Ali Keshavarz Mohammadian, Negar Ashari Astani, Farzaneh Shayeganfar
Hole transporting materials (HTMs) play a crucial role in the performance and stability of perovskite solar cells (PSCs). The interaction of HTMs with water significantly affects the overall stability and efficiency of these devices. Hydrophilic HTMs or those lacking adequate water resistance can absorb moisture, leading to degradation of both the HTM and the perovskite layer. In this study, we employed a proof-of-principle approach to investigate the effect of various chemical modifications on a promising HTM candidate, 8,11-bis(4-(N,N-bis(4-methoxyphenyl)amino)-1-phenyl)-dithieno [1,2- b:4,3-b’]phenazine (TQ4). Using molecular dynamics simulations, we examined the collective be- havior of chemically modified TQ4 molecules in the presence of water at different concentrations. To ensure that enhanced water resistance did not compromise the desirable electronic properties of the HTM, we analyzed both the individual and collective electronic structures of the HTM molecule and its molecular crystal. Additionally, we calculated the charge transport rate in different directions within the HTM crystal using Marcus theory. Our findings indicate that chemical modifications at the periphery of TQ4, particularly the symmetric addition of two F-chains, result in the optimal combination of electronic, crystal structure, and water-resistant properties. HOMO shape analysis reveals that the HOMO does not extend onto the added F-chains, reducing the maximum pre- dicted hole mobility relative to TQ4 by an order of magnitude. Despite this, a hole mobility of 2.8×10−4cm2V−1s−1 is successfully achieved for all designed HTMs, reflecting a compromise be- tween stability and charge transport. This atomistic insight into the collective behavior of chemically modified HTMs and its effect on hole transport pathways paves the way for designing more effective HTMs for PSC applications.
{"title":"Computational Design of Dopant-Free Hole Transporting Materials: Achieving an Optimal Balance Between Water Stability and Charge Transport","authors":"Ali Keshavarz Mohammadian, Negar Ashari Astani, Farzaneh Shayeganfar","doi":"10.1039/d5cp00082c","DOIUrl":"https://doi.org/10.1039/d5cp00082c","url":null,"abstract":"Hole transporting materials (HTMs) play a crucial role in the performance and stability of perovskite solar cells (PSCs). The interaction of HTMs with water significantly affects the overall stability and efficiency of these devices. Hydrophilic HTMs or those lacking adequate water resistance can absorb moisture, leading to degradation of both the HTM and the perovskite layer. In this study, we employed a proof-of-principle approach to investigate the effect of various chemical modifications on a promising HTM candidate, 8,11-bis(4-(N,N-bis(4-methoxyphenyl)amino)-1-phenyl)-dithieno [1,2- b:4,3-b’]phenazine (TQ4). Using molecular dynamics simulations, we examined the collective be- havior of chemically modified TQ4 molecules in the presence of water at different concentrations. To ensure that enhanced water resistance did not compromise the desirable electronic properties of the HTM, we analyzed both the individual and collective electronic structures of the HTM molecule and its molecular crystal. Additionally, we calculated the charge transport rate in different directions within the HTM crystal using Marcus theory. Our findings indicate that chemical modifications at the periphery of TQ4, particularly the symmetric addition of two F-chains, result in the optimal combination of electronic, crystal structure, and water-resistant properties. HOMO shape analysis reveals that the HOMO does not extend onto the added F-chains, reducing the maximum pre- dicted hole mobility relative to TQ4 by an order of magnitude. Despite this, a hole mobility of 2.8×10−4cm2V−1s−1 is successfully achieved for all designed HTMs, reflecting a compromise be- tween stability and charge transport. This atomistic insight into the collective behavior of chemically modified HTMs and its effect on hole transport pathways paves the way for designing more effective HTMs for PSC applications.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"34 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806213","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}
Emily Gross, Mark D. Driver, Areesha Saif, Oliver N. Evans, Christopher A. Hunter
The surface site interaction model for liquids at equilibrium (SSIMPLE) is a method for calculating thermodynamic properties in a fluid phase based on the use of surface site interaction points (SSIP) to represent all of the non-covalent interactions that molecules make with the environment. Interactions between the SSIPs of two different molecules are governed by a non-polar term and a polar term. Here the formulation originally made for room temperature liquids is generalized to any temperature. We show that the non-polar interaction term is temperature independent while the polar interaction term depends on temperature. This formulation was used to develop a description of the temperature dependence of fluid phase density in terms of an expansion energy, which is based on net intermolecular SSIP interactions. The method is shown to accurately model the temperature dependence of experimentally measured association constants for the formation of 1 : 1 H-bonded complexes in carbon tetrachloride. The atomic interaction point (AIP) version of the SSIP descripiton of 171 different compounds was used in SSIMPLE to calculate room temperature liquid densities that are in good agreement with experimental data. Since non-covalent interactions in the vapour phase can be treated in the same way as liquid phase interactions, SSIMPLE can also be used to calcuate vapour–liquid equilibria (VLE). Experimental VLE data for 196 binary mixtures of 30 miscible compounds was collected, and SSIMPLE was shown to reproduce the experimental behaviour well.
{"title":"Solvation energies from atomic surface site interaction points","authors":"Emily Gross, Mark D. Driver, Areesha Saif, Oliver N. Evans, Christopher A. Hunter","doi":"10.1039/d5cp00635j","DOIUrl":"https://doi.org/10.1039/d5cp00635j","url":null,"abstract":"The surface site interaction model for liquids at equilibrium (SSIMPLE) is a method for calculating thermodynamic properties in a fluid phase based on the use of surface site interaction points (SSIP) to represent all of the non-covalent interactions that molecules make with the environment. Interactions between the SSIPs of two different molecules are governed by a non-polar term and a polar term. Here the formulation originally made for room temperature liquids is generalized to any temperature. We show that the non-polar interaction term is temperature independent while the polar interaction term depends on temperature. This formulation was used to develop a description of the temperature dependence of fluid phase density in terms of an expansion energy, which is based on net intermolecular SSIP interactions. The method is shown to accurately model the temperature dependence of experimentally measured association constants for the formation of 1 : 1 H-bonded complexes in carbon tetrachloride. The atomic interaction point (AIP) version of the SSIP descripiton of 171 different compounds was used in SSIMPLE to calculate room temperature liquid densities that are in good agreement with experimental data. Since non-covalent interactions in the vapour phase can be treated in the same way as liquid phase interactions, SSIMPLE can also be used to calcuate vapour–liquid equilibria (VLE). Experimental VLE data for 196 binary mixtures of 30 miscible compounds was collected, and SSIMPLE was shown to reproduce the experimental behaviour well.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"2 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806212","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}
Jiaqi Zhang, Jiaxin Jiang, Hongyan Guo, Xiaowei Sheng, Weiyi Wang, Zhiwen Zhuo, Ning Lu
The development of high-comprehensive-performance cathode materials is significant and urgent for ion battery systems. Based on density functional theory methods, we systematically expand and investigate a porous and van der Waals layered bulk structure of carbon nitride as a versatile cathode material for varied ion batteries. The calculated results indicate that the layered bulk carbon nitride structure is a semiconductor material with good thermal stability. The structure has high-density one-dimensional transport channels for fast K/Na/Ca ions migration with low activation energy barriers of only 0.125, 0.281, and 0.296 eV, respectively. The theoretical specific capacity, open-circuit voltage, and energy density can reach 137, 150, and 273 mAh·g-1, 3.788-3.614, 3.251-3.037, and 3.376-2.821 V, and 506.1, 470.8, and 847.3 Wh·kg-1 for K, Na and Ca ion, respectively. Compared to common cathode materials, the layered carbon nitride possesses significant advantages such as fast ion, high energy density, low cost, and environmental friendliness.
{"title":"Layered carbon nitride bulk as a versatile cathode material for fast ion batteries","authors":"Jiaqi Zhang, Jiaxin Jiang, Hongyan Guo, Xiaowei Sheng, Weiyi Wang, Zhiwen Zhuo, Ning Lu","doi":"10.1039/d5cp00187k","DOIUrl":"https://doi.org/10.1039/d5cp00187k","url":null,"abstract":"The development of high-comprehensive-performance cathode materials is significant and urgent for ion battery systems. Based on density functional theory methods, we systematically expand and investigate a porous and van der Waals layered bulk structure of carbon nitride as a versatile cathode material for varied ion batteries. The calculated results indicate that the layered bulk carbon nitride structure is a semiconductor material with good thermal stability. The structure has high-density one-dimensional transport channels for fast K/Na/Ca ions migration with low activation energy barriers of only 0.125, 0.281, and 0.296 eV, respectively. The theoretical specific capacity, open-circuit voltage, and energy density can reach 137, 150, and 273 mAh·g-1, 3.788-3.614, 3.251-3.037, and 3.376-2.821 V, and 506.1, 470.8, and 847.3 Wh·kg-1 for K, Na and Ca ion, respectively. Compared to common cathode materials, the layered carbon nitride possesses significant advantages such as fast ion, high energy density, low cost, and environmental friendliness.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"93 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806217","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}
Ziga Casar, Davide Tisi, Samuel J. Page, Chris Greenwell, Franco Zunino
Calcium and silicon are critical components of cement. While 29Si nuclear magnetic resonance (NMR) is widely used in cement science, 43Ca NMR has received comparatively less attention given the experimental challenges associated with it. To investigate the potential of 43Ca NMR in cement research, a density functional theory study was carried out. The study focused on distinct calcium sites within the calcium silicate hydrate (C-S-H) structure. Four unique calcium sites were identified, each predicted to display distinct 43Ca chemical shifts due to differences in their local environments. These findings were used to generate theoretical 43Ca NMR spectra for C-S-H. Furthermore, theoretical 43Ca NMR spectra for the hydration reaction of triclinic tricalcium silicate were developed, illustrating the potential of 43Ca NMR for tracking the hydration process in multiphase systems.
{"title":"Is there a future for 43Ca nuclear magnetic resonance in cement science?","authors":"Ziga Casar, Davide Tisi, Samuel J. Page, Chris Greenwell, Franco Zunino","doi":"10.1039/d5cp00491h","DOIUrl":"https://doi.org/10.1039/d5cp00491h","url":null,"abstract":"Calcium and silicon are critical components of cement. While <small><sup>29</sup></small>Si nuclear magnetic resonance (NMR) is widely used in cement science, <small><sup>43</sup></small>Ca NMR has received comparatively less attention given the experimental challenges associated with it. To investigate the potential of <small><sup>43</sup></small>Ca NMR in cement research, a density functional theory study was carried out. The study focused on distinct calcium sites within the calcium silicate hydrate (C-S-H) structure. Four unique calcium sites were identified, each predicted to display distinct <small><sup>43</sup></small>Ca chemical shifts due to differences in their local environments. These findings were used to generate theoretical <small><sup>43</sup></small>Ca NMR spectra for C-S-H. Furthermore, theoretical <small><sup>43</sup></small>Ca NMR spectra for the hydration reaction of triclinic tricalcium silicate were developed, illustrating the potential of <small><sup>43</sup></small>Ca NMR for tracking the hydration process in multiphase systems.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"1 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806260","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}
Nathalie Kanchena Fernando, Claire A. Murray, Amber L Thompson, Katherine Milton, Andrew B Cairns, Anna Regoutz
With the advent of ever more intense and focused X-ray sources, including in laboratories, at synchrotrons, and at X-ray free electron lasers, radiation-induced sample change and damage are becoming increasingly challenging. Therefore, the exploration of possible mitigation strategies is crucial to continue to allow the collection of robust and repeatable data. One mitigation approach is the introduction of short, X-ray-free "dark'' periods. However, it is unclear whether this strategy minimises damage or, in actuality, promotes it through a phenomenon called "dark progression'', i.e. the increase or progression of radiation damage that occurs after the X-ray beam is turned off. This work discusses the influence of introducing dark periods and their duration on the radiation-induced changes in two model small-molecule catalysts, [Ir(COD)Cl]2 and [Rh(COD)Cl]2, exposed to X-ray radiation in powder diffraction (PXRD) and photoelectron spectroscopy (XPS) experiments. This provides, for the first time, insights into how damage progresses under varying radiation regimes and allows the distinction between the processes that affect the unit cell itself, the individual molecular units, and the respective atomic chemical environments. Furthermore, it provides the basis for informed decision-making in the design of future experiments where the need to minimise radiation-induced damage is crucial.
{"title":"Investigating Discontinuous X-ray Irradiation as a Damage Mitigation Strategy for [M(COD)Cl]2 Catalysts","authors":"Nathalie Kanchena Fernando, Claire A. Murray, Amber L Thompson, Katherine Milton, Andrew B Cairns, Anna Regoutz","doi":"10.1039/d5cp00089k","DOIUrl":"https://doi.org/10.1039/d5cp00089k","url":null,"abstract":"With the advent of ever more intense and focused X-ray sources, including in laboratories, at synchrotrons, and at X-ray free electron lasers, radiation-induced sample change and damage are becoming increasingly challenging. Therefore, the exploration of possible mitigation strategies is crucial to continue to allow the collection of robust and repeatable data. One mitigation approach is the introduction of short, X-ray-free \"dark'' periods. However, it is unclear whether this strategy minimises damage or, in actuality, promotes it through a phenomenon called \"dark progression'', i.e. the increase or progression of radiation damage that occurs after the X-ray beam is turned off. This work discusses the influence of introducing dark periods and their duration on the radiation-induced changes in two model small-molecule catalysts, [Ir(COD)Cl]<small><sub>2</sub></small> and [Rh(COD)Cl]<small><sub>2</sub></small>, exposed to X-ray radiation in powder diffraction (PXRD) and photoelectron spectroscopy (XPS) experiments. This provides, for the first time, insights into how damage progresses under varying radiation regimes and allows the distinction between the processes that affect the unit cell itself, the individual molecular units, and the respective atomic chemical environments. Furthermore, it provides the basis for informed decision-making in the design of future experiments where the need to minimise radiation-induced damage is crucial.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"38 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806148","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}
Alternative splicing engineering is a potential strategy to improve the thermoelectric conversion efficiency of low-dimensional nanodevices. The unique thermal/electrical transport properties of 5-carbon ring-based structures can significantly improve thermoelectric performance. The thermoelectric properties of three carbon nanomaterials and devices containing five-carbon ring structures, namely, penta-graphene (PG), penta-octa-penta-graphene (POPG) and Θ-graphene (ΘG), were investigated using density functional theory and non-equilibrium Green's function methods. The results demonstrated that the folded structure of PG gave rise to ring-like electrical transport properties, which greatly reduced effective conductance. POPG exhibited smooth charge transport behavior without scattering loops, leading to relatively higher conductance compared to PG. Meanwhile, embedded 8-carbon ring structures effectively flattened the folded structure of PG and significantly reduced vertical oscillation behavior, resulting in an increase in thermal conductance. For ΘG, the addition of distorted 6-carbon ring structures excited reverse charge transport paths, resulting in lower conductance compared to POPG. The splicing geometry between the 5-carbon ring and 6-carbon ring structure disrupted the original grain boundaries, leading to enhanced phonon scattering and more localized vibrational modes. As a result, ΘG achieved a ZT value of 0.54 near the Fermi energy level at room temperature (300 K).
{"title":"Alternative splicing engineering modulation of thermal/electrical transmission properties in low-dimensional nanodevices based on five-carbon ring structures","authors":"Meng Qian, Bei Zhang","doi":"10.1039/d4cp04772a","DOIUrl":"https://doi.org/10.1039/d4cp04772a","url":null,"abstract":"Alternative splicing engineering is a potential strategy to improve the thermoelectric conversion efficiency of low-dimensional nanodevices. The unique thermal/electrical transport properties of 5-carbon ring-based structures can significantly improve thermoelectric performance. The thermoelectric properties of three carbon nanomaterials and devices containing five-carbon ring structures, namely, penta-graphene (PG), penta-octa-penta-graphene (POPG) and Θ-graphene (ΘG), were investigated using density functional theory and non-equilibrium Green's function methods. The results demonstrated that the folded structure of PG gave rise to ring-like electrical transport properties, which greatly reduced effective conductance. POPG exhibited smooth charge transport behavior without scattering loops, leading to relatively higher conductance compared to PG. Meanwhile, embedded 8-carbon ring structures effectively flattened the folded structure of PG and significantly reduced vertical oscillation behavior, resulting in an increase in thermal conductance. For ΘG, the addition of distorted 6-carbon ring structures excited reverse charge transport paths, resulting in lower conductance compared to POPG. The splicing geometry between the 5-carbon ring and 6-carbon ring structure disrupted the original grain boundaries, leading to enhanced phonon scattering and more localized vibrational modes. As a result, ΘG achieved a <em>ZT</em> value of 0.54 near the Fermi energy level at room temperature (300 K).","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"36 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806214","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}
In this work, we successfully fabricated a series of Bi2SexTe3-x thin films with similar thickness using radio-frequency magnetron sputtering. The influence of elemental composition on the films' structure, optical constants, optical band gap, and nonlinear absorption properties was studied by techniques such as X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, spectroscopic ellipsometry, spectrophotometry, and open-aperture Z-scan. Linear optical property measurements indicate that as the proportion of Te increases, the metallic characteristics of the films are enhanced, which is reflected in a decrease in refractive index, an increase in extinction coefficient, and a redshift of the optical bandgap. Regarding nonlinear absorption properties, the annealed crystalline Bi2Te3 thin film exhibits the largest modulation depth, with its nonlinear optical absorption coefficient approximately eight times that of the amorphous Bi2Se3 thin film. However, the amorphous Bi2Se3 thin film possesses the highest damage threshold. All Bi2SexTe3-x thin films display saturable absorption behavior and exhibit large third-order nonlinear optical absorption coefficients, suggesting their potential as promising materials in ultrafast nonlinear optics. Our findings indicate the optical properties of Bi2SexTe3-x thin films can be effectively tuned through composition adjustment, demonstrating the potential device application in mode-locked lasers, Q-switching, all-optical diodes, and so on.
{"title":"Tunable Structural and Optical Properties of Bi2SexTe3-x Thin Films: Implications for Nonlinear Optical Applications","authors":"Tengfei Zhang, Shenjin Wei, Shubo Zhang, Menghan Li, Jiawei Wang, Jingze Liu, Junhua Wang, Er-Tao Hu, Jing Li","doi":"10.1039/d5cp00264h","DOIUrl":"https://doi.org/10.1039/d5cp00264h","url":null,"abstract":"In this work, we successfully fabricated a series of Bi2SexTe3-x thin films with similar thickness using radio-frequency magnetron sputtering. The influence of elemental composition on the films' structure, optical constants, optical band gap, and nonlinear absorption properties was studied by techniques such as X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, spectroscopic ellipsometry, spectrophotometry, and open-aperture Z-scan. Linear optical property measurements indicate that as the proportion of Te increases, the metallic characteristics of the films are enhanced, which is reflected in a decrease in refractive index, an increase in extinction coefficient, and a redshift of the optical bandgap. Regarding nonlinear absorption properties, the annealed crystalline Bi2Te3 thin film exhibits the largest modulation depth, with its nonlinear optical absorption coefficient approximately eight times that of the amorphous Bi2Se3 thin film. However, the amorphous Bi2Se3 thin film possesses the highest damage threshold. All Bi2SexTe3-x thin films display saturable absorption behavior and exhibit large third-order nonlinear optical absorption coefficients, suggesting their potential as promising materials in ultrafast nonlinear optics. Our findings indicate the optical properties of Bi2SexTe3-x thin films can be effectively tuned through composition adjustment, demonstrating the potential device application in mode-locked lasers, Q-switching, all-optical diodes, and so on.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"6 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806257","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}
Harald Agelii, Ellen L S Jakobsson, Emiliano De Santis, Gideon Elfrink, Thomas Mandl, Erik Marklund, Carl Caleman
In the aerosolization of single proteins from solution, the proteins may be covered by a layer of water. This is relevant to consider in sample delivery for Single Particle Imaging (SPI) with X-ray free-electron lasers. Previous studies suggest that the presence of a 3 Å water layer stabilizes the molecular structure and decreases structural heterogeneity which is important since it facilitates the structure determination in SPI. It has also been shown that SPI would benefit from the possibility of controlling the particle orientation in the interaction region. It has been proposed that such controll would be possible by applying a DC electric field that interacts with the intrinsic dipole of the particle. This study investigates how SPI experiments, including dipole orientation, would be affected by the presence of a hydration layer covering the proteins. We investigated this by performing classical MD simulations of a globular protein in gas phase interacting with an external electric field. Two hydration levels were used: a fully desolvated molecule and one with a water layer corresponding to 3 Åcovering the proteins surface surface. Our simulations show that a water layer enables the molecules to orient at lower field amplitudes, and on shorter time scales, as compared to the desolvated case. We also see a marginally larger stability of the molecular structure in the hydrated case at field strengths below 2 V/nm. The presence of a water layer, in combination with an electric field, also tend to stabilize the dipole axis significantly within the molecular structure.
{"title":"Dipole orientation of hydrated gas-phase proteins","authors":"Harald Agelii, Ellen L S Jakobsson, Emiliano De Santis, Gideon Elfrink, Thomas Mandl, Erik Marklund, Carl Caleman","doi":"10.1039/d5cp00073d","DOIUrl":"https://doi.org/10.1039/d5cp00073d","url":null,"abstract":"In the aerosolization of single proteins from solution, the proteins may be covered by a layer of water. This is relevant to consider in sample delivery for Single Particle Imaging (SPI) with X-ray free-electron lasers. Previous studies suggest that the presence of a 3 Å water layer stabilizes the molecular structure and decreases structural heterogeneity which is important since it facilitates the structure determination in SPI. It has also been shown that SPI would benefit from the possibility of controlling the particle orientation in the interaction region. It has been proposed that such controll would be possible by applying a DC electric field that interacts with the intrinsic dipole of the particle. This study investigates how SPI experiments, including dipole orientation, would be affected by the presence of a hydration layer covering the proteins. We investigated this by performing classical MD simulations of a globular protein in gas phase interacting with an external electric field. Two hydration levels were used: a fully desolvated molecule and one with a water layer corresponding to 3 Åcovering the proteins surface surface. Our simulations show that a water layer enables the molecules to orient at lower field amplitudes, and on shorter time scales, as compared to the desolvated case. We also see a marginally larger stability of the molecular structure in the hydrated case at field strengths below 2 V/nm. The presence of a water layer, in combination with an electric field, also tend to stabilize the dipole axis significantly within the molecular structure.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"40 5 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806210","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}
Intracellular lipid binding proteins (iLBPs) possess different characteristics, including a rigid protein structure consisting of a β-barrel, an α-helix cap, and a substantial internalized water cluster. Despite X-ray crystallographic research providing insights into the three dimensional structures of iLBPs, the protein conformations, and the function of the internal water molecules inside the protein remain uncertain. In this study, we conducted molecular dynamics (MD) simulations on free (apo) and oleate-bound (holo) rat Liver Fatty Acid Binding Proteins (rLFABP), which are common intracellular lipid binding proteins (iLBP) found in the liver of rats. Efforts have been undertaken to comprehensively comprehend the specific structural movements occurring in various segments of the proteins, namely the β-strands, the helix-turn-helix (HTH) region, the loop region and the impact of ligand binding on the microscopic structure and order of water molecules inside and around the proteins. Our calculations demonstrate the fluctuating nature of the HTH region, characterized by the development and disruption of distinct secondary structural components. Furthermore, the calculations showed the coexistence of highly ordered and disordered water molecules within the core regions of the apo and holo-protein, which exhibit spatial heterogeneity. The high level of organization is attributed to a significant portion of core water molecules that are doubly neighbored. In contrast, the randomly oriented ones have three neighboring water molecules in their first coordination shells. So, the core water molecules can play a crucial role in the ligand binding process in the rLFABP.
{"title":"Elucidating the microscopic properties of a β-barrel protein and the solvent confined in and around it","authors":"Gourab Saha, Sanjoy Bandyopadhyay","doi":"10.1039/d4cp04835k","DOIUrl":"https://doi.org/10.1039/d4cp04835k","url":null,"abstract":"Intracellular lipid binding proteins (iLBPs) possess different characteristics, including a rigid protein structure consisting of a β-barrel, an α-helix cap, and a substantial internalized water cluster. Despite X-ray crystallographic research providing insights into the three dimensional structures of iLBPs, the protein conformations, and the function of the internal water molecules inside the protein remain uncertain. In this study, we conducted molecular dynamics (MD) simulations on free (apo) and oleate-bound (holo) rat Liver Fatty Acid Binding Proteins (rLFABP), which are common intracellular lipid binding proteins (iLBP) found in the liver of rats. Efforts have been undertaken to comprehensively comprehend the specific structural movements occurring in various segments of the proteins, namely the β-strands, the helix-turn-helix (HTH) region, the loop region and the impact of ligand binding on the microscopic structure and order of water molecules inside and around the proteins. Our calculations demonstrate the fluctuating nature of the HTH region, characterized by the development and disruption of distinct secondary structural components. Furthermore, the calculations showed the coexistence of highly ordered and disordered water molecules within the core regions of the apo and holo-protein, which exhibit spatial heterogeneity. The high level of organization is attributed to a significant portion of core water molecules that are doubly neighbored. In contrast, the randomly oriented ones have three neighboring water molecules in their first coordination shells. So, the core water molecules can play a crucial role in the ligand binding process in the rLFABP.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"25 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806216","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}
Letícia Almeida Souza, Beatriz Rocha de Moraes, Rafael M. de Souza, Gabriel A. L. Porto, Adriaan van den Bruinhorst, Margarida Costa Gomes, Mauro Ribeiro, Rômulo Augusto Ando
Elucidating the liquid structure of Deep Eutectic Solvents (DES) is crucial to understand how local interactions determine their properties. In this work, the impact of the anion on the liquid structure and local interactions was investigated for mixtures of tetrabutylammonium chloride and bromide ([N4444]Cl and [N4444]Br) with glycerol (Gly). The phase behavior was explored across various compositions using Differential Scanning Calorimetry (DSC) showing that these mixtures form a (meta)stable liquid at room temperature and xsalt=0.25. At this composition, infrared spectroscopy (IR) revealed strong hydrogen bonding between glycerol and the anion that is more pronounced for chloride than bromide. This finding is supported by the enthalpy of mixing measurements and by quantum chemical calculations. Molecular dynamics (MD) simulations demonstrated that intermolecular hydrogen bonds between glycerol molecules persist, maintaining a long-range liquid structure even in the presence of salt. Far-infrared spectroscopy (FIR) combined with MD simulations revealed changes in local intermolecular dynamics due to a confinement effect caused by the strong anion–glycerol interactions. These results highlight the critical influence of local interactions driven by the anion on DES properties.
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