Journal of Molecular Modeling最新文献

Microstructure evolution and properties of liquid Fe–P with different phosphorus content: molecular dynamic investigation

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-10 DOI: 10.1007/s00894-025-06350-7

Chunhe Jiang, Bo Liu, Wang Liang, Jianliang Zhang, Kejiang Li

Context

With the scarcity of high-quality iron ore, high-phosphorus ores have become increasingly prevalent, posing challenges to maintaining the quality of steel. Phosphorus has emerged as a key factor affecting the fluidity of molten iron and the quality of steel products. Therefore, molecular dynamics method was conducted to analyze phosphorus’s impact on the microstructure and properties of liquid iron. The research examined phosphorus contents of 1 mol%, 3 mol%, 5 mol%, and 7 mol%, focusing on parameters like radial distribution functions, coordination numbers, and mean square displacements. Results showed that phosphorus decreases the viscosity, disrupts Fe–Fe bonds, and increases the self-diffusion coefficients of both Fe and P atoms. Microstructural analysis revealed phosphorus’s role in forming complex clusters, affecting the liquid iron’s local structural order. This research provides a deeper understanding of phosphorus behavior in liquid iron, offering insights for optimizing impurity control in ironmaking and enhancing the quality of steel products.

Method

Lammps software was conducted to do the molecular dynamics simulation using EAM potential with NVT ensemble at 1873 K. The research subject is Fe–P melts. The initial state model is created by randomly substituting Fe atoms in the iron crystal with P atoms based on the specific number of P atoms. The ISAACS software was used to analyze the trajectories of the Fe–P melt, including structural factors, radial distribution functions, coordination numbers, bond lengths, bond angles, and microscopic clusters. Additionally, mean square displacement and atomic diffusion coefficients are analyzed. The calculated viscosity is compared with experimental data from published literature.

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引用次数: 0

Theoretical study on the structures and properties of neutral and anionic molecular clusters Y6Sn0/− (n = 1—12)

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-07 DOI: 10.1007/s00894-025-06362-3

Xinchun Wu, Jucai Yang, Yaqing Chen, Caixia Dong

Context

Transition metal (TM) doped sulfur clusters, because of their novel physicochemical properties, have significant applications in fields such as new energy and nanomaterials, and have thus received widespread attention from scientists. Theoretical studies on the structures and properties of TM doped sulfur clusters are essential for designing novel nanomaterials. Therefore, we deeply studied the ground state structures, evolutionary patterns, electronic and optical properties of molecular clusters Y₆S_n^0/− (n = 1—12). The relative stability, HOMO–LUMO gaps, and thermodynamic stability of the ground state structure Y₆S_n^0/− (n = 1—12) indicate that the Y₆S₈⁻ cluster not only has thermodynamic stability, but also possesses relative stability. The aforementioned findings suggest that the Y₆S₈⁻ cluster are the most suitable building block for further development into a potential optoelectronic material.

Methods

The ground state structures were studied using global search Artificial Bee Colony (ABC) algorithm combined with density functional theory (DFT) and implemented in Gaussian 09 software package. The photoelectron spectra as well as Infrared and Raman spectra were simulated using Multiwfn and Gaussian View software, respectively. The adaptive natural density partitioning (AdNDP) analysis was performed on the most stable configuration Y₆S₈⁻ using visual molecular dynamics (VMD) software.

{"title":"Theoretical study on the structures and properties of neutral and anionic molecular clusters Y6Sn0/− (n = 1—12)","authors":"Xinchun Wu, Jucai Yang, Yaqing Chen, Caixia Dong","doi":"10.1007/s00894-025-06362-3","DOIUrl":"10.1007/s00894-025-06362-3","url":null,"abstract":"<div><h3>Context</h3><p>Transition metal (TM) doped sulfur clusters, because of their novel physicochemical properties, have significant applications in fields such as new energy and nanomaterials, and have thus received widespread attention from scientists. Theoretical studies on the structures and properties of TM doped sulfur clusters are essential for designing novel nanomaterials. Therefore, we deeply studied the ground state structures, evolutionary patterns, electronic and optical properties of molecular clusters Y<sub>6</sub>S<sub><i>n</i></sub><sup>0/−</sup> (<i>n</i> = 1—12). The relative stability, HOMO–LUMO gaps, and thermodynamic stability of the ground state structure Y<sub>6</sub>S<sub><i>n</i></sub><sup>0/−</sup> (<i>n</i> = 1—12) indicate that the Y<sub>6</sub>S<sub>8</sub><sup>−</sup> cluster not only has thermodynamic stability, but also possesses relative stability. The aforementioned findings suggest that the Y<sub>6</sub>S<sub>8</sub><sup>−</sup> cluster are the most suitable building block for further development into a potential optoelectronic material.</p><h3>Methods</h3><p>The ground state structures were studied using global search Artificial Bee Colony (ABC) algorithm combined with density functional theory (DFT) and implemented in Gaussian 09 software package. The photoelectron spectra as well as Infrared and Raman spectra were simulated using Multiwfn and Gaussian View software, respectively. The adaptive natural density partitioning (AdNDP) analysis was performed on the most stable configuration Y<sub>6</sub>S<sub>8</sub><sup>−</sup> using visual molecular dynamics (VMD) software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A study of asphaltene solubility and aggregation due to sulfur heteroatoms: molecular dynamics simulation

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-07 DOI: 10.1007/s00894-025-06358-z

Ulviyya J. Yolchuyeva, Orhan R. Abbasov, Rena A. Jafarova, Gunay A. Hajiyeva, Ravan A. Rahimov, Nazli A. Mehdiyeva, Elnur E. Baloglanov

Context

This study describes the molecular dynamics (MD) simulations to investigate the effects of sulfur atom position on the solubility and aggregation properties of asphaltenes extracted from Zaghli crude oil (East Azerbaijan). Two different asphaltene models were studied, i.e., A1 with sulfur in the aromatic ring and A2 with sulfur in the aliphatic side chain. The radial distribution function (RDF) analysis revealed significant differences in aggregation trends. A1 exhibited rapid aggregation in both solvents used in the experiments, as evidenced by a significant decrease in the radius of gyration from 0.6 to 0.4 Å in octane and from 0.8 to 0.5 Å in xylene. In contrast, A2 showed increased solubility; especially in xylene with a marked increase in the radius of gyration from 0.5 to 2 Å. Furthermore, the energy analysis confirmed these results, i.e., A2 exhibited a higher total energy (451.16 kcal/mol) than A1 (221.28 kcal/mol); indicating a more energetically favorable and less aggregated state of A2. These computational results open up new possibilities for understanding the critical role of the sulfur atom position in the asphaltene structure on its aggregation propensity, which can be used to prevent asphaltene-related problems in the petroleum industry. The work is very useful in the oil industry for enhancing oil production by studying asphaltene solubility and aggregation.

Methods

MD simulations were performed using the COMPASS force field and Material Studio V.6 2017 software to evaluate the solubility of asphaltenes in octane and xylene solvents. Geometric optimization was carried out to address unstable interactions, with periodic boundary conditions applied. Simulations were conducted in the NVT ensemble at 298 K and 1 atm pressure, using a time step of 1 fs, a Nose thermostat for temperature control, and a Berendsen thermostat for pressure control. RDF analysis was utilized to examine the behavior of two distinct asphaltene models, which differed in the positioning of the sulfur atom, in the solvents. The total energy contributions, including van der Waals and electrostatic interactions, were also analyzed.

{"title":"A study of asphaltene solubility and aggregation due to sulfur heteroatoms: molecular dynamics simulation","authors":"Ulviyya J. Yolchuyeva, Orhan R. Abbasov, Rena A. Jafarova, Gunay A. Hajiyeva, Ravan A. Rahimov, Nazli A. Mehdiyeva, Elnur E. Baloglanov","doi":"10.1007/s00894-025-06358-z","DOIUrl":"10.1007/s00894-025-06358-z","url":null,"abstract":"<div><h3>Context</h3><p>This study describes the molecular dynamics (MD) simulations to investigate the effects of sulfur atom position on the solubility and aggregation properties of asphaltenes extracted from Zaghli crude oil (East Azerbaijan). Two different asphaltene models were studied, i.e., A1 with sulfur in the aromatic ring and A2 with sulfur in the aliphatic side chain. The radial distribution function (RDF) analysis revealed significant differences in aggregation trends. A1 exhibited rapid aggregation in both solvents used in the experiments, as evidenced by a significant decrease in the radius of gyration from 0.6 to 0.4 Å in octane and from 0.8 to 0.5 Å in xylene. In contrast, A2 showed increased solubility; especially in xylene with a marked increase in the radius of gyration from 0.5 to 2 Å. Furthermore, the energy analysis confirmed these results, i.e., A2 exhibited a higher total energy (451.16 kcal/mol) than A1 (221.28 kcal/mol); indicating a more energetically favorable and less aggregated state of A2. These computational results open up new possibilities for understanding the critical role of the sulfur atom position in the asphaltene structure on its aggregation propensity, which can be used to prevent asphaltene-related problems in the petroleum industry. The work is very useful in the oil industry for enhancing oil production by studying asphaltene solubility and aggregation.</p><h3>Methods</h3><p>MD simulations were performed using the COMPASS force field and Material Studio V.6 2017 software to evaluate the solubility of asphaltenes in octane and xylene solvents. Geometric optimization was carried out to address unstable interactions, with periodic boundary conditions applied. Simulations were conducted in the NVT ensemble at 298 K and 1 atm pressure, using a time step of 1 fs, a Nose thermostat for temperature control, and a Berendsen thermostat for pressure control. RDF analysis was utilized to examine the behavior of two distinct asphaltene models, which differed in the positioning of the sulfur atom, in the solvents. The total energy contributions, including van der Waals and electrostatic interactions, were also analyzed.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Theoretical study of the nature of σ-hole regium bond between CuX/AgX/AuX and pyridine

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-07 DOI: 10.1007/s00894-025-06360-5

Junyong Wu, Hua Yan, Hao Chen, Guoliang Dai

Context

The σ-hole regium bond complexes between coinage metal monohalide molecule CuX/AgX/AuX (X = F, Cl, and Br) and pyridine (C₅H₅N), which have linear orientation and perpendicular orientation, have been systematically probed at the MP2/aug-cc-pVTZ level. By comparing the calculated interaction energy, we can see that the linear orientation interactions are a little stronger than the corresponding perpendicular orientation interactions in C₅H₅N-CuX/AgX/AuX complexes. The binding energies for linear orientation regium bond complexes range from − 34 to − 60 kcal/mol, while those perpendicular orientation regium bond complexes are from − 24 to − 50 kcal/mol. Both types of interactions energies all tend to follow the Au > Cu > Ag order and reduced with the decrease in electronegativity F > Cl > Br in C₅H₅N-CuX/AgX/AuX complexes. The electrostatic energy is the major source of the attraction for the linear orientation regium bond interactions, while for the perpendicular orientation regium bond interactions are mainly due to electrostatic and induction energy.

Methods

All the complexes and respective monomers were optimized at the MP2/aug-cc-pVTZ level. Relativistic effects were considered for Cu, Ag, Au, and Br by using the aug-cc-pVTZ-PP basis set. The NBO population analysis and AIM and IRI analysis were carried out. The interaction energies of the σ-hole regium bonds complexes were decomposed by using the symmetric adaptive perturbation theory (SAPT).

{"title":"Theoretical study of the nature of σ-hole regium bond between CuX/AgX/AuX and pyridine","authors":"Junyong Wu, Hua Yan, Hao Chen, Guoliang Dai","doi":"10.1007/s00894-025-06360-5","DOIUrl":"10.1007/s00894-025-06360-5","url":null,"abstract":"<div><h3>Context</h3><p>The σ-hole regium bond complexes between coinage metal monohalide molecule CuX/AgX/AuX (X = F, Cl, and Br) and pyridine (C<sub>5</sub>H<sub>5</sub>N), which have linear orientation and perpendicular orientation, have been systematically probed at the MP2/aug-cc-pVTZ level. By comparing the calculated interaction energy, we can see that the linear orientation interactions are a little stronger than the corresponding perpendicular orientation interactions in C<sub>5</sub>H<sub>5</sub>N-CuX/AgX/AuX complexes. The binding energies for linear orientation regium bond complexes range from − 34 to − 60 kcal/mol, while those perpendicular orientation regium bond complexes are from − 24 to − 50 kcal/mol. Both types of interactions energies all tend to follow the Au > Cu > Ag order and reduced with the decrease in electronegativity F > Cl > Br in C<sub>5</sub>H<sub>5</sub>N-CuX/AgX/AuX complexes. The electrostatic energy is the major source of the attraction for the linear orientation regium bond interactions, while for the perpendicular orientation regium bond interactions are mainly due to electrostatic and induction energy.</p><h3>Methods</h3><p>All the complexes and respective monomers were optimized at the MP2/aug-cc-pVTZ level. Relativistic effects were considered for Cu, Ag, Au, and Br by using the aug-cc-pVTZ-PP basis set. The NBO population analysis and AIM and IRI analysis were carried out. The interaction energies of the σ-hole regium bonds complexes were decomposed by using the symmetric adaptive perturbation theory (SAPT).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular docking of Cu(II) and Zn(II) complexes for tyrosinase inhibition and drug loading on boron nitride nanotube scaffolds using Monte Carlo simulations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-07 DOI: 10.1007/s00894-025-06355-2

Najeeb Ullah, Amir Karim, Muhammad Iqbal, Rahime Eshaghi Malekshah, Saqib Ali, Jebiti Haribabu, Sodio C. N. Hsu

Context

Recent studies on drug delivery systems incorporating boron nitride nanostructures (BNNTs) highlight their excellent chemical stability and non-cytotoxic properties, positioning them as a promising platform for drug release in biomedical applications. This study aimed to optimize the mono-nuclear structures of Cu(II) and Zn(II) complexes and to functionalize zigzag (13, 13) boron nitride nanotubes with glutamic acid (GABNNTs). Based on Monte Carlo, the results revealed that complexes 6 and 19 exhibited stronger interactions with GABNNTs, attributed to π-π stacking between bipyridine/phenanthroline ligands and GABNNTs. This interaction suggests a greater challenge in their release compared to other compounds. The interaction energy analysis further revealed that complexes 1, 4, and 12/GABNNTs exhibited the lowest stability, indicating weaker binding interactions between these complexes and the GABNNT surface. The adsorption of all complexes on GABNNTs was primarily found to be physisorption. Molecular docking with mushroom tyrosinase (2Y9X) identified complexes 5, 10, 11, 15, and 20 as having the strongest interactions, a trend that is partially supported by chemical hardness analysis. However, DFT-D results indicated that complexes 5, 11, and 20 exhibited the lowest chemical stability, suggesting a trade-off between strong interactions and lower stability in these complexes.

Methods

The energies of these systems were estimated using dispersion-corrected density functional theory (DFT-D) calculations performed in Materials Studio 2017. To evaluate the drug delivery potential of GABNNTs for Cu(II) and Zn(II) complexes, the Monte Carlo (MC) method was employed. The structural and electronic properties, as well as the relationship between biological activities and ΔE_g, were analyzed by calculating the HOMO–LUMO energy gap using the dispersion-corrected density functional theory (DFT-D) method. Molecular docking was used to interact with mushroom tyrosinase (2Y9X).

{"title":"Molecular docking of Cu(II) and Zn(II) complexes for tyrosinase inhibition and drug loading on boron nitride nanotube scaffolds using Monte Carlo simulations","authors":"Najeeb Ullah, Amir Karim, Muhammad Iqbal, Rahime Eshaghi Malekshah, Saqib Ali, Jebiti Haribabu, Sodio C. N. Hsu","doi":"10.1007/s00894-025-06355-2","DOIUrl":"10.1007/s00894-025-06355-2","url":null,"abstract":"<div><h3>Context</h3><p>Recent studies on drug delivery systems incorporating boron nitride nanostructures (BNNTs) highlight their excellent chemical stability and non-cytotoxic properties, positioning them as a promising platform for drug release in biomedical applications. This study aimed to optimize the mono-nuclear structures of Cu(II) and Zn(II) complexes and to functionalize zigzag (13, 13) boron nitride nanotubes with glutamic acid (GABNNTs). Based on Monte Carlo, the results revealed that complexes <b>6</b> and <b>19</b> exhibited stronger interactions with GABNNTs, attributed to π-π stacking between bipyridine/phenanthroline ligands and GABNNTs. This interaction suggests a greater challenge in their release compared to other compounds. The interaction energy analysis further revealed that complexes <b>1</b>, <b>4</b>, and <b>12</b>/GABNNTs exhibited the lowest stability, indicating weaker binding interactions between these complexes and the GABNNT surface. The adsorption of all complexes on GABNNTs was primarily found to be physisorption. Molecular docking with mushroom tyrosinase (2Y9X) identified complexes <b>5</b>, <b>10</b>, <b>11</b>, <b>15</b>, and <b>20</b> as having the strongest interactions, a trend that is partially supported by chemical hardness analysis. However, DFT-D results indicated that complexes <b>5</b>, <b>11</b>, and <b>20</b> exhibited the lowest chemical stability, suggesting a trade-off between strong interactions and lower stability in these complexes.</p><h3>Methods</h3><p>The energies of these systems were estimated using dispersion-corrected density functional theory (DFT-D) calculations performed in Materials Studio 2017. To evaluate the drug delivery potential of GABNNTs for Cu(II) and Zn(II) complexes, the Monte Carlo (MC) method was employed. The structural and electronic properties, as well as the relationship between biological activities and ΔE<sub>g</sub>, were analyzed by calculating the HOMO–LUMO energy gap using the dispersion-corrected density functional theory (DFT-D) method. Molecular docking was used to interact with mushroom tyrosinase (2Y9X).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study 一些植物化学物质与 Er2O3 纳米粒子的相互作用：第一原理研究

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-03 DOI: 10.1007/s00894-025-06361-4

Mahmood Akbari

Context

The interaction between phytochemicals and nanoparticles plays a crucial role in nanotechnology and biomedical applications. This study investigates the binding behavior and stability of six phytochemicals—Catechin, Limonene, Sabinene, Sinapic Acid, Vanillic Acid, and Luteolin 7-O-ß-glucuronide—with Er₂O₃ nanoparticles using Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. The findings indicate that Luteolin, Catechin, and Sinapic Acid exhibit the strongest binding affinities and highest structural stability with Er₂O₃, attributed to their balanced hydrophilicity-lipophilicity and favorable electronic properties. These insights contribute to the design and functionalization of phytochemical-based nanomaterials, with potential applications in drug delivery, bioimaging, and photodynamic therapy.

Methods

DFT calculations were conducted using Gaussian 09 at the B3LYP/6–311 + + G(d,p) level to determine HOMO–LUMO energy gaps, dipole moments, and polarizability of the phytochemicals. MD simulations, performed using GROMACS 2019 with the CHARMM36 force field and TIP3P water model, analyzed the dynamics of phytochemical adsorption on a 5 nm Er₂O₃ nanoparticle over 50 ns. Key parameters such as interaction energies, root mean square deviations (RMSD), radial distribution functions (RDF), and water solubility (logS) were evaluated using ALOPGPS 2.1 software.

{"title":"Interaction of some phytochemical compounds with Er2O3 nanoparticle: First principle study","authors":"Mahmood Akbari","doi":"10.1007/s00894-025-06361-4","DOIUrl":"10.1007/s00894-025-06361-4","url":null,"abstract":"<div><h3>Context</h3><p>The interaction between phytochemicals and nanoparticles plays a crucial role in nanotechnology and biomedical applications. This study investigates the binding behavior and stability of six phytochemicals—Catechin, Limonene, Sabinene, Sinapic Acid, Vanillic Acid, and Luteolin 7-O-ß-glucuronide—with Er₂O₃ nanoparticles using Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. The findings indicate that Luteolin, Catechin, and Sinapic Acid exhibit the strongest binding affinities and highest structural stability with Er<sub>2</sub>O<sub>3</sub>, attributed to their balanced hydrophilicity-lipophilicity and favorable electronic properties. These insights contribute to the design and functionalization of phytochemical-based nanomaterials, with potential applications in drug delivery, bioimaging, and photodynamic therapy.</p><h3>Methods</h3><p>DFT calculations were conducted using Gaussian 09 at the B3LYP/6–311 + + G(d,p) level to determine HOMO–LUMO energy gaps, dipole moments, and polarizability of the phytochemicals. MD simulations, performed using GROMACS 2019 with the CHARMM36 force field and TIP3P water model, analyzed the dynamics of phytochemical adsorption on a 5 nm Er<sub>2</sub>O<sub>3</sub> nanoparticle over 50 ns. Key parameters such as interaction energies, root mean square deviations (RMSD), radial distribution functions (RDF), and water solubility (logS) were evaluated using ALOPGPS 2.1 software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06361-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adsorption attributes of β-phosphoborophane nanosheets towards some vapors emitted from cosmetics—a first-principles study

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-03 DOI: 10.1007/s00894-025-06352-5

V. Nagarajan, Lakshitaa B., R. Chandiramouli

Context

Recently, new two-dimensional (2D) materials have emerged and are used for various engineering applications. One such new 2D material is beta (β-)phosphoborophane. Initially, we ensured the structural and dynamic stability of β-phosphoborophane. The semiconducting behavior of β-phosphoborophane with an energy band of 1.252 eV reveals that it is a suitable material for chemical nanosensors. We used β-phosphoborophane as adsorbing material for some of the molecules emitted from cosmetics such as hydroxycitronellal and alpha isomethyl ionone. The adsorption of target molecules changes the energy band gap of β-phosphoborophane, inferred based on the results of band structure and projected density of states. Furthermore, the changes in the electronic properties of β-phosphoborophane upon adsorption of target molecules are observed with regard to charge transfer and electron density difference results. The chemo-resistive nature of β-phosphoborophane is revealed from the relative energy gap changes owing to hydroxycitronellal and alpha isomethyl ionone adsorption.

Methods

The structural stability, dynamical firmness, electronic properties, and interaction behavior of hydroxycitronellal and alpha isomethyl ionone on β-phosphoborophane are explored within the framework of the DFT method. The hybrid GGA/B3LYP functional is used for optimizing the base material β-phosphoborophane. All the calculation in the research study is carried out by the QuantumATK simulation package. The result of the proposed work supports that β-phosphoborophane can be a suitable sensing material for hydroxycitronellal and alpha isomethyl ionone, which are found in cosmetics.

{"title":"Adsorption attributes of β-phosphoborophane nanosheets towards some vapors emitted from cosmetics—a first-principles study","authors":"V. Nagarajan, Lakshitaa B., R. Chandiramouli","doi":"10.1007/s00894-025-06352-5","DOIUrl":"10.1007/s00894-025-06352-5","url":null,"abstract":"<div><h3>Context</h3><p>Recently, new two-dimensional (2D) materials have emerged and are used for various engineering applications. One such new 2D material is beta (β-)phosphoborophane. Initially, we ensured the structural and dynamic stability of β-phosphoborophane. The semiconducting behavior of β-phosphoborophane with an energy band of 1.252 eV reveals that it is a suitable material for chemical nanosensors. We used β-phosphoborophane as adsorbing material for some of the molecules emitted from cosmetics such as hydroxycitronellal and alpha isomethyl ionone. The adsorption of target molecules changes the energy band gap of β-phosphoborophane, inferred based on the results of band structure and projected density of states. Furthermore, the changes in the electronic properties of β-phosphoborophane upon adsorption of target molecules are observed with regard to charge transfer and electron density difference results. The chemo-resistive nature of β-phosphoborophane is revealed from the relative energy gap changes owing to hydroxycitronellal and alpha isomethyl ionone adsorption.</p><h3>Methods</h3><p>The structural stability, dynamical firmness, electronic properties, and interaction behavior of hydroxycitronellal and alpha isomethyl ionone on β-phosphoborophane are explored within the framework of the DFT method. The hybrid GGA/B3LYP functional is used for optimizing the base material β-phosphoborophane. All the calculation in the research study is carried out by the QuantumATK simulation package. The result of the proposed work supports that β-phosphoborophane can be a suitable sensing material for hydroxycitronellal and alpha isomethyl ionone, which are found in cosmetics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Excited-state proton transfer in the rare isoguanine-isocytosine base pair in water solution

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-02 DOI: 10.1007/s00894-025-06351-6

Tsvetina D. Cherneva, Mina M. Todorova, Rumyana I. Bakalska, Ernst Horkel, Vassil B. Delchev

Context

With the current research, we aim to study the mechanism of the excites state proton transfer (ESPT) between the nucleobases isoguanine (iG) and isocytosine (iC) in their Watson–Crick model. Such research is proposed for the first time and it can partially reveal the question why the nature “has chosen” guanine and cytosine for pairing in the DNA duplex and not their analogs (isoforms). The UV irradiation of the water solution of equimolar mixture of iG and iC implies a tautomeric conversion between the nucleobases. In the research, the mechanism of the ESPT was followed and clarified for the first time. All this reflects to the photostability of the iG-iC base pair in water solution.

Methods

For the purposes of the current research, we chose to use the TD DFT with the hybrid functional B3LYP in combination with the aug-cc-pVDZ basis set. The water surroundings are modeled according to the polarizable continuum model (PCM) modeling the solvation effects on the studying systems. Linear interpolation and intrinsic reaction coordinate approach were applied for the reaction path follow of the ESPT.

{"title":"Excited-state proton transfer in the rare isoguanine-isocytosine base pair in water solution","authors":"Tsvetina D. Cherneva, Mina M. Todorova, Rumyana I. Bakalska, Ernst Horkel, Vassil B. Delchev","doi":"10.1007/s00894-025-06351-6","DOIUrl":"10.1007/s00894-025-06351-6","url":null,"abstract":"<div><h3>Context</h3><p>With the current research, we aim to study the mechanism of the excites state proton transfer (ESPT) between the nucleobases isoguanine (iG) and isocytosine (iC) in their Watson–Crick model. Such research is proposed for the first time and it can partially reveal the question why the nature “has chosen” guanine and cytosine for pairing in the DNA duplex and not their analogs (isoforms). The UV irradiation of the water solution of equimolar mixture of iG and iC implies a tautomeric conversion between the nucleobases. In the research, the mechanism of the ESPT was followed and clarified for the first time. All this reflects to the photostability of the iG-iC base pair in water solution.</p><h3>Methods</h3><p>For the purposes of the current research, we chose to use the TD DFT with the hybrid functional B3LYP in combination with the aug-cc-pVDZ basis set. The water surroundings are modeled according to the polarizable continuum model (PCM) modeling the solvation effects on the studying systems. Linear interpolation and intrinsic reaction coordinate approach were applied for the reaction path follow of the ESPT.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effect of fabrication process parameters and graphene reinforcement on mechanical behaviour of additively manufactured AlSi10Mg alloy: A molecular dynamics simulation study

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-02 DOI: 10.1007/s00894-025-06354-3

Sunita K. Srivastava, N. Rajesh Mathivanan

Context

AlSi10Mg alloy is among the most widely recognised aluminium alloys due to its dimensional stability and exceptional properties for additive manufacturing. However, the alloy’s performance can be improved and optimized through appropriate reinforcement and control of the manufacturing process parameters. This work focuses on the impact of process parameters (laser power, scan speed and layer thickness) and graphene reinforcement on the mechanical properties of SLM-fabricated AlSi10Mg alloy. The results indicate that, increasing the laser power within the studied range enhances both tensile and compressive strength. Furthermore, reducing the laser scanning speed improved these properties, although further reduction beyond a threshold value minimizes the impact. However, increasing the layer thickness while maintaining the same laser power reduces the material properties, the effect can be mitigated by supplying more laser energy. The addition of graphene as reinforcement has markedly improved the composite properties, improving its elastic and plastic behaviour. The graphene reinforcement also improved the stiffness, yield strength, toughness, and ultimate strength making it a highly effective way to enhance the AlSi10Mg alloy performance.

Methods

In this study, molecular dynamics (MD) was performed to model the selective laser melting (SLM) process using LAMMPS (large-scale atomic/molecular massively parallel simulator) software. The simulation setup was programmed to analyse the impact of process parameters, including laser power (500, 600, and 700 μW), scanning speed (1, 1.5, and 2 nm/ps) and layer thickness (two and three-particle layer system) on the mechanical properties (tensile and compressive strength) of AlSi10Mg alloy. Additionally, the impact of graphene reinforcement was also examined using nano-scale simulation. The simulation provides insights into both the SLM process and the mechanical behaviour of the alloy and its composite under different processing conditions.

{"title":"Effect of fabrication process parameters and graphene reinforcement on mechanical behaviour of additively manufactured AlSi10Mg alloy: A molecular dynamics simulation study","authors":"Sunita K. Srivastava, N. Rajesh Mathivanan","doi":"10.1007/s00894-025-06354-3","DOIUrl":"10.1007/s00894-025-06354-3","url":null,"abstract":"<div><h3>Context</h3><p>AlSi10Mg alloy is among the most widely recognised aluminium alloys due to its dimensional stability and exceptional properties for additive manufacturing. However, the alloy’s performance can be improved and optimized through appropriate reinforcement and control of the manufacturing process parameters. This work focuses on the impact of process parameters (laser power, scan speed and layer thickness) and graphene reinforcement on the mechanical properties of SLM-fabricated AlSi10Mg alloy. The results indicate that, increasing the laser power within the studied range enhances both tensile and compressive strength. Furthermore, reducing the laser scanning speed improved these properties, although further reduction beyond a threshold value minimizes the impact. However, increasing the layer thickness while maintaining the same laser power reduces the material properties, the effect can be mitigated by supplying more laser energy. The addition of graphene as reinforcement has markedly improved the composite properties, improving its elastic and plastic behaviour. The graphene reinforcement also improved the stiffness, yield strength, toughness, and ultimate strength making it a highly effective way to enhance the AlSi10Mg alloy performance.</p><h3>Methods</h3><p>In this study, molecular dynamics (MD) was performed to model the selective laser melting (SLM) process using LAMMPS (large-scale atomic/molecular massively parallel simulator) software. The simulation setup was programmed to analyse the impact of process parameters, including laser power (500, 600, and 700 μW), scanning speed (1, 1.5, and 2 nm/ps) and layer thickness (two and three-particle layer system) on the mechanical properties (tensile and compressive strength) of AlSi10Mg alloy. Additionally, the impact of graphene reinforcement was also examined using nano-scale simulation. The simulation provides insights into both the SLM process and the mechanical behaviour of the alloy and its composite under different processing conditions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico study of a new class of DNA fluorescent probes: docking, molecular dynamics and quantum chemistry calculations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-04-01 DOI: 10.1007/s00894-025-06342-7

Guilherme Saldanha Henkin, Simone Cristina Baggio Gnoatto, Diego Defferrari, Bruno Bercini de Araújo, Paulo Fernando Bruno Gonçalves, Paulo Augusto Netz

Context

Natural fluorescence in biochemical structures can result in unsatisfactory outcomes in cell imaging. This drawback can be addressed by using probe molecules that fluoresce via Excited State Intramolecular Proton Transfer (ESIPT), thereby improving resolution and the signal-to-noise ratio. A docking study was conducted to estimate the binding free energy of 132 benzazoles and to determine their binding modes (minor groove (MG) or intercalation (INT)) to DNA, comparing them with the commercial probes 4’,6-Diamidino-2-phenylindole dihydrochloride (DAPI) and acridine orange (AO). Atomistic molecular dynamics simulations under physiological conditions were performed for the five top-ranked ligands, as well as for AO and DAPI. Three of the investigated ligands exhibited stronger binding energy than both commercial probes, while the other two showed stronger binding energy than AO, but not than DAPI. The proposed benzazoles acted as intercalators and MG binders. Using molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations to estimate the binding free energy of the ligand-receptor complexes, we could confirm the strong interaction of these molecules with DNA. Quantum Chemical Calculations were performed to estimate the emission energies upon excitation of the selected ligands, which showed large Stokes shift values and, for some molecules, favorable ESIPT processes. Benzazoles 1–5 demonstrated strong interactions with DNA, surpassing the commercial probes in binding strength and displaying promising photophysical properties. Consequently, these ligands are promising fluorescent DNA probes, suitable for various diagnostic techniques.

Methods

132 Benzazole ligands were constructed and optimized using Gabedit and docked to a B-DNA oligomer using AutoDock. Molecular dynamics simulations were run in GROMACS, using AMBER-parmbsc0 and GAFF force fields. Quantum chemical calculations (TD-DFT) in Gaussian 16 provided excited-state properties, optimized at the CAM-B3LYP/cc-pVDZ level of theory.

{"title":"In silico study of a new class of DNA fluorescent probes: docking, molecular dynamics and quantum chemistry calculations","authors":"Guilherme Saldanha Henkin, Simone Cristina Baggio Gnoatto, Diego Defferrari, Bruno Bercini de Araújo, Paulo Fernando Bruno Gonçalves, Paulo Augusto Netz","doi":"10.1007/s00894-025-06342-7","DOIUrl":"10.1007/s00894-025-06342-7","url":null,"abstract":"<div><h3>Context</h3><p>Natural fluorescence in biochemical structures can result in unsatisfactory outcomes in cell imaging. This drawback can be addressed by using probe molecules that fluoresce via Excited State Intramolecular Proton Transfer (ESIPT), thereby improving resolution and the signal-to-noise ratio. A docking study was conducted to estimate the binding free energy of 132 benzazoles and to determine their binding modes (minor groove (MG) or intercalation (INT)) to DNA, comparing them with the commercial probes 4’,6-Diamidino-2-phenylindole dihydrochloride (DAPI) and acridine orange (AO). Atomistic molecular dynamics simulations under physiological conditions were performed for the five top-ranked ligands, as well as for AO and DAPI. Three of the investigated ligands exhibited stronger binding energy than both commercial probes, while the other two showed stronger binding energy than AO, but not than DAPI. The proposed benzazoles acted as intercalators and MG binders. Using molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations to estimate the binding free energy of the ligand-receptor complexes, we could confirm the strong interaction of these molecules with DNA. Quantum Chemical Calculations were performed to estimate the emission energies upon excitation of the selected ligands, which showed large Stokes shift values and, for some molecules, favorable ESIPT processes. Benzazoles 1–5 demonstrated strong interactions with DNA, surpassing the commercial probes in binding strength and displaying promising photophysical properties. Consequently, these ligands are promising fluorescent DNA probes, suitable for various diagnostic techniques.</p><h3>Methods</h3><p>132 Benzazole ligands were constructed and optimized using Gabedit and docked to a B-DNA oligomer using AutoDock. Molecular dynamics simulations were run in GROMACS, using AMBER-parmbsc0 and GAFF force fields. Quantum chemical calculations (TD-DFT) in Gaussian 16 provided excited-state properties, optimized at the CAM-B3LYP/cc-pVDZ level of theory.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143740690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0