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  • 101.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bast, Radovan
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Quantum chemistry on a heterogeneous computer system: Accelerating the Kohn-Sham method for hybrid CPU/GPGPU and CPU/Intel MIC platforms2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Article in journal (Other academic)
  • 102.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Palevicius, Paulius
    Kaunas Univ Technol, Dept Math Modeling, Kaunas, Lithuania..
    Kaminskas, Marius
    Kaunas Univ Technol, Dept Phys, Kaunas, Lithuania..
    Bockute, Kristina
    Kaunas Univ Technol, Dept Phys, Kaunas, Lithuania..
    Ragulskis, Minvydas
    Kaunas Univ Technol, Dept Math Modeling, Kaunas, Lithuania..
    Laukaitis, Giedrius
    Kaunas Univ Technol, Dept Phys, Kaunas, Lithuania..
    Polarizable coarse grain force field for metallic systems: A discrete interacting multipole model2019In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 257Article in journal (Other academic)
  • 103.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Xin, Li
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ringholm, Magnus
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. UiT, Dept Chem, Tromso, Norway..
    List, Nanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory2019In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 257Article in journal (Other academic)
  • 104.
    Rolland, Nicolas
    et al.
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Franco-Gonzalez, Juan Felipe
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Volpi, Riccardo
    Linkoping Univ, Dept Phys Chem & Biol IFM, SE-58183 Linkoping 3, Sweden.;RIST, Machine Learning & Optimizat Grp, Cluj Napoca, Romania..
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Zozoulenko, Igor, V
    Linkoping Univ, Lab Organ Elect, Dept Sci & Technol ITN, Campus Norrkoping, SE-60174 Norrkoping, Sweden..
    Understanding morphology-mobility dependence in PEDOT:Tos2018In: Physical Review Materials, ISSN 2475-9953, Vol. 2, no 4, article id 045605Article in journal (Refereed)
    Abstract [en]

    The potential of conjugated polymers to compete with inorganic materials in the field of semiconductor is conditional on fine-tuning of the charge carriers mobility. The latter is closely related to the material morphology, and various studies have shown that the bottleneck for charge transport is the connectivity between well-ordered crystallites, with a high degree of pi-pi stacking, dispersed into a disordered matrix. However, at this time there is a lack of theoretical descriptions accounting for this link between morphology and mobility, hindering the development of systematic material designs. Here we propose a computational model to predict charge carriers mobility in conducting polymer PEDOT depending on the physicochemical properties of the system. We start by calculating the morphology using molecular dynamics simulations. Based on the calculated morphology we perform quantum mechanical calculation of the transfer integrals between states in polymer chains and calculate corresponding hopping rates using the Miller-Abrahams formalism. We then construct a transport resistive network, calculate the mobility using a mean-field approach, and analyze the calculated mobility in terms of transfer integrals distributions and percolation thresholds. Our results provide theoretical support for the recent study [Noriega et al., Nat Mater 12, 1038 (2013)] explaining why the mobility in polymers rapidly increases as the chain length is increased and then saturates for sufficiently long chains. Our study also provides the answer to the long-standing question whether the enhancement of the crystallinity is the key to designing high-mobility polymers. We demonstrate, that it is the effective pi-pi stacking, not the long-range order that is essential for the material design for the enhanced electrical performance. This generic model can compare the mobility of a polymer thin film with different solvent contents, solvent additives, dopant species or polymer characteristics, providing a general framework to design new high mobility conjugated polymer materials.

  • 105.
    Rubio-Magnieto, Jenifer
    et al.
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium.;Univ Jaume 1, Dept Quim Inorgan & Organ, Bioinspired Supramol Chem & Mat Grp, Avda Sos Baynat S-N, E-12071 Castellon de La Plana, Spain..
    Kajouj, Sofia
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Di Meo, Florent
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Fossepre, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Trouillas, Patrick
    Univ Limoges, Sch Pharm, INSERM, U1248,IPPRITT, 2 Rue Dr Marcland, F-87025 Limoges, France.;Palacky Univ, Fac Sci, RCPTM, Slechtitelu 27, Olomouc 78371, Czech Republic..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Moucheron, Cecile
    Univ Libre Bruxelles, Chim Organ & Photochim CP160 08, 50 Ave FD Roosevelt, B-1050 Brussels, Belgium..
    Surin, Mathieu
    Univ Mons UMONS, Ctr Innovat Mat & Polymers, Lab Chem Novel Mat, 20 Pl Parc, B-7000 Mons, Belgium..
    Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G-Quadruplexes2018In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 58, p. 15577-15588Article in journal (Refereed)
    Abstract [en]

    Metal complexes constitute an important class of DNA binders. In particular, a few ruthenium polyazaaromatic complexes are attractive as light switches because of their strong luminescence enhancement upon DNA binding. In this paper, a comprehensive study on the binding modes of several mononuclear and binuclear ruthenium complexes to human telomeric sequences, made of repeats of the d(TTAGGG) fragment is reported. These DNA sequences form G-quadruplexes (G4s) at the ends of chromosomes and constitute a relevant biomolecular target in cancer research. By combining spectroscopy experiments and molecular modelling simulations, several key properties are deciphered: the binding modes, the stabilization of G4 upon binding, and the selectivity of these complexes towards G4 versus double-stranded DNA. These results are rationalized by assessing the possible deformation of G4 and the binding free energies of several binding modes via modelling approaches. Altogether, this comparative study provides fundamental insights into the molecular recognition properties and selectivity of Ru complexes towards this important class of DNA G4s.

  • 106.
    Samuelsen, SimoneV.
    et al.
    Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark..
    Santilli, Carola
    Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark..
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Madsen, Robert
    Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark..
    Development and mechanistic investigation of the manganese(iii) salen-catalyzed dehydrogenation of alcohols2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 4, p. 1150-1157Article in journal (Refereed)
    Abstract [en]

    The first example of a manganese(III) catalyst for the acceptorless dehydrogenation of alcohols is presented. N,N'-Bis(salicylidene)-1,2-cyclohexanediaminomanganese(III) chloride (2) has been shown to catalyze the direct synthesis of imines from a variety of alcohols and amines with the liberation of hydrogen gas. The mechanism has been investigated experimentally with labelled substrates and theoretically with DFT calculations. The results indicate a metal-ligand bifunctional pathway in which both imine groups in the salen ligand are first reduced to form a manganese(III) amido complex as the catalytically active species. Dehydrogenation of the alcohol then takes place by a stepwise outer-sphere hydrogen transfer generating a manganese(III) salan hydride from which hydrogen gas is released.

  • 107.
    Tan, Shijing
    et al.
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China.;Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Feng, Hao
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Ji, Yongfei
    Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Zheng, Qijing
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Shi, Yongliang
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Zhao, Jin
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Zhao, Aidi
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Yang, Jinlong
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Bing
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Hou, J. G.
    Univ Sci & Technol China, Microscale & Synerget Innovat Ctr Quantum Informa, Hefei Natl Res Ctr Phys Sci, Hefei 230026, Anhui, Peoples R China..
    Visualizing Elementary Reactions of Methanol by Electrons and Holes on TiO2(110) Surface2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 50, p. 28805-28814Article in journal (Refereed)
    Abstract [en]

    Direct visualization and comparison of the elementary reactions induced by electrons and holes are of importance for finding a way to conduct chemical reactions and reaction sequences in a controllable manner. As a semiconductor, TiO2 provides a playground to perform the measurements, and moreover, the information can be useful for design of high-performance TiO2-based catalysts and photocatalysts. Here, we present our investigation on the elementary reactions of CH3OH on TiO2 surface through visualization of specific elementary steps by highly controllable electron and hole injection using scanning tunneling microscopy. The distinct sequential routes and their kinetics, namely, breaking C-O and O-H bonds by electrons and breaking O-H and C-H bonds by holes, respectively, have been experimentally identified and well elucidated by density functional theory calculations. Our nonlocal h-injection experimental and theoretical results suggest that the delocalized holes in the TiO2 substrate should be responsible for the temperature-dependent h-route reactions. The locally triggered e-route reaction is associated with the fact that the location of the unoccupied hybridization states is much higher than that of the conduction band onset. Our findings resolve the long-standing debate about the intermediate species and reaction mechanism in photocatalytic oxidation of CH3OH. Our proposed protocol offers a powerful means to study elementary reactions induced by electrons and holes on a semiconductor surface in general.

  • 108.
    Ti, Huihui
    et al.
    Guangzhou Med Univ, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Sch Pharmaceut Sci, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China..
    Zhou, Yang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Guangzhou Med Univ, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Sch Pharmaceut Sci, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China.
    Liang, Xue
    Guangzhou Med Univ, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Sch Pharmaceut Sci, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China..
    Li, Runfeng
    Guangzhou Med Univ, State Key Lab Resp Dis, Natl Clin Res Ctr Resp Dis, Guangzhou Inst Resp Hlth,Affiliated Hosp 1, Guangzhou 510120, Guangdong, Peoples R China..
    Ding, Ke
    Jinan Univ, Int Cooperat Lab Tradit Chinese Med Modernizat &, Chinese Minist Educ MOE, Sch Pharm,Guangzhou City Key Lab Precis Chem Drug, Guangzhou 510632, Guangdong, Peoples R China.;Guangzhou Med Univ, State Key Lab Resp Dis, Natl Clin Res Ctr Resp Dis, Guangzhou Inst Resp Hlth,Affiliated Hosp 1, Guangzhou 510120, Guangdong, Peoples R China..
    Zhao, Xin
    Guangzhou Med Univ, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Sch Pharmaceut Sci, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China.;Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong 999077, Peoples R China..
    Targeted Treatments for Chronic Obstructive Pulmonary Disease (COPD) Using Low-Molecular-Weight Drugs (LMWDs)2019In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 62, no 13, p. 5944-5978Article in journal (Refereed)
    Abstract [en]

    Chronic obstructive pulmonary disease (COPD) is a very common and frequently fatal airway disease. Current therapies for COPD depend mainly on long-acting bronchodilators, which cannot target the pathogenic mechanisms of chronic inflammation in COPD. New pharmaceutical therapies for the inflammatory processes of COPD are urgently needed. Several anti-inflammatory targets have been identified based on increased understanding of the pathogenesis of COPD, which raises new hopes for targeted treatment of this fatal respiratory disease. In this review, we discuss the recent advances in bioactive low-molecular-weight drugs (LMWDs) for the treatment of COPD and, in addition to the first-line drug bronchodilators, focus particularly on low-molecular-weight anti-inflammatory agents, including modulators of inflammatory mediators, inflammasome inhibitors, protease inhibitors, antioxidants, PDE4 inhibitors, kinase inhibitors, and other agents. We also provide new insights into targeted COPD treatments using LMWDs, particularly small-molecule agents.

  • 109.
    Urbanaviciute, Indre
    et al.
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Bhattacharjee, Subham
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Lugger, Jody A. M.
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Cornelissen, Tim D.
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sijbesma, Rint P.
    Eindhoven Univ Technol, Lab Macromol & Organ Chem, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Kemerink, Martijn
    Linkoping Univ, Complex Mat & Devices, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Suppressing depolarization by tail substitution in an organic supramolecular ferroelectric2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 4, p. 2069-2079Article in journal (Refereed)
    Abstract [en]

    Despite being very well established in the field of electro-optics, ferroelectric liquid crystals so far lacked interest from a ferroelectric device perspective due to a typically high operating temperature, a modest remnant polarization and/or poor polarization retention. Here, we experimentally demonstrate how simple structural modification of a prototypical ferroelectric liquid-crystal benzene-1,3,5-trisamide (BTA) - introduction of branched-tail substituents - results in materials with a wide operating temperature range and a data retention time of more than 10 years in thin-film solution-processed capacitor devices at room temperature. The observed differences between linear- and branched-tail compounds are analyzed using density functional theory (DFT) and molecular dynamics (MD) simulations. We conclude that morphological factors like improved packing quality and reduced disorder, rather than electrostatic interactions or intra/inter-columnar steric hindrance, underlay the superior properties of the branched-tailed BTAs. Synergistic effects upon blending of compounds with branched and linear side-chains can be used to further improve the materials' characteristics.

  • 110.
    Valiev, R. R.
    et al.
    Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, POB 55,AI Virtanens Plats 1, FIN-00014 Helsinki, Finland..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.
    Sundholm, D.
    Univ Helsinki, Dept Chem, POB 55,AI Virtanens Plats 1, FIN-00014 Helsinki, Finland..
    Relations between the aromaticity and magnetic dipole transitions in the electronic spectra of hetero[8]circulenes2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 48, p. 30239-30246Article in journal (Refereed)
    Abstract [en]

    Magnetically induced current densities have been calculated at the second-order MOller-Plesset perturbation theory (MP2) level for seven hetero[8]circulenes and their dicationic and dianionic forms. Calculations of the magnetic dipole transition moments have also been carried out at the algebraic diagrammatic construction (ADC(2)) and the second-order approximate coupled-cluster (CC2) levels. The calculations show that the degree of aromaticity and the size of the magnetic dipole transition moment of the lowest magnetic-dipole allowed excited state are related. We show that neutral hetero[8]circulenes are weakly antiaromatic when the first excited state with a large magnetic dipole transition moment of 10-16 a.u. lies at high energies (approximate to 2.8-3.5 eV). For the dications, this transition often lies at much lower energies. Hetero[8]circulene dications with large magnetic dipole transition moments are strongly antiaromatic. The lowest excited states of the hetero[8]circulene dianions have very small magnetic dipole transition moments implying that they are aromatic.

  • 111.
    Vaz da Cruz, Vinicius
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Quantum Nuclear Dynamics in Resonant X-ray Scattering of Gas-Phase and Liquid Systems2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the role of the nuclear degrees of freedom in X-ray induced molecular processes. An important part of it is devoted to establishing theoretical principles to model and interpret high-resolution resonant X-ray scattering experiments in gases and liquids. Our investigations address the resonant inelastic x-ray scattering (RIXS) of H2O(g), H2O(l) and CH3OH(g) and Auger emission induced by hard X-rays in CO(g). The simulations for gas-phase systems are based on a multi-mode wave packet formalism and on potential energy surfaces computed with multi-configurational approaches.

    For liquid systems, we propose a classical/quantum formalism for simulating RIXS based on a combination of ab initio molecular dynamics, density functional theory calculations and quantum nuclear wave packet propagation. The developed model is able to reproduce the experimental observation of shortening of the vibrational progression in H2O(l).

    We show that electronically-elastic RIXS has an intrinsic capability to map the potential energy surface and to carry out vibrational analysis of the electronic ground state in free molecules as well as liquids. For gas-phase water, we see that the landscape of different core-excited states cause the nuclear wave packet to be localized along specific directions thus allowing to reconstruct one-dimensional potential energy curves. For liquid water, we propose a model for deriving, from experiment, confidence intervals for the molecular potential energy curves along the OH bonds, which are determined by the local arrangement of the hydrogen bond network.

    We also investigate the role of ultra-fast rotations induced by photoionization by hard X-rays. In this case, the ejection of a fast photoelectron results in an ultra-fast rotational motion of the molecule, which combined with the anisotropy of the Auger process causes the spectral profile to be split due to a dynamical Doppler effect.

  • 112.
    Vaz da Cruz, Vinicius
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH.
    Ertan, Emelie
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Carvalho Couto, Rafael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Odelius, Michael
    Kimberg, Victor
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Anomalous polarization dependence in vibrationally resolved RIXS of H2OManuscript (preprint) (Other academic)
    Abstract [en]

    It is well established that different electronic channels, in resonant inelastic X-ray scattering (RIXS), display different polarization dependences due to different orientations of their corresponding transition dipole moments in the molecular frame. However, this effect does not influence the vibrational progression in the Franck-Condon approximation. We have found that the transition dipole moments of core-excitation and de-excitation experience ultrafast rotation during the dissociation in intermediate core-excited state. This rotations makes the vibrational progression in RIXS spectra sensitive to the polarisation of the X-ray photons. The studied effect is exemplified for the RIXS of the water molecule through the dissociative core-excited state where the vibrational scattering anisotropy is accompanied also by violation of parity selection rules for vibrations.

  • 113.
    Vaz da Cruz, Vinicius
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Eckert, Sebastian
    Pietzsch, Annette
    Iannuzzi, Marcella
    Carvalho Couto, Rafael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Niskanen, Johannes
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Lu, Xingye
    McNally, Daniel
    Jay, Raphael
    Kimberg, Victor
    Föhlisch, Alexander
    Odelius, Michael
    Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scatteringManuscript (preprint) (Other academic)
    Abstract [en]

    The potential energy surface is widely used powerful concept in chemical physics. However, direct experimental access to the local potential energy surface in liquid especially in systems  with strong hydrogen bonds is lacking. We develop general technique demonstrated  for liquid water how to reconstruct from state-of-the-art  sub-natural linewidth resonant inelastic X-ray scattering (RIXS)  the local distribution of OH potential energy curves,  separately for OH bonds with weak and strong hydrogen bond. By this we are able to look on the local structure by characterising  selectively the strength of the hydrogen bond. We present a detailed analysis of the formation of the vibrationally resolved RIXS of liquids using a classical/quantum formalism  based on a combination of {\it ab initio} molecular dynamics, density functional theory calculations and quantum nuclear wave packet propagation. Theory nicely explains shortening of the vibrational progression in liquid phase in comparison with RIXS of free water molecules seen in the experiment by fluctuation of the hydrogen bond  network and coherent excitation of both OH bonds.

  • 114.
    Vaz da Cruz, Vinicius
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Carvalho Couto, Rafael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fedotov, Daniil
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Robert Rehn, Dirk
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Savchenko, Viktoriia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    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.
    Polyutov, Sergey
    Niskanen, Johannes
    Fondell, Mattis
    Eckert, Sebastian
    Jay, Raphael
    Schmitt, Thorsten
    Pietzsch, Annette
    Föhlisch, Alexander
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Odelius, Michael
    Kimberg, Victor
    Resonant inelastic X-ray scattering and X-ray absorption of methanol at the near oxygen K-edgeManuscript (preprint) (Other academic)
    Abstract [en]

    We report on a theoretical analysis of core-excitation spectra of gas and liquid phase methanol asobtained with use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering(RIXS). The electronic transitions are studied with complementary computational methods includ-ing strict and extended second-order algebraic diagrammatic construction (ADC(2) and ADC(2)-x),restricted active space second-order perturbation theory (RASPT2), and time-dependent densityfunctional theory (TDDFT)—providing a complete assignment of the near oxygen K-edge XAS.We show that multimode nuclear dynamics is of crucial importance for explaining the availableexperimental XAS and RIXS spectra. Multimode nuclear motions was considered in a developedmixed representation where dissociative states and highly excited vibrational modes are accuratelytreated with a time-dependent wave packet technique while the remaining active vibrational modesare described using Franck–Condon amplitudes. Particular attention is paid to the polarizationdependence of RIXS and the effects of the isotope substitution on the RIXS profile in the case ofdissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to bedue to an interplay between molecular and atomic-like features arising in the course of transitionsbetween dissociative core- and valence-excited states. The dynamical nature of the splitting of the2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical resultsare in good agreement with available experimental data.

  • 115.
    Wang, Xiaojiang
    et al.
    Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
    Liu, Yang
    Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai Synchrotron Radiat Facil, Shanghai 201204, Peoples R China..
    Wang, Ying
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ren, Rong
    Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
    Chen, Hengquan
    Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
    Jiang, Zheng
    Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai Synchrotron Radiat Facil, Shanghai 201204, Peoples R China..
    He, Qinggang
    Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
    Electrochemical and Spectroscopic Study of Homo- and Hetero-Dimetallic Phthalocyanines as Catalysts for the Oxygen Reduction Reaction in Acidic Media2018In: CHEMELECTROCHEM, ISSN 2196-0216, Vol. 5, no 22, p. 3478-3485Article in journal (Refereed)
    Abstract [en]

    Metallophthalocyanines (MPc, M=Fe or Co) have been investigated extensively as a typical type of transition metal macrocyclic catalysts for the oxygen reduction reaction (ORR). However, the understanding about ORR catalyzed by binuclear even heterodimetallic phthalocyanines in acidic condition is still not sufficient. Herein we synthesized two homodimetallicphthalocyanine (FePc-PcFe and CoPc-PcCo) and a heterodimetallic phthalocyanine (FePc-PcCo). The electrocatalytic activity of as-synthesized compounds were characterized by cyclic voltammetry (CV) and rotating disk electrode (RDE). Generally, the binuclear metallophthalocyanines show higher activity than their monomeric analogues including FePc and CoPc. Also, the Fe compounds exhibit better catalytic performance than the Co phthalocyanines. However, interestingly the heterodimetallic phthalocyanine FePc-PcCo shows similar half-wave potential and ORR activity with FePc-PcFe, rather than CoPc-PcCo. This may be explained by XPS and XAS, which reveal a similar square-planar structure existed in FePc-PcCo and FePc-PcFe and a non-planar structure in CoPc-PcCo. Furthermore, the increasing of the ORR activity among those five catalysts is well in agreement with the descending LUMO energies in DFT calculations. A lower LUMO energy indicates a favorable adsorption of O-2, which in turn affects the ORR performance.

  • 116.
    Wang, Ying
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhan, Shaoqi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nucleophilic Attack by OH2 or OH-: A Detailed Investigation on pH Dependent Performance of a Ru Catalyst2019In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 38, no 6, p. 1264-1268Article in journal (Refereed)
    Abstract [en]

    The considerable rate enhancements along with the increase in pH values may be due to the direct involvement of hydroxide anion in attacking electrophilic [Ru-V(tda)(py)(2)O](+) (1; tda = [2,2':6',2 ''-terpyridine]-6,6 ''-dicarboxylate, py = pyridine). The enhanced reaction rate is well in agreement with the descending activation barriers in our calculation. The addition of four extra water molecules in the geometry optimization plays a key role in stabilizing hydroxide anion as well as building a reasonable hydrogen-bonding network, and three of these molecules are required to stabilize the OH as an anion instead of a radical.

  • 117. Wang, Z.
    et al.
    Fu, Y.
    Kang, Zhengzhong
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, X.
    Chen, N.
    Wang, Q.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, L.
    Song, S.
    Ling, D.
    Song, H.
    Kong, X.
    Fan, C.
    Organelle-Specific Triggered Release of Immunostimulatory Oligonucleotides from Intrinsically Coordinated DNA-Metal-Organic Frameworks with Soluble Exoskeleton2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 44, p. 15784-15791Article in journal (Refereed)
    Abstract [en]

    DNA has proven of high utility to modulate the surface functionality of metal-organic frameworks (MOFs) for various biomedical applications. Nevertheless, current methods for preparing DNA-MOF nanoparticles rely on either inefficient covalent conjugation or specific modification of oligonucleotides. In this work, we report that unmodified oligonucleotides can be loaded on MOFs with high density (∼2500 strands/particle) via intrinsic, multivalent coordination between DNA backbone phosphate and unsaturated zirconium sites on MOFs. More significantly, surface-bound DNA can be efficiently released in either bulk solution or specific organelles in live cells when free phosphate ions are present. As a proof-of-concept for using this novel type of DNA-MOFs in immunotherapy, we prepared a construct of immunostimulatory DNA-MOFs (isMOFs) by intrinsically coordinating cytosine-phosphate-guanosine (CpG) oligonucleotides on biocompatible zirconium MOF nanoparticles, which was further armed by a protection shell of calcium phosphate (CaP) exoskeleton. We demonstrated that isMOFs exhibited high cellular uptake, organelle specificity, and spatiotemporal control of Toll-like receptors (TLR)-triggered immune responses. When isMOF reached endolysosomes via microtubule-mediated trafficking, the CaP exoskeleton dissolved in the acidic environment and in situ generated free phosphate ions. As a result, CpG was released from isMOFs and stimulated potent immunostimulation in living macrophage cells. Compared with naked CpG-MOF, isMOFs exhibited 83-fold up-regulation in stimulated secretion of cytokines. We thus expect this isMOF design with soluble CaP exoskeleton and an embedded sequential "protect-release" program provides a highly generic approach for intracellular delivery of therapeutic nucleic acids.

  • 118.
    Wei, Yong
    et al.
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China..
    Pei, Huan
    Yanshan Univ, Coll Informat Sci & Engn, Qinhuangdao 066004, Hebei, Peoples R China..
    Sun, Dexian
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China..
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tian, Guangjun
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China..
    Numerical investigations on the electromagnetic enhancement effect to tip-enhanced Raman scattering and fluorescence processes2019In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 31, no 23, article id 235301Article in journal (Refereed)
    Abstract [en]

    In the present work, we theoretically study the electromagnetic (EM) enhancement of the Raman and fluorescence signals for a molecule placed in a nanocavity formed by a metallic tip and substrate that mimics a tip-enhanced Raman scattering (TERS) setup using three-dimensional finite element method calculations. The influence of tip size and tip-molecule distance on the EM enhancements of the incident field as well as the radiative and non-radiative decay rates of the molecule are systematically investigated. Simulation results show that the maximum EM enhancement to the incident light as provided by the localized surface plasmon resonance in the nanocavity can reach similar to 285 for the configuration considered in the present work. Meanwhile, it was found that, at the classical limit, decreasing the apex radius or the tip-molecule distance can both reduce the spatial distribution (as characterized by the full width at half maximum) of the Raman enhancement in a linear fashion. Moreover, simulation results show that the nonlocal dielectric response of the tip and the substrate plays a key role to the fluorescence quantum yield of the molecule. However, it was found that the strong EM excitation enhancement is the dominating factor for the tip enhanced fluorescence (TEF) effect and stronger fluorescence enhancement has been found when increasing the apex radius or reducing the tip-molecule distance with an incident wavelength of 532 nm. The best TERS and TEF enhancements were found to be similar to 6 x 10(9) and similar to 1.7 x 10(4), respectively, with the tip-molecule distance around 1 nm.

  • 119.
    Widengren, Jerker
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Jamshidi, AhmadReza
    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. KTH, Superseded Departments (pre-2005), Biotechnology. KTH, Superseded Departments (pre-2005), Chemistry. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, Superseded Departments (pre-2005), Chemistry. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Chmyrov, Volodymyr
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Yuan, C
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Efficiency enhancedcolloidal Mn-doped type-II core/shell ZnSe/CdS quantum dot sensitized hybridsolar cells2015In: Journal of Nanomaterials, ISSN 1687-4110, E-ISSN 1687-4129, article id 921903Article in journal (Refereed)
    Abstract [en]

    Colloidal Mn-doped ZnSe/CdS core/shell quantum dots (QDs) are synthesized for the first time and employed as a strategy to boost the power conversion efficiency of quantum dot sensitized solar cells. By using Mn-doping as a band gap engineering tool for core/shell QDs an effective improvement of absorption spectra could be obtained. The mid-states generated by a proper Mn content alleviate carrier separation and enhance the electron injection rate, thus facilitating electron transport to the TiO2 substrate. It is demonstrated that a device constructed with 0.25% Mn-doped ZnSe/CdS leads to an enhancement of the electron injection rate and power conversion efficiency by 4 times and 1.3, respectively.

  • 120.
    Wu, Hongwei
    et al.
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China.;Nanyang Technol Univ, Sch Phys & Math Sci, Div Chem & Biol Chem, 21 Nanyang Link, Singapore 637371, Singapore..
    Chi, Weijie
    Singapore Univ Technol & Design, 8 Somapah Rd, Singapore 487372, Singapore..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wu, Bin
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Gong, Yifan
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Zheng, Dongxiao
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Nanyang Technol Univ, Sch Phys & Math Sci, Div Chem & Biol Chem, 21 Nanyang Link, Singapore 637371, Singapore..
    Liu, Xiaogang
    Singapore Univ Technol & Design, 8 Somapah Rd, Singapore 487372, Singapore..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhu, Liangliang
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Crystal Multi-Conformational Control Through Deformable Carbon-Sulfur Bond for Singlet-Triplet Emissive Tuning2019In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 13, p. 4328-4333Article in journal (Refereed)
    Abstract [en]

    Crystal-state luminophores have been of great interest in optoelectronics for years, whereas the excited state regulation at the crystal level is still restricted by the lack of control ways. We report that the singlet-triplet emissive property can be profoundly regulated by crystal conformational distortions. Employing fluoro-substituted tetrakis(arylthio)benzene luminophores as prototype, we found that couples of molecular conformations formed during different crystallizations. The deformable carbon-sulphur bond essentially drove the distortion of the molecular conformation and varied the stacking mode, together with diverse non-covalent interactions, leading to the proportional adjustment of the fluorescence and phosphorescence bands. This intrinsic strategy was further applied for solid-state multicolor emissive conversion and mechanoluminescence, probably offering new insights for design of smart crystal luminescent materials.

  • 121.
    Xie, Zhen
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techo, Jinan 250014, Shandong, Peoples R China.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tian, Guangjun
    Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China..
    Wang, Chuan-Kui
    Shandong Normal Univ, Sch Phys & Elect, Shandong Prov Key Lab Med Phys & Image Proc Techo, Jinan 250014, Shandong, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China..
    Theoretical modeling of tip-enhanced resonance Raman images of switchable azobenzene molecules on Au(111)2018In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 10, no 25, p. 11850-11860Article in journal (Refereed)
    Abstract [en]

    With a highly localized plasmonic field, tip-enhanced Raman spectroscopy (TERS) images have reached atomic-scale resolution, providing an optical means to explore the structure of a single molecule. We have applied the recently developed theoretical method to simulate the TERS images of trans and cis azobenzene as well as its derivatives on Au(111). Our theoretical results reveal that when the first excited state is resonantly excited, TERS images from a highly confined plasmonic field can effectively distinguish the isomer configurations of the adsorbates. The decay of the plasmonic field along the surface normal can be further used to distinguish different nonplanar cis configurations. Moreover, subtle characteristics of different molecular configurations can also be identified from the TERS images of other resonant excited states with a super-high confined plasmonic field. These findings serve as good references for future TERS experiments on molecular isomers.

  • 122.
    Xie, Zhen
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Chuan-Kui
    Shandong Normal Univ, Shandong Prov Key Lab Med Phys & Image Proc Techn, Sch Phys & Elect, Jinan 250014, Shandong, Peoples R China..
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Monitoring Hydrogen/Deuterium Tautomerization in Transient Isomers of Single Porphine by Highly Localized Plasmonic Field2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 17, p. 11081-11093Article in journal (Refereed)
    Abstract [en]

    Inner proton transfer between two trans isomers (tautomerization) in porphyrins plays a crucial role in many biological systems as well as molecular nanotechnology. Although the stepwise mechanism of tautomerization is well accepted, the involved intermediate cis-isomer has not been directly detected owing to its short lifetime and the extremely low intensities of corresponding hydrogen vibrations. Here, taking a single porphine as the prototype, we theoretically demonstrate that Raman intensities of the hydrogen vibrations become accessible under the highly localized plasmonic field because of the symmetry breaking effect. In addition, with the ultrafast incident excitations, we find that Raman signals of cis-porphine could be distinguished from the stable trans isomer, suggesting a general protocol for the direct characterization of transient isomers. Moreover, calculated results reveal that the position of inner hydrogen/deuterium can be unambiguously visualized from Raman images of the corresponding stretching modes, providing a unique optical means for the chemical monitoring of tautomerization in porphine and its derivatives.

  • 123. Xue, Yuhan
    et al.
    Li, Junhao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wu, Zengrui
    Liu, Guixia
    Tang, Yun
    Li, Weihua
    Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 toward schisantherin E2019In: Chemical Biology and Drug Design, ISSN 1747-0277, E-ISSN 1747-0285, Vol. 93, no 5, p. 854-864Article in journal (Refereed)
    Abstract [en]

    The cytochromes CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities toward some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes toward SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5-SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B-C loop and the I helix mediated different hydrogen-bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe-cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.

  • 124.
    Yang, Huiqing
    et al.
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Zheng, Danning
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Zhang, Jingshun
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Chen, Ke
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Li, Junfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Wang, Li
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Zhang, Jinglai
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    He, Hongyan
    Chinese Acad Sci, Inst Proc Engn, Beijing Key Lab Ion Liquids Clean Proc, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China..
    Zhang, Suojiang
    Chinese Acad Sci, Inst Proc Engn, Beijing Key Lab Ion Liquids Clean Proc, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China..
    Protic Quaternary Ammonium Ionic Liquids for Catalytic Conversion of CO2 into Cyclic Carbonates: A Combined Ab Initio and MD Study2018In: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 57, no 21, p. 7121-7129Article in journal (Refereed)
    Abstract [en]

    The mechanism of CO2 fixation catalyzed by protic hydroxyl-functionalized quaternary ammonium ionic liquids (ILs) is investigated by two different models, the Single-IL model and the Double-IL model. The relative sequence of catalytic activity calculated by the Single-IL model is contradictory with the experimental result. The situation is totally varied when the Double-IL model is utilized. In this system, ILs are not limited to the catalyst but solvent. The ILs are incorporated into the catalytic system to consider the solvent effect rather than by the existing solvent model. When the solvent effect is included, it is better to distinguish the catalytic activity of three ILs. According to the noncovalent interaction and the atoms in molecules analysis, the highest catalytic activity of tris(2-hydroxyethyl)ammonium bromide ([HTEA]Br) is attributed to its strongest nucleophilic attack and moderate hydrogen bond interaction between IL and reactant. It is necessary to consider the interaction between ILs to get a reliable result. Moreover, the solvent effect aroused by ILs should be carefully considered.

  • 125.
    Zakomirnyi, Vadim
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Karpov, Sergei, V
    Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.;Siberian State Univ Sci & Technol, Krasnoyarsk 660014, Russia.;RAS, KSC SB, Fed Res Ctr, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Rasskazov, Ilia L.
    Univ Rochester, Inst Opt, 601 Elmwood Ave, Rochester, NY 14627 USA..
    Collective lattice resonances in disordered and quasi-random all-dielectric metasurfaces2019In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 36, no 7, p. E21-E29Article in journal (Refereed)
    Abstract [en]

    Collective lattice resonances in disordered 2D arrays of spherical Si nanoparticles (NPs) have been thoroughly studied within the framework of the coupled dipole approximation. Three types of defects have been analyzed: positional disorder, size disorder, and quasi-random disorder. We show that the positional disorder strongly suppresses either the electric dipole (ED) or the magnetic dipole (MD) coupling, depending on the axis along which the NPs are shifted. Contrarily, size disorder strongly affects only the MD response, while the ED resonance can be almost intact, depending on the lattice configuration. Finally, random removing of NPs from an ordered 2D lattice reveals a quite surprising result: hybridization of the ED and MD resonances with lattice modes remains observable even in the case of random removing of up to 84% of the NPs from the ordered array. The reported results could be important for rational design and utilization of metasurfaces, solar cells, and other alldielectric photonic devices. 

  • 126.
    Zhan, Shaoqi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dynamics and Reactions of Molecular Ru Catalysts at Carbon Nanotube-Water Interfaces2018In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 24, p. 7498-7503Article in journal (Refereed)
    Abstract [en]

    Immobilization of molecular catalysts to electrode surfaces can improve the recyclability and electron transfer rates. The drawback is that most experimental techniques and theoretical methods are not applicable. Here we present results from a study of a ruthenium water oxidation catalyst [(RuO)-O-V(bda)L-2] in explicit water at a carbon nanotube water interface, forming the key O-O bond between two 128 atom catalysts, all fully dynamically. Our methodology is based on a recently developed empirical valence bond (EVB) model. We follow the key steps of the reaction including diffusion of the catalysts at the interface, formation of the prereactive dimer, and the bond formation between the two catalysts. On the basis of the calculated parameters, we compute the turnover frequency (TOF) at the experimental loading, in excellent agreement with the experiments. The key O-O bond formation was significantly retarded at the surface, and limiting components were identified that could be improved by catalyst modification.

  • 127.
    Zhan, Shaoqi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    De Gracia Triviño, Juan Angel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    The Carboxylate Ligand as an Oxide Relay in Catalytic Water Oxidation2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 26, p. 10247-10252Article in journal (Refereed)
    Abstract [en]

    Carboxylate groups have diverse functionalities in ligands of transition metal catalysts. Here we present a conceptually different function of the carboxylates: the oxide relay. It functions by providing an intramolecular nucleophilic oxygen close to the oxo group to facilitate O-O bond formation and at a later stage a remote electrophilic center to facilitate OH- nucleophilic attack. Empirical valence bond-molecular dynamics (EVB-MD) models were generated for key bond forming steps, diffusion coefficients and binding free energies from potential of mean force estimations were calculated from molecular dynamics (MD) simulations, activation free energies of chemical steps were calculated using density functional theory (DFT). The catalyst studied is the extremely active Ru(tda)(py)(2) water oxidation catalyst. The combination of simulation methods allowed for estimation of the turnover frequencies, which were within 1 order of magnitude from the experimental results at different pH values. From the calculated reaction rates we find that at low pH the OH- anion nucleophilic attack is the rate limiting step, which changes at high pH to the O-O bond formation step. Both steps are extremely rapid, and key to the efficiency is the oxide relay functionality of a pendant carboxylate group. We cannot exclude all alternative mechanisms and suggest isotope experiments using O-18-labeled water to support or invalidate the oxide relay mechanism. The functionality was discovered for a ruthenium catalyst, but since there is nothing in the mechanism restricting it to this metal, the oxide relay functionality could open new ways to design the next-generation water oxidation catalysts with improved activity.

  • 128.
    Zhan, Shaoqi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Triviño, Juan Angel De Gracia
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    The Carboxylate Ligand as an Oxide Relay in Catalytic Water Oxidation.In: Article in journal (Other academic)
    Abstract [en]

    Carboxylate groups have diverse functionality in ligands of transiton metal catalysts. Here we present a conceptuallydifferent function of the carboxylates – the oxide relay. It functions by providing an intramolecular nucleophilic oxygen close tothe oxo group to facilitate O-O bond formation, and at a later stage a remote electrophilic center to facilitate OH- nucleophilic attack.EVB-MD models were generated for key bond forming steps, diffusion coefficients and binding free energies from potentialof mean force estimations were calculated from MD simulations, activation free energies of chemical steps were calculated usingdensity functional theory. The catalyst studied is the extremely active Ru(tda)(py)2 water oxidation catalyst. The combination ofsimulation methods allowed for estimation of the turnover frequencies, which were within one order of magnitude from the experimentalresults at different pH values. From the calculated reaction rates we find that at low pH the OH- anion nucleophilic attack isthe rate-limiting step, which changes at high pH to the O-O bond formation step. Both steps are extremely rapid and key to theefficiency is the oxide relay functionality of a pendant carboxylate group. The functionality was discovered for a ruthenium catalyst,but since there is nothing in the mechanism restricting it to this metal, the oxide relay functionality could open new ways todesign the next generation water oxidation catalysts with improved activity.

  • 129.
    Zhan, Shaoqi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zou, Rongfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dynamics with Explicit Solvation Reveals Formation of the Prereactive Dimer as Sole Determining Factor for the Efficiency of Ru(bda)L-2 Catalysts2018In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 8, no 9, p. 8642-8648Article in journal (Refereed)
    Abstract [en]

    This report describes all key steps in the O-O bond formation from two separated [Ru-V=O(bda)L-2](+) cations to form the dinuclear [(bda)L2RuIV-O-Ru-IV(bda)L-2](2+) in explicit solvent. The three steps involve the diffusion of the catalysts in the water phase, formation of the prereactive dimer, and the bond formation between the two catalysts. On the basis of the calculated parameters, we compute the rate constant of two catalysts with different L-ligands, isoquinoline and picoline, and the computed values are in excellent agreement with the experimental ones. The interaction of the axial ligands is key to the improved rates of the larger ligand, mainly by facilitating the formation of the prereactive dimer from the solvated monomer. By comparing the binding free energy of hydrophilic Ru-IV-OH and hydrophobic Ru-V=O, the hydrophobic driving force of Ru-V=O in this system has been estimated to 1 kcal mol(-1).

  • 130.
    Zhang, Fuguo
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Cong, Jiayan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Li, Yuanyuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Bergstrand, Jan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Cai, Bin
    State Key Laboratory of Fine Chemicals, Dalian University of Technology (DUT).
    Hajian, Alireza
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Yao, Zhaoyang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Wang, Linqin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Hao, Yan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Yang, Xichuan
    State Key Laboratory of Fine Chemicals, Dalian University of Technology (DUT).
    Gardner, James M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Widengren, Jerker
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Kloo, Lars
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Sun, Licheng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry. State Key Laboratory of Fine Chemicals, Dalian University of Technology (DUT).
    A facile route to grain morphology controllable perovskite thin films towards highly efficient perovskite solar cells2018In: Nano Energy, ISSN 2211-2855, E-ISSN 2211-3282, Vol. 53, p. 405-414Article in journal (Refereed)
    Abstract [en]

    Perovskite photovoltaics have recently attracted extensive attention due to their unprecedented high power conversion efficiencies (PCEs) in combination with primitive manufacturing conditions. However, the inherent polycrystalline nature of perovskite films renders an exceptional density of structural defects, especially at the grain boundaries (GBs) and film surfaces, representing a key challenge that impedes the further performance improvement of perovskite solar cells (PSCs) and large solar module ambitions towards commercialization. Here, a novel strategy is presented utilizing a simple ethylammonium chloride (EACl) additive in combination with a facile solvent bathing approach to achieve high quality methyammonium lead iodide (MAPbI3) films. Well-oriented, micron-sized grains were observed, which contribute to an extended carrier lifetime and reduced trap density. Further investigations unraveled the distinctively prominent effects of EACl in modulating the perovskite film quality. The EACl was found to promote the perovskite grain growing without undergoing the formation of intermediate phases. Moreover, the EACl was also revealed to deplete at relative low temperature to enhance the film quality without compromising the beneficial bandgap for solar cell applications. This new strategy boosts the power conversion efficiency (PCE) to 20.9% and 19.0% for devices with effective areas of 0.126 cm2 and 1.020 cm2, respectively, with negligible current hysteresis and enhanced stability. Besides, perovskite films with a size of 10 × 10 cm2, and an assembled 16 cm2(5 × 5 cm2 module) perovskite solar module with a PCE of over 11% were constructed.

  • 131. Zhang, J.
    et al.
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tian, Y.
    Bertagnin, C.
    Fang, Z.
    Kang, D.
    Kong, X.
    Jia, H.
    Sun, Z.
    Jia, R.
    Gao, P.
    Poongavanam, V.
    Loregian, A.
    Xu, W.
    Ma, X.
    Ding, X.
    Huang, B.
    Zhan, P.
    Liu, X.
    Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 22, p. 9976-9999Article in journal (Refereed)
    Abstract [en]

    Due to the emergence of highly pathogenic and oseltamivir-resistant influenza viruses, there is an urgent need to develop new anti-influenza agents. Herein, five subseries of oseltamivir derivatives were designed and synthesized to improve their activity toward drug-resistant viral strains by further exploiting the 150-cavity in the neuraminidases (NAs). The bioassay results showed that compound 21h exhibited antiviral activities similar to or better than those of oseltamivir carboxylate (OSC) against H5N1, H5N2, H5N6, and H5N8. Besides, 21h was 5- to 86-fold more potent than OSC toward N1, N8, and N1-H274Y mutant NAs in the inhibitory assays. Computational studies provided a plausible rationale for the high potency of 21h against group-1 and N1-H274Y NAs. In addition, 21h demonstrated acceptable oral bioavailability, low acute toxicity, potent antiviral activity in vivo, and high metabolic stability. Overall, the above excellent profiles make 21h a promising drug candidate for the treatment of influenza virus infection.

  • 132.
    Zhang, Peili
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry. State Key Laboratory of Fine Chemicals, Institute of Artificial Photosynthesis, DUT-KTH Joint Education and Research Centre on Molecular Devices, Dalian University of Technology, Dalian, 116024, China.
    Sheng, Xia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry. State Key Laboratory of Fine Chemicals, Institute of Artificial Photosynthesis, DUT-KTH Joint Education and Research Centre on Molecular Devices, Dalian University of Technology, Dalian, 116024, China.
    Chen, Xiaoyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fang, Zhiyong
    Jiang, Jian
    Wang, Mei
    Li, Fusheng
    Fan, Lizhou
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Ren, Yansong
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Zhang, Biaobiao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Timmer, Brian J. J.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Sun, Licheng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry. State Key Laboratory of Fine Chemicals, Institute of Artificial Photosynthesis, DUT-KTH Joint Education and Research Centre on Molecular Devices, Dalian University of Technology, Dalian, 116024, China.
    Paired Electrocatalytic Oxygenation and Hydrogenation of Organic Substrates with Water as the Oxygen and Hydrogen Source2019In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 27, p. 9155-9159Article in journal (Refereed)
    Abstract [en]

    The use of water as an oxygen and hydrogen source for the paired oxygenation and hydrogenation of organic substrates to produce valuable chemicals is of utmost importance as a means of establishing green chemical syntheses. Inspired by the active Ni3+ intermediates involved in electro-catalytic water oxidation by nickel-based materials, we prepared NiBx as a catalyst and used water as the oxygen source for the oxygenation of various organic compounds. NiBx was further employed as both an anode and a cathode in a paired electrosynthesis cell for the respective oxygenation and hydrogenation of organic compounds, with water as both the oxygen and hydrogen source. Conversion efficiency and selectivity of >= 99% were observed during the oxygenation of 5-hydroxy-methylfurfural to 2,5-furandicarboxylic acid and the simultaneous hydrogenation of p-nitrophenol to p-aminophenol. This paired electrosynthesis cell has also been coupled to a solar cell as a stand-alone reactor in response to sunlight.

  • 133.
    Zhang, Qi
    et al.
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Rao, Si-Jia
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Xie, Tao
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Xu, Tian-Yi
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Da-Wei
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Qu, Da-Hui
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Long, Yi-Tao
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Tian, He
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Sch Chem & Mol Engn, Joint Int Res Lab Precis Chem & Mol Engn, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Muscle-like Artificial Molecular Actuators for Nanoparticles2018In: CHEM, ISSN 2451-9294, Vol. 4, no 11, p. 2670-2684Article in journal (Refereed)
    Abstract [en]

    Muscle tissue performs crucial contraction/extension motions that generate mechanical force and work by consuming chemical energy. Inspired by this naturally created biomolecular machine, artificial molecular muscles are designed and synthesized to undertake linear actuation functions. However, most of these muscle-like actuators are performed at large ensembles, while to realize the nanoscale actuation at the single-to few-molecule level remains challenging. Herein, we developed an artificial muscle-like molecular actuator that can reversibly control the proximity of the attached nano-objects, gold nanoparticles, within the single-molecule length level by its stimuli-responsive muscle-like linear contraction/extension motion. The molecular actuation motion is accompanied by an optical signal output resulting from the plasmonic resonance properties of gold nanoparticles. Meanwhile, the thermal noise of the muscle-like molecular actuator can be overcome by integrating the optical signal over a sufficiently long period.

  • 134.
    Zhang, T.
    et al.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Brumboiu, I. E.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Grazioli, C.
    Sincrotrone Trieste, CNR, ISM, I-34149 Trieste, Basovizza, Italy..
    Guarnaccio, A.
    CNR, ISM, I-85050 Potenza, Italy..
    Coreno, M.
    Sincrotrone Trieste, CNR, ISM, I-34149 Trieste, Basovizza, Italy..
    de Simone, M.
    Sincrotrone Trieste, Lab TASC, CNR, IOM, I-34149 Trieste, Basovizza, Italy..
    Santagata, A.
    CNR, ISM, I-85050 Potenza, Italy..
    Rensmo, H.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Brena, B.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Lanzilotto, V.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Puglia, C.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Lone-Pair Delocalization Effects within Electron Donor Molecules: The Case of Triphenylamine and Its Thiophene-Analog2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 31, p. 17706-17717Article in journal (Refereed)
    Abstract [en]

    Triphenylamine (TPA) and its thiophene-analog, N,N-diphenyl-2-thiophenamine (DPTA), are both well-known as electron-donating molecules implemented in optoelectronic devices such as organic solar cells and LEDs. Comprehensive valence and core level photoelectron spectroscopy, as well as near edge X-ray absorption spectroscopy (NEXAFS), measurements have been performed on gas phase TPA and DPTA. The experimental results have been compared to density functional theory calculations, providing a detailed description of the molecular electronic structure. Specifically, the C 1s photoelectron lines of both TPA and DPTA were resolved in the different C atom contributions and their binding energies explained as the result of two counter-acting effects: (1) the electronegativity of the nitrogen atom (and sulfur atom in DPTA) and (2) the the N (and S in DPTA) lone-pair electrons. In addition, the C K-edge NEXAFS spectrum of DPTA reveals that the lowest unoccupied molecular orbital (LUMO) energy position is affected differently if the core hole site is on the phenyl compared to the thiophene ring. The electron-donating properties of these two molecules are largely explained by the significant contribution of the N lone-pair electrons (p(z)) to the highest occupied molecular orbital. The contribution to the LUMO and to the empty density of states of the sulfur of the thiophene ring in DPTA explains the better performance of donor-pi-acceptor molecules containing this moiety and implemented in photoenergy conversion devices.

  • 135.
    Zhang, Wei
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Sadollahkhani, Azar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Yuanyuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Leandri, Valentina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Gardner, James M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Kloo, Lars
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Mechanistic Insights from Functional Group Exchange Surface Passivation: A Combined Theoretical and Experimental Study2019In: ACS APPLIED ENERGY MATERIALS, ISSN 2574-0962, Vol. 2, no 4, p. 2723-2733Article in journal (Refereed)
    Abstract [en]

    Four different functional groups including amino (-NH2), phosphine (-PH2), hydroxyl (-OH), and thiol (-SH) were combined with POSS (polyhedral oligomeric silsesquioxane) molecules to investigate how functional groups affect the surface passivation of POSS systems. Results from density-functional theory (DFT) calculations indicate that functional group amino (-NH2) with adsorption energy 86 (56) kJ mol(-1) is consistently better than that of thiol (-SH) with adsorption energy 68 (43) kJ mor(-1) for different passivation mechanisms. Theoretical studies on the analogous POSS-OH and POSS-PH2 systems show similar adsorption energies. Two of the systems were also investigated experimentally; aminopropyl isobutyl POSS (POSS-NH2) and mercaptopropyl isobutyl POSS (POSS-SH) were applied as passivation materials for MAPbI(3) (MA = methylammonium) perovskite and (FA)(0.85)(MA)(0.15)Pb(I-3)(0.85)(Br-3)(0)(.15)(FA = formamidinium) perovskite films. The same conclusion was drawn based on the results from contact angle studies, X-ray diffraction (XRD), and the stability of solar cells in ambient atmosphere, indicating the vital importance of choice of functional groups for passivation of the perovskite materials.

  • 136.
    Zhang, Weiwei
    et al.
    Univ Sci & Technol China, Dept Astron, CAS Key Lab Res Galaxies & Cosmol, Hefei 230026, Anhui, Peoples R China.;Univ Sci & Technol China, Sch Astron & Space Sci, Hefei 230026, Anhui, Peoples R China.;Penn State Univ, Dept Mech & Nucl Engn, University Pk, PA 16802 USA..
    Si, Yubing
    Huanghe Sci & Technol Coll, Inst Nanostruct Funct Mat, Henan Prov Key Lab Nanocomposites & Applicat, Zhengzhou 450006, Henan, Peoples R China..
    Zhen, Junfeng
    Univ Sci & Technol China, Dept Astron, CAS Key Lab Res Galaxies & Cosmol, Hefei 230026, Anhui, Peoples R China.;Univ Sci & Technol China, Sch Astron & Space Sci, Hefei 230026, Anhui, Peoples R China..
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linnartz, Harold
    Leiden Univ, Leiden Observ, Sackler Lab Astrophys, POB 9513, NL-2300 RA Leiden, Netherlands..
    Tielens, Alexander G. G. M.
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Laboratory Photochemistry of Covalently Bonded Fluorene Clusters: Observation of an Interesting PAH Bowl-forming Mechanism2019In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 872, no 1, article id 38Article in journal (Refereed)
    Abstract [en]

    The fullerene C-60, one of the largest molecules identified in the interstellar medium (ISM), has been proposed to form top-down through the photochemical processing of large (more than 60 C atoms) polycyclic aromatic hydrocarbon (PAH) molecules. In this article, we focus on the opposite process, investigating the possibility that fullerenes form from small PAHs, in which bowl-forming plays a central role. We combine laboratory experiments and quantum chemical calculations to study the formation of larger PAHs from charged fluorene clusters. The experiments show that with visible laser irradiation, the fluorene dimer cation-[C13H9-C13H9](+)-and the fluorene trimer cation-[C13H9-C13H8-C13H9](+)-undergo photodehydrogenation and photoisomerization, resulting in bowl-structured aromatic cluster ions, C26H12+ and C39H20+, respectively. To study the details of this chemical process, we employ quantum chemistry that allows us to determine the structures of the newly formed cluster ions, to calculate the dissociation energies for hydrogen loss, and to derive the underlying reaction pathways. These results demonstrate that smaller PAH clusters (with less than 60 C atoms) can convert to larger bowled geometries that might act as building blocks for fullerenes, because the bowl-forming mechanism greatly facilitates the conversion from dehydrogenated PAHs to cages. Moreover, the bowl-forming induces a permanent dipole moment that-in principle-allows one to search for such species using radio astronomy.

  • 137.
    Zhang, Xiaoliang
    et al.
    Beihang Univ, Sch Mat Sci & Engn, Beijing 100191, Peoples R China..
    Cappel, Ute B.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Jia, Donglin
    Beihang Univ, Sch Mat Sci & Engn, Beijing 100191, Peoples R China..
    Zhou, Qisen
    Beihang Univ, Sch Mat Sci & Engn, Beijing 100191, Peoples R China..
    Du, Juan
    Beihang Univ, Sch Mat Sci & Engn, Beijing 100191, Peoples R China..
    Sloboda, Tamara
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Svanström, Sebastian
    Uppsala Univ, Dept Phys & Astron, Div Mol & Condensed Matter Phys, Box 516, SE-75120 Uppsala, Sweden..
    Johansson, Fredrik O. L.
    Uppsala Univ, Dept Phys & Astron, Div Mol & Condensed Matter Phys, Box 516, SE-75120 Uppsala, Sweden..
    Lindblad, Andreas
    Uppsala Univ, Dept Phys & Astron, Div Mol & Condensed Matter Phys, Box 516, SE-75120 Uppsala, Sweden..
    Giangrisostomi, Erika
    Helmholtz Zentrum Berlin GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Ovsyannikov, Ruslan
    Helmholtz Zentrum Berlin GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Liu, Jianhua
    Beihang Univ, Sch Mat Sci & Engn, Beijing 100191, Peoples R China..
    Rensmo, Håkan
    Uppsala Univ, Dept Phys & Astron, Div Mol & Condensed Matter Phys, Box 516, SE-75120 Uppsala, Sweden..
    Gardner, James M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Johansson, Erik M. J.
    Uppsala Univ, Phys Chem, Dept Chem Angstrom, S-75120 Uppsala, Sweden..
    Probing and Controlling Surface Passivation of PbS Quantum Dot Solid for Improved Performance of Infrared Absorbing Solar Cells2019In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 31, no 11, p. 4081-4091Article in journal (Refereed)
    Abstract [en]

    Surface properties of colloidal quantum dots (CQDs) are critical for the transportation and recombination of the photoinduced charge carrier in CQD solar cells, therefore dominating the photovoltaic performance. Herein, PbS CQD passivated using liquid-state ligand exchange (LSLX) and solid-state ligand exchange (SSLX) strategies are in detail investigated using photoelectron spectroscopy (PES), and solar cell devices are prepared to understand the link between the CQD surface properties and the solar cell function. PES using different energies in the soft and hard Xray regime is applied to study the surface and bulk properties of the CQDs, and the results show more effective surface passivation of the CQDs prepared with the LSLX strategy and less formation of lead-oxide. The CQD solar cells prepared with LSLX strategy show higher performance, and the photoelectric measurements suggest that the recombination of photoinduced charges is reduced for the solar cell prepared with the LSLX approach. Meanwhile, the fabricated solar cells exhibit good stability. This work provides important insights into how to fine-tune the CQD surface properties by improving the CQD passivation, and how this is linked to further improvements of the device photovoltaic performance.

  • 138. Zhao, Pei
    et al.
    Li, Xuping
    Baryshnikov, Glib
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bogdan Khmelnitsky National University, Ukraine.
    Wu, Bin
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University, Russian Federation.
    Zhang, Junji
    Zhu, Liangliang
    One-step solvothermal synthesis of high-emissive amphiphilic carbon dots via rigidity derivation2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 5, p. 1323-1329Article in journal (Refereed)
    Abstract [en]

    In nanoscience, amphiphilic carbon dots (ACDs) are of great importance due to their excellent transferability for application in biological sensing, imaging and labelling. However, facile synthetic strategies are still limited, especially for obtaining high-emissive ACDs. Since the development of a high-emissive feature is strongly desired for improving the practical resolution in vivo, here we report a chemical strategy that uses rigid molecules to straightforwardly construct amphiphilic carbon dots (ACDs) with high luminescence quantum yields (QYs). By using 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate (HATU), a typical coplanar compound, as the only precursor, well-defined ACDs were prepared via a one-step solvothermal process which exhibited a superior QY of up to 29%, largely superior to those prepared from precursors with less rigid structures. The effect can be mainly attributed to a significant suppression of the competition of non-radiative decay through rigidity derivation. Metal ionic doping during the synthesis resulted in a further improvement of the crystallinity and monodispersity of the materials, with retention of the high-emissive ability. This high-emissive photoluminescence behavior of the ACDs is accompanied with an excitation-wavelength dependence, a high biocompatibility and a low toxicity, which together make the ACDs advantageous for application in multi-channel bioimaging.

  • 139.
    Zhao, Xin
    et al.
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China.;Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Guangzhou 510530, Guangdong, Peoples R China.;Univ Arizona, Coll Pharm, Dept Pharmacol & Toxicol, Tucson, AZ 85721 USA..
    Li, Runfeng
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China..
    Zhou, Yang
    AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Biotechnol, Div Theoret Chem & Biol, SE-10044 Stockholm, Sweden..
    Xiao, Mengjie
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China.;Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Guangzhou 510530, Guangdong, Peoples R China..
    Ma, Chunlong
    Univ Arizona, Coll Pharm, Dept Pharmacol & Toxicol, Tucson, AZ 85721 USA.;Univ Arizona, BIO5 Inst, Tucson, AZ 85721 USA..
    Yang, Zhongjin
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China..
    Zeng, Shaogao
    Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Guangzhou 510530, Guangdong, Peoples R China..
    Du, Qiuling
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China..
    Yang, Chunguang
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China..
    Jiang, Haiming
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China..
    Hu, Yanmei
    Univ Arizona, Coll Pharm, Dept Pharmacol & Toxicol, Tucson, AZ 85721 USA.;Univ Arizona, BIO5 Inst, Tucson, AZ 85721 USA..
    Wang, Kefeng
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China..
    Mok, Chris Ka Pun
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China.;Univ Hong Kong, HKU Li Ka Shing Fac Med, Sch Publ Hlth, HKU Pasteur Res Pole, 5 Sassoon Rd, Hong Kong, Peoples R China..
    Sun, Ping
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China..
    Dong, Jianghong
    Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Guangzhou 510530, Guangdong, Peoples R China..
    Cui, Wei
    Wang, Jun
    Univ Arizona, Coll Pharm, Dept Pharmacol & Toxicol, Tucson, AZ 85721 USA.;Univ Arizona, BIO5 Inst, Tucson, AZ 85721 USA..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Yang, Zifeng
    Guangzhou Med Univ, Guangzhou Inst Resp Hlth, Affiliated Hosp 1, Natl Clin Res Ctr Resp Dis,State Key Lab Resp Dis, Guangzhou 510120, Guangdong, Peoples R China..
    Hu, Wenhui
    Guangzhou Med Univ, Sch Pharmaceut Sci, Key Lab Mol Target & Clin Pharmacol, State Key Lab Resp Dis, Guangzhou 511436, Guangdong, Peoples R China.;Guangzhou Med Univ, Affiliated Hosp 5, Guangzhou 511436, Guangdong, Peoples R China.;Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Guangzhou 510530, Guangdong, Peoples R China..
    Discovery of Highly Potent Pinanamine-Based Inhibitors against Amantadine- and Oseltamivir-Resistant Influenza A Viruses2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 12, p. 5187-5198Article in journal (Refereed)
    Abstract [en]

    Influenza pandemic is a constant major threat to public health caused by influenza A viruses (IAVs). IAVs are subcategorized by the surface proteins hemagglutinin (HA) and neuraminidase (NA), in which they are both essential targets for drug discovery. While it is of great concern that NA inhibitor oseltamivir resistant strains are frequently identified from human or avian influenza virus, structural and functional characterization of influenza HA has raised hopes for new antiviral therapies. In this study, we explored a structure-activity relationship (SAR) of pinanamine-based antivirals and discovered a potent inhibitor M090 against amantadine-resistant viruses, including the 2009 H1N1 pandemic strains, and oseltamivir-resistant viruses. Mechanism of action studies, particularly hemolysis inhibition, indicated that M090 targets influenza HA and it occupied a highly conserved pocket of the HA(2) domain and inhibited virus-mediated membrane fusion by "locking" the bending state of HA(2) during the conformational rearrangement process. This work provides new binding sites within the HA protein and indicates that this pocket may be a promising target for broad-spectrum anti-influenza A drug design and development.

  • 140.
    Zhen, Junfeng
    et al.
    Univ Sci & Technol China, Dept Astron, CAS Key Lab Res Galaxies & Cosmol, Hefei 230026, Anhui, Peoples R China.;Univ Sci & Technol China, Sch Astron & Space Sci, Hefei 230026, Anhui, Peoples R China..
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tielens, Alexander G. G. M.
    Leiden Univ, Leiden Observ, POB 9513, NL-2300 RA Leiden, Netherlands..
    Laboratory Photochemistry of Pyrene Clusters: An Efficient Way to Form Large PAHs2018In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 863, no 2, article id 128Article in journal (Refereed)
    Abstract [en]

    In this work, we study the photodissociation processes of small PAH clusters (e.g., pyrene clusters). The experiments are carried out using a quadrupole ion trap in combination with time-of-flight (QIT-TOF) mass spectrometry. The results show that pyrene clusters are converted into larger PAHs under the influence of a strong radiation field. Specifically, pyrene dimer cations (e.g., [C16H10-C16H9](+) or C32H19 (+)), will photodehydrogenate and photo-isomerize to fully aromatic cations (PAHs) (e.g., C32H16 (+)) with laser irradiation. The structure of new formed PAHs and the dissociation energy for these reaction pathways are investigated with quantum chemical calculations. These studies provide a novel efficient evolution routes for the formation of large PAHs in the interstellar medium in a bottom-up process that will counteract the top-down conversion of large PAHs into rings and chains, and provide a reservoir of large PAHs that can be converted into C-60 and other fullerenes and large carbon cages.

  • 141.
    Zhou, Yang
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Structural Mechanics.
    Hussain, M.
    Guanglin, Kuang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhang, J.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Mechanistic insights into peptide and ligand binding of the ATAD2-bromodomain via atomistic simulations disclosing a role of induced fit and conformational selection2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 36, p. 23222-23232Article in journal (Refereed)
    Abstract [en]

    ATAD2 has emerged as a promising bromodomain (BRD)-containing therapeutic drug target in multiple human cancers. However, recent druggability assessment studies predicted ATAD2's BRD as a target 'difficult to drug' because its binding pocket possesses structural features that are unfeasible for ligand binding. Here, by using all-atom molecular dynamics simulations and an advanced metadynamics method, we demonstrate a dynamic view of the binding pocket features which can hardly be obtained from the "static" crystal data. The most important features disclosed from our simulation data, include: (1) a distinct 'open-to-closed' conformational switch of the ZA loop region in the context of peptide or ligand binding, akin to the induced fit mechanism of molecular recognition, (2) a dynamic equilibrium of the BC loop "in" and "out" conformations, highlighting a role in the conformational selection mechanism for ligand binding, and (3) a new binding region identified distal to the histone-binding pocket that might have implications in bromodomain biology and in inhibitor development. Moreover, based on our simulation results, we propose a model for an "auto-regulatory" mechanism of ATAD2's BRD for histone binding. Overall, the results of this study will not only have implications in bromodomain biology but also provide a theoretical basis for the discovery of new ATAD2's BRD inhibitors.

  • 142.
    Zhou, Yunyun
    et al.
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200433, Peoples R China..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Li, Xuping
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200433, Peoples R China..
    Zhu, Mingjie
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200433, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Zhu, Liangliang
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200433, Peoples R China..
    Anti-Kasha's Rule Emissive Switching Induced by Intermolecular H-Bonding2018In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 30, no 21, p. 8008-8016Article in journal (Refereed)
    Abstract [en]

    The exploration of emission pathways from high-excited states in organic luminogens has recently become prosperous owing to improved possibilities to study so-called anti-Kasha's rule emission with the potential of improving the luminescent quantum efficiency. However, emission pathway switching among different high-excited states has rarely been addressed through external control. We here present a rational design and synthesis of a novel azulene-based emitter to achieve a responsive control of its anti-Kasha's rule emissive switching. The emitter initially gives rise to an S-3-to-S-0 dominant emission as indicated by our experimental and theoretical studies. On this basis, it can be toggled into an S-2-to-S-0 dominant emission upon the H-bond formation between the triformyl groups and water molecules. Such a process, which originates from the H-bonding regulated distribution of excited state energy, is accompanied by a remarkable fluorescent color conversion and a significant improvement of the fluorescent quantum yield in the azulene family. Moreover, a reversible emissive switching in doped films was observed to depend on a solid-state H-bond tuning process with moisture sensitivity. These results may provide new insight for building advanced chemical systems for visualized sensing with high distinguishability.

  • 143.
    Zhovtobriukh, Iurii
    et al.
    Stockholm Univ, FYSIKUM, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Pettersson, Lars G. M.
    Stockholm Univ, FYSIKUM, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden..
    X-ray absorption spectrum simulations of hexagonal ice2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 3, article id 034501Article in journal (Refereed)
    Abstract [en]

    We calibrate basis sets and performance of two theoretical approaches to compute X-ray absorption spectra (XAS) of condensed water by comparison to experiments on hexagonal ice Ih. We apply both the transition-potential half-core-hole approach and the complex polarization propagator using four different models of the crystal with increasing oxygen and proton disorder but find poor agreement with experiments. We note that there are large variations in experimental spectra depending on detection mode and how the ice samples were prepared, which leads us to critically investigate what structures were actually prepared and measured in each case. This is done by using a Monte Carlo-based fitting technique which fits the spectra based on a library of precomputed spectra and assigns weights to contributions from different model structures. These are then used to generate O-O and O-H radial distribution functions and tetrahedrality parameters associated with each of the measured spectra. We find that all spectra are associated with sharp peaks at the oxygen positions in the perfect lattice, but with significant disorder around these positions. We suggest that presently available XAS of hexagonal ice are not fully representative of the perfect crystalline lattice, but contain varying amounts of defects and possible contributions from low-density amorphous ice.

  • 144.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Guanglin, Kuang
    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. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Nordberg, Agneta
    Karolinska Univ Hosp, Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res,Clin Geriatr Neo & Theme Aging, S-14183 Huddinge, Sweden..
    Långström, Bengt
    Uppsala Univ, Phys Organ Chem, Dept Chem, BMC, S-75123 Uppsala, Sweden..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Free Energy Profile for Penetration of Pittsburgh Compound-B into the Amyloid beta Fibril2019In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 10, no 3, p. 1783-1790Article in journal (Refereed)
    Abstract [en]

    The amyloid beta (A beta) fibril is a hallmark of Alzheimer's disease (AD) and has therefore served as an important target for early diagnosis of AD. The Pittsburgh Compound-B (PiB) is one of the most famous positron emission tomography (PET) tracers commonly used for in vivo detection of A beta fibrils. Many theoretical studies have predicted the existence of various core binding sites with different microenvironments for probes binding to the A beta fibril. However, little attention has been devoted to how the probes actually penetrate into the different core binding sites. In this study, an integrated molecular modeling scheme is used to study the penetration of PiB into the core binding sites of the A beta(1-42) fibril structure recently obtained by cryogenic electron microscopy. We find that there are two core binding sites for PiB with dramatic differences in cavity size and microenvironment properties, and furthermore that the penetration of PiB into site-1 is energetically prohibitive, whereas the penetration into site 2 is much more favorable. Therefore, the binding capacity at site-2 may be larger than that at site-1 despite its lower binding affinity. Our results thus suggest that site-2 may be a major binding site for PiB binding to A beta fibril and emphasize the importance to adopt a full dynamical picture when studying tracer fibril binding problems in general, something that in turn can be used to guide the development of tracers with higher affinity and selectivity for the A beta fibril.

  • 145.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Wang, Yong
    Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    An Efficient Strategy for the Estimation of Rare Event Transition Times in Biomolecular SystemsManuscript (preprint) (Other academic)
    Abstract [en]

    Studies of kinetics in biological systems are important for understanding functions of biomolecules and can provide valuable information for drug discovery. However, how to obtain the kinetics closely related to a rare event occurring in a biomolecular system from conventional unbiased molecular dynamics (MD) simulations remains a big challenge. Recently, an enhanced sampling method, namely infrequent metadynamics (InMetaD), has been developed and has the capability to recover the unbiased transition time from metadynamic runs. However, in this method a bias potential is deposited to the system at a low frequency, which often makes most of the computational time spend in waiting for the simulated system escaping from the initial state. Here we propose a strategy to achieve the same goal as InMetaD with increased efficiency. In this strategy, we first accelerate the occurring of a rare event using metadynamics simulations with a high bias deposition frequency, and subsequently restart the simulations at a time point before the rare event occurs, but with a low bias deposition frequency. Through combining these simulation data, the unbiased transition time can be recovered in the same way as in InMetaD. We applied this strategy to the studies of three systems including the conformational change of a small peptide, unfolding of a protein, and unbinding of an intrinsically disordered protein from its target. We show that our strategy can improve the efficiency in estimating the unbiased transition times in a very convenient way.

  • 146.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Zhou, Yang
    KTH, School of Engineering Sciences (SCI), Mechanics, Structural Mechanics.
    Wang, Yong
    Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen.
    Guanglin, Kuang
    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).
    Wu, Junchen
    Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Free Energy Profile and Kinetics for Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2Manuscript (preprint) (Other academic)
    Abstract [en]

    Intrinsically disordered proteins (IDPs) exert their functions by binding to partner proteins via a complex process that includes coupled folding and binding. Motivated by that inhibiting the binding of the IDP p53 to its partner MDM2 has become a promising strategy for drug design and that understanding of this process poses a most significant challenging task, we present an atomistic level simulation of the coupled folding and binding process linking the IDP p53 to MDM2. Using bias-exchange metadynamics (BE-MetaD) and infrequent metadynamics (InMetaD) we estimate the binding free energy, the unbinding rate and the binding rate. By analyzing the stable intermediates, we uncover the role of nonnative interactions played in the p53-MDM2 binding/unbinding process. We use a three-state model to describe the whole binding/unbinding process and to obtain the corresponding rate constants. Our work shows that the binding of p53 favors an induced fit mechanism which proceeds in a stepwise fashion. In general, InMetaD gave consistent results with BE-MetaD in terms of binding mechanism and intermediates, proving the robustness of our studies of the p53-MDM2 system using metadynamics. The results contribute to the in-depth understanding for the coupled folding and binding process that is needed for the design of MDM2 inhibitors.

  • 147.
    Zou, Rongfeng
    et al.
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Inst Fine Chem, Shanghai 200237, Peoples R China.;KTH Royal Inst Technol, Div Theoret Chem & Biol, Sch Biotechnol, SE-10691 Stockholm, Sweden..
    Zhu, Xiaomin
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Inst Fine Chem, Shanghai 200237, Peoples R China..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wu, Junchen
    East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Sch Chem & Mol Engn, Inst Fine Chem, Shanghai 200237, Peoples R China.;Univ Calif Berkeley, Dept Chem & Biomol Engn, 476 Stanley Hall, Berkeley, CA 94720 USA..
    Landry, Markita P.
    Univ Calif Berkeley, Dept Chem & Biomol Engn, 476 Stanley Hall, Berkeley, CA 94720 USA.;Chan Zuckerberg Biohub, San Francisco, CA USA.;Univ Calif Berkeley, Calif Inst Quantitat Biosci Qb3, Berkeley, CA 94720 USA..
    Activity of Antimicrobial Peptide Aggregates Decreases with Increased Cell Membrane Embedding Free Energy Cost2018In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 57, no 18, p. 2606-2610Article in journal (Refereed)
    Abstract [en]

    Antimicrobial peptides (AMPs) are a promising alternative to antibiotics for mitigating bacterial infections, in light of increasing bacterial resistance to antibiotics. However, predicting, understanding, and controlling the antibacterial activity of AMPs remain a significant challenge. While peptide intramolecular interactions are known to modulate AMP antimicrobial activity, peptide intermolecular interactions remain elusive in their impact on peptide bioactivity. Herein, we test the relationship between AMP intermolecular interactions and antibacterial efficacy by controlling AMP intermolecular hydrophobic and hydrogen bonding interactions. Molecular dynamics simulations and Gibbs free energy calculations in concert with experimental assays show that increasing intermolecular interactions via interpeptide aggregation increases the energy cost for the peptide to embed into the bacterial cell membrane, which in turn decreases the AMP antibacterial activity. Our findings provide a route for predicting and controlling the antibacterial activity of AMPs against Gram-negative bacteria via reductions of intermolecular AMP interactions.

  • 148.
    Ågren, Hans
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Harczuk, Ignat
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Decomposition of molecular properties2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 5, p. 2251-2270Article in journal (Refereed)
    Abstract [en]

    We review recent work on property decomposition techniques using quantum emical methods and discuss some topical applications in terms of antum mechanics-molecular mechanics calculations and the constructing properties of large molecules and clusters. Starting out from the -called LoProp decomposition scheme [Gagliardi et al., J. Chem. Phys., 04, 121, 4994] for extracting atomic and inter-atomic contributions to lecular properties we show how this method can be generalized to calized frequency-dependent polarizabilities, to localized perpolarizabilities and to localized dispersion coefficients. Some plications of the generalized decomposition technique are reviewed - lculations of frequency-dependent polarizabilities, Rayleigh attering of large clusters, and calculations of hyperpolarizabilities proteins.

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