166 research outputs found
Unusual bending patterns of spermidine3+ bound to DNA double helix
No full textNatural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq. 389, 122828 (2023)], we have shown how the interactions between spermidine(3+) and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine(3+) molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine(3+) molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine(3+) molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine(3+) in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA's biological function
195Pt NMR and Molecular Dynamics Simulation Study of the Solvation of [PtCl6]2-in Water-Methanol and Water-Dimethoxyethane Binary Mixtures
No full textThe experimental195Pt NMR chemical shift, δ(195Pt), of the [PtCl6]2-anion dissolved in binary mixtures of water and a fully miscible organic solvent is extremely sensitive to the composition of the mixture at room temperature. Significantly nonlinear δ(195Pt) trends as a function of solvent composition are observed in mixtures of water-methanol, or ethylene glycol, 2-methoxyethanol, and 1,2-dimethoxyethane (DME). The extent of the deviation from linearity of the δ(195Pt) trend depends strongly on the nature of the organic component in these solutions, which broadly suggests preferential solvation of the [PtCl6]2-anion by the organic molecule. This simplistic interpretation is based on an accepted view pertaining to monovalent cations in similar binary solvent mixtures. To elucidate these phenomena in detail, classical molecular dynamics computer simulations were performed for [PtCl6]2-in water-methanol and water-DME mixtures using the anionic charge scaling approach to account for the effect of electronic dielectric screening. Our simulations suggest that the simplistic model of preferential solvation of [PtCl6]2-by the organic component as inferred from nonlinear δ(195Pt) trends is not entirely accurate, particularly for water-DME mixtures. The δ(195Pt) trend in these mixtures levels off for high DME mole fractions, which results from apparent preferential location of [PtCl6]2-anions at the borders of water-rich regions or clusters within these inherently micro-heterogeneous mixtures. By contrast in water-methanol mixtures, apparently less pronounced mixed solvent micro-heterogeneity is found, suggesting the experimental δ(195Pt) trend is consistent with a more moderate preferential solvation of [PtCl6]2-anions. This finding underlines the important role of solvent-solvent interactions and micro-heterogeneity in determining the solvation environment of [PtCl6]2-anions in binary solvent mixtures, probed by highly sensitive195Pt NMR. The notion that preferential solvation of [PtCl6]2-results primarily from competing ion-solvent interactions as generally assumed for monatomic ions, may not be appropriate in general
Deep Eutectic Solvents Meet Non-Aqueous Cosolvents: A Modeling and Simulation Perspective─A Tutorial Review
No full textDeep eutectic solvents (DESs) have recently gained attention due to their tailorable properties and versatile applications in several fields, including green chemistry, pharmaceuticals, and energy storage. Their tunable properties can be enhanced by mixing DESs with cosolvents such as ethanol, acetonitrile, and water. DESs are structurally complex, and molecular modeling techniques, including quantum mechanical calculations and molecular dynamics simulations, play a crucial role in understanding their intricate behavior when mixed with cosolvents. While the most studied cosolvent is water, in some applications, even a small content of water is considered a contaminant, for example, when the processes of interest require dry conditions. Only quite recently have modeling studies begun to focus on DES mixed with cosolvents other than water. This tutorial provides the first comprehensive overview of these studies. It highlights how modern molecular modeling increases our understanding of their structural organization, transport properties, phase behavior, and thermodynamic properties. Additionally, case studies and recent developments in the field are discussed along with the challenges and future directions in molecular modeling of DES in cosolvent mixtures. Overall, this review offers valuable insights into the molecular-level understanding of DES-cosolvent systems and their implications for designing novel solvent mixtures with tailored properties for various applications. Validerad;2025;Nivå 2;2025-04-07 (u8);Full text license: CC BY-NC-ND</p
Molecular Perspective on Solutions and Liquid Mixtures from Modelling and Experiment
No full textLiquid 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
MD simulations explain the excess molar enthalpies in pseudo-binary mixtures of a choline chloride-based deep eutectic solvent with water or methanol
No full textThe addition of molecular liquid cosolvents to choline chloride (ChCl)-based deep eutectic solvents (DESs) is increasingly investigated for reducing the inherently high bulk viscosities of the latter, which represent a major obstacle for potential industrial applications. The molar enthalpy of mixing, often referred to as excess molar enthalpy H (E)—a property reflecting changes in intermolecular interactions upon mixing—of the well-known ChCl/ethylene glycol (1:2 molar ratio) DES mixed with either water or methanol was recently found to be of opposite sign at 308.15 K: Mixing of the DES with water is strongly exothermic, while methanol mixtures are endothermic over the entire mixture composition range. Knowledge of molecular-level liquid structural changes in the DES following cosolvent addition is expected to be important when selecting such “pseudo-binary” mixtures for specific applications, e.g., solvents. With the aim of understanding the reason for the different behavior of selected DES/water or methanol mixtures, we performed classical MD computer simulations to study the changes in intermolecular interactions thought to be responsible for the observed H (E) sign difference. Excess molar enthalpies computed from our simulations reproduce, for the first time, the experimental sign difference and composition dependence of the property. We performed a structural analysis of simulation configurations, revealing an intriguing difference in the interaction modes of the two cosolvents with the DES chloride anion: water molecules insert between neighboring chloride anions, forming ionic hydrogen-bonded bridges that draw the anions closer, whereas dilution of the DES with methanol results in increased interionic separation. Moreover, the simulated DES/water mixtures were found to contain extended hydrogen-bonded structures containing water-bridged chloride pair arrangements, the presence of which may have important implications for solvent applications
Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices
No full textPolyamines 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
Conformational flexibility of spermidine3+ interacting with DNA double helix
No full textNatural 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.Validerad;2023;Nivå 2;2023-12-12 (marisr);Funder: National Academy of Sciences of Ukraine (0123U102290); COST Action CA21101, COST (European Cooperation in Science and Technology);Full text license: CC BYBioMat4CAS
Aspects of the biology of the pink-billed lark (Spizocorys conirostris) in the Limpopo Province, South Africa
No full textThesis (M.Sc. ( Zoology)) --University of Limpopo, 2013The fieldwork for this study was carried out from October 2008 to October 2010, under the supervision of Professor D. Engelbrecht of the Department of Biodiversity at the University of Limpopo. Professor Engelbrecht kindly agreed to provide me with raw breeding data of the same population collected during 2008. This study represents original work by the author and where work of other authors has been used; they are duly acknowledged in the text and listed as references.
Chapter 1 is a general introduction to the family Alaudidae in which their characteristics and taxonomy are discussed. This is followed by a brief overview of the general biology and ecology of larks of the world in general, followed by a more specific emphasis on the genus Spizocorys, and finally the Pink-billed Lark. In this section, gaps in the available knowledge of Pink-billed Larks are highlighted. This chapter culminates in the aim and objectives of this study. In Chapter 2 the various aspects of the breeding biology of the Pink-billed Lark are reported. This includes, amongst others, aspects such as breeding seasonality, clutch sizes, roles of the sexes during the breeding cycle and breeding success. Chapter 3 provides the results of a morphometric study of museum study skins from across the species range. This includes an analysis of sexual size dimorphism and geographical variation of the different subspecies. This chapter also provides a brief description of the timing and pattern of moult and the various vocalizations of the Pink-billed Lark. Chapter 4 concludes the dissertation with a summary of the results of this study and highlights avenues for future research on the species and the family.
The format of Chapters 2 and 3 takes the form of research papers that can be submitted for publication with minimum editing. Chapter 2 has been published in the Journal of African Zoology (see below). Chapter 3 is in preparation for submission to a peer-reviewed journal. As such, there is some repetition in the introductory paragraphs and concluding remarks of chapters 2, 3 and 4. To give this manuscript a degree of uniformity, the literature cited in all chapters has been formatted according to the manuscript requirements of the Journal of African Zoology, and a reference list appears at the end of the dissertation. Tables and figures are arranged at the end of each chapter
Carbon Nanodots from an In Silico Perspective
No full text[Image: see text] 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
Theoretical and Experimental Study of the Excess Thermodynamic Properties of Highly Nonideal Liquid Mixtures of Butanol Isomers + DBE
No full textBinary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (HE and VE), have been extensively measured. Butanol isomer + di-n-butyl ether (DBE) mixtures received significant attention because of interesting differences in their VE, changing from negative (1- and isobutanol) to positive (2- and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol self-association and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1- and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the HE and VE in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures
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