| 1. |
- Ali, Asad, et al.
(författare)
-
Emerging strategies and developments in oxygen reduction reaction using high-performance platinum-based electrocatalysts
- 2024
-
Ingår i: Nano Reseach. - : Tsinghua University Press. - 1998-0124 .- 1998-0000. ; 17:5, s. 3516-3532
-
Forskningsöversikt (refereegranskat)abstract
- The global practical implementation of proton exchange membrane fuel cells (PEMFCs) heavily relies on the advancement of highly effective platinum (Pt)-based electrocatalysts for the oxygen reduction reaction (ORR). To achieve high ORR performance, electrocatalysts with highly accessible reactive surfaces are needed to promote the uncovering of active positions for easy mass transportation. In this critical review, we introduce different approaches for the emerging development of effective ORR electrocatalysts, which offer high activity and durability. The strategies, including morphological engineering, geometric configuration modification via supporting materials, alloys regulation, core-shell, and confinement engineering of single atom electrocatalysts (SAEs), are discussed in line with the goals and requirements of ORR performance enhancement. We review the ongoing development of Pt electrocatalysts based on the syntheses, nanoarchitecture, electrochemical performances, and stability. We eventually explore the obstacles and research directions on further developing more effective electrocatalysts.
|
|
| 2. |
- An, Rong, et al.
(författare)
-
Atomic force microscopy probing interactions and microstructures of ionic liquids at solid surfaces
- 2022
-
Ingår i: Nanoscale. - : Royal Society of Chemistry. - 2040-3364 .- 2040-3372. ; :14, s. 11098-11128
-
Forskningsöversikt (refereegranskat)abstract
- Ionic liquids (ILs) are room temperature molten salts that possess preeminent physicochemical properties and have shown great potential in many applications. However, the use of ILs in surface-dependent processes, e.g. energy storage, is hindered by the lack of a systematic understanding of the IL interfacial microstructure. ILs on the solid surface display rich ordering, arising from coulombic, van der Waals, solvophobic interactions, etc., all giving near-surface ILs distinct microstructures. Therefore, it is highly important to clarify the interactions of ILs with solid surfaces at the nanoscale to understand the microstructure and mechanism, providing quantitative structure–property relationships. Atomic force microscopy (AFM) opens a surface-sensitive way to probe the interaction force of ILs with solid surfaces in the layers from sub-nanometers to micrometers. Herein, this review showcases the recent progress of AFM in probing interactions and microstructures of ILs at solid interfaces, and the influence of IL characteristics, surface properties and external stimuli is thereafter discussed. Finally, a summary and perspectives are established, in which, the necessities of the quantification of IL–solid interactions at the molecular level, the development of in situ techniques closely coupled with AFM for probing IL–solid interfaces, and the combination of experiments and simulations are argued.
|
|
| 3. |
|
|
| 4. |
- An, Rong, et al.
(författare)
-
Ti–Si–Zr–Zn Nanometallic Glass Substrate with a Tunable Zinc Composition for Surface-Enhanced Raman Scattering of Cytochrome c
- 2023
-
Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 15:21, s. 25275-25284
-
Tidskriftsartikel (refereegranskat)abstract
- As a remarkably powerful analytical technique, surface-enhanced Raman scattering (SERS) continues to find applications from molecular biology and chemistry to environmental and food sciences. In search of reliable and affordable SERS substrates, the development has moved from noble metals to other diverse types of structures, e.g., nano-engineered semiconductor materials, but the cost of the enhancement factors (EF) substantially decreasing. In this work, we employ biocompatible thin films of Ti–Si–Zr–Zn nanometallic glasses as the SERS substrates, while tuning the Zn composition. Aided by quartz crystal microbalance, we find that the composition of 4.3% Zn (Ti–Si–Zr–Zn4.3) gives an ultrasensitive detection of Cytochrome c (Cyt c) with an EF of 1.38 × 104, 10-fold higher than the previously reported EF in the semiconducting metal oxide nanomaterials, such as TiO2, and even comparable to the reported noble-metal-assisted semiconducting tungsten oxide hydrate. Ti–Si–Zr–Zn4.3 exhibits a stronger adhesion force toward Cyt c, which ensures the strong binding of Cyt c to the surface, facilitating the Cyt c adsorption onto the surface and thus enhancing the SERS signal. The high separation efficiency of photoinduced electrons and holes in Ti–Si–Zr–Zn4.3 is also acknowledged for promoting the SERS activity.
|
|
| 5. |
- Barroso da Silva, Fernando L., et al.
(författare)
-
Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule
- 2022
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:36, s. 6835-6852
-
Tidskriftsartikel (refereegranskat)abstract
- Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
|
|
| 6. |
- de Villiers Engelbrecht, Leon, et al.
(författare)
-
Molecular Perspective on Solutions and Liquid Mixtures from Modelling and Experiment
- 2022
-
Ingår i: Soft Matter Systems for Biomedical Applications. - Cham : Springer Nature. - 9783030809232 - 9783030809249 ; , s. 53-84
-
Konferensbidrag (refereegranskat)abstract
- Liquid solutions and mixtures are part of our everyday lives and also important for their chemical and industrial applications. While considered fairly unattractive substances when kept in bottles and containers, their behavior as molecules can be completely the opposite, continuously attracting scientists to explain it better. Very strong repulsive and attractive interactions between the molecules can create most intriguing local structures, aggregates and complexes, whose spatial organization is often difficult to rationalize. Also, the same mixture can behave completely differently depending on the composition ratio, affecting strongly its macroscopic properties. To gain insight into the complex world of binary liquid mixtures, deep eutectic solvents and ionic liquid systems, combined theoretical and experimental studies are necessary. In this chapter we introduce the methodology of computer simulations and illustrate with several examples of the often-unexpected behavior of many liquid mixtures.
|
|
| 7. |
- Dong, Yihui, et al.
(författare)
-
Complementary Powerful Techniques for Investigating the Interactions of Proteins with Porous TiO2 and Its Hybrid Materials: A Tutorial Review
- 2022
-
Ingår i: Membranes. - : MDPI. - 2077-0375. ; 12:4
-
Forskningsöversikt (refereegranskat)abstract
- Understanding the adsorption and interaction between porous materials and protein is of great importance in biomedical and interface sciences. Among the studied porous materials, TiO2 and its hybrid materials, featuring distinct, well-defined pore sizes, structural stability and excellent biocompatibility, are widely used. In this review, the use of four powerful, synergetic and complementary techniques to study protein-TiO2-based porous materials interactions at different scales is summarized, including high-performance liquid chromatography (HPLC), atomic force microscopy (AFM), surface-enhanced Raman scattering (SERS), and Molecular Dynamics (MD) simulations. We expect that this review could be helpful in optimizing the commonly used techniques to characterize the interfacial behavior of protein on porous TiO2 materials in different applications.
|
|
| 8. |
- Dong, Yihui, et al.
(författare)
-
Phosphonium-Based Ionic Liquid Significantly Enhances SERS of Cytochrome c on TiO2 Nanotube Arrays
- 2022
-
Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 14:23, s. 27456-27465
-
Tidskriftsartikel (refereegranskat)abstract
- Surface-enhanced Raman scattering (SERS) is an attractive technique for studying trace detection. It is of utmost importance to further improve the performance and understand the underlying mechanisms. An ionic liquid (IL), the anion of which is derived from biomass, [P6,6,6,14][FuA] was synthesized and used as a trace additive to improve the SERS performance of cytochrome c (Cyt c) on TiO2 nanotube arrays (TNAs). An increased and better enhancement factor (EF) by four to five times as compared to the system without an IL was obtained, which is better than that from using the choline-based amino acid IL previously reported by us. Dissociation of the ILs improved the ionic conductivity of the system, and the long hydrophobic tails of the [P6,6,6,14]+ cation contributed to a strong electrostatic interaction between Cyt c and the TNA surface, thereby enhancing the SERS performance. Atomic force microscopy did verify strong electrostatic interactions between the Cyt c molecules and TNAs after the addition of the IL. This work demonstrates the importance of introducing the phosphonium-based IL to enhance the SERS performance, which will stimulate further development of more effective ILs on SERS detection and other relevant applications in biology.
|
|
| 9. |
- Dong, Yihui, et al.
(författare)
-
Selective Separation of Highly Similar Proteins on Ionic Liquid-Loaded Mesoporous TiO2
- 2022
-
Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 38:10, s. 3202-3211
-
Tidskriftsartikel (refereegranskat)abstract
- Separating proteins from their mixtures is an important process in a great variety of applications, but it faces difficult challenges as soon as the proteins are simultaneously of similar sizes and carry comparable net charges. To develop both efficient and sustainable strategies for the selective separation of similar proteins and to understand the underlying molecular mechanisms to enable the separation are crucial. In this work, we propose a novel strategy where the cholinium-based amino acid [Cho][Pro] ionic liquid (IL) is used as the trace additive and loaded physically on a mesoporous TiO2 surface for separating two similar proteins (lysozyme and cytochrome c). The observed selective adsorption behavior is explained by the hydration properties of the [Cho][Pro] loaded on the TiO2 surface and their partially dissociated ions under different pH conditions. As the pH is increased from 5.0 to 9.8, the degree of hydration of IL ions also increases, gradually weakening the interaction strength of the proteins with the substrates, more for lysozymes, leading to their effective separation. These findings were further used to guide the detection of the retention behavior of a binary mixture of proteins in high-performance liquid chromatography, where the introduction of ILs did effectively separate the two similar proteins. Our results should further stimulate the use of ILs in the separation of proteins with a high degree of mutual similarity.
|
|
| 10. |
- Giron, Carolina Corrêa, et al.
(författare)
-
Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies
- 2023
-
Ingår i: Journal of Biomolecular Structure and Dynamics. - : Taylor & Francis. - 0739-1102 .- 1538-0254. ; 41:12, s. 5707-5727
-
Tidskriftsartikel (refereegranskat)abstract
- SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.
|
|
| 11. |
|
|
| 12. |
|
|
| 13. |
|
|
| 14. |
- Li, Fangfang, et al.
(författare)
-
Rotten Eggs Revaluated: Ionic Liquids and Deep Eutectic Solvents for Removal and Utilization of Hydrogen Sulfide
- 2022
-
Ingår i: Industrial & Engineering Chemistry Research. - : American Chemical Society (ACS). - 0888-5885 .- 1520-5045. ; 61:7, s. 2643-2671
-
Forskningsöversikt (refereegranskat)abstract
- Hydrogen sulfide (H2S) is highly toxic and one of the problematic impurities in industrial gas streams, calling for H2S removal down to single-digit ppm levels to protect health and environment, and not to harm to the downstream processes. Here, we discuss the recent developments and challenges of current H2S removal technologies. Furthermore, we present a comprehensive review of H2S removal in ionic liquids (ILs), IL-based solvents/adsorbents/membranes, and deep eutectic solvents (DESs) due to their unique advantages. We analyze theoretical studies to better understand the microscopic details behind H2S removal. We discuss new research on IL/DES-based H2S removal processes from an industrial perspective. Finally, we summarize the utilization of H2S in IL/DES-based systems for the recovery of sulfur and hydrogen, and synthesis of value-added chemicals. This review will provide both general and in-depth knowledge of the achievements, difficulties, and research priorities in developing novel ILs/DESs for efficient and sustainable H2S removal and utilization.
|
|
| 15. |
- Li, Yangshuo, et al.
(författare)
-
Electrochemical CO2 reduction with ionic liquids: review and evaluation
- 2023
-
Ingår i: Industrial Chemistry & Materials. - : Royal Society of Chemistry. - 2755-2608 .- 2755-2500. ; 1:3, s. 410-430
-
Forskningsöversikt (refereegranskat)abstract
- The increasing CO2 emission, as the chief culprit causing numerous environmental problems, could be addressed by the electrochemical CO2 reduction (CO2R) to the added-value carbon-based chemicals. Ionic liquids (ILs) as electrolytes and co-catalysts have been widely studied to promote CO2R owing to their unique advantages. Among the potential products of CO2R, those only containing one carbon atom, named C1 products, including CO, CH3OH, CH4, and syngas, are easier to achieve than others. In this study, we first summarized the research status on CO2R to these C1 products, and then, the state-of-the-art experimental results were used to evaluate the economic potential and environmental impact. Considering the rapid development in CO2R, future scenarios with better CO2R performances were reasonably assumed to predict the future business for each product. Among the studied C1 products, the research focuses on CO, where satisfactory results have been achieved. The evaluation shows that producing CO via CO2R is the only profitable route at present. CH3OH and syngas of H2/CO (1 : 1) as the targeted products can become profitable in the foreseen future. In addition, the life cycle assessment (LCA) was used to evaluate the environmental impact, showing that CO2R to CH4 is the most environmentally friendly pathway, followed by the syngas of H2/CO (2 : 1) and CO, and the further improvement of the CO2R performance can make all the studied C1 products more environmentally friendly. Overall, CO is the most promising product from both economic and environmental impact aspects.
|
|
| 16. |
|
|
| 17. |
- Lyubartsev, Alexander, 1962-, et al.
(författare)
-
Hierarchical multiscale modelling scheme from first principles to mesoscale
- 2009
-
Ingår i: Journal of Computational and Theoretical Nanoscience. - : American Scientific Publishers. - 1546-1955 .- 1546-1963. ; 6:5, s. 951-959
-
Tidskriftsartikel (refereegranskat)abstract
- We present a straight-forward implementation of a practical hierarchical multiscale modelling scheme which enables us to start from first-principles atomistic computer simulation and successively coarse-grain the model by leaving out uninteresting degrees of freedom. Using the Car-Parrinello method or our recently developed highly efficient tight-binding-like approximate density-functional quantum mechanical method,w e first perform first-principles simulations we obtain a set of atomistic pair-wise effective interaction potentials to be used as a force field with scaling up the system size 2–3 orders of magnitude. The atomistic simulations similarly provide a new set of effective potentials but at a chosen coarse-grain level suitable for large-scale mesoscopic or soft-matter simulations beyond the atomic resolution. Show several examples are shown of how this scheme is done based on effective interaction potentials to tie together the various scales of modelling.
|
|
| 18. |
- Mocci, Francesca, et al.
(författare)
-
Carbon Nanodots from an In Silico Perspective
- 2022
-
Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 122:16, s. 13709-13799
-
Forskningsöversikt (refereegranskat)abstract
- Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.
|
|
| 19. |
- Mocci, Francesca, et al.
(författare)
-
DNA-Polyamine Interactions : Insight from Molecular Dynamics Simulations on the Sequence-Specific Binding of Spermidine3
- 2022
-
Ingår i: Soft Matter Systems for Biomedical Applications. - Cham : Springer Nature. - 9783030809232 - 9783030809249 ; , s. 163-192
-
Konferensbidrag (refereegranskat)abstract
- DNA is a polyanion stabilized in vivo by positively charged counterions, including metal ions and small organic molecules, e.g., putrescine2+, spermidine3+, and spermine4+. In this chapter, after a brief review of previous studies on such DNA-counterion interactions, we focus the attention on the interactions between spermidine3+ and DNA. In this context, we present our original molecular dynamics simulation study to establish the specificity of the binding of polyamines to different nucleotide sequence motifs. Spermidine3+ molecules tend to be localized in the minor groove of the DNA double helix around the regions with AATT and ATAT nucleotide sequences. In the major groove, the polyamine does not bind to the AT-rich sequences, but instead localizes on the CG-region. The positioning of polyamines on the DNA surface also determines the DNA-DNA contacts due to the formation of polyamine cross-links. The cross-linking spermidine3+ molecules are localized parallel to the sugar-phosphate backbone of the double helix, neutralizing the negatively charged phosphate groups. The presented results are important for understanding the role of spermidine3+ in the biological functions of DNA and also have implications for possible technological applications.
|
|
| 20. |
- Neamtu, Andrei, et al.
(författare)
-
Molecular dynamics simulations reveal the hidden EF-hand of EF-SAM as a possible key thermal sensor for STIM1 activation by temperature
- 2023
-
Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 299:8
-
Tidskriftsartikel (refereegranskat)abstract
- Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca2+ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca2+ depletion. STIM1 is also activated by temperature independent of ER Ca2+ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca2+ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca2+-loaded form compared to the Ca2+-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca2+ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.
|
|
| 21. |
- Neamtu, Andrei, et al.
(författare)
-
Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants
- 2023
-
Ingår i: Colloids and Surfaces B. - : Elsevier. - 0927-7765 .- 1873-4367. ; 221
-
Tidskriftsartikel (refereegranskat)abstract
- A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.
|
|
| 22. |
- Perepelytsya, Sergiy, et al.
(författare)
-
Conformational flexibility of spermidine3+ interacting with DNA double helix
- 2023
-
Ingår i: Journal of Molecular Liquids. - : Elsevier. - 0167-7322 .- 1873-3166. ; 389
-
Tidskriftsartikel (refereegranskat)abstract
- Natural polyamines play a key role in many biological processes, particularly in the stabilization of DNA double helix structure in the cell nucleus. Among others, the conformational flexibility of polyamines, such as spermidine, is an essential property for the formation of complexes with DNA. Yet, the characterization of the conformational space of polyamines has not been fully elucidated. Using atomistic molecular dynamics (MD) simulations, we present a detailed study of the conformational space of spermidine3+ both in solution and in interaction with DNA. We have identified more than 2000 distinct conformations, which can be grouped into seven modes. Notably, the relative population of these modes is highly affected by the interaction of spermidine3+ with DNA, thus representing a fingerprint of complex formation. In particular, three of the seven dihedral angles of spermidine3+ are predominantly in trans conformation (with or without DNA), while the other four dihedral angles are observed to switch between trans, gauche+ and gauche-. The preference between the latter conformational states was analyzed in terms of the distinct energy contributions composing the potential energy. Overall, our results shed some light on the conformational equilibrium and dynamics of spermidine3+, which in turn is important for understanding the nature of its interaction with DNA.
|
|
| 23. |
|
|
| 24. |
- Sarman, Sten, et al.
(författare)
-
Nonequilibrium Molecular Dynamics Simulation of Liquid Crystals and Variational Principle for Nonequilibrium Steady States
- 2023
-
Ingår i: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. - : Elsevier.
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The purpose of this article is to review molecular dynamics simulation of transport processes of liquid crystal model systems carried out during the last 30 years. In those processes a thermodynamic force or an external dissipative field drives a thermodynamic flux. Well-known examples are shear-flow and elongational flow, where a velocity gradient gives rise to a shear stress, and heat conduction where a temperature gradient drives a heat flow. In these transport processes it has been found that the director of the liquid crystal orients at a constant angle relative to the external dissipative field: In shear-flow the director orients at a constant angle relative to the streamlines, in elongational flow the director is either parallel or perpendicular to the elongation direction and during heat conduction the director is either parallel or perpendicular to the temperature gradient. The alignment angle has been found to be the one that minimizes the irreversible energy dissipation rate. This is in accordance with a recently proven theorem stating that this quantity is minimal in the linear regime of a non-equilibrium steady state. The most commonly used model system is based on the Gay-Berne fluid which can be regarded as a Lennard-Jones fluid generalized to elliptical molecular cores.
|
|
| 25. |
|
|
| 26. |
- Vasiliu, Tudor, et al.
(författare)
-
Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices
- 2022
-
Ingår i: Frontiers in Chemistry. - : Frontiers Media S.A.. - 2296-2646. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine2+, spermidine3+, and spermine4+ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine3+ (Spd3+) cations were performed to study the structuring of Spd3+ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm3+ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd3+ interaction modes, with special attention given to Spd3+ conformational changes in the space between the two DNA molecules (caged Spd3+). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd3+ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.
|
|
| 27. |
- Wang, Hui, et al.
(författare)
-
Experimental and theoretical study on ion association in [Hmim][halide] + water/isopropanol mixtures
- 2023
-
Ingår i: Fluid Phase Equilibria. - : Elsevier. - 0378-3812 .- 1879-0224. ; 566
-
Tidskriftsartikel (refereegranskat)abstract
- The electrical conductivities of the dilute solutions containing ionic liquids (1-hexyl-3-methylimidazolium chloride [Hmim]Cl, 1-hexyl-3-methylimidazolium bromide [Hmim]Br, and 1-hexyl-3-methylimidazolium iodide [Hmim]I) with water and isopropanol were determined in the temperature ranging from 293.15 to 313.15 K. The liquid densities of all binary mixtures were further determined for model parameterization. In theoretical modeling, the limiting molar conductivities Λ0(T) were first obtained using the Debye-Hückel-Onsager (DHO) equation, and thereafter the ion association constants KA(T) were determined using the Shedlovsky equation. The effects of temperature, dielectric constant, and anion size on the values of Λ0(T) and KA(T) were systematically discussed. The Eyring activation enthalpy of charge transport ∆H* and the Walden values Λ0η for all studied binary mixtures were obtained from the temperature-dependent Λ0(T).
|
|
| 28. |
- Wang, Yonglei, et al.
(författare)
-
The Development of Hierarchical Ion Models and Multiscale Modeling of Tetraalkylphosphonium and Imidazolium Ionic Liquids
- 2023
-
Ingår i: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. - : Elsevier.
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Ionic liquid (IL) materials are promising electrolytes with striking physicochemical properties for energy and environmental applications. Heterogeneous structures and transport quantities of ILs are intrinsically intercorrelated and span multiple spatiotemporal scales. Multiscale modeling methodology unifying theoretical calculations, atomistic, and coarse-grained simulations based on successive coarse-graining schemes is an efficient approach to explore complex phase behaviors of these ion-containing materials at extended spatiotemporal scales with a modest computational cost. In this chapter, we will provide several examples concentrated on tetraalkylphosphonium and imidazolium ILs showing how to sketch an effective modeling protocol to obtain force field parameters derived at high-resolution scales being transferred to low-resolution levels in a self-consistent computational scheme using a bottom-up approach bridging different length and time scales. Concluding remarks and an outlook on multiscale strategies in understanding and predictive capabilities of ILs and their mixtures are addressed in the final section to highlight future challenges and opportunities associated with IL materials in multiscale modeling community.
|
|
| 29. |
- Wei, Yudi, et al.
(författare)
-
Molecular interactions of ionic liquids with SiO2 surfaces determined from colloid probe atomic force microscopy
- 2022
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:21, s. 12808-12815
-
Tidskriftsartikel (refereegranskat)abstract
- Ionic liquids (ILs) interact strongly with many different types of solid surfaces in a wide range of applications, e.g. lubrication, energy storage and conversion, etc. However, due to the nearly immeasurable large number of potential ILs available, identifying the appropriate ILs for specific solid interfaces with desirable properties is a challenge. Theoretical studies are highly useful for effective development of design and applications of these complex molecular systems. However, obtaining reliable force field models and interaction parameters is highly demanding. In this work, we apply a new methodology by deriving the interaction parameters directly from the experimental data, determined by colloid probe atomic force microscopy (CP-AFM). The reliability of the derived interaction parameters is tested by performing molecular dynamics simulations to calculate translational self-diffusion coefficients and comparing them with those obtained from NMR diffusometry.
|
|
| 30. |
- Zhang, Zhibo, et al.
(författare)
-
Novel artificial ionic cofactors for efficient electro-enzymatic conversion of CO2 to formic acid
- 2022
-
Ingår i: Journal of CO2 Utilization. - : Elsevier. - 2212-9820 .- 2212-9839. ; 60
-
Tidskriftsartikel (refereegranskat)abstract
- The low yield of enzymatic conversion of CO2 to formic acid as well as the high cost and instability of using the natural cofactor (NADH) hamper the large-scale application of the CO2 enzymatic utilization. To address these issues and to improve the production of formic acid, six bipyridinium-based artificial cofactors were developed for the enzymatic conversion of CO2 and further integrated with the electrocatalytic regeneration of the cofactors for the formic acid production. All of them did show a higher catalytic performance compared to NADH. Particularly, 1,1′-bis(2-(dimethylamino)ethyl)-4,4′-bipyridinium bromine did exhibit the highest catalytic performance with a high formic acid concentration of 4.76 mM in 60 min, which is 47 times higher than that of the natural cofactor NADH and is also currently the highest performance among the reported artificial cofactors in literature. Thermodynamic analysis, electrochemical investigations, and molecular dynamics simulations were performed to clarify the structure-energy relationship of the functional bipyridinium-based salts and to rationalize how it is affected by the different functional groups. This study gives a deep insight into the role of artificial cofactors in enzymatic reactions and can clearly promote the development of novel bioelectrochemical conversion of CO2.
|
|
