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Using the Quantum Chemistry for Genesis of a Nano Biomembrane with a Combination of the Elements Be, Li, Se, Si, C and H

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Using the Quantum Chemistry for Genesis of a Nano Biomembrane with a Combination of the Elements Be, Li, Se, Si, C and H

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Preliminary bibliographic studies did not reveal any works with characteristics studied here. With this arrangement of atoms and employees with such goals. Going beyond with imagination using quantum chemistry in calculations to obtain probable one new bio-inorganic molecule, to the Genesis of a biomembrane with a combination of the elements Be, Li, Se, Si, C and H. After calculation a bio-inorganic seed molecule from the previous combination, it led to the search for a molecule that could carry the structure of a membrane. From a simple molecular dynamics, through classical calculations, the structure of the molecule was stabilized. An advanced study of quantum chemistry using ab initio, HF (Hartree-Fock) method in various basis is applied and the expectation of the stabilization of the Genesis of this bio-inorganic was promising. The calculations made so far admit a seed molecule at this stage of the quantum calculations of the arrangement of the elements we have chosen, obtaining a highly reactive molecule with the shape polar-apolar-polar. Calculations obtained in the ab initio RHF method, on the set of basis 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. Even using a simple base set the polar-apolar-polar characteristic is predominant. The set of basis used that have the best compatible, more precise results 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 structure of the bio-inorganic seed molecule for a biomembrane genesis that challenge 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.
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1
Using the Quantum Chemistry for Genesis of a Nano Biomembrane
with a Combination of the Elements Be, Li, Se, Si, C and H.
Ricardo Gobato 1,*, Alireza Heidari 2, Abhijit Mitra3
1Laboratory of Biophysics and Molecular Modeling Genesis, State Secretariat for Education of
Paraná, Bela Vista do Paraíso, Paraná, Brazil.
2Faculty of Chemistry, California South University, Costa Mesa, USA.
3Department of Marine Science, University of Calcutta, 35 B. C Road, Kolkata, 700019, West Bengal,
India.
Email address:
ricardogobato@seed.pr.gov.br (R. Gobato), ricardogobato@hotmail.com (R. Gobato)
Scholar.Researcher.Scientist@gmail.com (A. Heidari), Alireza.Heidari@calsu.us (A. Heidari)
abhijit_mitra@hotmail.com (A. Mitra)
*Corresponding author
Abstract: Preliminary bibliographic studies did not reveal any works with characteristics studied
here. With this arrangement of atoms and employees with such goals. Going beyond with imagination
using quantum chemistry in calculations to obtain probable one new bio-inorganic molecule, to the
Genesis of a biomembrane with a combination of the elements Be, Li, Se, Si, C and H. After
calculation a bio-inorganic seed molecule from the previous combination, it led to the search for a
molecule that could carry the structure of a membrane. From a simple molecular dynamics, through
classical calculations, the structure of the molecule was stabilized. An advanced study of quantum
chemistry using ab initio, HF (Hartree-Fock) method in various basis is applied and the expectation of
the stabilization of the Genesis of this bio-inorganic was promising. The calculations made so far
admit a seed molecule at this stage of the quantum calculations of the arrangement of the elements we
have chosen, obtaining a highly reactive molecule with the shape polar-apolar-polar. Calculations
obtained in the ab initio RHF method, on the set of basis 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. Even using a simple base set the polar-apolar-polar characteristic is
predominant. The set of basis used that have the best compatible, more precise results 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 structure of the bio-inorganic seed molecule for a biomembrane genesis that challenge
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.
1. Introduction
Preliminary bibliographic studies did not reveal any works with characteristics studied here. With this
arrangement of atoms and employees with such goals. So the absence of a referential of the theme.
The initial idea was to construct a molecule that was stable, using the chemical elements Lithium,
Beryllium, alkaline and alkaline earth metals, respectively, as electropositive and electronegative
elements - Selenium and Silicon, semimetal and nonmetal, respectively. This molecule would be the
basis of the structure of a crystal, whose structure was constructed only with the selected elements.
The elements Li, Be, Se and Si were chosen due to their physicochemical properties, and their use in
several areas of technology [1, 2, 3, 4]. To construct such a molecule, which was called a seed
molecule, quantum chemistry was used by ab initio methods [5, 6, 7]. The equipment used was a
cluster of the Biophysics laboratory built specifically for this task. It was simulated computationally
via molecular dynamics, initially using Molecular Mechanics [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24] and ab initio methods [5, 6, 7]. The results were satisfactory. We found a
2
probable seed molecule of the BeLi2SeSi structure predicted by quantum chemistry [23]. Due to its
geometry, it presents a probable formation of a crystal with the tetrahedral and hexahedral crystal
structure [23].
The idea of a new molecule for a crystal has been upgraded. Why not build a molecule, in the form of
a lyotropic liquid crystal [25] that could be the basis of a new biomembrane? For this, the molecule
should be amphiphilic, with polar head and apolar tail. Are basic requirement of the construction of a
biomembrane [25]. Then it is necessary to add a hydrophobic tail, with atoms of carbon and hydrogen.
Therefore, the molecule seed with a polar hydrophilic "head". So would a new amphiphilic molecule.
Several simulations were performed, always having as initial dynamics the use of Molecular
Mechanics [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] for the initial molecular
structure, moving to ab initio calculations of quantum chemistry. All attempts were thwarted.
Quantum calculations of quantum chemistry did not accept the seed molecule as the polar head, even
changing its binding structure. The silicon atom binds in double bond with the carbon chain and
Selenium. It binds in double with beryllium and is simple with the two lithium atoms, thus making a
stable molecular structure for Molecular Mechanics [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
22, 23, 24], Mm+ and Bio+ Charmm [26]. But in quantum calculations the seed molecule changed all
its fundamental structure [1]. The linear structure of the tail with the polar head, in the form of a rope
climbing hook, collapsed, bending toward the apolar tail.
In another simulation carried out the Selenium was connected in double bond to two atoms of Carbon
added in double bond. As the +6 polarity of the selenium neutralized with the atoms two atoms of
lithium, forming a wing. In the double bonded sequence is the Carbon with the Silicon, and this in
double bond with the Beryllium. A new structure for a probable lyotropic liquid crystal has now been
formed. A polar tail with the seed molecule undone but retaining the five base atoms of its
fundamental structure [25]. The structure after Molecular Mechanics, Mm+ and Bio+ Charmm [26],
the shape of the molecule obtained had a structure like a boomerang. After calculations ab initio, the
polar tail was undone. The Beryllium atom did not remain in the structure of the molecule, releasing
itself from it.
There is then a new idea. Why not separate the electropositive and electronegative elements in two
polar heads? This would completely change the concepts known so far of a biomembrane with a lipid
bilayer. The next challenging step of building a biomembrane that runs away from known concepts,
with a single layer, with two polar heads and its non-polar backbone. Would it be a new way to have a
biomembrane? A challenge for quantum chemistry.
Then he concentrated the calculations on the probable structure of the molecule with polar ends.
Separately then in pairs the atoms of Selenium with Beryllium and Silicon with the two bonds. Again
the attempt failed, in quantum calculations. Beryllium was disconnected from the basic structure of
the new molecule, polar-polar-polar polar structure. They have decided to further innovate the theory
and "challenge" quantum chemistry.
Add an aromatic ring to the polar head. The polar-polar-polar linear structure was now maintained,
with a six-carbon cyclic chain. At a polar end, the Silicon is bonded to three atoms of the Hydrogen
and is connected to a Carbon from the central chain. This one connected to the two atoms of the
Lithium and the apolar central carbon chain. At the other polar end, the six-carbon cyclic chain
attached in single bond to the carbonic chain. The cyclic chain with simple bonds, having at its center
the Selenium with six bonds to the cyclic chain and a double with the Beryllium, thus forcing two
more covalent bonds. Now with a +2 cationic head, the dynamics of the minimization energy with
Mm+ and Bio+ Charmm [26] calculations have maintained a stable structure of the molecule. A polar
head similar to a “parabolic antenna”, with folded edges outward with the Hydrogen atoms. The
expected, the obvious, Beryllium playing the role of the "LNB (Low Noise Block) receiver". We then
proceeded to the ab initio calculations in several methods and basis, testing various possibilities with
ab initio methods. The polar-apolar-polar (parabolic) molecule in ab initio calculation, by RHF [5-6,
27, 28, 29, 30, 31, 32] in the TZV [33, 34] sets basis was shown to be stable by changing its covalent
cyclic chain linkages, which was expected, Figure (2). The set of basis used was that of Ahlrichs and
coworkers main utility are: the SV, SVP, TZV, TZVP keywords refer to the initial formations of the
3
split valence and triple zeta basis sets from this group [33, 34].
Calculations continue to challenge concepts, experimenting. Going where imagination can lead us,
getting results that challenge concepts.
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, technology, life, health.
2.1. Beryllium
Beryllium 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. 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. 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. [2, 35]
Beryllium is a health and safety issue for workers. Exposure to beryllium in the workplace can lead to
a sensitization immune response and can over time develop chronic beryllium disease (CBD).
[37] Approximately 35 micrograms of beryllium is found in the average human body, an amount not
considered harmful. [38] Beryllium is chemically similar to magnesium and therefore can displace it
from enzymes, which causes them to malfunction. [38] Because Be2+ is a highly charged and small
ion, it can easily get into many tissues and cells, where it specifically targets cell nuclei, inhibiting
many enzymes, including those used for synthesizing DNA. Its toxicity is exacerbated by the fact that
the body has no means to control beryllium levels, and once inside the body the beryllium cannot be
removed. [39] Chronic berylliosis is.a pulmonary and systemic granulomatous disease caused by
inhalation of dust or fumes contaminated with beryllium; either large amounts over a short time or
small amounts over a long time can lead to this ailment. Symptoms of the disease can take up to five
years to develop; about a third of patients with it die and the survivors are left disabled. [38]
The International Agency for Research on Cancer (IARC) lists beryllium and beryllium compounds as
Category 1 carcinogens. [38] In the US, the Occupational Safety and Health Administration (OSHA)
has designated apermissible exposure limit (PEL) in the workplace with a time-weighted average
(TWA) 0.002 mg/m3 and a constant exposure limit of 0.005 mg/m3 over 30 minutes, with a maximum
peak limit of 0.025 mg/m3. The National Institute for Occupational Safety and Health (NIOSH) has
set a recommended exposure limit (REL) of constant 0.0005 mg/m3. The IDLH(immediately
dangerous to life and health) value is 4 mg/m3. [40]
2.2. Lithium
Lithium like all alkali metals, lithium is highly reactive and flammable. 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. [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. [2]
4
As lithium salts, are primarily used as apsychiatric medication. This includes the treatment of major
depressive disorder that does not improve following the use of other antidepressants, and bipolar
disorder. [41] In these disorders, it reduces the risk of suicide [42].
Common side effects include increased urination, shakiness of the hands, and increased thirst. Serious
side effects include hypothyroidism, diabetes insipidus, and lithium toxicity. Blood level monitoring is
recommended to decrease the risk of potential toxicity. If levels become too high, diarrhea, vomiting,
poor coordination, sleepiness, and ringing in the ears may occur. If used during pregnancy, lithium
can cause problems in the baby. [42]
In the nineteenth century, lithium was used in people who had gout, epilepsy, and cancer. Its use in
the treatment of mental disorder began in 1948 by John Cade in Australia. [43] It is on the World
Health Organization's List of Essential Medicines, the most effective and safe medicines needed in
a health system. [44]
2.3. Selenium
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]
Although it is toxic in large doses, selenium is an essential micronutrient for animals. In plants, it
sometimes occurs in toxic amounts as forage, e.g. locoweed. Selenium is a component of the amino
acids selenocys teine and selenomethionine. In humans, selenium is a trace element nutrient that
functions as cofactor for glutathione peroxidases and certain forms ofthioredoxin reductase. [45]
Selenium-containing proteins are produced from inorganic selenium via the intermediacy of
selenophosphate (PSeO33−).
Selenium is an essential micronutrient in mammals, but is also recognized as toxic in excess.
Selenium exerts its biological functions through selenoproteins, which contain the amino
acid selenocysteine. Twenty-five selenoproteins are encoded in the human genome. [46]
Selenium also plays a role in the functioning of the thyroid gland. It participates as a cofactor for the
three thyroid hormonedeiodinases. These enzymes activate and then deactivate various thyroid
hormones and their metabolites. [47] It may inhibit Hashimotos's disease, an auto-immune disease in
which the body's own thyroid cells are attacked by the immune system. A reduction of 21% on TPO
antibodies was reported with the dietary intake of 0.2 mg of selenium. [48]
Selenium deficiency can occur in patients with severely compromised intestinal function, those
undergoing total parenteral nutrition, and [49] in those of advanced age (over 90).
2.4. Silicon
Silicon 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]
5
Although silicon is readily available in the form of silicates, very few organisms use it
directly. Diatoms, radiolaria and siliceous sponges use biogenic silica as a structural material for
skeletons. In more advanced plants, the silica phytoliths (opal phytoliths) are rigid microscopic bodies
occurring in the cell; some plants, for example rice, need silicon for their growth. [50, 51, 52]
There is some evidence that silicon is important to nail, hair, bone and skin health in humans, [53] for
example in studies that show that premenopausal women with higher dietary silicon intake have
higher bone density, and that silicon supplementation can increase bone volume and density in
patients with osteoporosis. [54] Silicon is needed for synthesis of elastin and collagen, of which
the aorta contains the greatest quantity in the human body [55] and has been considered an essential
element [56].
3. Methods
2.1. Molecular dynamics
In short the goal of molecular mechanics is to predict the detailed structure and physical properties of
molecules. Examples of physical properties that can be calculated include enthalpies of formation,
entropies, dipole moments, and strain energies. Molecular mechanics calculates the energy of a
molecule and then adjusts the energy through changes in bond lengths and angles to obtain the
minimum energy structure. [8-24]
 (1)
The steric energy, bond stretching, bending, stretch-bend, out of plane, and torsion interactions are
called bonded interactions because the atoms involved must be directly bonded or bonded to a
common atom. The van der Waals and electrostatic (qq) interactions are between non-bonded atoms.
[8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]
2.2. Hartree-Fock
The Hartree-Fock selfconsistent method [5-6, 27, 28, 29, 30, 31, 32] 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) [5, 6, 57, 58] perturbation theory in which the Hartree-Fock energy is improved
by obtaining a perturbation expansion for the correlation energy. [5] However, MP calculations are not
variational and can produce an energy value below the true energy. [6]
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. [27, 28, 29, 30].
A hybrid exchange-correlation functional is usually constructed as a linear combination of the
HartreeFock exact exchange functional,


 (2)
and any number of exchange and correlation explicit density functional. The parameters determining
the weight of each individual functional are typically specified by fitting the functional predictions to
experimental or accurately calculated thermochemical data, although in the case of the “adiabatic
connection functional” the weights can be set a priori. [32]
6
Terms like “Hartree–Fock”, or “correlation energy” have specific meanings and are pervasive in the
literature. [59]
The vast literature associated with these methods suggests that the following is a plausible hierarchy:
 (3)
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. [4] The use of HF in the case of
FCI was due to the computational cost.
For calculations a cluster of six 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+), Equation (1), after the quantum
computation was optimized via Mm+ and then by RHF [5-6, 27-32], in the TZV [33, 34] sets basis.
The molecular dynamics at algorithm Polak-Ribiere [60], conjugate gradient, at the termination
condition: RMS gradient [61] of 0, 1 kcal/A. mol or 405 maximum cycles in vacuum [6, 41].
The first principles calculations have been performed to study the equilibrium configuration of
C13H20BeLi2SeSi molecule using the Hyperchem 7.5 Evaluation [41], Mercury 3.8 a general
molecular and electronic structure processing program [18], GaussView 5.0.8 [64] an advanced
semantic chemical editor, visualization, and analysis platform 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 in the Restrict Hartree-
Fock [5-6, 27, 28, 29, 30, 31, 32] approach.
Figure 1. Above and to the left the representation of the molecular structure of C13H20BeLi2SeSi seed obtained
after dynamics with Molecular Mechanic. The geometry was optimized via Bio+ Charmm and Mm+ [8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26] obtained using computer programs HyperChem
7.5 Evaluation [26]. Above and to the right the representation of the molecular structure of C13H20BeLi2SeSi,
obtained through computer via ab initio calculation method RHF [5, 6, 27, 28, 29, 30, 31, 32], TZV [33, 34] sets
basis obtained using computer programs GAMESS [7]. Images obtained in the software Mercury 3.8 [18].
Represented in bluish gray color the atom of silicon, in the purple color lithium, in the lemon yellow color
beryllium, in the orange the selenium, in dark gray color carbon and in light gray color hydrogen.
7
Figure 2. Molecule seed Bio-inorganic after dynamics obtained through computer via ab initio calculation
method RHF [5-6, 27, 28, 29, 30, 31, 32] in several sets of basis obtained using computer software GAMESS
[7]. The length of the molecule C13H20BeLi2SeSi obtained in the base TZV [33, 34] is of 15.799Å. Represented
in green color the positive charge, passing through the absence of color - black - zero charge, for the positive
charge red color. A Δδ = 4.686 a.u. of TZV [33, 34], were the elemental charge e (e = ±1,607 x 10-19 C). Images
obtained in the software Gaussview, Version 5, 2009 [64].
8
Table 1. Molecular parameters of the atoms of the molecule C13H20BeLi2SeSi seed, obtained through
computer via ab initio calculation method RHF [5, 6, 27, 28, 29, 30, 31, 32] in base 6-311G**(3df,3pd)
[7, 30, 60, 71, 83, 84, 85, 86], with distance measured in Ångstron obtained using computer programs
GAMESS. [7] end software Gaussview, Version 5, 2009 [64], Figure (1) the right.
Atom
NA
NB
Bond(Å)
Angle(°)
Dihedral(°)
X(Å)
Y(Å)
Z(Å)
1
C
-1.26242
-0.70592
-0.42423
2
C
1
1.53480
-0.06893
0.18439
-0.05204
3
C
2
1
1.53093
112.18322
1.26653
-0.55102
-0.19161
4
C
3
2
1.53069
113.44084
-179.29326
2.47630
0.30595
0.18929
5
C
4
3
1.53110
113.38147
-179.18964
3.81253
-0.42447
0.03043
6
C
5
4
1.53541
114.58958
-179.94093
5.04538
0.40982
0.40663
7
C
6
5
1.53311
114.67586
178.19882
6.38117
-0.33345
0.28974
8
H
1
2
1.08630
109.60129
56.01538
-1.24660
-1.60818
0.18053
9
H
2
1
1.09155
109.44705
-121.57960
-0.18343
0.53488
0.97535
10
H
2
1
1.08866
110.12770
121.90002
-0.05558
1.07436
-0.67890
11
H
3
2
1.09143
109.20585
58.62273
1.38039
-0.89640
-1.22067
12
H
3
2
1.09170
109.32720
-57.02568
1.25092
-1.44924
0.42868
13
H
4
3
1.09179
109.20151
-57.02737
2.48344
1.20958
-0.42343
14
H
4
3
1.09309
108.99998
58.38218
2.36236
0.64306
1.22283
15
H
5
4
1.09230
109.73569
-57.29866
3.80861
-1.33579
0.63260
16
H
5
4
1.08963
109.77058
58.85455
3.93562
-0.74714
-1.00302
17
H
6
5
1.13356
104.33284
52.40686
4.81593
0.79604
1.44738
18
H
6
5
1.09475
107.93590
-54.73588
5.01649
1.33591
-0.17647
19
Si
7
6
1.79413
121.65815
136.77829
7.82853
0.43952
-0.43592
20
H
19
7
1.50992
124.28552
84.69432
8.78810
1.32685
0.32021
21
Li
7
6
1.93570
80.74382
-112.10209
6.30663
-0.12765
2.21303
22
Li
7
6
1.92362
143.90425
3.24326
7.19404
-1.99623
-0.23436
23
H
19
7
1.50180
119.09663
-46.46644
7.68620
1.18396
-1.73244
24
H
19
7
1.54205
103.31409
-162.37645
8.74534
-0.75726
-0.76009
25
C
1
2
1.52105
114.24539
177.75031
-2.61796
-0.03815
-0.25052
26
C
25
1
1.46418
120.89424
-81.54025
-3.25931
0.03044
1.06394
27
C
26
25
1.51753
113.61265
140.34232
-3.95470
1.35220
1.33276
28
C
27
26
1.48591
113.39891
48.25291
-4.83198
1.79485
0.21814
29
C
28
27
1.36511
114.89814
-47.40505
-4.26563
1.72402
-1.02192
30
C
29
28
1.48572
115.33270
-0.61608
-2.86438
1.23118
-1.05361
31
Se
26
25
1.99538
69.39050
-104.42811
-4.13246
-1.35838
-0.07199
32
H
1
25
1.08914
108.44414
155.98884
-1.16732
-1.02827
-1.46022
33
H
26
25
1.07812
118.39424
-0.49303
-2.75121
-0.41130
1.90598
34
H
27
26
1.07694
116.13448
-175.21216
-4.37152
1.47719
2.31786
35
H
29
28
1.07737
122.38587
-171.61761
-4.74014
2.13528
-1.89738
36
H
30
29
1.07769
114.61917
-174.45720
-2.39730
1.26818
-2.02411
37
H
28
27
1.07730
122.10981
140.86027
-5.78580
2.26452
0.39199
38
Be
27
26
1.73804
99.82664
-23.49895
-3.07790
2.37701
0.23650
Table 2. Table containing the dipole moments of the C13H20BeLi2SeSi molecule via ab initio methods.
Methods/Base
Dipole moment (Debye)
Charge (a. u.)
X
Y
Z
Total
δ±
Δδ
RHF/CC-PVDZ [66, 67, 68, 69, 70]
0.8737
1.3742
4.5091
4.7941
0.701
1.402
RHF/SDD [71, 72]
1.3174
1.6305
4.9663
5.3906
1.387
2.774
RHF/SDDAll [71, 72]
1.7948
2.1358
4.9435
5.6763
0.878
1.756
RHF/SDF [71, 72]
1.5980
1.9300
4.8708
5.4775
0.885
1.770
RHF/CEP-31G [73, 74, 75]
1.7449
2.4205
5.2556
6.0436
0.930
1.860
RHF/CEP-121G [73, 74, 75]
1.3866
1.8646
5.0880
5.5935
1.466
2.932
RHF/LanL2MB [76, 77, 78, 79, 80]
0.8205
3.7053
2.4894
4.5387
0.517
1.034
UHF/LanL2DZ [71, 78, 79, 80]
1.6712
1.7404
5.2270
5.7570
1.134
2.268
RHF/CC-PVTZ [66, 67, 68, 69, 70]
1.0338
1.6160
4.5925
4.9771
0.340
0.680
RHF/SV [81, 82]
-2.9614
-3.7195
1.2563
4.9176
1.696
3.792
RHF/TVZ [81, 82]
-2.5869
-3.5777
1.2328
4.5839
2.343
4.686
RHF/STO-3G [7, 30, 60, 71, 83, 84, 85, 86]
0.3240
3.8529
1.7622
4.2492
0.755
1.510
RHF/3-21G [7, 30, 60, 71, 83, 84, 85, 86]
0.7941
0.5881
4.6114
4.7161
0.961
1.922
RHF/6-31G [7, 30, 60, 71, 83, 84, 85, 86]
0.8486
1.4443
5.0166
5.2889
0.996
1.992
RHF/6-31(d’,p’) [7, 30, 60, 71, 83, 84, 85, 86]
0.6890
1.2778
4.4425
4.6737
0.984
1.968
RHF/6-31G(d’) [7, 30, 60, 71, 83, 84, 85, 86]
0.6809
1.2832
4.5040
4.7325
0.803
1.606
RHF/6-311G [7, 30, 60, 71, 83, 84, 85, 86]
1.3579
1.8774
5.1162
5.6164
1.256
2.512
RHF/6-311G(3df,3pd)[ 7, 30, 60, 71, 83, 84, 85, 86]
0.8366
1.0963
4.5910
4.7936
0.683
1.366
D95 up to Ar [56] and Stuttgart/Dresden ECPs on the remainder of the periodic table. [57] 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) [2, 4, 5, 6, 7].
9
4. Discussions
The Figure (2) shows the final stable structure of the Bio-inorganic molecule obtained by an ab initio
calculation with the method RHF [5-6, 27-32], in several sets of basis such as: STO-3G [7, 30, 60, 71,
83, 84, 85, 86]; 3-21G [7, 30, 60, 71, 83, 84, 85, 86]; 6-31G [7, 30, 60, 71, 83, 84, 85, 86]; 6-31(d’) [7,
30, 60, 71, 83, 84, 85, 86]; 6-31(d’,p’) [7, 30, 60, 71, 83, 84, 85, 86]; 6-311G [7, 30, 60, 71, 83, 84, 85,
86]; 6-311G(3df,3pd) [7, 30, 60, 71, 83, 84, 85, 86]; SV [81, 82]; SDF [71, 72]; SDD [71, 72];
SDDAll [71, 72]; TZV [81, 82]; CC-pVDZ [66, 67, 68, 69, 70]; CC-pVTZ [66, 67, 68, 69, 70]; CEP-
31G [66, 67, 68, 69, 70]; CEP-121G [66, 67, 68, 69, 70]; LanL2DZ [71, 78, 79, 80]; LanL2MB [71,
78, 79, 80], starting from the molecular structure of Figure (1) obtained through a molecular
mechanical calculation, method Mm+ and Bio+ Charmm [8-24, 26, 65].
The molecular structure shown in Figure (2) of the bio-inorganic molecule C13H20BeLi2SeSi, is
represented in structure in the form of the van der Walls radius [4, 5, 6]. As an example of analysis the
set of basis TZV [81, 82]. with the charge distribution (Δδ) through it, whose charge variation is Δδ =
4.686 au of elemental charge. In green color the intensity of positive charge displacement. In red color
the negative charge displacement intensity. Variable, therefore, of δ- = 2,343 a.u. negative charge,
passing through the absence of charge displacement, represented in the absence of black - for the
green color of δ+ = 2.343 a.u. positive charge. The electric dipole moment () total obtained was p =
5.5839 Debye, perpendicular to the main axis of the molecule, for sets basis TZV [81, 82]. By the
distribution of charge through the bio-inorganic molecule it is clear that the molecule has a polar-
apolar-polar structure, with neutral charge distributed on its main axis, the carbonic chain. A strong
positive charge displacement (cation) at the polar ends of the molecule, in the two lithium and silicon
atoms, bound to the carbon atom with strong negative (anion). Therefore, there is a displacement of
electrons from the two lithium and silicon atoms towards the carbon attached to them. At the other
end of the cyclic chain, attached to it is the totally neutral Selenium atom, while the beryllium is
extremely charged with positive charge (cationic), represented in green color. While the two carbon
atoms of the cyclic chain connected to Beryllium, with negatively charged (anionic), represented in
red color. It happened, therefore, a displacement of electrons of the Beryllium atom towards the
Carbons connected to it.
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-polar-
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 in all the 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.
Analyzing the charge distribution through the molecule:
In all the sets of basis used, the Silicon atom presents a strong positive charge, that is, cationic form,
represented in green color, except for the LanL2MB base, which presents a strong negative charge
displacement, represented in red color. The two Lithium atoms, accompany the cationic tendency of
Silicon, but with less intensity.
The Carbon atom connected to the central chain, and to Silicon and the two Lithiums, presents a
strong negative charge, that is, anionic form, represented in red color. There is, therefore, a shift of the
electric charges of the silicon atom and of the two Lithiums towards the Carbon. This charge
displacement is evident in all the base sets studied, except for the base STO-3G and LanL2MB, which
present almost neutral charge for the said Carbon atom.
The backbone of the molecule, that is, its central axis which has a chain of seven aligned Carbon
atoms, has a homogeneous charge distribution, with approximately neutral polarity, represented by the
10
absence of color (black). This charge neutrality is observed in the set of basis: STO-3G; 6-31 (d ', p');
TZV; SDD; CEP-31G; CC-cVDZ; SV and CEP-121G. In the set of basis: 3-21G; 6-31G; 6-31 (d '); 6-
311G; SDF; LanL2DZ and LanL2MB, the central axis of the molecule has a small distribution of
negative charge throughout its length, due to the negative charge displacement of Hydrogen atoms
(seen slightly in blackish green, tending to black) connected to each of their respective Carbon atoms,
whose charge is slightly negative (visualized in blackish red color, tending to black).
At the other end of the molecule is the cyclic chain of six Carbon atoms. Which has only one double
connection. The cyclic chain is attached to the Beryllium atom and to two Carbon atoms, symmetrical
and central to the cyclic chain. The Selenium atom is connected to two carbon atoms of the cyclic
chain, the first Carbon atom being connected to the central axis of the molecule and the second atoms
in sequence, being opposed to the double bonded cyclic chain atoms.
The Beryllium atom presents a strong positive charge, cationic character, visualized in green color, in
the set of basis: 3-21G; 6-31G; 6-311G; 6-311G (3df, 3pd); SV and TZV. Beryllium presents almost
totally neutral charge in the set of basis: 6-31 (d '); 6-31 (d, p '); CC-pVDZ; cc-pVTZ; CEP-31G and
CEP-121G. And charge, slightly positive in other basis studied.
The Selenium atom is visualized in Figure (2), as seen always behind the cyclic chain. This presents a
neutral charge distribution in all basis studied, with the exception of CC-pVTZ and LanL2MB.
The Table (1) presents the Molecular parameters of the atoms of the molecule C13H20BeLi2SeSi seed,
obtained through computer via ab initio calculation method RHF [5-6, 27-32] in base 6-
311G**(3df,3pd) [7, 30, 60, 71, 83, 84, 85, 86], obtained using computer programs GAMESS. [7]
end software Gaussview, Version 5, 2009 [64], Figure (1) the right. The distance between the atoms is
measured in Ångstron, as well as the position of the atoms in the coordinate axes x, y and z. The
angles formed, and the angles formed in the dihedral are given in degrees.
In the Table (2) containing the electric dipole moments, in the directions of the coordinate axes axes
x, y and z, given in Debye, are presented in all the sets of basis studied. The minimum and maximum
charge distributed through the molecule and the variation of the charge (in a.u.) by the extension of
the molecule (C13H20BeLi2SeSi). They are represented by the variation of the intensities of the green
color (positive charge), through black (zero charge) and red (negative charge), evenly distributed
according to the basic functions used in quantum calculations allowed by quantum chemistry.
The largest distributed charge variation (Δδ) per molecule was calculated on the base set TZV, with
Δδ = 4.686 a.u., and the lowest in the CC-pVTZ set, with Δδ = 0.680 a.u., Table (2).
The highest total electric dipole moment () was obtained using the CEP-31G method, with p =
6.0436 Debye, with Δδ = 1.860 a.u., and the lowest electric dipole moment in the STO-3G method,
with p = 4.2492 Debye, with Δδ = 1.510 a.u.
5. Conclusions
Calculations obtained in the ab initio RHF method, on the set of basis 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. Even using a simple base set the polar-apolar-polar
characteristic is predominant.
From the set of basis used in the RHF, based on 6-311G (3df, 3pd), the Silicon atoms, the two
Lithium, have a strong density of positive charge, cationic, from the displacement of charges of these
atoms towards the atom which Carbon are connected, which consequently exhibits strong negative
charge density, anionic. It is observed a cyclic displacement and constant electric charges originating
from the sp orbitals of the Carbon atom, Figure (2). At the other end of the molecule, a similar
situation occurs. The Beryllium atom presents a high density of positive charge, cationic character,
due to the displacement of the electronic cloud of that one towards the Carbon atoms that is
connected. These Carbon atoms also receive a displacement of negative charges, originating from the
11
two Carbon atoms that are linked in the cyclic chain, in covalent double bonds. Now presenting these
latter a strong density of positive, cationic charges, such as Beryllium, leaving the anionic Beryllium
bound Carbon. The Selenium atom has a small anionic character.
Among all simulated base assemblies, 6-311G (3df, 3pd), is unique that 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, with
characteristics similar to those shown in the Silicon and the two Lithium atoms. However, the central
chain presents an anionic feature, for all its extension, originating from the displacement of charges of
the Hydrogen atoms connected to them. At the other end of the cyclic chain, the Selenium atom
presents high density of negative charges, anionic, as well as in the cyclic chain the Carbon atoms
present anionic characteristics, with little intensity, distributed proportionally by these atoms,
originating from the displacement of charges of the Hydrogens linked to these. Except for the Carbon
atom, connected to the central axis of the molecule that is not bound to Hydrogens atoms.
The structure of the 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 bio-inorganic 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.
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