Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115022
Bin Liu , Wen-Lu Wang , Yan-Ni Su , Ya-Ling Ye , Wei-Ming Sun
The interaction between a boron-based Zn@B38 superatom and five drugs, including cisplatin (DDP), 5-fluorouracil (FU), mercaptopurine (MP), hydroxyurea (HU) and nitrogen mustard (CM) have been investigated. The adsorption of these anticancer drugs onto Zn@B38 reduces the energy gap of this superatom. Except for DDP, these drugs exhibit strong covalent interaction with the vertex of Zn@B38 because the lone pair of N/O atom of FU, MP, HU, and CM can fill into the empty atomic orbital of the electron-deficient boron atom of Zn@B38 to form polar covalent bonds, resulting in the charge transfer from drugs to Zn@B38. Hence, the adsorption energies of drug@[Zn@B38] (drug = FU, MP, HU, and CM) are −37.67 to −57.21 kcal/mol, but can be significantly decreased to −8.63–5.48 kcal/mol upon protonation, suggesting that these drugs can be efficiently adsorbed by the Zn@B38 carrier in neutral aqueous solution but are easily released in the acidic tumor microenvironment.
{"title":"On the potential of Zn@B38 superatom as a drug delivery vehicle for several anticancer drugs: A DFT study","authors":"Bin Liu , Wen-Lu Wang , Yan-Ni Su , Ya-Ling Ye , Wei-Ming Sun","doi":"10.1016/j.comptc.2024.115022","DOIUrl":"10.1016/j.comptc.2024.115022","url":null,"abstract":"<div><div>The interaction between a boron-based Zn@B<sub>38</sub> superatom and five drugs, including cisplatin (DDP), 5-fluorouracil (FU), mercaptopurine (MP), hydroxyurea (HU) and nitrogen mustard (CM) have been investigated. The adsorption of these anticancer drugs onto Zn@B<sub>38</sub> reduces the energy gap of this superatom. Except for DDP, these drugs exhibit strong covalent interaction with the vertex of Zn@B<sub>38</sub> because the lone pair of N/O atom of FU, MP, HU, and CM can fill into the empty atomic orbital of the electron-deficient boron atom of Zn@B<sub>38</sub> to form polar covalent bonds, resulting in the charge transfer from drugs to Zn@B<sub>38</sub>. Hence, the adsorption energies of drug@[Zn@B<sub>38</sub>] (drug = FU, MP, HU, and CM) are −37.67 to −57.21 kcal/mol, but can be significantly decreased to −8.63–5.48 kcal/mol upon protonation, suggesting that these drugs can be efficiently adsorbed by the Zn@B<sub>38</sub> carrier in neutral aqueous solution but are easily released in the acidic tumor microenvironment.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115022"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115074
Linian Li
This study examines the sensing performance of transition metal doped C7N3 sensor structures for four toxic gases (H2S, SO2, NO2, and NO). A series of sensor configurations with single transition metal atoms doped with C7N3 (TM-C7N3) are constructed. The results of the stability analysis indicate that, with the exception of Ni-C7N3, all sensor configurations demonstrate excellent structural stability. Notably, Os-C7N3 exhibits a high adsorption strength for four toxic gases. Furthermore, the adsorption strength of TM-C7N3 towards NO consistently surpasses that of the other gases investigated. Ultimately, by comparing recovery times, the most effective gas sensor is identified. At 298 K, Pd-C7N3 is a suitable H2S gas sensor, and Fe-C7N3 and Co-C7N3 are suitable SO2 gas sensors. At 398 K and above temperatures, Fe- and Rh-C7N3 are promising H2S gas sensors, and Pt-C7N3 is a promising SO2 and NO2 gas sensor.
{"title":"Investigating the adsorption and sensing of H2S, SO2, NO, and NO2 on transition metal atom doped C7N3 using DFT","authors":"Linian Li","doi":"10.1016/j.comptc.2025.115074","DOIUrl":"10.1016/j.comptc.2025.115074","url":null,"abstract":"<div><div>This study examines the sensing performance of transition metal doped C<sub>7</sub>N<sub>3</sub> sensor structures for four toxic gases (H<sub>2</sub>S, SO<sub>2</sub>, NO<sub>2</sub>, and NO). A series of sensor configurations with single transition metal atoms doped with C<sub>7</sub>N<sub>3</sub> (TM-C<sub>7</sub>N<sub>3</sub>) are constructed. The results of the stability analysis indicate that, with the exception of Ni-C<sub>7</sub>N<sub>3</sub>, all sensor configurations demonstrate excellent structural stability. Notably, Os-C<sub>7</sub>N<sub>3</sub> exhibits a high adsorption strength for four toxic gases. Furthermore, the adsorption strength of TM-C<sub>7</sub>N<sub>3</sub> towards NO consistently surpasses that of the other gases investigated. Ultimately, by comparing recovery times, the most effective gas sensor is identified. At 298 K, Pd-C<sub>7</sub>N<sub>3</sub> is a suitable H<sub>2</sub>S gas sensor, and Fe-C<sub>7</sub>N<sub>3</sub> and Co-C<sub>7</sub>N<sub>3</sub> are suitable SO<sub>2</sub> gas sensors. At 398 K and above temperatures, Fe- and Rh-C<sub>7</sub>N<sub>3</sub> are promising H<sub>2</sub>S gas sensors, and Pt-C<sub>7</sub>N<sub>3</sub> is a promising SO<sub>2</sub> and NO<sub>2</sub> gas sensor.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115074"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The quest for organic molecules with tunable optoelectronic properties for specific purposes is still continuing and computational designing strategies gain momentum in recent years. In this context, BOAPY core moiety attracts our attention due to its excellent photophysical properties and structural flexibility. Therefore, here we made an attempt to further enhance the photophysical properties of BOAPY molecule by introducing electron donating tuner group such as –OCH3, –NH2, –NH(CH3) and –N(CH3)2 as well as electron withdrawing flanking groups such as –F, –CF3 and –CN, one on each side of the tuner group. Totally, we have designed 25 molecules and analyzed their optical and Non-Linear Optical (NLO) properties using Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculations. These calculations are done at M06-2X/6-31+G(d,p) level of theory. The wavelength dependent NLO properties of the designed molecules are also determined. Our studies reveal that the HOMO-LUMO energy gap (ΔE) decreases with an increase in the electron donating nature of the tuner group. The electron withdrawing flanking groups such as –CF3 and –CN are acting well in reducing the ΔE value. The simulated absorption spectra of the designed molecules show that the λmax increases with the electron donating power of the tuner group. Electron Localization Function (ELF) and Localized Orbital Locator (LOL) topological analyses are done to ascertain the presence of delocalization in the designed molecules. Transition Density Matrix (TDM) Analysis is also done to quantify the intramolecular charge transfer. The NLO calculations show that all the designed molecules show superior NLO characteristics, with enhanced <α>, βtotal and <γ> values, surpassing urea, which is a standard NLO material. The wavelength dependent NLO calculations of a selected molecule reveal that the dynamic NLO descriptors fluctuate with wavelength and they are reaching their highest values at 450 nm. In summary, this study laid the foundation for the designing principles to tune the BOAPY derivatives to get enhanced optoelectronic and NLO properties.
{"title":"Tuning the BOAPY derivatives for enhancing the NLO properties using flanking groups – A DFT & TD-DFT study","authors":"Serangolam Krishnasami Sridhar , Rajadurai Vijay Solomon","doi":"10.1016/j.comptc.2024.115062","DOIUrl":"10.1016/j.comptc.2024.115062","url":null,"abstract":"<div><div>The quest for organic molecules with tunable optoelectronic properties for specific purposes is still continuing and computational designing strategies gain momentum in recent years. In this context, BOAPY core moiety attracts our attention due to its excellent photophysical properties and structural flexibility. Therefore, here we made an attempt to further enhance the photophysical properties of BOAPY molecule by introducing electron donating tuner group such as –OCH<sub>3</sub>, –NH<sub>2</sub>, –NH(CH<sub>3</sub>) and –N(CH<sub>3</sub>)<sub>2</sub> as well as electron withdrawing flanking groups such as –F, –CF<sub>3</sub> and –CN, one on each side of the tuner group. Totally, we have designed 25 molecules and analyzed their optical and Non-Linear Optical (NLO) properties using Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculations. These calculations are done at M06-2X/6-31+G(d,p) level of theory. The wavelength dependent NLO properties of the designed molecules are also determined. Our studies reveal that the HOMO-LUMO energy gap (ΔE) decreases with an increase in the electron donating nature of the tuner group. The electron withdrawing flanking groups such as –CF<sub>3</sub> and –CN are acting well in reducing the ΔE value. The simulated absorption spectra of the designed molecules show that the λ<sub>max</sub> increases with the electron donating power of the tuner group. Electron Localization Function (ELF) and Localized Orbital Locator (LOL) topological analyses are done to ascertain the presence of delocalization in the designed molecules. Transition Density Matrix (TDM) Analysis is also done to quantify the intramolecular charge transfer. The NLO calculations show that all the designed molecules show superior NLO characteristics, with enhanced <α>, β<sub>total</sub> and <γ> values, surpassing urea, which is a standard NLO material. The wavelength dependent NLO calculations of a selected molecule reveal that the dynamic NLO descriptors fluctuate with wavelength and they are reaching their highest values at 450 nm. In summary, this study laid the foundation for the designing principles to tune the BOAPY derivatives to get enhanced optoelectronic and NLO properties.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115062"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115064
A. Subashini , P. Venkatesan , G.Thulasi Prasanna , R. Kumaravel , M.Judith Percino , Helen Stoeckli-Evans , K. Ramamurthi
A new benzylideneaniline derivative, N-(4-nitrobenzylidene)-4’-fluoroaniline (I), was synthesized by a condensation reaction between 4-nitrobenzaldehyde and 4-fluoroaniline. The crystal structure of I was analyzed and compared with two regioisomeric benzylideneaniline derivatives, viz.N-(3-nitrobenzylidene)-4’-fluoroaniline (II) and N-(4-nitrobenzylidene)-2’-fluoroaniline (III), reported in the literature. The crystal structures of I-III were subjected to evaluation of their interatomic interactions in the crystal using Hirshfeld surface (HS) analysis and Coulomb-London-Pauli-PIXEL (CLP-PIXEL)and DFT calculations. The investigation reveals that the crystal packing of I–III was stabilized by the weak C–H⋅⋅⋅O, C–H⋅⋅⋅F and C–H⋅⋅⋅π interactions. Intermolecular interaction energies for different molecular pairs in the crystal packing of I-III, as well as the total lattice energies were quantified. The total lattice energies of the three regioisomeric benzylideneanilines (I-III) are compared and the dipole moment (μ), the polarizability (αtot) and the first-order hyperpolarizability (βtot) of I-III were computed using the M06-2X/cc-pVTZ level of theory.
{"title":"Evaluation of weak noncovalent interactions in three regioisomeric benzylideneaniline derivatives: An integrated crystallographic and theoretical approach","authors":"A. Subashini , P. Venkatesan , G.Thulasi Prasanna , R. Kumaravel , M.Judith Percino , Helen Stoeckli-Evans , K. Ramamurthi","doi":"10.1016/j.comptc.2024.115064","DOIUrl":"10.1016/j.comptc.2024.115064","url":null,"abstract":"<div><div>A new benzylideneaniline derivative, <em>N</em>-(4-nitrobenzylidene)-4’-fluoroaniline (<strong>I</strong>), was synthesized by a condensation reaction between 4-nitrobenzaldehyde and 4-fluoroaniline. The crystal structure of <strong>I</strong> was analyzed and compared with two regioisomeric benzylideneaniline derivatives, <em>viz.N</em>-(3-nitrobenzylidene)-4’-fluoroaniline (<strong>II</strong>) and <em>N</em>-(4-nitrobenzylidene)-2’-fluoroaniline (<strong>III</strong>), reported in the literature. The crystal structures of <strong>I-III</strong> were subjected to evaluation of their interatomic interactions in the crystal using Hirshfeld surface (HS) analysis and Coulomb-London-Pauli-PIXEL (CLP-PIXEL)and DFT calculations. The investigation reveals that the crystal packing of <strong>I</strong>–<strong>III</strong> was stabilized by the weak C–H⋅⋅⋅O, C–H⋅⋅⋅F and C–H⋅⋅⋅π interactions. Intermolecular interaction energies for different molecular pairs in the crystal packing of <strong>I-III</strong>, as well as the total lattice energies were quantified. The total lattice energies of the three regioisomeric benzylideneanilines (<strong>I-III</strong>) are compared and the dipole moment (μ), the polarizability (α<sub>tot</sub>) and the first-order hyperpolarizability (β<sub>tot</sub>) of <strong>I-III</strong> were computed using the M06-2X/cc-pVTZ level of theory.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115064"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115090
Wei Song , Zhe Fu , Jiale Liu , Jinqiang Li , Chaozheng He
NH3, as a carbon-free energy carrier that can replace H2, is also an important raw material for fertilizer. Compared with Haber–Bosch process, electrocatalytic NH3 synthesis has the green advantage of using renewable resources under ambient conditions. Herein, the catalytic performance of 3d transition metal single atom anchored in MoS2 (TM@MoS2) as electrocatalyst for nitrogen reduction reaction (NRR) has been investigated by first-principles calculation. By evaluating the stability, activity and selectivity of the catalysts, V@MoS2 was found to be a potential catalyst. After simulating the entire NRR pathway, it was found that the limiting potential was only −0.311 V, indicating that V@MoS2 had high catalytic activity. Finally, the partial density of states, charge density difference and crystal orbital Hamilton population were calculated to reveal the reason for the high catalytic activity of V@MoS2. We hope that this work can provide new design concepts for the development of efficient MoS2-based electrocatalysts.
{"title":"First-principles study of transition metal atom doped MoS2 as single-atom electrocatalysts for nitrogen fixation","authors":"Wei Song , Zhe Fu , Jiale Liu , Jinqiang Li , Chaozheng He","doi":"10.1016/j.comptc.2025.115090","DOIUrl":"10.1016/j.comptc.2025.115090","url":null,"abstract":"<div><div>NH<sub>3</sub>, as a carbon-free energy carrier that can replace H<sub>2</sub>, is also an important raw material for fertilizer. Compared with Haber–Bosch process, electrocatalytic NH<sub>3</sub> synthesis has the green advantage of using renewable resources under ambient conditions. Herein, the catalytic performance of 3d transition metal single atom anchored in MoS<sub>2</sub> (TM@MoS<sub>2</sub>) as electrocatalyst for nitrogen reduction reaction (NRR) has been investigated by first-principles calculation. By evaluating the stability, activity and selectivity of the catalysts, V@MoS<sub>2</sub> was found to be a potential catalyst. After simulating the entire NRR pathway, it was found that the limiting potential was only −0.311 V, indicating that V@MoS<sub>2</sub> had high catalytic activity. Finally, the partial density of states, charge density difference and crystal orbital Hamilton population were calculated to reveal the reason for the high catalytic activity of V@MoS<sub>2</sub>. We hope that this work can provide new design concepts for the development of efficient MoS<sub>2</sub>-based electrocatalysts.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115090"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115051
Indah Miftakhul Janah , Reka Mustika Sari , Faris Hermawan , Aulia Sukma Hutama , Lala Adetia Marlina
This study explores the potential of transition metal-doped Si12C12 nanocages for detecting volatile amines released during fish spoilage, using density functional theory (ωB97XD). The analysis focuses on structural stability, electronic properties, adsorption mechanisms, thermodynamics, sensitivity, and selectivity. Results indicate that TM doping enhances the adsorption of amines, with most interactions being spontaneous and exothermic. The trimethylamine∙∙∙TiSi11C12 complex exhibits particularly favorable thermodynamic properties. Sensitivity tests reveal that Cr, Cu, and Zn-doped nanocages demonstrate high responsiveness to trimethylamine at room temperature, with significant electronic property shifts upon adsorption. These findings highlight the potential of TM-doped Si12C12 nanocages as effective, selective, and sensitive sensors for monitoring volatile amines, aiding food quality control and fish freshness assessment. The study provides a theoretical basis for designing Si12C12-based gas sensors, contributing to advancements in food safety technology.
{"title":"A DFT study of doped first-row transition metals on Si12C12 nanocages as promising nanosensors for detecting volatile amines of fish spoilage","authors":"Indah Miftakhul Janah , Reka Mustika Sari , Faris Hermawan , Aulia Sukma Hutama , Lala Adetia Marlina","doi":"10.1016/j.comptc.2024.115051","DOIUrl":"10.1016/j.comptc.2024.115051","url":null,"abstract":"<div><div>This study explores the potential of transition metal-doped Si<sub>12</sub>C<sub>12</sub> nanocages for detecting volatile amines released during fish spoilage, using density functional theory (ωB97XD). The analysis focuses on structural stability, electronic properties, adsorption mechanisms, thermodynamics, sensitivity, and selectivity. Results indicate that TM doping enhances the adsorption of amines, with most interactions being spontaneous and exothermic. The trimethylamine∙∙∙TiSi<sub>11</sub>C<sub>12</sub> complex exhibits particularly favorable thermodynamic properties. Sensitivity tests reveal that Cr, Cu, and Zn-doped nanocages demonstrate high responsiveness to trimethylamine at room temperature, with significant electronic property shifts upon adsorption. These findings highlight the potential of TM-doped Si<sub>12</sub>C<sub>12</sub> nanocages as effective, selective, and sensitive sensors for monitoring volatile amines, aiding food quality control and fish freshness assessment. The study provides a theoretical basis for designing Si<sub>12</sub>C<sub>12</sub>-based gas sensors, contributing to advancements in food safety technology.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115051"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115085
Lucas Sousa Martins , Beatriz Alves Bentes , Tricia Naicker , Thavendran Govender , Hendrik Gerhardus Kruger , Cláudio Nahum Alves , Jerônimo Lameira , José Rogério A. Silva
Melanogenesis produces human melanin, which protects against UV radiation but can lead to skin issues and severe cancers if not appropriately regulated. The enzyme tyrosinase (TYR) plays a crucial role in melanin production, so inhibiting it is an essential target for controlling melanin levels. This study applied classical and quantum computational methods to examine how TYR interacts with inhibitors based on arylpiperidine and arylpiperazine. Using classical molecular dynamics (MD) simulations and the Linear Interaction Energy (LIE) method, we identified a strong correlation (r2 = 0.963) between computational and experimental binding free energies, underscoring the accuracy of these approaches. Additionally, residual decomposition analysis revealed the critical role of electrostatic interactions with Cu2+ ions at the active site, along with van der Waals interactions involving key residues, including Phe197, Pro201, Val218, Asn205, and Arg209, which are pivotal for inhibitor effectiveness. These findings are further supported by Free Energy Perturbation (FEP) calculations, which demonstrate excellent agreement with experimental data (r2 = 0.843), providing robust validation of the computational models. Additionally, quantum mechanical (QM) calculations using the DFT (wB97XD/6-311++G(d,p)) method uncovered electronic factors that influence inhibitor binding. Analyzing the frontier molecular orbitals (FMOs) and QM descriptors for L04, L08 and L19 inhibitors provided insights into TYR binding by arylpiperidine and arylpiperazine-based compounds. This thorough computational analysis improves our understanding of TYR inhibition and helps guide the development of treatments for conditions related to melanogenesis.
{"title":"Unravelling the mechanism of tyrosinase inhibition by arylpiperidine and arylpiperazine derivatives: A computational approach","authors":"Lucas Sousa Martins , Beatriz Alves Bentes , Tricia Naicker , Thavendran Govender , Hendrik Gerhardus Kruger , Cláudio Nahum Alves , Jerônimo Lameira , José Rogério A. Silva","doi":"10.1016/j.comptc.2025.115085","DOIUrl":"10.1016/j.comptc.2025.115085","url":null,"abstract":"<div><div>Melanogenesis produces human melanin, which protects against UV radiation but can lead to skin issues and severe cancers if not appropriately regulated. The enzyme tyrosinase (TYR) plays a crucial role in melanin production, so inhibiting it is an essential target for controlling melanin levels. This study applied classical and quantum computational methods to examine how TYR interacts with inhibitors based on arylpiperidine and arylpiperazine. Using classical molecular dynamics (MD) simulations and the Linear Interaction Energy (LIE) method, we identified a strong correlation (<em>r</em><sup>2</sup> = 0.963) between computational and experimental binding free energies, underscoring the accuracy of these approaches. Additionally, residual decomposition analysis revealed the critical role of electrostatic interactions with Cu<sup>2+</sup> ions at the active site, along with van der Waals interactions involving key residues, including Phe197, Pro201, Val218, Asn205, and Arg209, which are pivotal for inhibitor effectiveness. These findings are further supported by Free Energy Perturbation (FEP) calculations, which demonstrate excellent agreement with experimental data (<em>r</em><sup>2</sup> = 0.843), providing robust validation of the computational models. Additionally, quantum mechanical (QM) calculations using the DFT (wB97XD/6-311++G(d,p)) method uncovered electronic factors that influence inhibitor binding. Analyzing the frontier molecular orbitals (FMOs) and QM descriptors for L04, L08 and L19 inhibitors provided insights into TYR binding by arylpiperidine and arylpiperazine-based compounds. This thorough computational analysis improves our understanding of TYR inhibition and helps guide the development of treatments for conditions related to melanogenesis.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115085"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115020
Xiru Cao, Zhibin Tan, Chen Ji, Changwei Pan
The oxygen evolution reaction (OER) counterbalances the hydrogen evolution reaction (HER) during water dissociation under an electric field. Platinum (Pt) group metals and their oxides exhibit considerable durability as electrocatalysts for water dissociation. However, an atomic-level understanding of the OER on Pt-oxide surfaces at high potential remains elusive because of the limited experimental techniques for tracking dynamic surface species involved in adsorption, electron transfer, or interactions. Herein, the OER mechanisms involving water nucleophilic attack (WNA) and intramolecular oxygen coupling (IMOC) were studied on Pt and platinum dioxide (PtO2) surfaces using density functional theory (DFT) calculations, indicating that the WNA mechanism dominates the OER on Pt and PtO2 electrode surfaces. The OER activity on the PtO2(100) surface is better than the PtO2(111) surface due to the high overpotential obtained on PtO2(111). These findings offer valuable insights into the OER mechanism on oxidized Pt surfaces and suggest new strategies for designing and optimizing Pt-based catalysts for improved stability and performance.
{"title":"Oxygen evolution reaction mechanism on platinum dioxide surfaces based on density functional theory calculations","authors":"Xiru Cao, Zhibin Tan, Chen Ji, Changwei Pan","doi":"10.1016/j.comptc.2024.115020","DOIUrl":"10.1016/j.comptc.2024.115020","url":null,"abstract":"<div><div>The oxygen evolution reaction (OER) counterbalances the hydrogen evolution reaction (HER) during water dissociation under an electric field. Platinum (Pt) group metals and their oxides exhibit considerable durability as electrocatalysts for water dissociation. However, an atomic-level understanding of the OER on Pt-oxide surfaces at high potential remains elusive because of the limited experimental techniques for tracking dynamic surface species involved in adsorption, electron transfer, or interactions. Herein, the OER mechanisms involving water nucleophilic attack (WNA) and intramolecular oxygen coupling (IMOC) were studied on Pt and platinum dioxide (PtO<sub>2</sub>) surfaces using density functional theory (DFT) calculations, indicating that the WNA mechanism dominates the OER on Pt and PtO<sub>2</sub> electrode surfaces. The OER activity on the PtO<sub>2</sub>(100) surface is better than the PtO<sub>2</sub>(111) surface due to the high overpotential obtained on PtO<sub>2</sub>(111). These findings offer valuable insights into the OER mechanism on oxidized Pt surfaces and suggest new strategies for designing and optimizing Pt-based catalysts for improved stability and performance.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115020"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Palladium oxide (PdO) possesses excellent adsorption activity and catalytic properties for CO oxidation reactions. In this study, density functional theory (DFT) was used to investigate CO oxidation reactions on PdO(1 0 1) surface via Eley-Rideal (E-R), Langmuir-Hinshelwood (L-H), and Mars-van Krevelen (MVK) mechanisms. Transition state theory was used to calculate the rate constants for elementary reactions. The oxidation of CO by lattice oxygen through the MVK mechanism is favored due to its lower rate-determining energy barrier compared to the E-R and L-H mechanisms. Furthermore, the secondary oxidation reaction of CO with an adsorbed oxygen atom was studied, revealing that the presence of adsorbed oxygen on the catalyst surface significantly enhances the oxidation of CO. These findings provide an in-depth insight into CO oxidation reactions on PdO and facilitate the development of CO catalytic oxidation models.
{"title":"A mechanistic study of CO oxidation on PdO(1 0 1) surface","authors":"Chengcheng Ao , Chunlan Qin , Lidong Zhang , Shanshan Ruan","doi":"10.1016/j.comptc.2024.115037","DOIUrl":"10.1016/j.comptc.2024.115037","url":null,"abstract":"<div><div>Palladium oxide (PdO) possesses excellent adsorption activity and catalytic properties for CO oxidation reactions. In this study, density functional theory (DFT) was used to investigate CO oxidation reactions on PdO(1<!--> <!-->0<!--> <!-->1) surface via Eley-Rideal (E-R), Langmuir-Hinshelwood (L-H), and Mars-van Krevelen (MVK) mechanisms. Transition state theory was used to calculate the rate constants for elementary reactions. The oxidation of CO by lattice oxygen through the MVK mechanism is favored due to its lower rate-determining energy barrier compared to the E-R and L-H mechanisms. Furthermore, the secondary oxidation reaction of CO with an adsorbed oxygen atom was studied, revealing that the presence of adsorbed oxygen on the catalyst surface significantly enhances the oxidation of CO. These findings provide an in-depth insight into CO oxidation reactions on PdO and facilitate the development of CO catalytic oxidation models.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115037"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115066
Maryam Touqir , G. Murtaza , Ahmad Ayyaz , Ahmad Usman , M.Basit Shakir , Saba Saleem , Hummaira khan , Muhammad Umair Ashraf , Khalid M. Elhindi
FeCoZ compounds (where Z = Si, Ge, or Pb) are essential for spintronics and thermoelectric applications. This study, using density functional theory and PBE-GGA for exchange–correlation, explores their structural, electrical, magnetic, thermoelectric, thermodynamic, and elastic properties. Density of states analysis and spin-polarized band structures indicate that all three compounds have an indirect bandgap in the spin-up (↑) channel and are metallic in the spin-down (↓) channel. The exchange mechanism is finally produced by splitting the degeneracy of Co’s 3d-states via the John-Teller distortion. Ferromagnetic stability in FeCoZ (Z = Si, Ge, or Pb) is shown by negative Noα and Noβ values. Thermoelectric properties are derived using the BoltzTraP method. The increasing PF in alloys indicates their potential use in high-temperature thermoelectric applications. Consequently, the elevated ZT value produced in the spin-up condition indicates that these alloys are suitable for thermoelectric applications, and the quasi-harmonic Debye model indicates thermodynamic stability. Poisson’s ratio, Pugh’s ratio, and Cauchy’s pressure confirm mechanical stability and ductility. Overall, these compounds, suited for spintronic applications, exhibit half-metallicity, ferromagnetism, and high intrinsic magnetic moments.
{"title":"First-principles calculations to investigate Electronic, half-metallicity, thermodynamics, thermoelectric and mechanical properties of new Half-Heusler alloys FeCoZ (Z = Si, Ge, and Pb)","authors":"Maryam Touqir , G. Murtaza , Ahmad Ayyaz , Ahmad Usman , M.Basit Shakir , Saba Saleem , Hummaira khan , Muhammad Umair Ashraf , Khalid M. Elhindi","doi":"10.1016/j.comptc.2025.115066","DOIUrl":"10.1016/j.comptc.2025.115066","url":null,"abstract":"<div><div>FeCoZ compounds (where Z = Si, Ge, or Pb) are essential for spintronics and thermoelectric applications. This study, using density functional theory and PBE-GGA for exchange–correlation, explores their structural, electrical, magnetic, thermoelectric, thermodynamic, and elastic properties. Density of states analysis and spin-polarized band structures indicate that all three compounds have an indirect bandgap in the spin-up (↑) channel and are metallic in the spin-down (↓) channel. The exchange mechanism is finally produced by splitting the degeneracy of Co’s 3d-states via the John-Teller distortion. Ferromagnetic stability in FeCoZ (Z = Si, Ge, or Pb) is shown by negative N<sub>o</sub>α and N<sub>o</sub>β values. Thermoelectric properties are derived using the BoltzTraP method. The increasing PF in alloys indicates their potential use in high-temperature thermoelectric applications. Consequently, the elevated ZT value produced in the spin-up condition indicates that these alloys are suitable for thermoelectric applications, and the quasi-harmonic Debye model indicates thermodynamic stability. Poisson’s ratio, Pugh’s ratio, and Cauchy’s pressure confirm mechanical stability and ductility. Overall, these compounds, suited for spintronic applications, exhibit half-metallicity, ferromagnetism, and high intrinsic magnetic moments.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115066"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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