| 431. |
- Li, Xin, et al.
(författare)
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Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins : Insight from Atomistic Simulations and First-Principles Calculations
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:11, s. 4766-4774
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Tidskriftsartikel (refereegranskat)abstract
- Electron paramagnetic resonance (EPR) imaging techniques provide a promising approach to detect amyloid structures which are of paramount importance in early-stage diagnosis of conformational diseases. Here, we report a combined molecular dynamics and density functional theory/molecular mechanics computational scheme for evaluation of the binding mechanism between a multifunctional spin label and the target amyloid protein. In addition, we consider evaluation of EPR spin Hamiltonian parameters with the aim of providing a better microscopic understanding and interpretation of EPR spectroscopy. The results from molecular dynamics simulations suggest that the oligothiophene conjugate part of the spin label interacts with hydrophobic residues of the amyloid protein through hydrophobic attraction and that both the N-O bond length and the N-O out-of-plane tilt angle in the nitroxide group are slightly diminished after, complexation with the protein. The translational and rotational motions of the protein bound spin label are considerably slowed compared to those of the free spin label in aqueous solution, but interestingly, hydrogen bonds formed between the nitroxide oxygen group and the surrounding water molecules are hardly affected by the presence Of the amyloid protein. First principles calculation's suggest that EPR spin Hamiltonian parameters including the nitroxide nitrogen hyperfine coupling tensor A(N) and electronic g tensor suffer noticeable changes upon complexation with the protein. The magnitude of the A(N) tensor is found,to:be. closely related to the nitroxide N-O out tilt angle, while the g tensor is affected by both the nitroxide N-O bond length as well as the interaction between the spin label and the amyloid protein With this work we show that state-of-the-art simulation techniques represent a promising way of providing a detailed understanding of the microscopic mechanisms responsible for the formation and stability of a spin label complexed with amyloid structures as well as the magnetic properties of the free and protein-bound spin label.
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| 432. |
- Li, Xin, et al.
(författare)
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Cloud droplet activation mechanisms of amino acid aerosol particles : insight from molecular dynamics simulations
- 2013
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Ingår i: Tellus. Series B, Chemical and physical meteorology. - : Stockholm University Press. - 0280-6509 .- 1600-0889. ; 65, s. 65-
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric amino acids constitute a large fraction of water-soluble organic nitrogen compounds in aerosol particles, and have been confirmed as effective cloud condensation nuclei (CCN) materials in laboratory experiments. We present a molecular dynamics (MD) study of six amino acids with different structures and chemical properties that are relevant to the remote marine atmospheric aerosol-cloud system, with the aim of investigating the detailed mechanism of their induced changes in surface activity and surface tension, which are important properties for cloud drop activation. Distributions and orientations of the amino acid molecules are studied; these L-amino acids are serine (SER), glycine (GLY), alanine (ALA), valine (VAL), methionine (MET) and phenylalanine (PHE) and are categorised as hydrophilic and amphiphilic according to their affinities to water. The results suggest that the presence of surface-concentrated amphiphilic amino acid molecules give rise to enhanced Lennard-Jones repulsion, which in turn results in decreased surface tension of a planar interface and an increased surface tension of the spherical interface of droplets with diameters below 10 nm. The observed surface tension perturbation for the different amino acids under study not only serves as benchmark for future studies of more complex systems, but also shows that amphiphilic amino acids are surface active. The MD simulations used in this study reproduce experimental results of surface tension measurements for planar interfaces and the method is therefore applicable for spherical interfaces of nano-size for which experimental measurements are not possible to conduct.
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| 433. |
- Li, Xin, et al.
(författare)
-
Cloud droplet activation mechanisms of amino acid aerosol particles : insight from molecular dynamics simulations
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Atmospheric amino acids constitute a large fraction of water-soluble organic nitrogen compounds in aerosol particles, and have been confirmed as effective cloud condensation nuclei materials in laboratory experiments. We here present a molecular dynamics study of six amino acids with different structures and chemical properties that are relevant to the remote marine atmospheric aerosol-cloud system, with the aim to investigate the detailed mechanism of their induced changes in surface activity and surface tension, which are important properties for cloud drop activation. Distributions and orientations of the amino acid molecules are studied; these L-amino acids are serine, glycine, alanine, valine, methionine and phenylalanine and are categorized as hydrophilic and hydrophobic according to their affinities to water. The results suggest that the presence of surface-concentrated hydrophobic amino acid molecules give rise to enhanced Lennard-Jones repulsion, which in turn results in decreased surface tension of a planar interface but an increased surface tension of the spherical interface of droplets with diameters below 10 nm. The observed surface tension perturbation for the different amino acids under study not only serves as benchmark for future studies of more complex systems, but also shows that hydrophobic amino acids are surface active. The molecular dynamics simulations used in this study reproduce experimental results of surface tension measurements for planar interfaces and the method is therefore applicable for spherical interfaces of nano-size for which experimental measurements are not possible to conduct.
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| 434. |
- Li, Xin, et al.
(författare)
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Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures
- 2010
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Ingår i: Journal of Chemical Physics. - Melville, USA : AIP Publishing. - 0021-9606 .- 1089-7690. ; 132:10, s. 104505-
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Tidskriftsartikel (refereegranskat)abstract
- Metal ions play essential roles in biological processes and have attracted much attention in both experimental and theoretical fields. By using the molecular dynamics simulation technology, we here present a fitting-refining procedure for deriving Lennard-Jones parameters of aqua metal ions toward the ultimate goal of accurately reproducing the experimentally observed hydration free energies and structures. The polarizable SWM4-DP water model {proposed by Lamoureux [J. Chem. Phys. 119, 5185 (2003)]} is used to properly describe the polarization effects of water molecules that interact with the ions. The Lennard-Jones parameters of the metal ions are first obtained by fitting the quantum mechanical potential energies of the hexahydrated complex and are subsequently refined through comparison between the calculated and experimentally measured hydration free energies and structures. In general, the derived Lennard-Jones parameters for the metal ions are found to reproduce hydration free energies accurately and to predict hydration structures that are in good agreement with experimental observations. Dynamical properties are also well reproduced by the derived Lennard-Jones parameters.
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| 435. |
- Li, Xin, et al.
(författare)
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Cross-Linked Polysaccharide Assemblies in Marine Gels : An Atomistic Simulation
- 2013
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 4:16, s. 2637-2642
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Tidskriftsartikel (refereegranskat)abstract
- Marine polymeric gels or colloidal nano- and microgels have been shown to contribute significantly to the primary marine aerosol and cloud condensation nuclei over remote marine areas. A microscopic understanding of such biologically derived matter at the sea air interface is important for future development of global climate models, but unfortunately cannot be obtained from modern characterization techniques. In this contribution, we employ molecular dynamics simulations to reveal the atomistic details of marine polymeric gels represented by anionic polysaccharide assemblies. The ionic bonds formed between polysaccharides and metal ions in seawater as well as the hydrophobic contribution to surface area are investigated in detail, and destabilization of the assemblies upon removal of Ca2+ or acidification is explained. These results provide insight into physicochemical properties of polysaccharide-Ca2+ structures and enable future studies of their roles of in the wetting process of cloud droplet activation.
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| 436. |
- Li, Xin, et al.
(författare)
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Density Functional Theory Study of Photophysical Properties of Iridium(III) Complexes with Phenylisoquinoline and Phenylpyridine Ligands
- 2011
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 115:42, s. 20724-20731
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Tidskriftsartikel (refereegranskat)abstract
- Linear and quadratic response time-dependent density functional theory is applied to study the photophysical properties of iridium complexes with phenylisoquinoline and phenylpyridine ligands. The ground-state geometries, frontier molecular orbitals, absorption spectra, phosphorescence wavelengths, and radiative rate constants are computed to facilitate better understanding of the structure-property relationships of these iridium complexes used in organic light-emitting diodes (OLEDs) to enhance spin-orbit coupling and triplet state emission. The agreement obtained between calculated and available experimental data indicates a possibility to guide the design of phosphorescence-based OLEDs by predicting their relevant properties through quantum mechanical calculations.
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| 437. |
- Li, X., et al.
(författare)
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Dual-Phase Thermally Activated Delayed Fluorescence Luminogens : A Material for Time-Resolved Imaging Independent of Probe Pretreatment and Probe Concentration
- 2020
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Ingår i: Angewandte Chemie International Edition. - : Wiley-VCH Verlagsgesellschaft. - 1433-7851 .- 1521-3773. ; 59:19, s. 7548-7554
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Tidskriftsartikel (refereegranskat)abstract
- Developing luminescent probes with long lifetime and high emission efficiency is essential for time-resolved imaging. However, the practical applications usually suffer from emission quenching of traditional luminogens in aggregated states, or from weak emission of aggregation-induced emission type luminogens in monomeric states. Herein, we overcome this dilemma by a rigid-and-flexible alternation design in donor–acceptor–donor skeletons, to achieve a thermally activated delayed fluorescence luminogen with high emission efficiency both in the monomeric state (quantum yield up to 35.3 %) and in the aggregated state (quantum yield up to 30.8 %). Such a dual-phase strong and long-lived emission allows a time-resolved luminescence imaging, with an efficiency independent of probe pretreatment and probe concentration. The findings open opportunities for developing luminescent probes with a usage in larger temporal and spatial scales.
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| 438. |
- Li, Xin, et al.
(författare)
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Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:11, s. 5833-5840
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Tidskriftsartikel (refereegranskat)abstract
- To promote a more comprehensive understanding of the influence of metal-adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMNI model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability-capacitance force fields for large metallic clusters representing surfaces or nanoparticles.
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| 439. |
- Li, Xin, et al.
(författare)
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Glycine in aerosol water droplets : a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations
- 2011
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 11:2, s. 519-527
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Tidskriftsartikel (refereegranskat)abstract
- Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Kohler theory which describes the nucleation and the equilibrium growth of cloud droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems, the pure water droplets and glycine in water droplets. The curvature dependence of the surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the Kohler equation could be improved by incorporating surface tension corrections.
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| 440. |
- Li, Xin, et al.
(författare)
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Modulation of iridium(III) phosphorescence via photochromic ligands : a density functional theory study
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - Stockholm, Sweden : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:41, s. 13730-13736
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Tidskriftsartikel (refereegranskat)abstract
- The photochromic iridium(III) complex (Py-BTE)(2)Ir(acac) synthesized by Tan et al. [W. Tan et al., Org. Lett. 2009, 11, 161-164] has shown distinct photo-reactivity and photo-controllable phosphorescence. We here present a density functional theory study on the (Py-BTE)(2)Ir(acac) complex to explore the mechanism at the molecular level and to help further design of photochromic iridium(III) complexes with the desirable properties. The hybrid functional PBE0, with 25% Hartree-Fock exchange, is found to give an optimal structure compared with X-ray crystallographic data. The absorption bands are well reproduced by using time-dependent density functional theory calculations, lending the possibility to assign the metal-to-ligand and intra-ligand charge transfer transitions. The radiative and nonradiative deactivation rate constants, k(r) and k(nr), are rationalized for both the open-ring and closed-ring forms of the complex. The very large k(nr) and small k(r) make the closed-ring form of the complex non-emissive. The triplet reactivity of the Py-BTE ligand is also studied by performing density functional theory calculations on the potential energy surfaces of the ground state and the lowest triplet state.
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