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Article ; Online: Conformational preference of dipeptide zwitterions in aqueous solvents.

Adasme-Carreño, Francisco / Ochoa-Calle, Alvaro / Galván, Marcelo / Ireta, Joel

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 10, Page(s) 8210–8218

Abstract: Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides ...

Abstract	Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy,
MeSH term(s)	Solvents/chemistry ; Dipeptides ; Water ; Glycine ; Protein Conformation
Chemical Substances	Solvents ; Dipeptides ; Water (059QF0KO0R) ; Glycine (TE7660XO1C)
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp05742a
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Article ; Online: Activated layered double hydroxides: assessing the surface anion basicity and its connection with the catalytic activity in the cyanoethylation of alcohols.

Castro, Guadalupe / Valente, Jaime S / Galván, Marcelo / Ireta, Joel

Physical chemistry chemical physics : PCCP

2022 Volume 24, Issue 38, Page(s) 23507–23516

Abstract: Layered double hydroxides (LDHs) act as catalysts in several reactions like in the cyanoethylation of alcohols with acrylonitrile to produce alkoxypropionitriles. Here we report an experimental and theoretical study in which it is shown that the ... ...

Abstract	Layered double hydroxides (LDHs) act as catalysts in several reactions like in the cyanoethylation of alcohols with acrylonitrile to produce alkoxypropionitriles. Here we report an experimental and theoretical study in which it is shown that the experimental catalytic activity of LDHs in the cyanoethylation of 2-propanol and methanol correlates with the predicted strength of the basicity of the adsorbed surface species. First, it is shown that using activated LDHs containing Mg
Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp02704f
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Article ; Online: Electronic structure behavior of PbO

Islas-Vargas, Claudia / Guevara-García, Alfredo / Galván, Marcelo

The Journal of chemical physics

2021 Volume 154, Issue 7, Page(s) 74704

Abstract: A detailed analysis of the electronic structure of three different electrochemical interfaces as a function of the chemical potential (μ) is performed using the grand canonical density functional theory in the joint density functional theory formulation. ...

Abstract	A detailed analysis of the electronic structure of three different electrochemical interfaces as a function of the chemical potential (μ) is performed using the grand canonical density functional theory in the joint density functional theory formulation. Changes in the average number of electrons and the density of states are also described. The evaluation of the global softness, which measures the tendency of the system to gain or lose electrons, is straightforward under this formalism. The observed behavior of these quantities depends on the electronic nature of the electrochemical interfaces.
Language	English
Publishing date	2021-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0035208
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Article ; Online: Hydrodesulfurization of Dibenzothiophene: A Machine Learning Approach.

Castro, Guadalupe / Cruz-Borbolla, Julián / Galván, Marcelo / Guevara-García, Alfredo / Ireta, Joel / Matus, Myrna H / Meneses-Viveros, Amilcar / Ignacio Perea-Ramírez, Luis / Pescador-Rojas, Miriam

ChemistryOpen

2024 , Page(s) e202400062

Abstract: The hydrodesulfurization (HDS) process is widely used in the industry to eliminate sulfur compounds from fuels. However, removing dibenzothiophene (DBT) and its derivatives is a challenge. Here, the key aspects that affect the efficiency of catalysts in ... ...

Abstract	The hydrodesulfurization (HDS) process is widely used in the industry to eliminate sulfur compounds from fuels. However, removing dibenzothiophene (DBT) and its derivatives is a challenge. Here, the key aspects that affect the efficiency of catalysts in the HDS of DBT were investigated using machine learning (ML) algorithms. The conversion of DBT and selectivity was estimated by applying Lasso, Ridge, and Random Forest regression techniques. For the estimation of conversion of DBT, Random Forest and Lasso offer adequate predictions. At the same time, regularized regressions have similar outcomes, which are suitable for selectivity estimations. According to the regression coefficient, the structural parameters are essential predictors for selectivity, highlighting the pore size, and slab length. These properties can connect with aspects like the availability of active sites. The insights gained through ML techniques about the HDS catalysts agree with the interpretations of previous experimental reports.
Language	English
Publishing date	2024-04-12
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2655605-4
ISSN	2191-1363 ; 2191-1363
ISSN (online)	2191-1363
ISSN	2191-1363
DOI	10.1002/open.202400062
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Article ; Online: Establishing the Relationship between Quantum Capacitance and Softness of N-Doped Graphene/Electrolyte Interfaces within the Density Functional Theory Grand Canonical Kohn-Sham Formalism.

Ochoa-Calle, Alvaro / Guevara-García, Alfredo / Vazquez-Arenas, Jorge / González, Ignacio / Galván, Marcelo

The journal of physical chemistry. A

2020 Volume 124, Issue 3, Page(s) 573–581

Abstract: The joint density functional theory (JDFT) is applied in the context of the grand canonical Kohn-Sham theory to calculate the global and local softness of pristine and N-substituted graphene structures. A comparison is established between the different ... ...

Abstract	The joint density functional theory (JDFT) is applied in the context of the grand canonical Kohn-Sham theory to calculate the global and local softness of pristine and N-substituted graphene structures. A comparison is established between the different theoretical approaches to evaluate total capacitance, revealing that the JDFT approach presents the closest result of this property with experimental data. A model of series capacitors is used to determine the quantum and nonquantum contributions of total capacitance, which enables us to determine the limitations of the rigid band approximation for the studied systems. It is found that global chemical softness is proportional to the total capacitance measured in the experiments, when the geometry relaxation is neglected. In this context, it is possible to obtain quantum and total capacitance (and consequently softness) from an average number of electrons vs applied potential plots and the model of series capacitors. Likewise, the relation of capacitance and softness gives rise to a new definition of local capacitance within the JDFT formalism. The evaluation of global and local softness paves the way to analyze electrochemical surface reactivity as a function of applied potential for a solid-electrolyte interface.
Language	English
Publishing date	2020-01-10
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.9b10885
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Article ; Online: Using local softness to reveal oxygen participation in redox processes in cathode materials.

Perea-Ramírez, Luis Ignacio / Guevara-García, Alfredo / Galván, Marcelo

Journal of molecular modeling

2018 Volume 24, Issue 9, Page(s) 227

Abstract: In this paper, the use of chemical local softness s(r) is proposed as an alternative way of analyzing the initial redox processes that occur in cathode materials used for lithium-ion batteries. It is shown that the chemical local softness is a quantity ... ...

Abstract	In this paper, the use of chemical local softness s(r) is proposed as an alternative way of analyzing the initial redox processes that occur in cathode materials used for lithium-ion batteries. It is shown that the chemical local softness is a quantity able to capture the same effects as the standard analysis based on the projected density of states. Because of its own nature, the local softness reveals the atomic sites involved in charge-transfer events and allows a quantitative comparative analysis between different materials. As pointed out by Johannes et al. (Solid State Ion 286:83-89, 2016), this analysis can be used as an indicator of stability of cathode materials for Li-ion batteries.
Language	English
Publishing date	2018-08-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-x
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-018-3754-0
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Article ; Online: Nature of Hydrogen Bonds and S···S Interactions in the l-Cystine Crystal.

Flores-Huerta, Anaid G / Tkatchenko, Alexandre / Galván, Marcelo

The journal of physical chemistry. A

2016 Volume 120, Issue 24, Page(s) 4223–4230

Abstract: The intermolecular interactions that govern the stability of the l-cystine crystal were studied. This task is accomplished by using density-functional theory (DFT) with the generalized-gradient approximation (GGA) and including many-body dispersion (MBD) ...

Abstract	The intermolecular interactions that govern the stability of the l-cystine crystal were studied. This task is accomplished by using density-functional theory (DFT) with the generalized-gradient approximation (GGA) and including many-body dispersion (MBD) interactions. The strengths of the different interactions within the molecular crystal were obtained by a decomposition of the total interaction energy in two-, three-, and four-body contributions. It was determined that most of the hydrogen bonds formed within the crystal are strong (13, 15, and 19 kcal/mol) and the van der Waals nature of the S···S interaction is fully confirmed. Also, the presence of strong repulsive three-body contributions is determined. The results obtained support the idea of designing crystal growth inhibitors for this system in such a way that, when inserted in the crystal, they maintain the disulfide bridge environment but its capacity of generate hydrogen-bond networks is removed.
Language	English
Publishing date	2016-06-23
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.6b03167
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Article ; Online: Sensing polarization effects through the analysis of the effective C6 dispersion coefficients in NaCl solutions.

Guevara-García, Alfredo / Ireta, Joel / Galván, Marcelo

The Journal of chemical physics

2015 Volume 142, Issue 1, Page(s) 14504

Abstract: Density functional theory based ab initio molecular dynamics is used to obtain microscopic details of the interactions in sodium chloride solutions. By following the changes in the atomic C6 coefficients under the Tkatchenko-Scheffler's scheme, we were ... ...

Abstract	Density functional theory based ab initio molecular dynamics is used to obtain microscopic details of the interactions in sodium chloride solutions. By following the changes in the atomic C6 coefficients under the Tkatchenko-Scheffler's scheme, we were able to identify two different coordination situations for the Cl(-) ion with significant different capabilities to perform dispersion interactions. This capability is enhanced when the ion-ion distance corresponds to the contact ion-pair situation. Also, the oxygen and hydrogen atoms of the water molecules change their aptitudes to interact through van der Waals like terms when they are close to the cation region of the ion-pair. These results have interesting implications on the design of force fields to model electrolyte solutions.
Language	English
Publishing date	2015-01-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4905125
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Article: Effect of double bonds on the conducting properties of ciguatoxin 3C and tetrahydropyrane-based polymers: a theoretical study.

Matus, Myrna H / Garza, Jorge / Galván, Marcelo

The journal of physical chemistry. B

2006 Volume 110, Issue 3, Page(s) 1172–1178

Abstract: The electronic structure of the ciguatoxin 3C is analyzed through the Kohn-Sham model by using two different kinds of basis sets: localized basis set (Gaussian functions) and nonlocalized basis set (plane wave functions). With the localized basis ... ...

Abstract	The electronic structure of the ciguatoxin 3C is analyzed through the Kohn-Sham model by using two different kinds of basis sets: localized basis set (Gaussian functions) and nonlocalized basis set (plane wave functions). With the localized basis functions, two approximations are used for the exchange-correlation functional: the local density approximation and the generalized gradient approximation. With the nonlocalized basis set, just the local density approximation is used. The energy gap, obtained from the frontier molecular orbitals, for this molecule predicts that this system is a semiconductor, even when the number of double bonds is increased inside the structure. However, as large molecules built with the basic unit--the tetrahydropyrane--of the ciguatoxin 3C are found in nature, it suggests studying the gap in polymeric systems built with the basic unit of this molecule. It is demonstrated that the presence of double bonds reduces considerably the gap, indicating the possibility of forming conducting materials by introducing double bonds in this kind of molecular systems. Thus, molecules strongly linked with biological systems can be used as precursor to build electric conducting systems.
MeSH term(s)	Ciguatoxins/chemistry ; Electric Conductivity ; Models, Chemical ; Molecular Conformation ; Polymers/chemistry ; Pyrans/chemistry
Chemical Substances	Polymers ; Pyrans ; ciguatoxin 3C ; Ciguatoxins (11050-21-8)
Language	English
Publishing date	2006-01-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-6106
ISSN	1520-6106
DOI	10.1021/jp053491o
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Article: Potential energy landscape of monolayer-surface systems governed by repulsive lateral interactions: the case of (3 x 3)-I-Pt(111).

Tkatchenko, Alexandre / Batina, Nikola / Galván, Marcelo

Physical review letters

2006 Volume 97, Issue 3, Page(s) 36102

Abstract: Combined density functional theory (DFT) and Monte Carlo (MC) approach is applied to study the potential energy landscape of four iodine atoms adsorbed on the Pt(111) surface in a (3 x 3) unit cell. Three critical points were identified: (3 x 3)-sym and ( ...

Abstract	Combined density functional theory (DFT) and Monte Carlo (MC) approach is applied to study the potential energy landscape of four iodine atoms adsorbed on the Pt(111) surface in a (3 x 3) unit cell. Three critical points were identified: (3 x 3)-sym and (3 x 3)-asym, corresponding to structures well known from experimental studies, while the third one (3 x 3)-zigzag is a new structure not reported before. An interaction model fitted to DFT calculations allows us to explain the difference between arrangements of iodine monolayer in vacuum, air, and solution environments as a result of different repulsion regimes.
Language	English
Publishing date	2006-07-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.97.036102
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