| 1. |
- Almeida, Joao, et al.
(författare)
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Molecular understanding of sulphuric acid-amine particle nucleation in the atmosphere
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 502:7471, s. 359-
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Tidskriftsartikel (refereegranskat)abstract
- Nucleation of aerosol particles from trace atmospheric vapours is thought to provide up to half of global cloud condensation nuclei(1). Aerosols can cause a net cooling of climate by scattering sunlight and by leading to smaller but more numerous cloud droplets, which makes clouds brighter and extends their lifetimes(2). Atmospheric aerosols derived from human activities are thought to have compensated for a large fraction of the warming caused by greenhouse gases(2). However, despite its importance for climate, atmospheric nucleation is poorly understood. Recently, it has been shown that sulphuric acid and ammonia cannot explain particle formation rates observed in the lower atmosphere(3). It is thought that amines may enhance nucleation(4-16), but until now there has been no direct evidence for amine ternary nucleation under atmospheric conditions. Here we use the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN and find that dimethylamine above three parts per trillion by volume can enhance particle formation rates more than 1,000-fold compared with ammonia, sufficient to account for the particle formation rates observed in the atmosphere. Molecular analysis of the clusters reveals that the faster nucleation is explained by a base-stabilization mechanism involving acid-amine pairs, which strongly decrease evaporation. The ion-induced contribution is generally small, reflecting the high stability of sulphuric acid-dimethylamine clusters and indicating that galactic cosmic rays exert only a small influence on their formation, except at low overall formation rates. Our experimental measurements are well reproduced by a dynamical model based on quantum chemical calculations of binding energies of molecular clusters, without any fitted parameters. These results show that, in regions of the atmosphere near amine sources, both amines and sulphur dioxide should be considered when assessing the impact of anthropogenic activities on particle formation.
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| 2. |
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| 3. |
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| 4. |
- 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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| 5. |
- Henschel, Henning, et al.
(författare)
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An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra
- 2020
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 11:14, s. 5471-5475
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Tidskriftsartikel (refereegranskat)abstract
- Computational chemistry has become a central tool in spectroscopic studies in most of chemical science. The quality of a calculated vibrational spectrum is commonly expressed as the deviation of the peak position from the experimental reference. With the increasing application of vibrational spectroscopy to complex (biological) systems, this is likely not sustainable. Here we present a quality measure for theoretical vibrational spectra based on matching the spectra to a reference database with the help of correlation coefficients. This approach can easily be applied to large sets of data and complex spectra without easily identifiable peak positions. We demonstrate this on a database of infrared spectra of 670 compounds using six different theoretical (DFT and force field) methods. Most importantly, it is intuitively understandable by both theoreticians and experimentalists.
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| 6. |
- Henschel, Henning, et al.
(författare)
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Computational and structural studies on the complexation of cobalt(II) acetate by water and pyridine
- 2012
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1007, s. 45-51
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Tidskriftsartikel (refereegranskat)abstract
- Four different complexes of the cobalt(II) acetate-pyridine-water system were obtained as dominant species by crystallization from a series of dichloromethane and toluene solutions. The complexes were characterized by terms of X-ray crystal structure determination. Factors in solution properties leading to crystallization of certain complexes are discussed. Furthermore, trends in terms of structure and binding energies in a systematic series of mononuclear cobalt(II) complexes were studied using density functional calculations.
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| 7. |
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| 8. |
- Henschel, Henning, et al.
(författare)
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Effect of the cross-linker on the general performance and temperature dependent behaviour of a molecularly imprinted polymer catalyst of a Diels-Alder reaction
- 2011
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Ingår i: Journal of Molecular Catalysis B. - : Elsevier BV. - 1381-1177 .- 1873-3158. ; 72:3-4, s. 199-205
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Tidskriftsartikel (refereegranskat)abstract
- Here we present a series of molecularly imprinted polymers capable of catalysing the Diels-Alder reaction between benzyl 1,3-butadienylcarbamate (1) and N,N-dimethyl acrylamide (2). The polymer systems studied here demonstrated an unusual cross-linker and temperature dependent behaviour, namely that polymer catalysis of the Diels-Alder reaction was lower at elevated temperature, in contrast to the solution reaction. Furthermore, not only was the catalytic activity significantly influenced by the choice of cross-linker, but in a similar fashion also the extent of the temperature effect, indicating a close relationship between catalysis and the observed inhibition. Molecular dynamics simulations of both the polymer systems studied were used to provide insight into the molecular background of transition state stabilisation, and differences in properties of the systems based on different cross-linkers.
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| 9. |
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| 10. |
- Henschel, Henning, et al.
(författare)
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Hydration of Atmospherically Relevant Molecular Clusters : Computational Chemistry and Classical Thermodynamics
- 2014
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 118:14, s. 2599-2611
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Tidskriftsartikel (refereegranskat)abstract
- Formation of new particles through clustering of molecules from condensable vapors is a significant source for atmospheric aerosols. The smallest clusters formed in the very first steps of the condensation process are, however, not directly observable by experimental means. We present here a comprehensive series of electronic structure calculations on the hydrates of clusters formed by up to four molecules of sulfuric acid, and up to two molecules of ammonia or dimethylamine. Though clusters containing ammonia, and certainly dimethylamine, generally exhibit lower average hydration than the pure acid clusters, populations of individual hydrates vary widely. Furthermore, we explore the predictions obtained using a thermodynamic model for the description of these hydrates. The similar magnitude and trends of hydrate formation predicted by both methods illustrate the potential of combining them to obtain more comprehensive models. The stabilization of some clusters relative to others due to their hydration is highly likely to have significant effects on the overall processes that lead to formation of new particles in the atmosphere.
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| 11. |
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| 12. |
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| 13. |
- Henschel, Henning, et al.
(författare)
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Insights into the Isomerisation Mechanism of Warfarin
- 2010
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Konferensbidrag (refereegranskat)abstract
- Warfarin is one of the most commonly used drugs in anticoagulent therapy. Notwithstanding its wide use, achieving correct dosage is often a major challenge due to its narrow therapeutic window.[1] The bioavailability of warfarin is believed to be greatly influenced by the environment-dependent composition of the ensemble of isomers present. While the different structures of warfarin have been discussed in earlier publications,[2] details of the mechanism underlying the formation of the cyclic hemiacetal (Figure 1) had not yet been investigated. Figure 1. Cyclization reaction of warfarin.Figure 2. Transition state in presence of one water molecule. We have now studied the reaction by means of density functional calculations. Comparison of results from calculations performed on the isolated warfarin molecule and in presence of water molecules (compare Figure 2) highlight the importance of intermolecular interactions in the key proton transfer step for the reaction to proceed. A viable model for the mechanism underlying the isomerisation shall be presented. References[1] J. Ansell, J. Hirsh, L. Poller, H. Bussey, A. Jacobsen and E. Hylek, Chest, 126, 204S (2004).[2] B. C. G. Karlsson, A. M. Rosengren, P. O. Andersson and I. A. Nicholls, J. Phys. Chem. B, 111,10520 (2007).
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| 14. |
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| 15. |
- Henschel, Henning, et al.
(författare)
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The Mechanistic Basis for Warfarin’s Structural Diversity and Implications for Its Bioavailability
- 2010
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 958, s. 7-9
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Tidskriftsartikel (refereegranskat)abstract
- The anticoagulent drug warfarin exhibits chameleon-like isomerism, where the environment-dependent composition of the ensemble of structures greatly influences its bioavailability. Here, the mechanism of conversion between the major isomeric forms is studied. The dramatic differences in transition state energies, as determined by density functional calculations, highlight the necessity for the involvement of intermolecular interactions in the key proton transfer step. A viable model for the mechanism underlying the isomerization reactions is presented.
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| 16. |
- Henschel, Henning, et al.
(författare)
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Theoretical Infrared Spectra : Quantitative Similarity Measures and Force Fields
- 2020
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Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:5, s. 3307-3315
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Tidskriftsartikel (refereegranskat)abstract
- Infrared spectroscopy can provide significant insight into the structures and dynamics of molecules of all sizes. The information that is contained in the spectrum is, however, often not easily extracted without the aid of theoretical calculations or simulations. We present here the calculation of the infrared spectra of a database of 703 gas phase compounds with four different force fields (CGenFF, GAFF-BCC, GAFF-ESP, and OPLS) using normal-mode analysis. Modern force fields increasingly use virtual sites to describe, e.g., lone-pair electrons or the o -holes on halogen atoms. This requires some adaptation of code to perform normal-mode analysis of such compounds, the implementation of which into the GROMACS software is briefly described as well. For the quantitative comparison of the obtained spectra with experimental reference data, we discuss the application of two different statistical correlation coefficients, Pearson and Spearman. The advantages and drawbacks of the different methods of comparison are discussed, and we find that both methods of comparison give the same overall picture, showing that present force field methods cannot match the performance of quantum chemical methods for the calculation of infrared spectra.
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| 17. |
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| 18. |
- Karjalainen, Jouni, et al.
(författare)
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Dipolar Relaxation of Water Protons in the Vicinity of a Collagen-like Peptide
- 2022
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:13, s. 2538-2551
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Tidskriftsartikel (refereegranskat)abstract
- Quantitative magnetic resonance imaging is one of the few available methods for noninvasive diagnosis of degenerative changes in articular cartilage. The clinical use of the imaging data is limited by the lack of a clear association between structural changes at the molecular level and the measured magnetic relaxation times. In anisotropic, collagen-containing tissues, such as articular cartilage, the orientation dependency of nuclear magnetic relaxation can obscure the content of the images. Conversely, if the molecular origin of the phenomenon would be better understood, it would provide opportunities for diagnostics as well as treatment planning of degenerative changes in these tissues. We study the magnitude and orientation dependence of the nuclear magnetic relaxation due to dipole-dipole coupling of water protons in anisotropic, collagenous structures. The water-collagen interactions are modeled with molecular dynamics simulations of a small collagen-like peptide dissolved in water. We find that in the vicinity of the collagen-like peptide, the dipolar relaxation of water hydrogen nuclei is anisotropic, which can result in orientation-dependent relaxation times if the water remains dose to the peptide. However, the orientation-dependency of the relaxation is different from the commonly observed magic-angle phenomenon in articular cartilage MRI.
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| 19. |
- Karlsson, Björn C. G., et al.
(författare)
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How warfarin’s structural diversity influences its phospholipid bilayer membrane permeation
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:8, s. 2384-2395
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Tidskriftsartikel (refereegranskat)abstract
- The role of the structural diversity of the widely used anticoagulant drug warfarin on its distribution in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer membranes was investigated using a series of both restrained (umbrella sampling) and unrestrained molecular dynamics simulations. Data collected from unrestrained simulations revealed favorable positions for neutral isomers of warfarin, the open side chain form (OCO), and the cyclic hemiketal (CCO), along the bilayer normal close to the polar headgroup region and even in the relatively distant nonpolar lipid tails. The deprotonated open side chain form (DCO) was found to have lower affinity for the DOPC bilayer membrane relative to the neutral forms, with only a small fraction interacting with the membrane, typically within the polar headgroup region. The conformation of OCO inside the lipid bilayer was found to be stabilized by intramolecular hydrogen bonding thereby mimicking the structure of CCO. Differences in free energies, for positions of OCO and CCO inside the bilayer membrane, as compared to positions in the aqueous phase, were −97 and −146 kJ·mol–1. Kinetic analysis based on the computed free energy barriers reveal that warfarin will diffuse through the membranes within hours, in agreement with experimental results on warfarin’s accumulation in the plasma, thus suggesting a passive diffusion mechanism. We propose that this membrane transport may be an isomerization-driven process where warfarin adapts to the various local molecular environments encountered under its journey through the membrane. Collectively, these results improve our understanding of the influence of warfarin’s structural diversity on the drug’s distribution and bioavailability, which in turn may provide insights for developing new formulations of this important pharmaceutical to better address its narrow therapeutic window.
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| 20. |
- Kirsch, Nicole, et al.
(författare)
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Molecularly imprinted polymer catalysis of a Diels-Alder reaction
- 2009
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Ingår i: Journal of Molecular Catalysis B. - : Elsevier BV. - 1381-1177 .- 1873-3158. ; 58:1-4, s. 110-117
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Tidskriftsartikel (refereegranskat)abstract
- A series of synthetic polymers were designed and synthesized for enhancing the rate of the Diels-Alder cycloaddition reaction of 1,3-butadiene carbamic acid benzyl ester (11) and N,N-dimethyl acrylamide (2), to yield the corresponding endo- (3) and exo- (4) reaction products. Putative transition state analogues (TSAs) for the endo- (5) and exo- (6) reaction pathways were used as templates for the synthesis of molecularly imprinted methacrylic acid (MAA)-divinylbenzene (DVB) copolymers. The polymer system utilized was selected based upon a series of (1)H NMR studies of complex formation between template and a functional monomer analogue (K(d) (app) approximate to 70 mM, d(8)-toluene, 293 K). Batch binding studies revealed that the imprinted polymers were selective for the TSA corresponding to the template used in the polymer synthesis. Studies on the influence of the polymers on the catalysis of the reaction of 1 and 2 demonstrated a 20-fold enhancement of the rate of the reaction relative to the solution reaction. A surprising temperature dependence of the reaction of 1 and 2 in the presence of the polymers was observed, which provides support for the role of template-functional monomer complexes in the catalysis of the Diels-Alder reaction.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
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| 25. |
- Mailhiot, Sarah E., et al.
(författare)
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Melting of aqueous NaCl solutions in porous materials: shifted phase transition distribution (SIDI) approach for determining NMR cryoporometry pore size distributions
- 2024
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : The Royal Society of Chemistry. - 1463-9076 .- 1463-9084.
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear magnetic resonance cryoporometry (NMRC) and differential scanning calorimetry thermoporometry (DSC-TPM) are powerful methods for measuring mesopore size distributions. The methods are based on the fact that, according to the Gibbs–Thomson equation, the melting point depression of a liquid confined to a pore is inversely proportional to the pore size. However, aqueous salt solutions, which inherently exist in a broad range of biological porous materials as well as technological applications such as electrolytes, do not melt at a single temperature. This causes artefacts in the pore size distributions extracted by traditional Gibbs–Thomson analysis of NMRC and DSC-TPM data. Bulk aqueous NaCl solutions are known to have a broad distribution of melting points between the eutectic and pure water phase transition points (252–273 K). Here, we hypothesize that, when aqueous NaCl solution (saline) is confined to a small pore, the whole melting point distribution is shifted toward lower temperatures by the value predicted by the Gibbs–Thomson equation. We show that this so-called shifted phase transition distribution (SIDI) approach removes the artefacts arising from the traditional Gibbs–Thomson analysis and gives correct pore size distributions for saline saturated mesoporous silica gel and controlled pore materials analyzed by NMR cryoporometry. Furthermore, we demonstrate that the method can be used for determining pore sizes in collagen–chondroitin sulphate hydrogels resembling the composition of the extracellular matrix of articular cartilage. It is straightforward to apply the SIDI analysis for DSC-TMP data as well.
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| 26. |
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| 27. |
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| 28. |
- 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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| 29. |
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| 30. |
- Nicholls, Ian A., et al.
(författare)
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Theoretical and Computational Strategies for Rational Molecularly Imprinted Polymer Design
- 2009
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Ingår i: Biosensors & bioelectronics. - : Elsevier BV. - 0956-5663 .- 1873-4235. ; 25:3, s. 543-552
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Tidskriftsartikel (refereegranskat)abstract
- The further evolution of molecularly imprinted polymer science and technology necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. A combination of the rapid growth in computer power over the past decade and significant software developments have 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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| 31. |
- Nicholls, Ian A., et al.
(författare)
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Warfarin : an environment-dependent switchable molecular probe
- 2010
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Ingår i: Journal of Molecular Recognition. - : Wiley. - 0952-3499 .- 1099-1352. ; 23:6, s. 604-608
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Tidskriftsartikel (refereegranskat)abstract
- The complex nature of the structure of the anticoagulant warfarin is reflected in the diversity of binding modes observed in warfarin-protein recognition systems. A series of theoretical, H-1-NMR and steady state and time resolved fluorescence spectroscopic studies, have been used to establish correlations between the molecular environment provided by various solvent systems and the relative concentrations of the various members of warfarin's ensemble of isomers. A consequence of these observations is that the judicious choice of solvent system or molecular environment of warfarin allows for manipulation of the position of the equilibrium between isomeric structures such as the hemiacetal and open phenol-keto forms, the latter even possible in a deprotonated form, where in each case unique spectroscopic properties are exhibited by the respective structures. Collectively, warfarin's capacity to adapt its structure as a function of environment in conjunction with the fluorescence behaviours of the various isomers together provide an environment-dependent molecular switch with reporter properties, which allows for the simultaneous detection of warfarin in different states with lifetimes spanning the range <0.10-5.5 ns. These characteristics are here used to examine warfarin binding domains in a series of materials (solvents, protein, inorganic matrix and synthetic polymer). Moreover, these studies demonstrate the potential for using warfarin, or other switchable analogues thereof, as a tool for studying molecular level characteristics, for example local dielectricity.
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| 32. |
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| 33. |
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| 34. |
- Olenius, Tinja, et al.
(författare)
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New particle formation from sulfuric acid and amines : Comparison of monomethylamine, dimethylamine, and trimethylamine
- 2017
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Ingår i: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 122:13, s. 7103-7118
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Tidskriftsartikel (refereegranskat)abstract
- Amines are bases that originate from both anthropogenic and natural sources, and they are recognized as candidates to participate in atmospheric aerosol particle formation together with sulfuric acid. Monomethylamine, dimethylamine, and trimethylamine (MMA, DMA, and TMA, respectively) have been shown to enhance sulfuric acid-driven particle formation more efficiently than ammonia, but both theory and laboratory experiments suggest that there are differences in their enhancing potentials. However, as quantitative concentrations and thermochemical properties of different amines remain relatively uncertain, and also for computational reasons, the compounds have been treated as a single surrogate amine species in large-scale modeling studies. In this work, the differences and similarities of MMA, DMA, and TMA are studied by simulations of molecular cluster formation from sulfuric acid, water, and each of the three amines. Quantum chemistry-based cluster evaporation rate constants are applied in a cluster population dynamics model to yield cluster concentrations and formation rates at boundary layer conditions. While there are differences, for instance, in the clustering mechanisms and cluster hygroscopicity for the three amines, DMA and TMA can be approximated as a lumped species. Formation of nanometer-sized particles and its dependence on ambient conditions is roughly similar for these two: both efficiently form clusters with sulfuric acid, and cluster formation is rather insensitive to changes in temperature and relative humidity. Particle formation from sulfuric acid and MMA is weaker and significantly more sensitive to ambient conditions. Therefore, merging MMA together with DMA and TMA introduces inaccuracies in sulfuric acid-amine particle formation schemes.
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| 35. |
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| 36. |
- Partanen, Lauri, et al.
(författare)
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Effect of Conformers on Free Energies of Atmospheric Complexes
- 2016
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 120:43, s. 8613-8624
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Tidskriftsartikel (refereegranskat)abstract
- In this article we show how to calculate free energies for atmospherically relevant complexes when multiple conformers and/or isomers are present. We explain why the thermal averaging methods used in several published works are incorrect. On the basis of our two sample cases, the sulfuric acid−pinic acid complex and the H2SO4)3(NH3)3(H2O)4 cluster, we provide numerical evidence that the use of these incorrect formulas can result in errors larger than 1 kcal/mol. We recommend that if vibrational frequencies and thus Gibbs free energies of the individual conformers are unavailable, one should not attempt to correct for the presence of multiple conformers and instead use only the global minimum conformers for both reactants and products. On the contrary, if the free energies for the conformers are calculated for both reactants and products, their effect can be accounted for by the statistical mechanical methods presented in this article.
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| 37. |
- Tolkkinen, Katja, et al.
(författare)
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SPICY : a method for single scan rotating frame relaxometry
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 25:18, s. 13164-13169
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Tidskriftsartikel (refereegranskat)abstract
- T 1ρ is an NMR relaxation mode that is sensitive to low frequency molecular motions, making it an especially valuable tool in biomolecular research. Here, we introduce a new method, SPICY, for measuring T1ρ relaxation times. In contrast to conventional T1ρ experiments, in which the sequence is repeated many times to determine the T1ρ time, the SPICY sequence allows determination of T1ρ within a single scan, shortening the experiment time remarkably. We demonstrate the method using 1H T1ρ relaxation dispersion experiments. Additionally, we combine the sequence with spatial encoding to produce 1D images in a single scan. We show that T1ρ relaxation times obtained using the single scan approach are in good agreement with those obtained using the traditional experiments.
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| 38. |
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| 39. |
- Van der Spoel, David, et al.
(författare)
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A potential for molecular simulation of compounds with linear moieties
- 2020
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Ingår i: Journal of Chemical Physics. - : AMER INST PHYSICS. - 0021-9606 .- 1089-7690. ; 153:8
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Tidskriftsartikel (refereegranskat)abstract
- The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180 degrees, which can lead to numeric instabilities. Angle bending of linear groups, such as alkynes or nitriles, or linear molecules, such as carbon dioxide, can be treated by a simple harmonic potential if we describe the fluctuations as a deviation from a reference position of the central atom, the position of which is determined by the flanking atoms. The force constant for the linear angle potential can be derived analytically from the corresponding force constant in the traditional potential. The new potential is tested on the properties of alkynes, nitriles, and carbon dioxide. We find that the angles of the linear groups remain about 2 degrees closer to 180 degrees using the new potential. The bond and angle force constants for carbon dioxide were tuned to reproduce the experimentally determined frequencies. An interesting finding was that simulations of liquid carbon dioxide under pressure with the new flexible model were stable only when explicitly modeling the long-range Lennard-Jones (LJ) interactions due to the very long-range nature of the LJ interactions (>1.7 nm). In the other tested liquids, we find that a Lennard-Jones cutoff of 1.1 nm yields similar results as the particle mesh Ewald algorithm for LJ interactions. Algorithmic factors influencing the stability of liquid simulations are discussed as well. Finally, we demonstrate that the linear angle potential can be used in free energy perturbation calculations. (c) 2020 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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| 40. |
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