Research

17 pages, 4200 KiB

Open AccessArticle

Molecular Dynamics Simulations of the Short-Chain Fluorocarbon Surfactant PFH_XA and the Anionic Surfactant SDS at the Air/Water Interface

by Jinqing Jiao, Tao Li, Guangwen Zhang, Jing Xiong, Xuqing Lang, Xiaolong Quan, Yiwei Cheng and Yuechang Wei

Molecules 2024, 29(7), 1606; https://doi.org/10.3390/molecules29071606 - 03 Apr 2024

Viewed by 444

Abstract

The research and development of alternatives to long-chain fluorocarbon surfactants are desperately needed because they are extremely toxic, difficult to break down, seriously harm the environment, and limit the use of conventional aqueous film-forming foam fire extinguishing agents. In this study, mixed surfactant [...] Read more.

The research and development of alternatives to long-chain fluorocarbon surfactants are desperately needed because they are extremely toxic, difficult to break down, seriously harm the environment, and limit the use of conventional aqueous film-forming foam fire extinguishing agents. In this study, mixed surfactant systems containing the short-chain fluorocarbon surfactant perfluorohexanoic acid (PFH_XA) and the hydrocarbon surfactant sodium dodecyl sulfate (SDS) were investigated by molecular dynamics simulation to investigate the microscopic properties at the air/water interface at different molar ratios. Some representative parameters, such as surface tension, degree of order, density distribution, radial distribution function, number of hydrogen bonds, and solvent-accessible surface area, were calculated. Molecular dynamics simulations show that compared with a single type of surfactant, mixtures of surfactants provide superior performance in improving the interfacial properties of the gas–liquid interface. A dense monolayer film is formed by the strong synergistic impact of the two surfactants. Compared to the pure SDS system, the addition of PFH_XA caused SDS to be more vertically oriented at the air/water interface with a reduced tilt angle, and a more ordered structure of the mixed surfactants was observed. Hydrogen bonding between SDS headgroups and water molecules is enhanced with the increasing PFH_XA. The surface activity is arranged in the following order: PFH_XA/SDS = 1:1 > PFH_XA/SDS = 3:1 > PFH_XA/SDS = 1:3. These results indicate that a degree of synergistic relationship exists between PFH_XA and SDS at the air/water interface. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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21 pages, 4948 KiB

Open AccessArticle

Assessment of Hydrazone Derivatives for Enhanced Steel Corrosion Resistance in 15 wt.% HCl Environments: A Dual Experimental and Theoretical Perspective

by Abdelilah El-khlifi, Fatima Zahrae Zouhair, Mustafa R. Al-Hadeethi, Hassane Lgaz, Han-seung Lee, Rachid Salghi, Belkheir Hammouti and Hamid Erramli

Molecules 2024, 29(5), 985; https://doi.org/10.3390/molecules29050985 - 23 Feb 2024

Viewed by 528

Abstract

This study evaluates the corrosion inhibition capabilities of two novel hydrazone derivatives, (E)-2-(5-methoxy-2-methyl-1H-indol-3-yl)-N′-(4-methylbenzylidene)acetohydrazide (MeHDZ) and (E)-N′-benzylidene-2-(5-methoxy-2-methyl-1H-indol-3-yl)acetohydrazide (HHDZ), on carbon steel in a 15 wt.% HCl solution. A comprehensive suite of analytical techniques, including gravimetric analysis, potentiodynamic polarization (PDP), electrochemical impedance spectroscopy (EIS), and [...] Read more.

This study evaluates the corrosion inhibition capabilities of two novel hydrazone derivatives, (E)-2-(5-methoxy-2-methyl-1H-indol-3-yl)-N′-(4-methylbenzylidene)acetohydrazide (MeHDZ) and (E)-N′-benzylidene-2-(5-methoxy-2-methyl-1H-indol-3-yl)acetohydrazide (HHDZ), on carbon steel in a 15 wt.% HCl solution. A comprehensive suite of analytical techniques, including gravimetric analysis, potentiodynamic polarization (PDP), electrochemical impedance spectroscopy (EIS), and scanning electron microscopy (SEM), demonstrates their significant inhibition efficiency. At an optimal concentration of 5 × 10⁻³ mol/L, MeHDZ and HHDZ achieve remarkable inhibition efficiencies of 98% and 94%, respectively. EIS measurements reveal a dramatic reduction in effective double-layer capacitance (from 236.2 to 52.8 and 75.3 µF/cm²), strongly suggesting inhibitor adsorption on the steel surface. This effect is further corroborated by an increase in polarization resistance and a significant decrease in corrosion current density at optimal concentrations. Moreover, these inhibitors demonstrate sustained corrosion mitigation over extended exposure durations and maintain effectiveness even under elevated temperatures, highlighting their potential for diverse operational conditions. The adsorption process of these inhibitors aligns well with the Langmuir adsorption isotherm, implying physicochemical interactions at the carbon steel surface. Density functional tight-binding (DFTB) calculations and molecular dynamics simulations provide insights into the inhibitor-surface interaction mechanism, further elucidating the potential of these hydrazone derivatives as highly effective corrosion inhibitors in acidic environments. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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14 pages, 1450 KiB

Open AccessArticle

Thermal Conductivity Calculation in Organic Liquids: Application to Poly-α-Olefin

by Jonathan Severin, Sophie Loehlé and Philippe Jund

Molecules 2024, 29(2), 291; https://doi.org/10.3390/molecules29020291 - 05 Jan 2024

Viewed by 677

Abstract

In this work, we aim to understand and predict the thermal properties of automotive lubricants using non-equilibrium molecular dynamics. After a previous study on model materials for the mechanical parts of a car engine, we now focus on the thermal conductivity

κ

of [...] Read more.

In this work, we aim to understand and predict the thermal properties of automotive lubricants using non-equilibrium molecular dynamics. After a previous study on model materials for the mechanical parts of a car engine, we now focus on the thermal conductivity

κ

of the poly-

α

-olefin base oil (PAO4) using the well-known sink and source method to study the response of the system to an imposed heat flux. We present a detailed methodology for the calculation of

κ

, taking into account specific constraints related to the system under study, such as large steady-state fluctuations and rapidly growing stationarization times. We provide thermal conductivity results using four different force fields, including OPLS-AA, PCFF and COMPASS, in a temperature range of 300 to 500 K, which corresponds to the typical operating range of a car engine. The results are compared to experimental measurements performed on the commercial compound using the laser flash method. Agreement at room temperature is shown to be excellent for our in-house force field. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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11 pages, 337 KiB

Open AccessArticle

Nuclear Motion Is Classical: Spectrum of a Magic Protonated Water Cluster

by Irmgard Frank

Molecules 2023, 28(18), 6454; https://doi.org/10.3390/molecules28186454 - 06 Sep 2023

Viewed by 555

Abstract

The assumption that nuclear motion is classical explains many phenomena. The problems of Schrödinger’s cat and the EPR paradoxon do not exist in a perfectly deterministic theory. All it needs is to describe nuclear motion classically right from the beginning. To establish this [...] Read more.

The assumption that nuclear motion is classical explains many phenomena. The problems of Schrödinger’s cat and the EPR paradoxon do not exist in a perfectly deterministic theory. All it needs is to describe nuclear motion classically right from the beginning. To establish this simple idea, it must be tested for as many examples as possible. In the present paper, we use ab initio molecular dynamics to investigate the infrared spectrum of a ‘magic’ protonated water cluster H

_{3}

O

^{+}

(H

_{2}

O)

_{20}

which exhibits some features that were believed to afford a quantum treatment of nuclear motion. The role of the temperature in contrast to a quantum mechanical description is discussed. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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25 pages, 2020 KiB

Open AccessArticle

Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

by Andreas Schöller, H. Lee Woodcock and Stefan Boresch

Molecules 2023, 28(10), 4006; https://doi.org/10.3390/molecules28104006 - 10 May 2023

Cited by 3 | Viewed by 1515

Abstract

Non-equilibrium work switching simulations and Jarzynski’s equation are a reliable method for computing free energy differences,

Δ A^{low \to high}

, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular mechanical (QM/MM) description of a [...] Read more.

Non-equilibrium work switching simulations and Jarzynski’s equation are a reliable method for computing free energy differences,

Δ A^{low \to high}

, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular mechanical (QM/MM) description of a system of interest. Despite the inherent parallelism, the computational cost of this approach can quickly become very high. This is particularly true for systems where the core region, the part of the system to be described at different levels of theory, is embedded in an environment such as explicit solvent water. We find that even for relatively simple solute–water systems, switching lengths of at least 5 ps are necessary to compute

Δ A^{low \to high}

reliably. In this study, we investigate two approaches towards an affordable protocol, with an emphasis on keeping the switching length well below 5 ps. Inserting a hybrid charge intermediate state with modified partial charges, which resembles the charge distribution of the desired high level, makes it possible to obtain reliable calculations with 2 ps switches. Attempts using step-wise linear switching paths, on the other hand, did not lead to improvement, i.e., a faster convergence for all systems. To understand these findings, we analyzed the solutes’ properties as a function of the partial charges used and the number of water molecules in direct contact with the solute, and studied the time needed for water molecules to reorient themselves upon a change in the solute’s charge distribution. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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10 pages, 2208 KiB

Open AccessArticle

Sulphur- and Selenium-for-Oxygen Replacement as a Strategy to Obtain Dual Type I/Type II Photosensitizers for Photodynamic Therapy

by Mario Prejanò, Marta Erminia Alberto, Bruna Clara De Simone, Tiziana Marino, Marirosa Toscano and Nino Russo

Molecules 2023, 28(7), 3153; https://doi.org/10.3390/molecules28073153 - 01 Apr 2023

Cited by 5 | Viewed by 1529

Abstract

The effect on the photophysical properties of sulfur- and selenium-for-oxygen replacement in the skeleton of the oxo-4-dimethylaminonaphthalimide molecule (DMNP) has been explored at the density functional (DFT) level of theory. Structural parameters, excitation energies, singlet–triplet energy gaps (ΔE_S-T), and spin–orbit coupling [...] Read more.

The effect on the photophysical properties of sulfur- and selenium-for-oxygen replacement in the skeleton of the oxo-4-dimethylaminonaphthalimide molecule (DMNP) has been explored at the density functional (DFT) level of theory. Structural parameters, excitation energies, singlet–triplet energy gaps (ΔE_S-T), and spin–orbit coupling constants (SOC) have been computed. The determined SOCs indicate an enhanced probability of intersystem crossing (ISC) in both the thio- and seleno-derivatives (SDMNP and SeDMNP, respectively) and, consequently, an enhancement of the singlet oxygen quantum yields. Inspection of Type I reactions reveals that the electron transfer mechanisms leading to the generation of superoxide is feasible for all the compounds, suggesting a dual Type I/Type II activity. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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15 pages, 4078 KiB

Open AccessArticle

Theoretical and Anti-Klebsiella pneumoniae Evaluations of Substituted 2,7-dimethylimidazo[1,2-a]pyridine-3-carboxamide and Imidazopyridine Hydrazide Derivatives

by Suraj N. Mali, Amit Anand, Magdi E. A. Zaki, Sami A. Al-Hussain, Rahul D. Jawarkar, Anima Pandey and Aleksey Kuznetsov

Molecules 2023, 28(6), 2801; https://doi.org/10.3390/molecules28062801 - 20 Mar 2023

Cited by 4 | Viewed by 1369

Abstract

A series of multistep synthesis protocols was adopted to synthesize substituted imidazopyridines (IMPs) (SM-IMP-01 to SM-IMP-13, and DA-01-05). All substituted IMPs were then characterized using standard spectroscopic techniques such as ¹H-NMR, ¹³C-NMR, elemental analyses, and mass spectrometry. Our both in vitro [...] Read more.

A series of multistep synthesis protocols was adopted to synthesize substituted imidazopyridines (IMPs) (SM-IMP-01 to SM-IMP-13, and DA-01-05). All substituted IMPs were then characterized using standard spectroscopic techniques such as ¹H-NMR, ¹³C-NMR, elemental analyses, and mass spectrometry. Our both in vitro qualitative and quantitative results for antibacterial analysis, against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 suggested that all compounds essentially exhibited activity against selected strains of bacteria. Our DFT analyses suggested that the compounds of the SM-IMP-01–SM-IMP-13 series have HOMO/LUMO gaps within 4.43–4.69 eV, whereas the compounds of the DA-01–DA-05 series have smaller values of the HOMO/LUMO gaps, 3.24–4.17 eV. The lowest value of the global hardness and the highest value of the global softness, 2.215 and 0.226 eV, respectively, characterize the compound SM-IMP-02; thus, it is the most reactive compound in the imidazopyridine carboxamide series (except hydrazide series). This compound also depicted lesser MIC values against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 as 4.8 µg/mL, each. In terms of another series, hydrazide DA-05 depicted strong antimicrobial actions (MIC: 4.8 µg/mL against both bacterial strains) and also had the lowest energy gap (3.24 eV), higher softness (0.309 eV), and lesser hardness (1.62 eV). Overall, when we compare qualitative and quantitative antimicrobial results, it is been very clear that compounds with dibromo substitutions on imidazopyridine (IMP) rings would act as better antimicrobial agents than those with -H at the eighth position on the IMP ring. Furthermore, substituents of higher electronegativities would tend to enhance the biological activities of dibromo-IMP compounds. DFT properties were also well comparable to this trend and overall, we can say that the electronic behavior of compounds under investigation has key roles in their bioactivities. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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15 pages, 16567 KiB

Open AccessArticle

The Network Basis for the Structural Thermostability and the Functional Thermoactivity of Aldolase B

by Guangyu Wang

Molecules 2023, 28(4), 1850; https://doi.org/10.3390/molecules28041850 - 15 Feb 2023

Cited by 5 | Viewed by 1879

Abstract

Thermostability is important for the thermoactivity of proteins including enzymes. However, it is still challenging to pinpoint the specific structural factors for different temperature thresholds to initiate their specific structural and functional perturbations. Here, graph theory was used to investigate how the temperature-dependent [...] Read more.

Thermostability is important for the thermoactivity of proteins including enzymes. However, it is still challenging to pinpoint the specific structural factors for different temperature thresholds to initiate their specific structural and functional perturbations. Here, graph theory was used to investigate how the temperature-dependent noncovalent interactions as identified in the structures of aldolase B and its prevalent A149P mutant could form a systematic fluidic grid-like mesh network with topological grids to regulate the structural thermostability and the functional thermoactivity upon cyclization against decyclization in an extended range of a subunit. The results showed that the biggest grid may determine the melting temperature thresholds for the changes in their secondary and tertiary structures and specific catalytic activities. Further, a highly conserved thermostable grid may serve as an anchor to secure the flexible active site to achieve the specific thermoactivity. Finally, higher grid-based systematic thermal instability may disfavor the thermoactivity. Thus, this computational study may provide critical clues for the structural thermostability and the functional thermoactivity of proteins including enzymes. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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22 pages, 1072 KiB

Open AccessArticle

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

by Kacper Rzepiela, Jakub Kaminský, Aneta Buczek, Małgorzata A. Broda and Teobald Kupka

Molecules 2022, 27(23), 8230; https://doi.org/10.3390/molecules27238230 - 25 Nov 2022

Cited by 4 | Viewed by 1574

Abstract

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical [...] Read more.

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H₃PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry)

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