| 1. |
- Nicholls, Ian A., et al.
(författare)
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Rational design of biomimetic molecularly imprinted materials : theoretical and computational strategies for guiding nanoscale structured polymer development
- 2011
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:6, s. 1771-1786
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Forskningsöversikt (refereegranskat)abstract
- In principle, molecularly imprinted polymer science and technology provides a means for ready access to nano-structured polymeric materials of predetermined selectivity. The versatility of the technique has brought it to the attention of many working with the development of nanomaterials with biological or biomimetic properties for use as therapeutics or in medical devices. Nonetheless, the further evolution of the field necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. The rapid growth in computer power and software over the past decade has opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.
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| 2. |
- Wiklander, Jesper G., 1974-, et al.
(författare)
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Towards a synthetic avidin mimic
- 2011
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:5, s. 1397-1404
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Tidskriftsartikel (refereegranskat)abstract
- A series of streptavidin-mimicking molecularly imprinted polymers has been developed and evaluated for their biotin binding characteristics. A combination of molecular dynamics and NMR spectroscopy was used to examine potential polymer systems, in particular with the functional monomers methacrylic acid and 2-acrylamidopyridine. The synthesis of copolymers of ethylene dimethacrylate and one or both of these functional monomers was performed. A combination of radioligand binding studies and surface area analyses demonstrated the presence of selectivity in polymers prepared using methacrylic acid as the functional monomer. This was predicted by the molecular dynamics studies showing the power of this methodology as a prognostic tool for predicting the behavior of molecularly imprinted polymers.
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| 3. |
- Friedman, Ran
(författare)
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Ions and the protein surface revisited : extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115, s. 9213-9223
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Tidskriftsartikel (refereegranskat)abstract
- Proteins interact with ions in various ways. The surface of proteins has an innate capability to bind ions, and it is also influenced by the screening of the electrostatic potential owing to the presence of salts in the bulk solution. Alkali metal ions and chlorides interact with the protein surface, but such interactions are relatively weak and often transient. In this paper, computer simulations and analysis of protein structures are used to characterize the interactions between ions and the protein surface. The results show that the ion-binding properties of protein residues are highly variable. For example, alkali metal ions are more often associated with aspartate residues than with glutamates, whereas chlorides are most likely to be located near arginines. When comparing NaCl and KCl solutions, it was found that certain surface residues attract the anion more strongly in NaCl. This study demonstrates that protein–salt interactions should be accounted for in the planning and execution of experiments and simulations involving proteins, particularly if subtle structural details are sought after.
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| 4. |
- Friedman, Ran, et al.
(författare)
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Surfactant Effects on Amyloid Aggregation Kinetics
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 414, s. 303-312
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Tidskriftsartikel (refereegranskat)abstract
- There is strong experimental evidence of the influence of surfactants (e.g., fatty acids) on the kinetics of amyloid fibril formation. However, the structures of mixed assemblies and interactions between surfactants and fibril-forming peptides are still not clear. Here, coarse-grained simulations are employed to study the aggregation kinetics of amyloidogenic peptides in the presence of amphiphilic lipids. The simulations show that the lower the fibril formation propensity of the peptides, the higher the influence of the surfactants on the peptide self-assembly kinetics. In particular, the lag phase of weakly aggregating peptides increases because of the formation of mixed oligomers, which are promoted by hydrophobic interactions and favorable entropy of mixing. A transient peak in the number of surfactants attached to the growing fibril is observed before reaching the mature fibril in some of the simulations. This peak originates from transient fibrillar defects consisting of exposed hydrophobic patches on the fibril surface, which provide a possible explanation for the temporary maximum of fluorescence observed sometimes in kinetic traces of the binding of small-molecule dyes to amyloid fibrils.
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| 5. |
- Xu, Yuan, et al.
(författare)
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Understanding intermolecular interactions of large systems in ground state and excited state by using density functional based tight binding methods
- 2021
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:19
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Tidskriftsartikel (refereegranskat)abstract
- A novel energy decomposition analysis scheme, named DFTB-EDA, is proposed based on the density functional based tight-binding method (DFTB/TD-DFTB), which is a semi-empirical quantum mechanical method based on Kohn–Sham-DFT for large-scale calculations. In DFTB-EDA, the total interaction energy is divided into three terms: frozen density, polarization, and dispersion. Owing to the small cost of DFTB/TD-DFTB, DFTB-EDA is capable of analyzing intermolecular interactions in large molecular systems containing several thousand atoms with high computational efficiency. It can be used not only for ground states but also for excited states. Test calculations, involving the S66 and L7 databases, several large molecules, and non-covalent bonding complexes in their lowest excited states, demonstrate the efficiency, usefulness, and capabilities of DFTB-EDA. Finally, the limits of DFTB-EDA are pointed out.
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| 6. |
- Henschel, Henning, et al.
(författare)
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A Density Functional Study on the Factors Governing Metal Catalysis of the Direct Aldol Reaction
- 2011
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Ingår i: Journal of Molecular Catalysis A. - : Elsevier BV. - 1381-1169 .- 1873-314X. ; 351, s. 76-80
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Tidskriftsartikel (refereegranskat)abstract
- Density functional calculations are employed in the study of the C-C bond formation step of an aldol reaction in presence of a series of metals. Focus was placed on first row d-block metals that have been used in catalysis of direct aldol reactions. The obtained energy profiles are analysed in order to differentiate between factors governing catalysis. Results demonstrate a major influence of d-orbital occupation, and suggest some of the so far less commonly used metals as promising candidates for development of new catalytic systems.
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| 7. |
- Friedman, Ran
(författare)
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Proton Transfer on the Molecular Surface of Proteins and Model Systems
- 2009
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Ingår i: Israel Journal of Chemistry. - 0021-2148. ; 49:2, s. 149-153
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Tidskriftsartikel (refereegranskat)abstract
- Proton transfer (PT) reactions take place oil the molecular Surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions oil the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed oil a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions oil the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few A apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface.
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| 8. |
- Lindwall, Katrin, 1959-, et al.
(författare)
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Maker Tour - Mot nya höjder : Make IT flow, del 2
- 2018
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Annan publikation (populärvet., debatt m.m.)abstract
- Utmaningarna är en del av projektet Maker tour - Mot nya höjder ( tidigare Mot nya höjder). Projektets mål är att öka intresset för naturvetenskap, teknik och matematik bland skolelever.Läs gärna mer på http://motnyahojder.com/
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| 9. |
- Lindwall, Katrin, 1959-, et al.
(författare)
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Maker tour: mot nya höjder : make space HT-19
- 2019
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Annan publikation (populärvet., debatt m.m.)abstract
- Utmaningarna är en del av projektet Maker tour - Mot nya höjder (tidigare Mot nya höjder). Projektets mål är att öka intresset för naturvetenskap, teknik och matematik bland skolelever.
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| 10. |
- Lindwall, Katrin, 1959-, et al.
(författare)
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Maker tour: mot nya höjder : make IT shine HT-18
- 2018
-
Annan publikation (populärvet., debatt m.m.)abstract
- Utmaningarna är en del av projektet Maker tour - Mot nya höjder (tidigare Mot nya höjder). Projektets mål är att öka intresset för naturvetenskap, teknik och matematik bland skolelever.
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