Conjugation | Definition of Conjugation by Oxford

It's my first week in OChem and I'm stuck on a homework problem. The problem asks to rank the basicity of 4 different compounds given in the form of bond-line structures. We are given 3 attempts to solve the problem correctly, of which I have used 2. On my first attempt, I took the completely wrong approach (used acid rules). On my second attempt, I figured out the chemical formulas and then researched the pKas of their conjugate acids to figure out which is the strongest. This still didn't seem to be right, although I think my approach is on the right track.
The pKas for the conjugate acids for these specific structures are not provided in the textbook. I've never heard analogous structures in this context and could not find a chemistry definition online, so I'm not quite sure what that means. The order displayed in the screen shot below is my most recent attempt. I would appreciate any help.
https://preview.redd.it/ak8zd5b7brc61.png?width=1372&format=png&auto=webp&s=70ee3353540a2e304c64ca1cccf0c9cbae89eefd

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Abstract
The work is an evolution of research already begin and in development. Therefore, we can observe a part that has already been commented that presents the whole development of the research from its beginning. 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 bioinorganic membrane 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 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 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. Even using a simple base set the polar-apolar-polar characteristic is predominant. The set of bases 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 bio-membrane genesis that challenge the current concepts of a protective mantle structure of a cell such as bio-membrane to date is promising, challenging. Leaving to the biochemists their experimental synthesis.
Introduction
The work is an evolution of research already begin and in development. Therefore, we can observe a part that has already been commented that presents the whole development of the research from its beginning. A small review of the main compounds employed some of their known physicochemical and biological properties and the ab initio methods used. 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 [1-4]. 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 [8-24] and ab initio methods [5,6,7]. The results were satisfactory. We found a 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 bio-membrane? For this, the molecule should be amphiphilic, with polar head and apolar tail. Are basic requirement of the construction of a bio-membrane [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 [8-24] 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 [8-24], 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 a polar 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 polarities 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 bio-membrane 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 bio-membrane? 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, polarpolar- 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 a polar 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 like 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 [5-6,27-32] 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 bases used was that of Ahlrichs and coworker’s main utility are: the SV, SVP, TZV, TZVP keywords refer to the initial formations of the 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.
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 (PSeO3 3−). 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).
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]. 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].
Methods
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 [8-24].
Hartree-Fock
The Hartree-Fock self–consistent method [5-6,27- 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 considers 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 exchangecorrelation 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 [27-30]. A hybrid exchange-correlation functional is usually constructed as a linear combination of the Hartree-Fock exact exchange functional,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]. 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:
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, 1kcal/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 [5-6,27-32] approach.
Discussions
The Figure 2 shows the final stable structure of the Bioinorganic 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 [66-70]; CEP- 31G [66-70]; CEP-121G [66-70]; 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 bases 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 polarpolar- 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 bases 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 absence of color (black). This charge neutrality is observed in the set of bases: STO-3G; 6-31 (d ‘, p’); TZV; SDD; CEP-31G; CCcVDZ; SV and CEP-121G. In the set of bases: 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 bases: 3-21G; 6-31G; 6-311G; 6-311G (3df, 3pd); SV and TZV. Beryllium presents almost totally neutral charge in the set of bases: 6-31 (d ‘); 6-31 (d, p ‘); CC-pVDZ; cc-pVTZ; CEP-31G and CEP-121G. And charge, slightly positive in another 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 CCpVTZ 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], obtained using computer programs GAMESS [7]. end software [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 bases 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.
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. Even using a simple base set the polar-apolar-polar characteristic is predominant. From the set of bases 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 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 like 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 bio-membrane genesis that defies the current concepts of a protective mantle structure of a cell such as bio-membrane to date is promising, challenging. Leaving to the Biochemists their experimental synthesis. The quantum calculations must continue to obtain the structure of the bioinorganic bio-membrane. 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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