1
|
Lgaz H, Lee HS, Kaya S, Salghi R, Ibrahim SM, Chafiq M, Bazzi L, Ko YG. Unraveling Bonding Mechanisms and Electronic Structure of Pyridine Oximes on Fe(110) Surface: Deeper Insights from DFT, Molecular Dynamics and SCC-DFT Tight Binding Simulations. Molecules 2023; 28:molecules28083545. [PMID: 37110779 PMCID: PMC10141362 DOI: 10.3390/molecules28083545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. The computational assessment of organic corrosion inhibitors' performance is a crucial step towards the design of new task-specific materials. Herein, the electronic features, adsorption characteristics and bonding mechanisms of two pyridine oximes, namely 2-pyridylaldoxime (2POH) and 3-pyridylaldoxime (3POH), with the iron surface were investigated using molecular dynamics (MD), and self-consistent-charge density-functional tight-binding (SCC-DFTB) simulations. SCC-DFTB simulations revealed that the 3POH molecule can form covalent bonds with iron atoms in its neutral and protonated states, while the 2POH molecule can only bond with iron through its protonated form, resulting in interaction energies of -2.534, -2.007, -1.897, and -0.007 eV for 3POH, 3POH+, 2POH+, and 2POH, respectively. Projected density of states (PDOSs) analysis of pyridines-Fe(110) interactions indicated that pyridine molecules were chemically adsorbed on the iron surface. Quantum chemical calculations (QCCs) revealed that the energy gap and Hard and Soft Acids and Bases (HSAB) principles were efficient in predicting the bonding trend of the molecules investigated with an iron surface. 3POH had the lowest energy gap of 1.706 eV, followed by 3POH+ (2.806 eV), 2POH+ (3.121 eV), and 2POH (3.431 eV). In the presence of a simulated solution, MD simulation showed that the neutral and protonated forms of molecules exhibited a parallel adsorption mode on an iron surface. The excellent adsorption properties and corrosion inhibition performance of 3POH may be attributed to its low stability compared to 2POH molecules.
Collapse
Affiliation(s)
- Hassane Lgaz
- Innovative Durable Building and Infrastructure Research Center, Center for Creative Convergence Education, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si 15588, Gyeonggi-do, Republic of Korea
| | - Han-Seung Lee
- Department of Architectural Engineering, Hanyang University-ERICA, 55 Hanyangdaehak-ro, San-grok-gu, Ansan-si 15588, Gyeonggi-do, Republic of Korea
| | - Savaş Kaya
- Department of Pharmacy, Health Services Vocational School, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Rachid Salghi
- Laboratory of Applied Chemistry and Environment, Applied Science National School (ENSA), University Ibn Zohr, P.O. Box 1136, Agadir 80000, Morocco
- Laboratoire de Génie Industriel, de l'Énergétique et de l'Environnement (LGI2E), SupMTI, Rabat 10000, Morocco
| | - Sobhy M Ibrahim
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Maryam Chafiq
- Materials Electrochemistry Group, School of Materials Science and Engineering, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| | - Lahcen Bazzi
- Laboratoire de Génie Industriel, de l'Énergétique et de l'Environnement (LGI2E), SupMTI, Rabat 10000, Morocco
| | - Young Gun Ko
- Materials Electrochemistry Group, School of Materials Science and Engineering, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| |
Collapse
|
2
|
Tolosa S, Sansón J, Hidalgo A. A procedure to understanding the C-G to A-T transversion. SMD simulations from guanine oxidation pathways assisted by one H2O2 molecule in the C-G basis pair. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
4
|
Tolosa S, Sansón J, Hidalgo A. Theoretical study of mechanisms for double proton transfer in adenine–uracil base pair via steered molecular dynamic simulations. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
6
|
Tolosa S, Sansón JA, Hidalgo A. Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations. RSC Adv 2018; 8:34867-34876. [PMID: 35547048 PMCID: PMC9087476 DOI: 10.1039/c8ra07390b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations. Two pathways were considered to explain the mechanism of this process, where the water molecule attacks the C–N bond to give an intermediate (an amino–hydroxy–oxo structure in the A-path, and a hydroxy–oxo in the B-path) as the determinant step of reaction. Stationary structures along both energy profiles were analyzed at molecular dynamics level, obtaining states with higher free energies than those from electronic calculations in the gas phase and in solution described as a continuous medium. From the results obtained, the more complex A-pathway, with five steps, was kinetically the most favorable (with an endergonic reaction energy of 7.41 kcal mol−1, a high barrier of 67.53 kcal mol−1, and a small velocity constant k2 = 1.80 × 10−37 s−1), concluding that the uracil base can participate in a spontaneous genetic mutation since the uracil–ammonia complex has a long lifetime of 6.10 × 1027 s. This process turns out exergonic and faster when carried out in gas phase simulation or electronic calculation with a continuous medium, due to the disappearance of explicit water molecules that can compete with the assistant molecule. Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.![]()
Collapse
Affiliation(s)
- S. Tolosa
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz
- Spain
| | - J. A. Sansón
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz
- Spain
| | - A. Hidalgo
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz
- Spain
| |
Collapse
|
7
|
Tolosa S, Sánchez J, Sansón J, Hidalgo A. Steered molecular dynamic simulations of the tautomeric equilibria in solution of DNA bases. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
8
|
Shi H, Koskinen P, Ramasubramaniam A. Self-Consistent Charge Density-Functional Tight-Binding Parametrization for Pt–Ru Alloys. J Phys Chem A 2017; 121:2497-2502. [DOI: 10.1021/acs.jpca.7b00701] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hongbo Shi
- Department
of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Pekka Koskinen
- Department
of Physics, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Ashwin Ramasubramaniam
- Department
of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| |
Collapse
|
9
|
Tolosa S, Sansón JA, Hidalgo A, Mora-Diez N. Theoretical determination of aqueous acid–base pK values: electronic structure calculations and steered molecular dynamic simulations. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2008-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
10
|
Tolosa S, Hidalgo A, Sansón JA. Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations. J Mol Model 2016; 22:44. [PMID: 26815031 DOI: 10.1007/s00894-016-2914-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
The thermodynamics and kinetics of enzymatically assisted reactions of carbon acids were studied theoretically in this work. Quantum electronic (QE) structure calculations and steered molecular dynamics (SMD) simulations were carried out. Three 3-butenal tautomerization reactions that proceed from the β,γ-unsaturated reactant (R) to the α,β-unsaturated carbon acid product (P) and occur in two elementary steps through an intermediate (I) were studied, ignoring or including the surrounding aqueous medium in the calculations. The Gibbs free energies of activation of the R ⇆ I enolization and I ⇆ P ketonization steps were found to decrease considerably when residues simulating enzymes were introduced into these processes. Although the processes became slightly more favorable thermodynamically when the solution was included in the simulations, they became less favorable kinetically. The results from SMD simulations of these reactions were qualitatively consistent with the values we obtained using QE as well as those found by other authors in similar studies. Our simulations also allowed us to perform a detailed study of these reactions in solution.
Collapse
Affiliation(s)
- Santiago Tolosa
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain.
| | - Antonio Hidalgo
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain
| | - Jorge A Sansón
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain
| |
Collapse
|
11
|
Tolosa S, Mora-Diez N, Hidalgo A, Sansón JA. Amide-imide tautomerism of acetohydroxamic acid in aqueous solution: quantum calculation and SMD simulations. RSC Adv 2014. [DOI: 10.1039/c4ra06124a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The kinetics and the thermodynamics of the amide-imide tautomerizations of acetohydroxamic acid in aqueous solution are studied from a theoretical point of view.
Collapse
Affiliation(s)
- S. Tolosa
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz, Spain
| | - N. Mora-Diez
- Department of Chemistry
- Thompson Rivers University
- Kamloops, Canada
| | - A. Hidalgo
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz, Spain
| | - J. A. Sansón
- Departamento de Ingeniería Química y Química Física
- Universidad de Extremadura
- Badajoz, Spain
| |
Collapse
|
12
|
Seabra GDM, Walker RC, Roitberg AE. Are current semiempirical methods better than force fields? A study from the thermodynamics perspective. J Phys Chem A 2010; 113:11938-48. [PMID: 19848431 DOI: 10.1021/jp903474v] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(N),H(alpha)) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.
Collapse
Affiliation(s)
- Gustavo de M Seabra
- Quantum Theory Project and Department of Chemistry, University of Florida, 2234 New Physics Building #92, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
| | | | | |
Collapse
|