
exchange and dynamic correlation effects are treated
approximately. [26]
A hybrid exchange-correlation functional is usually
constructed as a linear combination of the Hartree–Fock
exact exchange functional,
 =  −
Ψ
, Ψ
  (1)
and any number of exchange and correlation explicit density
functionals. The parameters determining the weight of each
individual functional are typically specified by fitting the
functional’s predictions to experimental or accurately
calculated thermochemical data, although in the case of the
“adiabatic connection functionals” the weights can be set a
priori. [27]
3.2. B3LYP
The B3LYP (Becke, three-parameter, Lee-Yang-Parr) [28,
29] exchange-correlation functional is:

 =  
 + "#

 + "$
%% −
 +
 + "&&
%% − &
 (2)
Are generalized gradient approximations: the Becke 88
exchange functional [30] and the correlation functional of
Lee, Yang and Parr [31] for B3LYP, and EcDA is the VWN
local-density approximation to the correlation functional.
[32]
The three parameters defining B3LYP have been taken
without modification from Becke’s original fitting of the
analogous B3PW91 functional to a set of atomization
energies, ionization potentials, proton affinities, and total
atomic energies. [33]
The first principles methods (i.e. HF and DFT) discussed
above can be implemented with the aid of the GAMESS set
of programs to study the electronic structure and to determine
the various physical properties of many-electron systems. [7]
A basis set is the mathematical description of the orbitals
within a system (which in turn combine to approximate the
total electronic wavefunction) used to perform the theoretical
calculation. [34] 3-21G, 3-21G*, 6-31G, 6-31G*, 6-31G**,
6-311G, 6-311G*, 6-311G** are the basis sets used in the
calculations. The functional Becke-style one parameter
40 Ricardo Gobato and Alireza Heidari: Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi2SeSi
functional using modified Perdew-Wang exchange and
Perdew-Wang 91 correlation is used for DFT Calculations.
[26, 35]
The SCF method and extensions to it are mathematically
and physically considerably more complicated than the one-
electron methods already discussed. Thus, one normally does
not perform such calculations with pencil and paper, but
rather with complicated computer programs. Terms like
“Hartree–Fock”, or “correlation energy” have specific
meanings and are pervasive in the literature. [36]
The vast literature associated with these methods suggests
that the following is a plausible hierarchy:
HF << MP2 < CISD < CCSD < CCSD (T) < FCI
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.
[37]
For calculations a cluster of 6 computer models was used:
Prescott-256 Celeron D processors, [2] featuring double the
L1 cache (16 KB) and L2 cache (256 KB), Socket 478 clock
speeds of 2.13 GHz; Memory DDR2 PC4200 512MB;
Hitachi HDS728080PLAT20 80 GB and CD-R.
The dynamic was held in Molecular Mechanics Force
Field (Mm+), Eq. (1), after the quantum computation was
optimized via PM3 and then by DFT, [21, 26] with functional
B3LYP [38] and base 6-311G** [7, 21, 26]. The molecular
dynamics at algorithm Polak-Ribiere [39], conjugate
gradient, at the termination condition: RMS gradient [40] of
0, 1 kcal/A. mol or 405 maximum cycles in vacuum [6].
The first principles calculations have been performed to
study the equilibrium configuration of BeLi2SeSi molecule
using the Hyperchem 7.5 Evaluation [41], Mercury 3.8 a
general molecular and electronic structure processing
program [18], Avogadro: an advanced semantic chemical
editor, visualization, and analysis platform [19] and
GAMESS is a computational chemistry software program
and stands for General Atomic and Molecular Electronic
Structure System [7] set of programs. The first principles
approaches can be classified into two main categories: the
Hartree-Fock approach and the density functional approach.
[22]
4. Discussions
The BeLi2SeSi molecular has:
Chemical formula: BeLi2SeSi
Molecular mass: 130.93764 amu
Crystal system: triclinic
Density: 215.757 g/cm3
Wyckoff sequence: a5
A covalent bonding structure between the atoms was
initially suggested as shown in Figure (1). Selenium valences
+6, Silicon +4, Beryllium +2 and Lithium +1 were
considered as valences. Selenium binding to the silicon in
triple bond, and this to Beryllium in simple bond. Two
lithium and beryllium atoms and simple covalent bond to
Selenium.
The structure of the molecule was initially parameterized
and made to the optimization of its geometry using
Molecular Mechanics Mm+. [42] After optimization of the
geometry via Mm+, it was optimized via PM3 [12, 13, 14,
15, 16], Figure (1), being the software used was the Hyper
Chem 7.5 Evaluation [6]. Above the center and to the right of
Figure (1), the molecular structure of the BeLi2SeSi molecule
was obtained by DFT [21] in the UB3LYP/6-311G**(3df,
3pd) using the GAMESS software. [7]
A detailed analysis of the molecular structure of the
BeLi2SeSi molecule was obtained using the GAMESS
software [7]. We obtained the dipole moment and vibration
frequencies of the BeLi2SeSi molecule through ab initio
calculations by the B3LYP, HF, MP2, CISD, CCSD,
CCSD(T) and FCI methods [21], Tables (3) and (6).
We represent the BeLi2SeSi molecule in this sequence of
Figure (3) for a better understanding of its three-dimensional
structure.
Figure (3) contains 16 images of the molecular structure
of BeLi2SeSi molecule in different positions under-rotation
of the x and y axes. From the first image at the top left, a
sequence of 16 images in turn sequence is displayed, from
left to right and from top to bottom. The molecule is rotated
in the x-direction from the first image until it returns to its
initial position in the ninth image. From which you rotate y
until you return to the starting position, last image in the
lower right corner. The atoms are represented in four
different colors. Silicon in golden color, Selenium in
orange, Beryllium in lime-green and two lithium atoms in
purple.
Analyzing Figures (1) and Figure (2) obtained by
quantum chemistry by the ab initio method, we can see the
structure of the simulated molecule. Making the necessary
turns of visualization with the atom of Be in front of the
screen, or the atom of Se, and centralizing these in a
segment of line between them, Be and Se, these form a
tetrahedron each. Six planes are formed, with six triangles
belonging to these planes formed by the atoms, occupying
its vertices: Be-Si-Li2, Be-Si-Li1 and Be-Li1-Li2 for the
tetrahedron of the atom Beryllium, and Se-Si-L1, Se-Si-Li2
and Se-Li1-Li2 to the tetrahedron of the Selenium atom.
Both tetrahedrons connected to the same base, formed by
the plane, with the atoms Si-Li1-Li2, as vertices of the base
triangle of these.
The covalent bonds between the atoms of the simulated
molecule have now changed with the covalent bonding
sequence Li2-Be-Si-Se-Li1, i.e. Li-Be-Si-Se-Li, Figure (2),
(in the center and the left).
In Tables (1) and (2) the pdb files of the simulated
molecule are displayed. The Table (1) the pdb file of the
molecular structure of molecule BeLi2SeSi, obtained through
computer via ab initio calculation method HF in base STO-
3G [43, 44], obtained using computer programs Hyper Chem
7.5 Evaluation [6]. The Table (2) the pdb file of the
molecular structure of molecule BeLi2SeSi, obtained through
computer via ab initio calculation method B3LYP in base 6-
American Journal of Quantum Chemistry and Molecular Spectroscopy 2017; 2(3): 37-46 41
311G**(3df, 3pd), obtained using computer programs
GAMESS [7].
The Table (3) presents some thermochemical properties
of the simulated molecule, such as: thermal energy,
vaporization heat and molar entropy. All values obtained
after a end optimization of the molecular geometry, using
the DFT method, with B3LYP functional and base 6-
311G** (3df, 3pd). The thermochemical values for the HF,
MP2, CISD, CCSD(T), CC, CID and CI methods were
calculated at the end geometry point B3LYP/6-311G**(3df,
3pd). [21]
The lowest and highest thermal energy obtained were
7,622 kcal/mol and 8,560 kcal/mol in the HF/3-21G and
MP2/STO-3G methods, respectively.
The lowest and highest heat of vaporization were 18.592
kcal/mol.K and 20.718 kcal/mol.K in the HF/3-21G and
B3LYP/6-311G** (3df, 3pd) methods, respectively.
The lowest and highest molar entropy obtained were
80.298 kcal/mol.K and 84.426 kcal/mol.K, in the HF/6-
311G** (3df, 3pd) and CIS-FC/CC-PVDZ methods,
respectively.
The Tables (4) and (5) present the parameters of the
molecular geometry of the simulated molecule, such as
spatial coordinates, length of the bonds between the atoms,
angles and dihedral. The Table (1) shows the values for the
dynamics via the HF method in the STO-3G base and Table
(2) for the DFT method, functional B3LYP in base 6-
311G**(3df, 3pd).
The Figures (1) and (2), to the left of these, the
representation of the molecular structure of BeLi2SeSi seed
[8, 9, 45, 46], obtained through computer via Molecular
Mechanics Mm+ calculation, and then its geometry was
optimized via PM3 [12, 13, 14, 15, 16] and the representation
of the molecular structure of BeLi2SeSi seed, obtained
through computer via ab initio calculation method HF in base
STO-3G [43, 44], with distance measured in Ångstron and
loads obtained using computer programs Hyper Chem 7.5
Evaluation [6], respectively.
There is a reduction of the average distance between atoms
of the simulated molecule.
Through the calculations presented in Table (6) show that
the lowest and highest electric dipole moment, have the
values 0.9869 Debye and 8.9298 Debye, in the B3LYP/STO-
3G and UHF/TVZ methods, respectively.
5. Conclusions
As a result of the likely molecular structure of the
arrangement of a crystal was obtained. The techniques of
micro-crushing and conoscopic [47] analysis can lead to
evidence and obtaining such crystals.
Calculations using quantum chemistry admit inorganic
molecule BeLi2SeSi.
As a result of calculations ab initio the molecular structure
with a feature proposed by the simulated seed molecule, it is
likely by quantum chemistry that a crystal structure of the
arrangement can be obtained.
The simulated molecule has a cationic molecular structure,
in the atoms Selenium and Silicon. As a consequence, it has a
strong electric dipole moment, 8.9298 Debye, in UHF/TVZ
methods. Due to its geometry, it presents a probable
formation structure of a crystal with the tetrahedral and
hexahedral crystal structure.
6. Tables and Figures
Table 1. Description of the. pdb file of the molecular structure of molecule
BeLi2SeSi, obtained through computer via ab initio calculation method HF
in base STO-3G [43, 44], obtained using computer programs Hyper Chem
7.5 Evaluation [6].
HETATM 1 Si 1 -0.892 1.300 0.917
HETATM 2 Se 2 -0.010 -1.387 -0.224
HETATM 3 Be 3 -1.646 -0.283 -0.066
HETATM 4 Li 4 0.494 0.829 -0.850
HETATM 5 Li 5 -0.199 -0.606 1.992
CONECT 1 2 3
CONECT 2 1 3 4 5
CONECT 3 1 2
CONECT 4 2
CONECT 5 2
END
Table 2. Description of the. pdb file of the molecular structure of molecule
BeLi2SeSi, obtained through computer via ab initio calculation method
B3LYP in base 6-311G**(3df, 3pd), obtained using computer programs
GAMESS [7].
HETATM 1 Se 1 0.883 -0.055 0.000
HETATM 2 Li 2 -0.319 1.382 -1.484
HETATM 3 Si 3 -1.359 -0.805 0.000
HETATM 4 Li 4 -0.319 1.382 1.484
HETATM 5 Be 5 -2.273 1.212 0.000
CONECT 1 2 3
CONECT 2 1
CONECT 3 1 5
CONECT 4 5
CONECT 5 3 4
END
Table 3. Thermochemical parameters of the molecule BeLi2SeSi obtained by ab initio methods.
Methods/Base
Thermochemistry
E
Thermal CV S
(Kcal/mol) (cal/mol.K) (cal/mol.K)
B3LYP/6-311G**(3df, 3pd) 8.152 20.718 83.606
CIS-FC/CC-pVDZ 8.523 19.714 80.298
HF/3-21G 7.622 18.592 82.660
HF/6-311G**(3df, 3pd) 8.158 20.706 84.426
42 Ricardo Gobato and Alireza Heidari: Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi2SeSi
Methods/Base
Thermochemistry
E
Thermal CV S
(Kcal/mol) (cal/mol.K) (cal/mol.K)
MP2/STO-3G 8.560 19.648 80.457
CISD/STO-3G 8.552 19.662 80.457
CCSD(T)/STO-3G 8.518 19.749 80.714
CI/STO-3G 8.552 19.662 80.457
B3LYP/STO-3G 8.438 19.944 80.979
CC/STO-3G 8.545 19.686 80.609
CID/STO-3G 8.560 19.645 80.445
Table 4. Molecular parameters of the atoms of the molecule BeLi2SeSi seed, obtained through computer via ab initio calculation method HF in base STO-3G
[43, 44], with distance measured in Ångstron obtained using computer programs Hyper Chem 7.5 Evaluation [6].
Atom NA NB
NC
Bond Angle Dihedral X(A)
˚
Y(A)
˚
Z(A)
˚
Si -0,379 -1,080 1,707
Se 1 3,0272777 -0,671 0,681 -0,738
Be 2 1 1,8506712 40,6512698 -1,661 -0,539 0,240
Li 1 3 2 2,4351417 69,0527075 53,4172985 -0,624 1,341 1,614
Li 3 2 1 2,4492640 68,7308859 -58,1835086 0,412 -1,542 -0,594
Table 5. Molecular parameters of the atoms of the molecule BeLi2SeSi seed, obtained through computer via ab initio calculation method DFT, functional
B3LYP in base 6-311G**(3df, 3pd), with distance measured in Ångstron obtained using computer programs GAMESS. [7].
Atom NA NB
NC
Bond Angle Dihedral X(A)
˚
Y(A)
˚
Z(A)
˚
Se
0.883497
-0.054990
0.000003
Li 1 2.390969
-0.319339
1.382430
-1.484498
Si 1 2 2.364837 73.358
-1.359205
-0.805152
-0.000012
Li 1 3 4 2.390972 73.357 40.393
-0.319392
1.382375 1.484518
Be 3 3 2 2.214531 95.889
-40.393
-2.273460
1.211847
0.000006
Table 6. Table containing the dipole moments of the BeLi2SeSi molecule via ab initio methods.
Methods/Base Dipole moment (Debye)
X Y Z Total
UHF/CC-PVQZ [48, 49, 50, 51, 52] 0.8228 4.3880 0.0000 4.4645
UHF/CEP-31G [53, 54, 55] 0.7997 5.2102 0.0002 5.2712
UHF/CEP-121G [53, 54, 55] 0.7864 5.3204 0.0001 5.3782
UHF/SDD [56, 57] -0.8772 6.8195 0.0000 6.8757
SDD All [56, 57] 0.5963 5.4523 0.0001 5.4848
UHF/SDD Ar/STO-3G [43, 44, 56, 57] -1.3862 0.7216 0.0000 1.5627
UHF/SDF [56, 57] 0.6394 5.3161 0.0003 5.3544
UHF/UGBS1P [58, 59, 60, 61, 62, 63, 64, 65, 66] 0.5085 4.6007 0.0002 4.6287
UCISD-FC/STO-3G [43, 44, 67, 68, 69] -0.8474 -0.9167 0.0022 1.2484
UHF/CEP-4G [53, 54, 55] -0.1523 3.8818 0.0000 3.8848
UHF/CEP-31G [53, 54, 55] -1.2259 5.1166 0.0000 5.2614
UHF/CEP-121G [53, 54, 55] -1.1199 5.0853 0.0000 5.2071
UHF/LanL2MB [43, 44, 70, 71, 72] -2.5964 5.5830 -0.2414 6.1620
UHF/LanL2DZ [56, 70, 71, 72] -1.3022 4.3037 -0.1042 4.4976
UHF/LanL2MB/STO-3G [43, 44, 70, 71, 72] -1.6159 0.5603 -0.0001 1.7103
LanL2DZ [43, 44, 70, 71, 72] -1.3022 4.3037 -0.1042 4.4976
UHF/SDD † [56, 57] -1.8520 5.9664 0.0000 6.2472
UHF/SDDAII [56, 57] -1.1776 5.0344 0.0000 5.1703
UHF/CC-PVTZ[48, 49, 50, 51, 52] -0.4389 5.0838 0.0000 5.1028
UHF/CC-PVQZ [48, 49, 50, 51, 52] -0.4379 5.1418 0.0000 5.1604
UHF/SV [73, 74] -1.3423 8.3589 0.0000 8.4660
UHF/TVZ [73, 74] -1.4678 8.8083 0.0000 8.9298
UHF/STO-3G [7, 25, 39, 56, 75, 76, 77, 78] -1.3862 0.7216 0.0000 1.5627
UBLYP/STO-3G [7, 25, 39, 56, 75, 76, 77, 78] -0.4887 -1.0666 -0.0001 1.1732
UB3LYP/STO-3G [7, 25, 39, 56, 75, 76, 77, 78] 0.8327 -0.6992 0.0000 1.0873
UB3LYP/3-21G [7, 25, 39, 56, 75, 76, 77, 78] -0.0682 4.6195 0.0000 4.6200
UB3LYP/6-31G(d)[ 7, 25, 39, 56, 75, 76, 77, 78] 0.2063 4.0714 0.0000 4.0766
UB3LYP/6-31G [7, 25, 39, 56, 75, 76, 77, 78] -0.0435 4.9571 0.0000 4.9573
UB3LYP/6-311G [7, 25, 39, 56, 75, 76, 77, 78] -0.4081 4.6962 0.0000 4.7139
UB3LYP/6-311G(d) [7, 25, 39, 56, 75, 76, 77, 78] 0.0271 4.0669 0.0000 4.0670
UB3LYP/6-311G(3df, 3pd) [7, 25, 39, 56, 75, 76, 77, 78] 0.1373 3.9598 0.0000 3.9622
UB3LYP/6-311G(d, p) [7, 25, 39, 56, 75, 76, 77, 78] 0.0271 4.0669 0.0000 4.0670
UB3LYP/6-311G**(3df, 3pd) [7, 25, 39, 56, 75, 76, 77, 78] 0.1374 3.9526 0.6081 4.0015
American Journal of Quantum Chemistry and Molecular Spectroscopy 2017; 2(3): 37-46 43
Methods/Base Dipole moment (Debye)
X Y Z Total
UCIS-FC/CC-PVDZ [48, 49, 50, 51, 52, 79] -0.5403 5.0436 0.0000 5.0724
UHF/3-21G [7, 25, 39, 56, 75, 76, 77, 78] -0.8811 4.9453 0.0000 5.0232
UHF/6-311G**(3df, 3pd) [7, 25, 39, 56, 75, 76, 77, 78] -0.4440 5.1327 0.0000 5.1519
UMP2-FC/STO-3G [43, 44, 80, 81, 82, 83, 84, 85] -1.6159 0.5603 -0.0001 1.7103
UCCSD(T)-FC/STO-3G [43, 44, 86, 87, 88, 89, 90, 91] -1.6152 0.5864 0.0181 1.7185
UCISD-FC/STO-3G [43, 44, 92, 93, 94] -0.8474 -0.9167 0.0022 1.2484
B3LYP/STO-3G [7, 25, 39, 43, 44, 56, 75, 76, 77, 78] -0.7344 -0.6592 -0.0001 0.9869
UCCD-FC/STO-3G [43, 44, 86, 87] -0.7643 -1.1334 0.0022 1.3670
UCID-FC/STO-3G [43, 44, 92, 93, 94] -0.8846 -0.8808 0.0022 1.2483
D95 up to Ar [56] and Stuttgart/Dresden ECPs on the remainder of the periodic table. [57] Selects Stuttgart potentials for Z > 2.
Figure 2. Above and to the left the representation of the molecular structure of BeLi2SeSi seed, obtained through computer via ab initio calculation method HF
in base STO-3G [43, 44], with distance measured in Ångstron and loads obtained using computer programs Hyper Chem 7.5 Evaluation [6], after the
structure of the molecule was initially parameterized and made to the optimization of its geometry using Molecular Mechanics Mm+. [42] After optimization
of the geometry via Mm+, it was optimized via PM3 [12, 13, 14, 15, 16], Figure (1). Above, in the center and to the right the representation of the molecular
structure of BeLi2SeSi, [18] obtained through computer via ab initio calculation method DFT [21], functional B3LYP in base 6-311G**(3df, 3pd), with
distance measured in Ångstron and loads in units of atomic charge obtained using computer programs GAMESS [7].
Figure 3. Representation of the molecular structure of BeLi2SeSi, [18] obtained through computer via ab initio calculation method DFT, functional B3LYP in
base 6-311G** (3df, 3pd), obtained using computer software GAMESS [7]. Images obtained in the software Mercury 3.8 [18]. Represented in cornsilk color
the atom of Silicon, in the purple color Lithium, in the lemon yellow color Beryllium, and in the pumpkin the Selenium.
44 Ricardo Gobato and Alireza Heidari: Calculations Using Quantum Chemistry for Inorganic Molecule Simulation BeLi2SeSi
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... As its scientific name 3-lithio-3-(6-{3-selena-8-beryllatricyclo[3.2.1.0²,⁴]oct-6-en-2-yl} hexyl)-1-sila-2-lithacyclopropane [1][2][3][4][5][6][7][8]. Getting Kurumi name [8], which means boy in Tupi-Guarani language, which are indigenous inhabitants of southern Brazil. ...
... [6]. The kurumi seed molecule has been well characterized, [1][2][3][4][5][6][7][8][9] and is in accordance with the ab initio computational methods [10][11][12][13][14]. Now the challenge is to build the basic structure of the bioinorganic membrane. The study evolved to construct a biomembrane from the seed molecule (kurumi) [1][2][3][4][5][6][7][8]. ...
... The kurumi seed molecule has been well characterized, [1][2][3][4][5][6][7][8][9] and is in accordance with the ab initio computational methods [10][11][12][13][14]. Now the challenge is to build the basic structure of the bioinorganic membrane. The study evolved to construct a biomembrane from the seed molecule (kurumi) [1][2][3][4][5][6][7][8]. The calculations default already performed admit a hydrophobic and hydrophilic molecule, the basis of the formation of a micelle and or biomembrane, as the default template [9]. ...
Article
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The work characterizes develop a single layer bioinorganic membrane using nano-molecule Kurumi C13H20BeLi2 SeSi / C13H19BeLi2SeSi, is well characterize computationally. As its scientific name 3-lithio-3-(6-{3-selena-8-beryllatricyclo [3.2.1.02,⁴]oct-6-en-2-yl}hexyl)-1-sila-2-lithacyclopropane. The work was based on a molecular dynamics (MD) of 1ns, using the CHARMM22 force field, with step 0.001 ps. Calculations indicate that the final structure, arrangement have the tendency to form a single layer micellar structure, when molecular dynamics is performed with a single layer. However, when molecular dynamics were carried out in several layers, indicates the behavior of a liotropic nematic liquid crystal order. Kurumi features the structure polar-apolar-polar predominant. Limitations our study has so far been limited to computational simulation via quantum mechanics e molecular mechanics (QM/MM), an applied theory. Our results and calculations are compatible and with the theory of QM/MM, but their physical experimental verification depend on advanced techniques for their synthesis, obtaining laboratory for experimental biochemical. Going beyond imagination, the most innovative and challenging proposal of the work advances the construction of a structure compatible with the formation of a “new DNA”, based now on the kurumi molecule
... As its scientific name 3-lithio-3-(6-{3selena-8-beryllatricyclo[3.2.1.0²,⁴]oct-6-en-2-yl}hexyl)-1-sila-2-lithacyclopropane [1][2][3][4][5][6][7][8]. ...
... The kurumi seed molecule has been well characterized, [1][2][3][4][5][6][7][8][9] and is in accordance with the ab initio computational methods [10][11][12][13][14]. Now the challenge is to build the basic structure of the bioinorganic membrane. The study evolved to construct a biomembrane from the seed molecule (kurumi) [1][2][3][4][5][6][7][8]. ...
... The kurumi seed molecule has been well characterized, [1][2][3][4][5][6][7][8][9] and is in accordance with the ab initio computational methods [10][11][12][13][14]. Now the challenge is to build the basic structure of the bioinorganic membrane. The study evolved to construct a biomembrane from the seed molecule (kurumi) [1][2][3][4][5][6][7][8]. The calculations default already performed admit a hydrophobic and hydrophilic molecule, the basis of the formation of a micelle and or biomembrane, as the default template [9]. ...
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The work characterizes develop a single layer bioinorganic membrane using nano-molecule Kurumi C13H20BeLi2SeSi / C13H19BeLi2SeSi, is well characterize computationally. As its scientific name 3-lithio-3-(6-{3-selena-8-beryllatricyclo[3.2.1.02,⁴]oct-6-en-2-yl}hexyl)-1-sila-2-lithacyclopropane. The work was based on a molecular dynamics (MD) of 1ns, using the CHARMM22 force field, with step 0.001 ps. Calculations indicate that the final structure, arrangement have the tendency to form a single layer micellar structure, when molecular dynamics is performed with a single layer. However, when molecular dynamics were carried out in several layers, indicates the behavior of a liotropic nematic liquid crystal order. Kurumi features the structure polar-apolar-polar predominant. Limitations our study has so far been limited to computational simulation via quantum mechanics e molecular mechanics (QM/MM), an applied theory. Our results and calculations are compatible and with the theory of QM/MM, but their physical experimental verification depend on advanced techniques for their synthesis, obtaining laboratory for experimental biochemical. Going beyond imagination, the most innovative and challenging proposal of the work advances the construction of a structure compatible with the formation of a “new DNA”, based now on the kurumi molecule.
... 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 (Gobato et al., -2021 [19][20][21][22][23][24][25][26][27][28][29][30]. ...
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The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, and thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in CNTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).
... 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 [19][20][21][22][23][24][25][26][27][28][29][30]. ...
Article
Full-text available
The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in NTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of bases used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).
... [2,3,4,5,6,7,8,9,10,11,12,13,14] 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 [19,20,21,22,23,24,25,26,27,28,29,30]. ...
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The core of the work is based on the replace- ment of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via "ab initio" Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in STP (Standard Temperature and Pressure), for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the "ab initio" Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CCpVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).
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The rhodochrosite (MnCO3) shows complete solid solution with siderite (FeCO3), and it may contain substantial amounts of Zn, Mg, Co, and Ca. The electric charge that accumulates in certain solid materials, such as crystals, certain ceramics, and biological matter such as bone, DNA and various proteins in response to applied mechanical stress, phenomenon called piezoelectricity. There is no precedent in the literature on the treatment of tumor tissues by eliminating these affected tissues, using rhodochrosite crystals in tissue absorption and eliminating cancerous tissues by synchrotron radiation. An in-depth study is necessary to verify the absorption by the tumoral and non-tumoral tissues of rhodochrosite, before and after irradiating of synchrotron radiation using Small. Later studies could check the advantages and disadvantages of rhodochrosite in the treatment of cancer through synchrotron radiation, such as one oscillator crystal. The studies that are found are the research papers of this team. Through an unrestricted Hartree-Fock (UHF) computational simulation, Compact effective potentials (CEP), the infrared spectrum of the protonated rhodochrosite crystal, CH19Mn6O8, and the load distribution by the unit molecule by two widely used methods, Atomic Polar Tensor (APT) and Mulliken, were studied. The rhodochrosite crystal unit cell of structure CMn6O8, where the load distribution by the molecule was verified in the UHF CEP-4G (Effective core potential (ECP) minimal basis), UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis). The largest load variation in the APT and Mulliken methods were obtained in the CEP-121G basis set, with δ = 2.922 e δ = 2.650 u. a., respectively, being δAPT > δMulliken. The maximum absorbance peaks in the CEP-4G, CEP-31G and CEP-121G basis set are present at the frequencies 2172.23 cm-1, with a normalized intensity of 0.65; 2231.4 cm-1 and 0.454; and 2177.24 cm-1 and 1.0, respectively. Studying the sites of rhodocrosite action may lead to a better understanding of its absorption by healthy and/or tumor tissues, thus leading to a better application of synchrotron radiation to the tumors to eliminate them.
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The work characterizes the Raman spectrum of the new nanomolecule C13H20BeLi2SeSi / C13H19BeLi2SeSi, nano-molecule Kurumi. Calculations obtained in the methods Restrict Hartree-Fock of the first principles (ab initio), on the set of basis used indicate that the simulated molecule C13H20BeLi2SeSi / C13H19BeLi2SeSi features the structure polar-apolar-polar predominant. The set of basis used that have been correlation-consistent polarized Triple-zeta (CC-pVTZ) and Pople’s basis sets six gaussian functions in the shell, three double zeta Gaussian functions, Slater type orbitals with polarization function (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 C13H20BeLi2 SeSi is of 15.799Å. The Raman spectrum was calculated indicating the characteristic of the nano-molecule and their frequency (cm-1) were obtained in the set of bases used. The highest for Raman scattering activities peaks are in the frequency 3,348cm-1 with 7.107609729 Å4/amu and 2,163 cm-1 with 8.902805583 Å4/amu, for CC-pVTZ and 6-311G** (3df, 3pd), respectively. 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. The new nano-molecule Kurumi is well characterizing computationally. As its scientific name 3-lithio-3-(6- {3-selena-8-beryllatricyclo [3.2.1.0²,⁴] oct-6-en-2-yl} hexyl) -1-sila-2-lithacyclopropane [1-100]
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