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Water and Dioxide Carbon Effects on Di or Tri Saccharides Degradation by Density Functional Theory at Level: B3LYP/6-311++G (d, p)

Koffi Kouassi Alain, Koné Soleymane, Bamba El Hadji Sawaliho
Journal of Materials Physics and Chemistry. 2021, 9(1), 1-8. DOI: 10.12691/jmpc-9-1-1
Received December 30, 2020; Revised January 19, 2021; Accepted February 03, 2021

Abstract

Storing paddy rice over a long period changes its physical properties. It transforms its chemical structure. But the mechanism of this degradation remains little known. This work aims to help elucidate it. It’s studying the possibilities of hydrogen bonding between the di or the trisaccharide with water or carbon dioxide. This research uses the methods of quantum chemistry. These make it feasible to determine the geometric and energy parameters of the complexes. These supramolecules consist of di or trisaccharide associated with water or carbon dioxide. The calculations lead to the following result. The trisaccharide remains stable during its interactions with water and carbon dioxide, the latter strengthening the hydrogen bonds of the complex disaccharide-water. It disadvantages its degradation.

1. Introduction

Oryza Sativa, known as rice, occupies a major place in the world’s diet. It’s an important source of carbohydrates, proteins and fats. The starch content reaches 90% of the dry seed’s weight 1. Moreover, its conservation over long periods of time changes its physical properties. It damages the bonding and gelling ones. It modifies its flavour and texture. It transforms its structure.

Rice loses its organoleptic characteristics. The ambient temperature and the water activity in the seeds (moisture) mainly contribute. They impact its physical, chemical, and biological parameters 2. The decrease in disaccharide concentrations during storage also explains rice degradation. It similarly results from oryzenine-starch interactions 3. Other research focuses on its conservation.

Chemicals 4, treatment with phosphine gas 5, storage 6 at low temperature and an inert atmosphere 7 are being used. All these solutions remain ineffective. They don’t prevent the rice grains degradation. These techniques incorporate carbon dioxide. According to Rajendran and al. 8, the brown one storage piles for 4 months under a controlled atmosphere kills 100% of its insects. It reduces its moisture content; the carbon dioxide can safeguard it over a long period. However, these authors don’t detail the mechanisms involved 8, 9. Its lack of knowledge hinders the discovery of a solution to protect the saccharides in starch.

This research aims to identify the interactions between water or carbon dioxide and rice starch. It uses disaccharide or trisaccharide to represent its basic components, amylose or amylopectin. This exploratory work plans to explain the roles of these molecules in its seed’s degradation. It exploits a method of quantum chemistry.

The Gaussian 09 software 10 allows performing gas phase calculations with the B3LYP 11 associated with the 6-311++G (d, p). On the other hand, this research examines the molecular interactions between di or trisaccharide and water or carbon dioxide. It also evaluates the effect of carbon dioxide on the complex water-disaccharide. It analyzes found on the geometric parameters of hydrogen bond (HB) and energy of the complexation reactions. Its results can help to understand how reagents contribute to the degradation or conservation of rice. This work contains two parts.

The first one announces the molecules studied. It explains the calculation techniques. It summarizes the methods for exploiting the Electrostatic Potential (ESP) of the interactions. This part elucidates the stability conditions of various supramolecules. The second presents and discusses its results. It presents the HB sites of glucose units. It details their reactions with water or carbon dioxide. Previously, the article reveals the structures of the molecules under study.

2. Structures of the Studied Molecules

Starch constitutes a mixture of two polymers, amylose and amylopectin. Amylose is a linear compound. It consists of α-D-glucose by α -1.4 bonds. Amylopectin has branching points at approximately every 20 synthons along the main chain. The shorter side chain glucose includes its α form associated through α -1.6 links 12. High degree of Amylopectin’s ramifications distinguishes it from amylose. Both polysaccharides share α-D-glucose of more than three units. The methods define the operational procedures. Theoretical calculations focus on a portion of amylose consisting of two or three synthons (Figure 1).

3. Methods of Calculation

This work performs ab initio calculations with the Gaussian 09 software. It optimizes the geometry of chemical entities. It computes different energies using DFT at level DFT/ (B3LYP/6-311++G [d, p]).

Frequency calculations validate it. DFT replaces wave function for the exact Hamiltonian. It allows obtaining it by means of a static density. It makes possible to describe long-range interactions such as those involved in the molecular studied 13. ESP contributes to this.

4. The Electrostatic Interaction Potential

The molecular ESP represents an effective descriptor to determine the preferred sites for electrophilic or nucleophilic attack; it contributes to the identification of HB in organic compounds 14, 15. It can relate to the energy of the proton’s interactions with its nuclei and electrons. Equation (1) defines it:

(1)

ZA designs the charge of the A nuclei. RA—r and r’—r correspond respectively to the proton-nucleus and proton-electron distances. ρ(r) represents electron density. The first term indicates the repulsion energy between nuclei and protons. The second one illustrates between electrons and these latter. On the other hand, the sign of becomes negative in regions where the electrons influence prevails on that of nuclei. It occurs around the free pairs of heteroatoms.

An HB donor will be captivated to the point where equals on the molecular surface, Bader and al. 16 define the latter as electronic iso-density one. If the strength of the nuclei becomes greater, is positive. This is for particles that behave like Lewis acids. ESP maximum study allows distinguishing HB donor sites. To do so, it uses the value and minimum one Then, it identifies and analyzes HB donor or acceptor sites for two or three glucose units (Figure 1). Moreover, the article focuses on complex stability conditions.

5. Stability of Two- and Three-Body Complex

Three fragments compose each complex. The first, labelled A, represents two or three glucose; the last two, B and C, designate respectively water and carbon dioxide. HB makes it possible to associate these three bodies. Their geometric parameters contribute to the discussion related to the establishment and strength of interactions. Figure 2 and Figure 3 illustrate them.

5.1. Geometric Parameters

Before any complex geometry optimization, equals at 180°. is 109.5° for oxygen and 120° for that of More, the distance between the latter atom and hydrogen is fixed at 2 Å. These seize correspond to their initial values 17. The article explains the criteria for exploiting the geometric parameters’ analysis.

According to Rowland and al 19, HB exists if is inferior to the sum of the Van der Waals radii of oxygen (1.52 Å) and hydrogen (1.1 Å) 20 or d ≤ 2.62 Å 21. It’s also strong if the interval is short. Furthermore, the more and differ from these ideal values, the more the HB topples. Here, an angular deviation becomes significant if it’s beyond 20°.

5.2. Calculations Interaction Energy of Two Body (AB) and Three Body (ABC)

The nature attractive or inductive of the interactions between fragments can apprehend complex stability. In the “super molecule” approach, the energy of two bodies calculate as follows. The interaction energy of A and B corresponds to the difference between that of the AB and its constituents. It writes according to equation (2) 22:

(2)

The term designates monomer X energy calculated in supramolecule AB geometry. The base developed on all its atomic orbital X () and phantoms X (). For Boys 23: the value overestimate interaction energy between A and B; the surplus comes from the base superposition error (Basis Sets Superposition Error: BSSE). The “counterpoise” method corrects this error.

The calculation of BSSE is done in two steps. The first one consists of determining the interaction energy with equation (2). The second considers the relaxation energy of fragments A and B. According to Diomandé and al 22, the latter translates monomer X geometry variations between its isolated and associated states. It’s defined:

(3)

The complexation energy ∆E becomes the sum of interaction and relaxation.

(4)
(5)

With

(6)

The term between brackets corresponds to the interaction energy without the corrective one. Moreover, in the case of the three-body ABC (supramolecule), it’s calculated from equation 7.

(7)

The terms refers to fragments X relaxation energy. corresponds to the n-body energy. Three ones specify how one of the fragments interacts with the already formed two subunits. Equation (8) defines this energy:

(8)

Equation (9) gives the corrected interaction energy BSSE

(9)

Table 1 presents interaction energy calculations and simplified formulas of the studied complex. Research results and discussion follow it.

6. Results and Discussion

This section explains the complex geometric and energetic parameters. It presents the ESP calculated. These allow analyzing AM2G and AM3G fragments at the level B3LYP/6-311++G (d, p). This investigation bases on oxygen sites and their corresponding values Vs, min, and Vs, max of

6.1. Electrostatic Potential: Molecular Interaction Sites

The ESP analyzes Table 2 shows ESP average values. The most negative Vs, min corresponds with oxygen and for AM3G and for AM2G. These atoms constitute the most important nucleophilic centres. Osidic Bridge oxygen (acceptor site) promotes the interaction between the AM2G or AM3G fragments and water hydrogen. This interaction causes the chain to break at this level. it results in an increase in monosaccharides; its high content induces rice degradation 24.

Hydrogen ESP likely to join in HB, corresponds to the maximum or hydrogen in AM2G or AM3G fragments meet this criterion. Likewise, that of in AM2G respects it. and hydrogen in AM3G owns very similar electrophilic properties; they make HB more easily with acceptors of other molecules. More, Figure 4 shows initials (I) and optimized (O) geometry examples of

6.2. Study

This section shows HB geometric parameters and energy data. Table 3 and Table 4 resume them respectively. Figure 4 illustrates this complex geometry before and after optimization at the level DFT/ (B3LYP/6-311++G [d, p]).


6.2.1. Geometric Parameters

The criteria listed in point 4.1 systematically guides the discussions on geometric parameters. The value Å indicates HB presence between the osidic bridge oxygen and water hydrogen

The angle of the osidic bridge equals to its ideal value after optimization. These results suggest the presence of a stable HB between and Furthermore, the distance is worth 1.87 Å. Angle measure 156.5°. The interaction corresponds to HB despite the weak measure of the angle

This connection remains unstable. On the other hand, the link length increases after optimization. It rises from 1.84 Å to 1.92 Å. The geometric parameters indicate that the interaction between water and AM2G leads to two intermolecular HB, and The first seems more stable than the second. More, HB intramolecular stabilizes glucose units. The energy aspects make it possible to specify these effects on AM2G.


6.2.2. Energy Parameters

Table 4 shows the total energy and its variation during the complex formation. It provides interaction energy enthalpy and free enthalpy The value of the first is low. More, its negative sign confirms that the complex is forming. It suggests that HB and remain relatively stable.

The negative enthalpy establishes that the formation of the complex corresponds to an exothermic process. The positive shows that complex doesn’t form spontaneously. The interaction of the fragment and stabilize the complex: the intramolecular HB and intermolecular and contribute to this. More, research concerns the complexation of the AM2G building with

6.3. Study

This part presents HB geometric and energetic parameters of the Table 5 and Table 6 show them, respectively. Figure 5 illustrates its initials and optimized geometries at the level DFT (B3LYP/6-311++G [d, p]).


6.3.1. Geometric Parameters

Table 5 summarizes HB geometric parameters. The first criteria guide discussion. The distance Å related to interaction exceeds the maximum length of HB. Moreover, angles and deviate from the expected values.

The geometric parameters demonstrate the intermolecular HB non-existence. The direct interaction of with AM2G moves the two entities apart ( increases from 2 Å to 3.09 Å). However, it enhances HB intramolecular stability. The energy parameters make it possible to verify this hypothesis.


6.3.2. Energy Parameters

This section presents complex energy parameters in Table 6. The interaction one is negative; it suggests existence. It contradicts the nonentity of an intermolecular HB between AM2G and However, the weak and the positive value establishes that the complexation remains difficult and not spontaneous.

In other words, HB instability don’t assemble The interaction between carbon dioxide and two glucose units don’t generate a HB. Moreover, this work focuses on buildings with three ones.

6.4. Study

This section presents complex geometric and energetic parameters. It summarizes them in Table 7 and Table 8 respectively. Figure 6 illustrates the first before and after its optimization.


6.4.1. Geometric Parameters

The distance varies slightly. It goes from 2 Å to 2.03 Å. Although and differ by 180° and 109.5° respectively. These results establish the presence of an intermolecular HB between and Furthermore, the value of 1.85 Å for pleads for another HB between these two atoms. The energy parameters analysis makes it possible to specify HB stability degree.


6.4.2. Energy Parameters

This section presents observations on interaction energies. Table 8 resume it’s parameters.

The interaction energy and enthalpy are very weak. The formation of the complex isn’t very probable. The positive supports this thesis. In sum, the osidic bridge oxygen doesn’t participate to HB. These two probable bonds remain too unstable.

6.5. AM3G … CO2 Study

This part presents HB geometric parameters and energetic data. Table 9 and Table 10 summarizes them respectively. Figure 7 shows the first. The previous criteria guide this discussion. The distance varies from 2 Å to 3.31 Å. For x=3 and 4, it’s 2.16 Å and 2.21 Å severally. On the other hand, moves from them; the intermolecular HB is unstable.


6.5.1. Geometric Parameters

The intramolecular HB becomes shorter in the optimized complex. It highlights a probable HB For the angles of the osidic bridge and remain almost close to their ideal values

It’s more reinforced by the presence of the Molecule. The analysis of the energy parameters makes it possible to clarify these observations.


6.5.2. Energy Parameters

This section presents Total, interaction energies and enthalpies. The interaction energy is for the It proves that doesn’t exist. This result agrees with the previous observations made with geometric parameters. instability is high.

Carbon dioxide action doesn’t generate intermolecular HB. It doesn’t form a complex with AM2G and AM3G. creates a stable one with AM2G only. This process bases on two intermolecular HB and Furthermore, this result suggests that the one more glucose unit to AM2G halts complexation between AM3G fragment and water. In other words, this latter degrading action on amylose synthons stops at disaccharide level. Moreover, the work focuses on the interactions of with the complex

6.6. Study

Figure 8 shows the optimized geometry of the three-body complex at the DFT/ (B3LYP/6-311++G [d, p]) level. The supramolecule contains two subunits of amylose, water and carbon dioxide


6.6.1. Geometric Parameters

Table 11 presents the geometric parameters of the interactions analyzed within the three bodies

These data indicate that one dioxide carbon more to the slightly increases the length of the HB; this latter locates between osidic bridge oxygen and water The distance grows from 1.87 Å to 1.90 Å. The angle and vary very little regarding the two-body complex. HB doesn’t disappear within the supramolecule establishes a weak HB with water. This result suggests that the approach doesn’t strongly destabilize aggregate. Carbon dioxide doesn’t contribute to the initial degradation of glucose units. The analysis of the energy parameters allows identifying the interaction modalities of with


6.6.2. Energy Parameters

Table 12 shows energy parameters. Its electronic energy is worth This weak value signifies that the complex remains robust. These of all two-body buildings are negative. They range from to They indicate that the group is the steadiest of the two-body complex. edifice is the most unbalanced; associates preferably with AM2G fragments.

The electronic energy of the one-body fragments, in the isolated geometry, ranges from to It indicates that AM2G remains the most stable component of the It reveals that water is the most unbalanced molecule.

The interaction energy related to formation corresponds to Its positive value means that the action of on AM2G is detrimental to existence. It varies between and remains the most stable of the two-body structures. The relaxation energies are zero for and

These molecules retain their initial geometries within the complex. The positive value of indicates that of changes. Under these conditions, is difficult to create. consolidate The carbon dioxide acts subjectively on the AM2G fragment. It stabilizes AM2G edifice also alters within the supramolecule.

7. Conclusion

This work aims to explain the extent to which water or carbon dioxide involve in the rice polysaccharides degradation. First reagent constitutes its moisture source. This article examines in turn the interactions of these reagents with two glucose units. It also analyzes the second product’s action on complex On another side, research performs calculations at level DFT/(B3LYP/6-311++G [d, p]) essentially. It generates geometric and energy parameters. Their analysis leads to the following results.

Water establishes two stable intermolecular HB with AM2G. It highlights the two HB and which conducts to complex Furthermore, AM2G remains inactive towards carbon dioxide. This latter stabilizes and It doesn’t stop AM2G aqueous degradation.

References

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In article      
 
[2]  M. L. Bason, P. W. Gras, H. J. Banks, and L. A. Esteves, “A quantitative study of the influence of temperature, water activity and storage atmosphere on the yellowing of paddy endosperm”, Journal of Cereal Science, vol. 12, no 2, p. 193-201, sept. 1990.
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[3]  Joseph. Chrastil and Z. M. Zarins, “Influence of storage on peptide subunit composition of rice oryzenin”, J. Agric. Food Chem., vol. 40, no 6, p. 927-930, juin 1992.
In article      View Article
 
[4]  P. L. Sholberg and A. P. Gaunce, “Fumigation of high moisture seed with acetic acid to control storage mold”, Can. J. Plant Sci., vol. 76, no 3, p. 551-555, juill. 1996.
In article      View Article
 
[5]  K. A. Buckman, J. F. Campbell and B. Subramanyam, “<I>Tribolium castaneum</I> (Coleoptera: Tenebrionidae) Associated With Rice Mills: Fumigation Efficacy and Population Rebound”, jnl. econ. entom., vol. 106, no 1, p. 499-512, févr. 2013.
In article      View Article  PubMed
 
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In article      
 
[7]  G. Pacaud, “Aperçu sur la désinsectisation par anoxie sous atmosphère inerte. 1. Systèmes statique et dynamique (1)”, La lettre de l’OCIM, no 58, p. 26-30, 19980000.
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In article      View Article
 
[10]  G. W. T. M. J. Frisch, G. E. S. H. B. Schlegel, J. R. C. M. A. Robb, V. B. G. Scalmani, G. A. P. B. Mennucci and H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, “Gaussian 09, Revision A.02”, Coordination Chemistry Reviews, vol. 252, no 3, p. 395-415, févr. 2008.
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[13]  D. Sulzer, “Modélisation des interactions faibles en théorie de la fonctionnelle de la densité”, phdthesis, Université de Strasbourg, 2012.
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[14]  J. S. Murray, M. C. Concha, P. Lane, P. Hobza and P. Politzer, “Blue shifts vs red shifts in σ-hole bonding”, J Mol Model, vol. 14, no 8, p. 699-704, août 2008.
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Normal Style
Koffi Kouassi Alain, Koné Soleymane, Bamba El Hadji Sawaliho. Water and Dioxide Carbon Effects on Di or Tri Saccharides Degradation by Density Functional Theory at Level: B3LYP/6-311++G (d, p). Journal of Materials Physics and Chemistry. Vol. 9, No. 1, 2021, pp 1-8. http://pubs.sciepub.com/jmpc/9/1/1
MLA Style
Alain, Koffi Kouassi, Koné Soleymane, and Bamba El Hadji Sawaliho. "Water and Dioxide Carbon Effects on Di or Tri Saccharides Degradation by Density Functional Theory at Level: B3LYP/6-311++G (d, p)." Journal of Materials Physics and Chemistry 9.1 (2021): 1-8.
APA Style
Alain, K. K. , Soleymane, K. , & Sawaliho, B. E. H. (2021). Water and Dioxide Carbon Effects on Di or Tri Saccharides Degradation by Density Functional Theory at Level: B3LYP/6-311++G (d, p). Journal of Materials Physics and Chemistry, 9(1), 1-8.
Chicago Style
Alain, Koffi Kouassi, Koné Soleymane, and Bamba El Hadji Sawaliho. "Water and Dioxide Carbon Effects on Di or Tri Saccharides Degradation by Density Functional Theory at Level: B3LYP/6-311++G (d, p)." Journal of Materials Physics and Chemistry 9, no. 1 (2021): 1-8.
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  • Figure 8. Initial (I) and optimized (O) structure of the supramolecule AM2G … H2O … CO2 at the level DFT/ (B3LYP/6-311++G [d, p])
  • Table 2. Electrostatic Potential of Interaction Average Vs (kj.mol-1) at the DFT/ (B3LYP/6-311++G [d, p]) level
  • Table 3. AM2G … H2O Initials (I) and Optimized (O) Geometric Parameters at Level DFT/ (B3LYP/6-311++G [d, p]).
  • Table 5. AM2G … CO2 Geometric Parameters of the Initials (I) and Optimized (O) Complex at the DFT/ (B3LYP/6-311++G [d, p]) Level.
  • Table 7. AM3G … H2O Geometric Parameters of the Initials (I) and Optimized (O) Complex at the DFT Level/ (B3LYP/6-311++G [d, p])
  • Table 9. AM3G … CO2 Geometric Parameters of Initials (I) and Optimized (O) at the Level DFT/ (B3LYP/6-31++G [d, p])
  • Table 11. AM2G … H2O … CO2 Geometric Parameters of the Complex Optimized (O) at the Level DFT/ (B3LYP/6-311++G [d, p]).
  • Table 12. Energy Parameters of the AM2G … H2O … CO2 Building at the Level DFT/ (B3LYP/6-311++G [d, p])
[1]  B. O. Juliano, “Polysaccharides, proteins, and lipids of rice”, Rice: Chemistry and Technology, p. 59-174, 1985.
In article      
 
[2]  M. L. Bason, P. W. Gras, H. J. Banks, and L. A. Esteves, “A quantitative study of the influence of temperature, water activity and storage atmosphere on the yellowing of paddy endosperm”, Journal of Cereal Science, vol. 12, no 2, p. 193-201, sept. 1990.
In article      View Article
 
[3]  Joseph. Chrastil and Z. M. Zarins, “Influence of storage on peptide subunit composition of rice oryzenin”, J. Agric. Food Chem., vol. 40, no 6, p. 927-930, juin 1992.
In article      View Article
 
[4]  P. L. Sholberg and A. P. Gaunce, “Fumigation of high moisture seed with acetic acid to control storage mold”, Can. J. Plant Sci., vol. 76, no 3, p. 551-555, juill. 1996.
In article      View Article
 
[5]  K. A. Buckman, J. F. Campbell and B. Subramanyam, “<I>Tribolium castaneum</I> (Coleoptera: Tenebrionidae) Associated With Rice Mills: Fumigation Efficacy and Population Rebound”, jnl. econ. entom., vol. 106, no 1, p. 499-512, févr. 2013.
In article      View Article  PubMed
 
[6]  B. Diawara, D. Richard-Molard, and B. Cahagnier, “Conservation des céréales humides sous atmosphère contrôlée. Limites théoriques and pratiques”, p. 12.
In article      
 
[7]  G. Pacaud, “Aperçu sur la désinsectisation par anoxie sous atmosphère inerte. 1. Systèmes statique et dynamique (1)”, La lettre de l’OCIM, no 58, p. 26-30, 19980000.
In article      
 
[8]  S. Rajendran, M. K. Bhashyam, and N. Muralldharan’, “Storage of Basmati Rice Under Carbon Dioxide -rich Atmosphere”, p. 6.
In article      
 
[9]  J. Le Torc’H and F. Fleurat-Lessard, “Étude des interactions d’adsorption-désorption entre le grain et les atmosphères enrichies en CO 2, destinées à la désinsectisation du riz paddy”, Agronomie, vol. 11, no 4, p. 305-314, 1991.
In article      View Article
 
[10]  G. W. T. M. J. Frisch, G. E. S. H. B. Schlegel, J. R. C. M. A. Robb, V. B. G. Scalmani, G. A. P. B. Mennucci and H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, “Gaussian 09, Revision A.02”, Coordination Chemistry Reviews, vol. 252, no 3, p. 395-415, févr. 2008.
In article      
 
[11]  Koch, W and Holthausen, “M.C.A in Chemist’s Guide to Density Fonctional Theory 2nd Ed”, 1999. .
In article      
 
[12]  S. Mezoudji, “Modification de l’amidon par un monomère organique, caractérisations et applications.”, PhD Thesis, 03-07-2018.
In article      
 
[13]  D. Sulzer, “Modélisation des interactions faibles en théorie de la fonctionnelle de la densité”, phdthesis, Université de Strasbourg, 2012.
In article      
 
[14]  J. S. Murray, M. C. Concha, P. Lane, P. Hobza and P. Politzer, “Blue shifts vs red shifts in σ-hole bonding”, J Mol Model, vol. 14, no 8, p. 699-704, août 2008.
In article      View Article  PubMed
 
[15]  T. Brinck, “The use of the electrostatic potential for analysis and prediction of intermolecular interactions”, in Theoretical and Computational Chemistry, vol. 5, C. Párkányi, Éd. Elsevier, 1998, p. 51-93.
In article      View Article
 
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