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  • 251.
    Karaush-Karmazin, Nataliya N.
    et al.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Valiulina, Lenara I.
    Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia..
    Valiev, Rashid
    Tomsk Polytech Univ, 36 Lenin Ave, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Inst Atmospher & Earth Syst Res, FIN-00014 Helsinki, Finland..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Impact of heteroatoms (S, Se, and Te) on the aromaticity of heterocirculenes2019In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 43, no 30, p. 12178-12190Article in journal (Refereed)
    Abstract [en]

    A series of thia[7]circulenes and novel Se-, Te-, S/Te-, and Se/Te-substituted [8]circulenes have been studied by calculations of nucleus-independent chemical shift indices and gauge including magnetically induced currents to interpret the impact of heteroatoms on the aromatic properties of these polyheterocyclic species. The calculations indicate that all the studied hetero[7]circulenes and hetero[8]circulenes consist of two concentric subsystems: an inner seven- or eight-membered core is antiaromatic because of the existence of a paratropic ring current, and an outer system of benzene and hetarene rings that exhibit aromatic behaviour due to the circulation of diatropic ring currents. Thus, most of the hetero[7]circulenes can be considered as slightly antiaromatic because of the slight domination of the paratropic ring currents over the diatropic ones, whereas hetero[8]circulenes represent aromatic species due to the prevailing contribution of the diatropic currents. The antiaromaticity gradually increases with more scattered arrangements of the thiophene and benzene rings in each series of di-, tri-, tetra-, and pentathia[7]circulenes because of the reduced conjugation effect between the neighboring thiophene and benzene rings. Loss of planarity with increased strain leads to an increased antiaromatic character of the lower representatives of the thia[n]circulenes, whereas higher thia[n]circulenes demonstrate a more pronounced aromatic nature because of the small deviation from planarity. The ring current topology is found to be quite insensitive to the heteroatom type, number of hetarene rings and the size of the inner ring; this clearly manifests the special electronic structure of hetero[n]circulenes containing two concentric cyclic subsystems.

  • 252. Karthigeyan, Dhanasekaran
    et al.
    Siddhanta, Soumik
    Kishore, Annavarapu Hari
    Perumal, Sathya S. R. R.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sudevan, Surabhi
    Bhat, Akshay V.
    Balasubramanyam, Karanam
    Subbegowda, Rangappa Kanchugarakoppal
    Kundu, Tapas K.
    Narayana, Chandrabhas
    SERS and MD simulation studies of a kinase inhibitor demonstrate the emergence of a potential drug discovery tool2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 29, p. 10416-10421Article in journal (Refereed)
    Abstract [en]

    We demonstrate the use of surface-enhanced Raman spectroscopy (SERS) as an excellent tool for identifying the binding site of small molecules on a therapeutically important protein. As an example, we show the specific binding of the common antihypertension drug felodipine to the oncogenic Aurora A kinase protein via hydrogen bonding interactions with Tyr-212 residue to specifically inhibit its activity. Based on SERS studies, molecular docking, molecular dynamics simulation, biochemical assays, and point mutation-based validation, we demonstrate the surface-binding mode of this molecule in two similar hydrophobic pockets in the Aurora A kinase. These binding pockets comprise the same unique hydrophobic patches that may aid in distinguishing human Aurora A versus human Aurora B kinase in vivo. The application of SERS to identify the specific interactions between small molecules and therapeutically important proteins by differentiating competitive and noncompetitive inhibition demonstrates its ability as a complementary technique. We also present felodipine as a specific inhibitor for oncogenic Aurora A kinase. Felodipine retards the rate of tumor progression in a xenografted nude mice model. This study reveals a potential surface pocket that may be useful for developing small molecules by selectively targeting the Aurora family kinases.

  • 253.
    Kashtanov, Stepan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Augustson, Andreas
    Uppsala Universitet.
    Rubensson, Jan-Erik
    Uppsala Universitet.
    Nordgren, Joseph
    Uppsala Universitet.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Guo, Jing. Hua
    Lawrence Berkeley National Laboratory.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chemical and electronic structures of liquid methanol from x-ray emission spectroscopy and density functional theory.2005In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 71, no 10Article in journal (Refereed)
    Abstract [en]

    We have applied x-ray emission spectroscopy and density functional theory (DFT) to study the chemical and electronic structures of liquid methanol. The x-ray emission spectra at carbon and oxygen K edges of methanol in different hydrogen-bonded clusters are simulated. It is shown that hydrogen bonding strongly influences the spectral profile of O K emission, but not the C K emission. The methanol chain and ring conformations show a distinct difference in their electronic structures. The molecular orbitals of chains are strongly localized, whereas for the ring structures they show strong delocalization characteristics and behaviorlike covalent pi orbitals in a conjugated system. A comparison of experimental spectra and DFT calculations suggests that liquid methanol comprises combinations of rings and chains of methanol molecules linked with hydrogen bonds and is dominated by structures with the size of six and eight molecules.

  • 254.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Augustsson, A.
    Uppsala Universitet.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Guo, J. H.
    Lawrence Berkeley National Laboratory.
    Såthe, C.
    Uppsala Universitet.
    Rubensson, J. E.
    Uppsala Universietet.
    Siegbahn, H.
    Uppsala Universitet.
    Nordgren, J.
    Uppsala Universietet.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Local structures of liquid water studied by x-ray emission spectroscopy2004In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 69, no 2Article in journal (Refereed)
    Abstract [en]

    The O Kalpha x-ray emission spectra of water clusters with different sizes and conformations embedded in a continuum medium are simulated. The calculations have successfully explained the experimental spectra of water in both gas and liquid phases. It is shown that the x-ray emission spectra are very sensitive to the local hydrogen bonding structures. Strong electron sharing between different water molecules is observed and its possible connection to the covalency of hydrogen bonding is discussed. The experimentally observed strong excitation energy dependence of the spectra has been interpreted in terms of the polarization and angular dependence for the gas phase, and in terms of variations of local hydrogen bonding structures for the liquid phase.

  • 255.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Guo, J.-H.
    Augustsson, A.
    Rubensson, J.-E.
    Nordgren, J.
    Uppsala Universitet.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Electronic structure of water clusters in tetrahedral, ring, and chain conformations.Manuscript (preprint) (Other academic)
  • 256.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Stäfstrom, Sven
    Linköpings Universitet.
    Csillag, Stefan
    Stockholms Universitet.
    Characterization of aza-fullerene C58N2 isomers by X-ray spectroscopy2003In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 371, no 02-jan, p. 98-104Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron and near-edge X-ray absorption fine-structure spectra (NEXAFS) of four isomers of C58N2 are predicted by means of density-functional theory calculations. A strong isomer dependence for both types of spectra are found. The spectroscopic findings are discussed in conjunction with results from electronic and geometric structure optimizations.

  • 257.
    Kayathri, Rajarathinam
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Premkumar, Albert
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    A plant alkaloid, azadirachtin as an inhibitor for glutathione-S-transferase from Proteus mirabilisArticle in journal (Other academic)
  • 258.
    Kayathri, Rajarathinam
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Palmatine, a nucleotide sequence specific inhibitor for cancer therapyManuscript (preprint) (Other academic)
  • 259. Kaznacheyev, K.
    et al.
    Osanna, A.
    Jacobsen, C.
    Plashkevych, O.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Innershell absorption Spectroscopy of amino acids2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 13, p. 3153-3168Article in journal (Refereed)
    Abstract [en]

    We present comprehensive measurements of the C (carbon) K edge near-edge X-ray absorption (NEXAFS) spectra of all 20 amino acids commonly occurring in nature. Qualitative trends among the spectra of amino acids with similar chemical character are identified and spectral features are compared with extensive ab initio calculations. The contributions of individual units and substitutional groups have been determined to explore their fingerprinting character using the building block concept. Several such units are found. Two that give particularly clear features in the C Is NEXAFS spectra are the carboxyl group (which can be clearly identified by a pronounced structure due to the C 1s-->pi*c-o transition with maximum at 288.65(5) eV) and modified phenol rings in aromatic amino acids (which give sharp C 1s-->pi*c=o structures). The latter transitions are located around 285 cV, and their shape is specific for each aromatic amino acid. Other building blocks, such as the CNHn group and the CH, CC, CO, CN pair bonds, are also identified, although their characteristic features are less pronounced in the C K edge spectra than the carboxylic and aromatic structures. This study provides the basis for rigorous assignment of the NEXAFS spectra of the amino acids, and will be helpful in developing X-ray absorption spectroscopy for quantitative analysis of proteins.

  • 260.
    Kimberg, Victor
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Angular anisotropy of the delay time of short pulses in impurity band based photonic crystals2005In: Journal of Optics. A, Pure and applied optics, ISSN 1464-4258, E-ISSN 1741-3567, Vol. 7, no 3, p. 118-122Article in journal (Refereed)
    Abstract [en]

    We investigate the transmission of short pulses through one-dimensional impurity band based photonic crystals. We found a strong dependence of the delay time on the angle of incidence. The delay time is larger for larger incident angles for the transverse electrical mode, while the delay time of the transverse magnetic mode has a qualitatively different angular dependence, especially in the region below the Brewster angle. The strong anisotropy of the delay time is traced to the anisotropy of the group velocity which is directly related to the angular dependence of the impurity band structure.

  • 261.
    Kimberg, Victor
    et al.
    KTH, Superseded Departments, Biotechnology.
    Gelmukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Pent, E.
    Plekhanov, A.
    Kuchin, I.
    Rodionov, M.
    Shelkovnikov, V.
    Angular properties of band structures in one-dimensional holographic photonic crystals2004In: Journal of Optics. A, Pure and applied optics, ISSN 1464-4258, E-ISSN 1741-3567, Vol. 6, no 10, p. 991-996Article in journal (Refereed)
    Abstract [en]

    One-dimensional photonic crystals with continuous distribution of the dielectric constant were fabricated by the use of photopolymer materials and laser holography. The angular dependence of light propagation through the system was studied experimentally and theoretically. It is shown that the Brewster angles for different bands are different, in contrast to the conventional two-layer Bragg reflector with a step-like distribution of the dielectric constant. Comparison of the theory with experimental data allowed us to define the parameters of the hologram-the dielectric contrast and the shrinkage of the structure.

  • 262.
    Kimberg, Victor
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Polyutov, Sergey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Baev, Alexander
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zheng, Q.D.
    Institute for Lasers, Photonics and Biophotonics, State University of New York at Buffalo.
    He, G. S.
    Institute for Lasers, Photonics and Biophotonics, State University of New York at Buffalo.
    Dynamics of cavityless lasing generated by ultrafast multiphoton excitation2006In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 74, no 3, article id 033814Article in journal (Refereed)
    Abstract [en]

    A dynamical theory is developed with the purpose of explaining recent experimental results on multiphoton-excited amplified stimulated emission (ASE). Several conspicuous features of this experiment are analyzed, like the threshold dependence of the spectral profile on the pump intensity, and spectral shifts of the ASE pulses co- and counterpropagating relative to the pump pulse. Two models are proposed and evaluated, one based on the isolated molecule and another which involves solvent interaction. The spectral shift between the forward and backward ASE pulses arises in the first model through the competition between the ASE transitions from the pumped vibrational levels and from the bottom of the excited-state well, while in the solvent-related model the dynamical solute-solvent interaction leads to a relaxed excited state, producing an additional ASE channel. In the latter model the additional redshifted ASE channel makes the dynamics of ASE essentially different from that in the molecular model because the formation of the relaxed state takes a longer time. The variation of the pump intensity influences strongly the relative intensities of the different ASE channels and, hence, the spectral shape of ASE in both models. The regime of ASE changes character when the pump intensity crosses a threshold value. Such a phase transition occurs when the ASE rate approaches the rate of vibrational relaxation or the rate of solute-solvent relaxation in the first excited state.

  • 263. Kitajima, M.
    et al.
    Ueda, K.
    De Fanis, A.
    Furuta, T.
    Shindo, H.
    Tanaka, H.
    Okada, K.
    Feifel, R.
    Sorensen, S. L.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Baev, A.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Doppler effect in resonant photoemission from SF6: Correlation between doppler profile and auger emission anisotropy2003In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 91, no 21Article in journal (Refereed)
    Abstract [en]

    Fragmentation of the SF6 molecule upon F 1s excitation has been studied by resonant photoemission. The F atomiclike Auger line exhibits the characteristic Doppler profile that depends on the direction of the photoelectron momentum relative to the polarization vector of the radiation as well as on the photon energy. The measured Doppler profiles are analyzed by the model simulation that takes account of the anisotropy of the Auger emission in the molecular frame. The Auger anisotropy extracted from the data decreases with an increase in the F-SF5 internuclear distance.

  • 264. Kolczewski, C.
    et al.
    Puttner, R.
    Plashkevych, O.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Staemmler, V.
    Martins, M.
    Snell, G.
    Schlachter, A. S.
    Sant'Anna, M.
    Kaindl, G.
    Pettersson, L. G. M.
    Detailed study of pyridine at the C1s and N1s ionization thresholds: The influence of the vibrational fine structure2001In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 115, no 14, p. 6426-6437Article in journal (Refereed)
    Abstract [en]

    High resolution, vibrationally resolved, near-edge x-ray absorption fine structure (NEXAFS) spectra at the C 1s and N 1s ionization thresholds of pyridine and deuterated d(5)-pyridine in the gas phase have been recorded. The high resolution of 65 meV (150 meV) at the C s (N 1s) ionization thresholds reveals vibrational structures in the spectra. Detailed ab initio and density functional theory (DFT) calculations were performed to interpret the experimental spectra and to assign the observed peaks. In particular we focused on the previously unexplained intensity ratio for the two components of the C1s -->1 pi* transition. For this transition the vibrational structure is included through a linear coupling model in the DFT calculations and leads to the experimentally observed similar to2:3 intensity ratio between the two pi* components in the C1s spectrum rather than the similar to3:2 ratio obtained without vibrational effects. After inclusion of relaxation effects in the excited states, in addition to the vibrational effects, both theoretical methods yield almost perfect agreement with experiment.

  • 265. Kong, Jiahui
    et al.
    Li, Qizhao
    Li, Minzhi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Xu
    Zhu, Weihua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Modulation of the structures and properties of bidipyrrin zinc complexes by introducing terminal alpha-methoxy groups2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 137, p. 430-436Article in journal (Refereed)
    Abstract [en]

    A bidipyrrin nickel complex was synthesized in a high yield by oxidatively coupling between the ligands in the corresponding 2:1 (L:M) type of dipyrrin nickel complex, and further demetallation afforded the free bidipyrrin ligand. Interestingly, when treating the bidipyrrin nickel complex or the free bidipyrrin with FeCl3 in CH2Cl2/MeOH, the symmetric di-alpha-methoxy bidipyrrin could be synthesized in a high yield, with two methoxy groups attached to the terminal pyrrolic alpha-positions. Moreover, the coordination of the unsubstituted and disubstituted bidipyrrins with Zn(OAc)(2),2H(2)O afforded two similar M2L2 type of bidipyrrin helical complexes with different ligand conformations and different Zn center dot center dot center dot Zn distances of 5.353 and 3.357 angstrom, respectively. The difference in the conformations may be related to the electrostatic repulsions between the methoxy substituents. These results indicate that the dyes based on helical bidipyrrin zinc complexes with tunable structures and photophysical properties may be developed simply by modulating the terminal alpha-substituents.

  • 266. Kong, Jiahui
    et al.
    Zhang, Qiong
    Savage, Mathew
    Li, Minzhi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yang, Sihai
    Liang, Xu
    Zhu, Weihua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Tetra- and Octapyrroles Synthesized from Confusion and Fusion Approaches2016In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, no 19, p. 5046-5049Article in journal (Refereed)
    Abstract [en]

    By oxidation of an alternately N-confused bilane in CH2Cl2, a C-N fused tetrapyrrin was synthesized that bears a 5.5.5-tricyclic ring generated from an intramolecular C-N linkage. When CH3CN was used as the reaction medium, a multiply C-N-fused octapyrrolic dimer was also obtained that contained two 5.5.5.7.5-pentacyclic moieties and a bipyrrole unit generated from the intramolecular C-N linkage and intermolecular C-C linkage, respectively. This could be coordinated with Ni(acac)(2) to afford a mixed-ligand complex.

  • 267.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Nordberg, Agneta
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-beta(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 35, p. 11560-11567Article in journal (Refereed)
    Abstract [en]

    Detecting deposits of amyloid beta fibrils in the brain is of paramount importance for an early diagnosis of Alzheimer's disease. A number of PET tracers have been developed for amyloid imaging, but many suffer from poor specificity and large signal to background ratio. Design of tracers with specificity and improved binding affinity requires knowledge about various potential binding sites in the amyloid beta fibril available for the tracers and the nature of the local microenvironment of these sites. In this study we investigate the local structure of fibrils using two important probes, namely, thioflavin T (a fluorescent probe) and AZD2184 (a PET tracer). The target structures for amyloid-beta(1-42) fibril are based on reported NMR solution models. By explicitly considering the effect of fibril flexibility on the available binding sites for all these models, the binding affinity of these probes has been investigated. The binding profiles of AZD2184 and thioflavin T were studied by molecular docking and molecular dynamics simulation methods. The two compounds were found to bind at the same sites of the fibril: three of which are within the fibril, and one is on the two sides of the Met35 residue on the surface. The binding affinity of AZD2184 and thioflavin T is found to be higher at the core sites than on the surface due to more contact residues. The binding affinity of AZD2184 is much higher than that of thioflavin T at every site due to electrostatic interaction and spatial restriction, which is in good agreement with experimental observation. However, the structural change of thioflavin T is much more significant than that of AZD2184, which is the chemical basis for its usage as a fluorescent probe. The ramifications of these results for the design and optimization of PET radioligands and fluorescent probes are briefly discussed.

  • 268.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhou, Yang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zou, Rongfeng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Halldin, C.
    Nordberg, A.
    Långström, B.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Characterization of the binding mode of the PET tracer [18F]ASEM to a chimera structure of the α7 nicotinic acetylcholine receptor2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 32, p. 19787-19793Article in journal (Refereed)
    Abstract [en]

    The α7 nicotinic acetylcholine receptor (α7-nAChR) is assumed to be implicated in a variety of neurological disorders, such as schizophrenia and Alzheimer's disease (AD). The progress of these disorders can be studied through imaging α7-nAChR with positron emission tomography (PET). [18F]ASEM is a novel and potent α7-nAChR PET radioligand showing great promise in recent tests. However, the mechanism of the molecular interaction between [18F]ASEM and α7-nAChR is still unclear. In this paper, the binding profile of [18F]ASEM to a chimera structure of α7-nAChR was investigated with molecular docking, molecular dynamics, and metadynamics simulation methods. We found that [18F]ASEM binds at the same site as the crystallized agonist epibatidine but with a different binding mode. The dibenzo[b,d]thiophene ring has a different orientation compared to the pyridine ring of epibatidine and has van der Waals interactions with residues from loop C on one side and π-π stacking interaction with Trp53 on the other side. The conformation of Trp53 was found to have a great impact on the binding of [18F]ASEM. Six binding modes in terms of the side chain dihedral angles χ1 and χ2 of Trp53 were discovered by metadynamics simulation. In the most stable binding mode, Trp53 adopts a different conformation from that in the crystalline structure and has a rather favorable π-π stacking interaction with [18F]ASEM. We believe that these discoveries can be valuable for the development of novel PET radioligands.

  • 269. Kuklin, A. V.
    et al.
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Minaev, B. F.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Strong Topological States and High Charge Carrier Mobility in Tetraoxa[8]circulene Nanosheets2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 38, p. 22216-22222Article in journal (Refereed)
    Abstract [en]

    Here we report structural and electronic properties of a new family of two-dimensional covalent metal-free organic frameworks based on tetraoxa[8]circulene with different types of fusing. All nanosheets demonstrate high thermodynamic stability and unique electronic properties depending on the fusing type. Among three types of nanosheets, only two demonstrate semiconducting properties exhibiting 1.37 and 1.84 eV direct band gaps, while another one is found to be a semimetal, which hosts strong topological states and enhances the band gap (∼87 meV) induced by spin-orbit coupling that exceeds by several orders of magnitude that gap in graphene. Tetraoxa[8]circulene-based nanosheets are also predicted to be good organic semiconductors due to a clearly observable quantum confinement effect on the band gap size in oligomers and relatively low effective masses, which result in high carrier mobility. Owing to the versatility of chemical design, these materials have the potential to expand applications beyond those of graphene.

  • 270. Kuklin, A. V.
    et al.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004, China.
    Quasiparticle electronic structure and optical spectra of single-layer and bilayer PdSe2: Proximity and defect-induced band gap renormalization2019In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 99, no 24, article id 245114Article in journal (Refereed)
    Abstract [en]

    The fundamental properties of recently synthesized single- and bilayer PdSe2 are investigated using accurate many-body perturbation GW theory to quantitatively examine their electronic structure and explain the insufficiency of previously reported experimental and theoretical results. Including electron-hole interactions responsible for exciton formation, we solve the Bethe-Salpeter equation on top of the GW0 approximation to predict the optical properties. The fundamental quasiparticle band gaps of single- and bilayer PdSe2 are 2.55 and 1.89 eV, respectively. The optical gap of monolayer PdSe2 reduces significantly due to a large excitonic binding energy of 0.65 eV comparable to that of MoSe2, while an increase of the layer number decreases the excitonic binding energy to 0.25 eV in bilayer PdSe2. The giant band gap renormalization of ∼36-38% in the bilayer (BL) PdSe2/graphene heterostructure has a high impact on the construction of PdSe2-based devices and explains the experimentally observed band gap. The small value of the experimental optical gap of single-layer (SL) PdSe2 (1.3 eV) can be explained by the presence of Se vacancies, which can drop the Tauc-estimated optical gap to ∼1.32 eV. The absorption spectra of both mono- and bilayer PdSe2 cover a wide region of photon energy, demonstrating promising application in solar cells and detectors. These findings provide a basis for a deeper understanding of the physical properties of PdSe2 and PdSe2-based heterostructures.

  • 271. Lao, X.
    et al.
    Li, Xiyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chen, G.
    Highly controllable synthesis and DFT calculations of double/triple-halide CsPBX 3 (X = Cl, Br, I) perovskite quantum dots: Application to light-emitting diodes2019In: Nanomaterials, ISSN 2079-4991, Vol. 9, no 2, article id 172Article in journal (Refereed)
    Abstract [en]

    Although all-inorganic CsPbX 3 (X = Cl, Br, I) perovskite quantum dots (PQDs) have evoked exciting new opportunities for optoelectronic applications due to their remarkable optical properties, their emission color tunability has not been investigated to any appreciable extent. In this work, double/triple CsPbX 3 perovskite quantum dots with precise ratios of Cl/Br or Br/I are synthesized and their luminescence (410–700 nm) is explored. A group of down-converted CsPbX 3 (X = Cl, Br, I) perovskite quantum dot light-emitting diode (LED) devices were constructed to demonstrate the potential use of such double/triple-halide CsPbX 3 perovskite quantum dots with full-spectrum luminescence. Based on density functional theory, we theoretically explored the properties of CsPbX 3 with double/triple anion atoms. The calculated band gaps provided strong support that the full-spectrum luminescence (410–700 nm) of double/triple CsPbX 3 can be realized with the change of the mixed-halide ratios, and hence that such PQDs are of potential use in optoelectronic devices.

  • 272.
    Li, Cui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Chemical and Physical Processes, Italy.
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Chemistry of Organometallic Compounds, Italy.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, V.
    Theoretical study of para-nitro-aniline adsorption on the Au(111) surface2016In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 649, p. 124-132Article in journal (Refereed)
    Abstract [en]

    The electronic structure, bonding properties and dynamics of para-nitro-aniline (PNA) adsorbed on the Au(111) surface for a sub-monolayer coverge have been investigated by density-functional theory (DFT) static calculations and quantum molecular dynamics simulations. Four main adsorption geometries have been identified by DFT energy optimization with the gradient corrected PBE functional and accounting for the role of the van del Waals (vdW) interaction. Quantum dynamics calculations starting from the four different structures have been performed at room temperature to estimate the relative stability of the adsorbates and the presence of barriers for their interconversion. Quantum simulations suggest that the most stable adsorption geometry at room temperature is that of PNA with a slightly distorted molecular plane almost parallel to the Au(111) surface. In a second less populated configuration the PNA molecule interacts with the substrate by its NO2 group while the molecular plane is orthogonal to the surface. The N 1s electron photoemission spectrum has been simulated for the identified adsorbate geometries and a measurable variation of the absolute and relative chemical shift for the two nitrogen atoms in comparison with the known values for PNA in gas phase is predicted.

  • 273.
    Li, Cui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, Vincenzo
    Cysteine on TiO2(110): A Theoretical Study by Reactive Dynamics and Photoemission Spectra Simulation2014In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 30, no 29, p. 8819-8828Article in journal (Refereed)
    Abstract [en]

    A coherent account of adsorption modes, dynamics, self aggregation, and spectroscopic properties of an indoline organic dye adsorbed on TiO2 anatase (101) substrates is reported. The study is performed by combining reactive molecular dynamics (reaxFF) simulations with time-dependent density functional theory calculations, and the reliability of the results is assessed through comparison with theoretical and experimental data available in the literature. The use of a theoretical multilevel approach has proven to be crucial to gain a deep understanding, at an atomistic level, of the morphology and electronic properties of dye-sensitized heterogeneous interfaces. A realistic description of the functionalized anatase (101) interface, where a variety of binding modes are present, has been achieved by means of extensive molecular dynamics simulations of the adsorption of dye clusters made of different molecular units on medium/large size TiO2 anatase slabs. Our results disclose that the main driving forces toward formation of ordered surface aggregates are pi stacking and T-shaped interactions between the aromatic rings of the donor moiety of the molecules, as well as the tendency to maximize the anchoring points with the surface. The dye aggregates were found to be organized in domains, characterized by a different orientation of the packing units, and, in the high coverage limit, presenting a certain degree of short-to-medium range order.

  • 274.
    Li, Deyang
    et al.
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China.
    Chen, Guanying
    Harbin Inst Technol, Sch Chem & Chem Engn, MIIT Key Lab Crit Mat Technol New Energy Convers, Harbin 150001, Heilongjiang, Peoples R China.;Harbin Inst Technol, Minist Educ, Key Lab Microsyst & Microstruct, Harbin 150001, Heilongjiang, Peoples R China..
    Near infrared harvesting dye-sensitized solar cells enabled by rare-earth upconversion materials2018In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 47, no 26, p. 8526-8537Article, review/survey (Refereed)
    Abstract [en]

    Dye-sensitized solar cells (DSSCs) have been deemed as promising alternatives to silicon solar cells for the conversion of clean sunlight energy into electricity. A major limitation to their conversion efficiency is their inability to utilize light in the infrared (IR) spectral range, which constitutes almost half the energy of the sun's radiation. This fact has elicited motivations and endeavors to extend the response wavelength of DSSCs to the IR range. Photon upconversion through rare-earth ions constitutes one of the most promising approaches toward the goal of converting near-IR (NIR) or IR light into visible or ultraviolet light, where DSSCs typically have high sensitivity. In the present review, we summarize recent progress based on the utilization of various upconversion materials and device structures to improve the performance of dye-sensitized solar cells.

  • 275. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zhan-Qi
    Qu, Da-Hui
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    A Switchable bis-Branched [1]Rotaxane featuring Dual-Mode Molecular Motions and Tunable Molecular Aggregation2014In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 6, no 21, p. 18921-18929Article in journal (Refereed)
    Abstract [en]

    A multifunctional bis-branched [1]rotaxane containing a perylene bisimide (PBI) core and two identical bistable[1]rotaxane arms terminated with ferrocene units was prepared and characterized by H-1 NMR, C-13 NMR, and 2D ROESY NMR spectroscopies and by HR-ESI spectrometry. The system is shown to possess several key features: (1) In acetone solution, external acid base stimuli can result in relative mechanical movements of its ring and thread, which can induce extension and contraction movements of the whole system accompanied by a rotational movement of the ferrocene units, thus realizing dual-mode molecular motions, and the optimized conformations at different states are obtained through molecular dynamics simulations employing the general Amber force field. (2) The introduction of PBI enables the system fluorescence encoding through distance-dependent photoinduced electron transfer process from the ferrocene units to the PBI fluorophore. (3) The addition of Zn2+ can increase the degree of aggregation of the system, while adding base hinders aggregation because of the movement of the macrocyde. The tunable aggregated nanostructural morphologies of [1]rotaxane were examined by scanning electron microscopy. These results can pave the way to achieve precise control of integrated and coupling nanomechanical motions at a single-molecule level and provide more insight into controlling the aggregate behavior of switchable mechanically interlocked molecules.

  • 276. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Ying
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Qu, Da-Hui
    A Musclelike [2](2)Rotaxane: Synthesis, Performance, and Molecular Dynamics Simulations2014In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 79, no 15, p. 6996-7004Article in journal (Refereed)
    Abstract [en]

    A novel bistable symmetric [2](2)rotaxane was prepared by a threading-followed-by-stoppering strategy and characterized with H-1, C-13, and 2D ROESY NMR spectroscopy and HR-ESI spectrometry. The symmetric [2] (2)rotaxane system consists of an anthracene-based bis(crown ether) as macrocycles, and each of the two dibenzo[24]crown-8 (DB24C8) rings is threaded by the pendant substituents a symmetrically substituted central rotatable ferrocene subunit that possesses two distinguishable recognition sites for the DB24C8 ring: namely, a dibenzylammonium site and an N-methyltriazolium site. The uniform shuttling motion of the thread relative to the two DB24C8 rings in [2](2)rotaxane can be driven by external acid base stimuli, which was evidenced by H-1 and 2D ROESY NMR spectroscopy. Furthermore, molecular dynamics simulations of the [2](2)rotaxane were carried out both in protonated (stretched) and in neutral (contracted) forms. The calculated percentage change in molecular length of the [2](2)rotaxane between the two end-capping bis(methoxyl)phenyl groups is about 48% in the two different states (in acetone), which is much larger than the percentage change (similar to 27%) in human muscle. Moreover, in the two states, the C*-Cp-Cp-C* dihedral angles are computed as -177 degrees in the stretched state and -112 degrees in the contracted state, indicating a correlation between the translational and rotational motions of the [2](2)rotaxane.

  • 277. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Qu, Da-Hui
    Two Switchable Star-Shaped [1](n)Rotaxanes with Different Multibranched Cores2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 18, p. 4940-4943Article in journal (Refereed)
    Abstract [en]

    Two novel star-shaped [1](n)rotaxanes with three and four identical [1]rotaxane arms but different multibranched cores were designed, synthesized, and well-characterized. In the two systems, external base acid stimuli result in the uniform relative mechanical movement of the macrocydic rings and threads of their [1]rotaxane arms. The energy-minimized structures of the two rotaxanes in different states were obtained using molecular dynamics simulations in acetone solution, suggesting the construction of more sophisticated molecular machines mimicking the extension and contraction motions.

  • 278.
    Li, Qizhao
    et al.
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Ishida, Masatoshi
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Kai, Hiroto
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Gu, Tingting
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Li, Chengjie
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Baryshnikov, Glib
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liang, Xu
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Zhu, Weihua
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Biotechnol, S-10691 Stockholm, Sweden..
    Furuta, Hiroyuki
    Kyushu Univ, Dept Chem & Biochem, Grad Sch Engn, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka 8190395, Japan..
    Xie, Yongshu
    East China Univ Sci & Technol, Key Lab Adv Mat, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Joint Int Res Lab Precis Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Skeletal Rearrangement of Twisted Thia-Norhexaphyrin: Multiply Annulated Polypyrrolic Aromatic Macrocycles2019In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 18, p. 5925-5929Article in journal (Refereed)
    Abstract [en]

    A hybrid thia-norhexaphyrin comprising a directly linked N-confused pyrrole and thiophene unit (1) revealed unique macrocycle transformations to afford multiply inner-annulated aromatic macrocycles. Oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone triggered a cleavage of the C-S bond of the thiophene unit, accompanied with skeletal rearrangement to afford unique pi-conjugated products: a thiopyrrolo-pentaphyrin embedded with a pyrrolo[1,2]isothiazole (2), a sulfur-free pentaphyrin incorporating an indolizine moiety (3), and a thiopyranyltriphyrinoid containing a 2H-thiopyran unit (4). Furthermore, 2 underwent desulfurization reactions to afford a fused pentaphyrin containing a pyrrolizine moiety (5) under mild conditions. Using expanded porphyrin scaffolds, oxidative thiophene cleavage and desulfurization of the hitherto unknown N-confused core-modified macrocycles would be a practical approach for developing unique polypyrrolic aromatic macrocycles.

  • 279.
    Li, Qizhao
    et al.
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Chengjie
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Kim, Jinseok
    Yonsei Univ, Dept Chem, Seoul 03722, South Korea.;Yonsei Univ, Spect Lab Funct Elect Syst, Seoul 03722, South Korea..
    Ishida, Masatoshi
    Kyushu Univ, Grad Sch Engn, Dept Chem & Biochem, Fukuoka, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka, Fukuoka 8190395, Japan..
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Gu, Tingting
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Liang, Xu
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Zhu, Weihua
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Kim, Dongho
    Yonsei Univ, Dept Chem, Seoul 03722, South Korea.;Yonsei Univ, Spect Lab Funct Elect Syst, Seoul 03722, South Korea..
    Furuta, Hiroyuki
    Kyushu Univ, Grad Sch Engn, Dept Chem & Biochem, Fukuoka, Fukuoka 8190395, Japan.;Kyushu Univ, Ctr Mol Syst, Fukuoka, Fukuoka 8190395, Japan..
    Xie, Yongshu
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Feringa Nobel Prize Scientist Joint Res Ctr, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Regioselectively Halogenated Expanded Porphyrinoids as Building Blocks for Constructing Porphyrin-Porphyrinoid Heterodyads with Tunable Energy Transfer2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 13, p. 5294-5302Article in journal (Refereed)
    Abstract [en]

    Expanded porphyrins have been attracting increasing attention owing to their unique optical and electrochemical properties as well as switchable aromaticity. Toward material applications, regioselective functionalization of the expanded porphyrins at their periphery is indeed challenging due to the presence of multiple reactive sites. Herein, a set of regioselective halogenated isomers (L5-Br-A/B/C) of neo-confused isosmaragdyrin (L5) are synthesized by a combination of the halogenation reaction of L5 and sequential macrocycleto-macrocycle transformation reactions of its halogenated isomers. On this basis, the regioselectively functionalized isosmaragdyrins are utilized as building blocks for constructing multichromophoric porphyrinoids, specifically, heterodyads L5-ZnP-A/B/C, in which a common zinc porphyrin is linked at three different pyrrolic positions of isosmaragdyrins, respectively, by Sonogashira coupling reactions. The highly efficient energy cascade from porphyrin to isosmaragdyrin is elucidated using steady-state/time-resolved spectroscopies and theoretical calculations. Notably, the energy transfer processes from the porphyrin to the isosmaragdyrin moieties as well as the excitation energy transfer rates in L5-ZnP-A/B/C are highly dependent on the linking sites by through-bond and Forster-type resonance energy transfer mechanisms. The site-selective functionalization and subsequent construction of a set of heterodyads of the expanded porphyrinoid would provide opportunities for developing new materials for optoelectronic applications.

  • 280. Li, T.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, J.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ma, X.
    Tian, H.
    Photoresponsive Supramolecular Assemblies Based on a C3-Symmetric Benzene-1,3,5-tricarboxamide Anchored Diarylethene2016In: Advanced Optical Materials, ISSN 2195-1071Article in journal (Refereed)
    Abstract [en]

    A functional C3-symmetric benzene-1,3,5-tricarboxamide-anchored diarylethene molecule (C3-BTE) is synthesized, which evolves into ordered superstructures with tunable morphology properties both in different solvent and via alternative light stimuli. The formation of rod-like assemblies from C3-BTE is reported and the self-assembly property of C3-BTE can be realized through alternative light stimuli in nonpolar solvents such as toluene.

  • 281. Li, Wenlong
    et al.
    Cai, Yunsong
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    Zhu, Wei-Hong
    Sterically hindered diarylethenes with a benzobis(thiadiazole) bridge: photochemical and kinetic studies2015In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 3, no 33, p. 8665-8674Article in journal (Refereed)
    Abstract [en]

    Four rationally designed diarylethenes (DAEs) 1-4 with a benzobis(thiadiazole) bridge are specifically designed for gaining insights into steric effects on photochromic performances. It is shown that, upon increasing steric hindrance, the exchanging rate between two main conformers in the ring-open form gradually slows down, offering the opportunity for isolating photoactive anti-parallel conformers. Impressively, the separated anti-parallel conformer shows high cyclization quantum yields over the unresolved common DAEs. The typical donor-pi-acceptor (D-pi-A) feature in ring-open DAEs 1-4 endows their prominent fluorescence, which can be conveniently modulated by photocyclization. In the ring-closed form, the excess steric hindrance is found to seriously disrupt the thermal bistability, and particularly 3c fades quickly with a half-life of several hours at ambient temperature. In contrast, both 1c and 2c exhibit excellent stability, which originates from the stabilization effects of intramolecular hydrogen bonds. This work demonstrates the steric effects on the photochemical and kinetic behaviors of DAEs, providing a unique approach to develop photochromic DAEs with high photosensitivity.

  • 282.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, Vincenzo
    Li, Cui
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. CNR-ICCOM, Italy .
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 7, p. 3325-3339Article in journal (Refereed)
    Abstract [en]

    Motivated by the growing importance of organometallic nanostructured materials and nanoparticles as microscopic devices for diagnostic and sensing applications, and by the recent considerable development in the simulation of such materials, we here choose a prototype system para-nitroaniline (pNA) on gold nanoparticles to demonstrate effective strategies for designing metal nanoparticles with organic conjugates from fundamental principles. We investigated the motion, adsorption mode, and physical chemistry properties of gold-pNA particles, increasing in size, through classical molecular dynamics (MD) simulations in connection with quantum chemistry (QC) calculations. We apply the quantum mechanics-capacitance molecular mechanics method [Z. Rinkevicius et al. J. Chem. Theory Comput. 2014, 10, 989] for calculations of the properties of the conjugate nanoparticles, where time dependent density functional theory is used for the QM part and a capacitance-polarizability parametrization of the MM part, where induced dipoles and charges by metallic charge transfer are considered. Dispersion and short-range repulsion forces are included as well. The scheme is applied to one- and two-photon absorption of gold-pNA clusters increasing in size toward the nanometer scale. Charge imaging of the surface introduces red-shifts both because of altered excitation energy dependence and variation of the relative intensity of the inherent states making up for the total band profile. For the smaller nanoparticles the difference in the crystal facets are important for the spectral outcome which is also influenced by the surrounding MM environment.

  • 283.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Hede, T.
    Tu, Y.
    Leck, C.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Glycine in aerosol water droplets: a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations2011In: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 11, no 2, p. 519-527Article in journal (Refereed)
    Abstract [en]

    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.

  • 284.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hede, Thomas
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cloud droplet activation mechanisms of amino acid aerosol particles: insight from molecular dynamics simulations2013In: Tellus. Series B, Chemical and physical meteorology, ISSN 0280-6509, E-ISSN 1600-0889, Vol. 65, p. 65-Article in journal (Refereed)
    Abstract [en]

    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.

  • 285.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hede, Thomas
    Tu, Yaoquan
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Molecular Dynamics Study on the Surface Tension of Atmospheric Water Droplets Containing Amino AcidsManuscript (preprint) (Other academic)
    Abstract [en]

    Atmospheric amino acids constitute an important fraction of the water-soluble organic nitrogen compounds in both marine and continental aerosols, and have been confirmed as effective cloud condensation nuclei materials in laboratory tests. We here present molecular dynamics study of six types of amino acids in atmospheric water droplets, in order to investigate molecular distributions, orientations and induced changes in surface tension, and to evaluate their indirect effects on optical properties of clouds. These amino acids, including serine, glycine, alanine, valine, methionine and phenylalanine, are categorized into hydrophilic and hydrophobic species according to their affinities to water. Different amino acids show distinct effects on the surface tension; even the same amino acid has different influence on the surface tension of planar and spherical interfaces. Finally the curvature dependence of the surface tension is modeled by a quadratic polynomial function of the inverse of droplet radius, and such relationship is used to improve the Köhler equation in predicting the critical supersaturation of droplet activation.

  • 286.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hede, Thomas
    Tu, Yaoquan
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Surface-Active cis-Pinonic Acid in Atmospheric Droplets: A Molecular Dynamics Study2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, Vol. 1, no 4, p. 769-773Article in journal (Refereed)
    Abstract [en]

    Water vapor in the atmosphere can condensate and form cloud droplets when there is a certain amount of humidity and a presence of cloud condensation nuclei, and organic solutes called surfactants can significantly lower the surface tension of water-one of the parameters determining cloud droplet population. We here present a molecular dynamics study of the behavior of cis-pinonic acid, a commonly found organic compound in cloud condensation nuclei, and its effect on the surface tension of water clusters. Specifically, the decrease in surface tension is found to depend on not only the concentration of the organic compound but also the droplet size due to the spontaneous assembly of the surfactant molecules on the droplet surface. This leads to the conclusion that the partitioning of the surfactant between the bulk and surface plays an important role in the behavior of atmospheric aerosol particles and thus in their availability for cloud formation.

  • 287.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, Caroline
    Sun, Lu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hede, Thomas
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cross-Linked Polysaccharide Assemblies in Marine Gels: An Atomistic Simulation2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 16, p. 2637-2642Article in journal (Refereed)
    Abstract [en]

    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.

  • 288.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Wenlong
    E China Univ Sci & Technol, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;E China Univ Sci & Technol, Inst Fine Chem, Shanghai Key Lab Funct Mat Chem, Shanghai 200237, Peoples R China..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    E China Univ Sci & Technol, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;E China Univ Sci & Technol, Inst Fine Chem, Shanghai Key Lab Funct Mat Chem, Shanghai 200237, Peoples R China..
    Zhu, Weihong
    E China Univ Sci & Technol, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;E China Univ Sci & Technol, Inst Fine Chem, Shanghai Key Lab Funct Mat Chem, Shanghai 200237, Peoples R China..
    Theoretical insight into the enhanced hindrance, thermal stability and optical properties of diarylethene with a benzobis(thiadiazole) bridge and benzothiophene rings2016In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 125, p. 348-355Article in journal (Refereed)
    Abstract [en]

    To rationalize the effects of intramolecular steric hindrance on the performance of diarylethene photoswitches, we here present a density functional theory study on the thermal bistability and optical properties of a photochromic diarylethene BBTE consisting of a benzobis(thiadiazole) bridge and benzothiophene rings, in which prominent steric hindrance exists owing to the extended structures of is-conjugated groups. Our calculations not only provide rational explanations for the isolation of enantiopure anti-parallel conformers of the open-ring isomer, but also elucidate the detailed pathway of a two-step ground-state ring-opening process, where the thermal stability of the closed-ring isomer is guaranteed by an overall free energy barrier of around 113 kJ mol(-1) (27 kcal mol(-1)). In addition, the tunable intramolecular charge transfer of the donor acceptor structure formed by the benzobis(thiadiazole) bridge and the bulky benzothiophene rings is also addressed within time-dependent density functional theory. Charge transfer excitations in the open- and the closed-ring isomers are characterized as long-range and medium-range, respectively. We show that the diarylethene derivative under investigation can serve as a promising platform for future development of optoelectronic materials.

  • 289.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Tian, He
    E China Univ Sci & Technol, Adv Mat Lab, Shanghai 200237, Peoples R China.;E China Univ Sci & Technol, Inst Fine Chem, Shanghai 200237, Peoples R China..
    Density Functional Theory Study of Photophysical Properties of Iridium(III) Complexes with Phenylisoquinoline and Phenylpyridine Ligands2011In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 42, p. 20724-20731Article in journal (Refereed)
    Abstract [en]

    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.

  • 290.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    E China Univ Sci & Technol, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;E China Univ Sci & Technol, Inst Fine Chem, Shanghai 200237, Peoples R China..
    Theoretical Study of Phosphorescence of Iridium Complexes with Fluorine-Substituted Phenylpyridine Ligands2011In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, no 16, p. 2517-2524Article in journal (Refereed)
    Abstract [en]

    Time-dependent density functional theory (TD-DFT) with linear and quadratic response approaches was applied to calculate absorption and luminescence spectra of a number of facial and meridional iridium complexes with fluorine-substituted phenylpyridine (F(n)ppy) ligands. The absorption and luminescence spectra were studied to simulate the photophysical properties of electroluminescent devices fabricated on the basis of these iridium complexes used to increase spin-orbit coupling and the triplet-state blue emission of the corresponding organic light-emitting diodes (OLEDs). By using the quadratic response technique, the phosphorescence radiative rate constant and lifetime of the studied iridium complexes were calculated through spin-orbit coupling perturbation and compared with the measured data in experiments. A satisfactory agreement between these data permits us to guide improvements in the design of phosphorescence-based OLEDs by predicting the structure-property relationships through quantum chemical calculations.

  • 291.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4766-4774Article in journal (Refereed)
    Abstract [en]

    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.

  • 292.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, p. 11347-11352Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the Cd-113(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic Shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in Cd-113 NMR experiments, due to the mutual cancelation between individual relativistic corrections.

  • 293.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, p. 10916-10922Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

  • 294.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 11, p. 5833-5840Article in journal (Refereed)
    Abstract [en]

    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.

  • 295.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Two-Photon Absorption of Metal-Assisted Chromophores2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5630-5639Article in journal (Refereed)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

  • 296.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 10, p. 104505-Article in journal (Refereed)
    Abstract [en]

    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.

  • 297.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tian, He
    Modulation of iridium(III) phosphorescence via photochromic ligands: a density functional theory study2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 41, p. 13730-13736Article in journal (Refereed)
    Abstract [en]

    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.

  • 298.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Liangliang
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aggregation-induced chiral symmetry breaking of a naphthalimide-cyanostilbene dyad2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 43, p. 23854-23860Article in journal (Refereed)
    Abstract [en]

    Spontaneously emerged supramolecular chirality and chiral symmetry breaking from achiral/racemic constituents remain poorly understood. We here report that supramolecular chirality may emerge from the structural flexibility of achiral aryl nitrogen centres which provide instantaneous chirality. Employing a naphthalimide-cyanostilbene dyad as a model, we explored the underlying mechanism of aggregation-induced chiral symmetry breaking and found that the conformations of the N-naphthylpiperazine and the N, N-dimethylaniline units facilitate the formation of ordered supramolecular structures and offer opposite handedness. Furthermore, chiral symmetry breaking of the monomers was amplified by the formation of dimers. The microscopic and the macroscopic observations from the theoretical simulations and experimental measurements are thus rationalized by connecting the population of the dihedral angles of the aryl nitrogen centres, the morphology of the self-assemblies, and the observed circular dichroism spectra.

  • 299.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zou, Qi
    Shanghai Univ Elect Power, Shanghai Key Lab Mat Protect & Adv Mat Elect Powr, Shanghai 200090, Peoples R China..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Photochromic Diarylethenes with Heterocyclic Aromatic Rings: Correlation between Thermal Bistability and Geometrical Characters of Transition States2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 34, p. 9140-9147Article in journal (Refereed)
    Abstract [en]

    We present a density functional theory study on the thermal bistability of a number of photochromic diarylethenes, with emphasis on the free energy barrier of the ground-state ring-opening process. We found that the free energy barrier is correlated with the geometrical and vibrational character of the transition state, in particular the distance between the two reactive carbon atoms, the out-of-plane angles of the methyl groups at the reactive carbon atoms, and the imaginary vibrational frequency. Based on these relationships we propose a linear fitting expression for the free energy barrier in terms of the three aforementioned transition-state quantities and obtained a correlation coefficient of R-2 = 0.971. In this way quantum chemical calculations may provide insight and structure property relationships, which can be applied in the development of novel photochromic materials.

  • 300.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular Dynamics Simulations Using a Capacitance-Polarizability Force Field2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 33, p. 19430-19437Article in journal (Refereed)
    Abstract [en]

    We present molecular dynamics (MD) simulations using a capacitance-polarizability force field. This force field allows an atomistic description of charge migration within a particle and hence the image charge effects at the interface of such a particle. By employing atomic capacitance and polarizability as the key parameters that describe fluctuating charges and dipoles, we can thus explore the effect of charge migration on the structural dynamics. We illustrate the method by exploring gold nanoparticles in aqueous solutions and compare with previous simulation work. We reach the conclusion that the capacitance polarizability force field MD method serves as a promising tool for simulating gold water systems, indicating probable extensions to other metal solutions and for studies of more complicated systems provided that a proper parametrization of the capacitance force field can be made. For the particular system studied, it is found that the water molecules interact with the surface through oxygen atoms, leading to more hydrogen-bond donors than acceptors at the gold water interface. A prominent shoulder peak is found in the radial distribution of oxygen atoms with respect to the gold surface, due to the fact that the oxygen atoms adsorbed at the on-top sites of the gold nanoparticle. The surface of the aqueous gold nanoparticle carries negative charge, which is balanced by the positive charge in the second outermost layer.

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