@misc{13388, abstract = {The Inside Cover picture illustrates the fluorescent properties of a gold nanocluster functionalized with several copies of a red-emitting merocyanine (image by Ella Marushchenko). The red fluorescence can be turned on and off reversibly by using an external stimulus.}, author = {Udayabhaskararao, T. and Kundu, Pintu K. and Ahrens, Johannes and Klajn, Rafal}, booktitle = {ChemPhysChem}, issn = {1439-7641}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {12}, pages = {1711--1711}, publisher = {Wiley}, title = {{Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016)}}, doi = {10.1002/cphc.201600480}, volume = {17}, year = {2016}, } @article{13389, abstract = {Au25 nanoclusters functionalized with a spiropyran molecular switch are synthesized via a ligand-exchange reaction at low temperature. The resulting nanoclusters are characterized by optical and NMR spectroscopies as well as by mass spectrometry. Spiropyran bound to nanoclusters isomerizes in a reversible fashion when exposed to UV and visible light, and its properties are similar to those of free spiropyran molecules in solution. The reversible photoisomerization entails the modulation of fluorescence as well as the light-controlled self-assembly of nanoclusters.}, author = {Udayabhaskararao, T. and Kundu, Pintu K. and Ahrens, Johannes and Klajn, Rafal}, issn = {1439-7641}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {12}, pages = {1805--1809}, publisher = {Wiley}, title = {{Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters}}, doi = {10.1002/cphc.201500897}, volume = {17}, year = {2016}, } @article{10376, abstract = {Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation.}, author = {Šarić, Anđela and Michaels, Thomas C. T. and Zaccone, Alessio and Knowles, Tuomas P. J. and Frenkel, Daan}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {physical and theoretical chemistry, general physics and astronomy}, number = {21}, publisher = {American Institute of Physics}, title = {{Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation}}, doi = {10.1063/1.4965040}, volume = {145}, year = {2016}, } @article{10380, abstract = {Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.}, author = {Wirnsberger, P. and Fijan, D. and Šarić, Anđela and Neumann, M. and Dellago, C. and Frenkel, D.}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {physical and theoretical chemistry, general physics and astronomy}, number = {22}, publisher = {American Institute of Physics}, title = {{Non-equilibrium simulations of thermally induced electric fields in water}}, doi = {10.1063/1.4953036}, volume = {144}, year = {2016}, } @article{13397, abstract = {Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light.}, author = {Singh, Gurvinder and Chan, Henry and Udayabhaskararao, T. and Gelman, Elijah and Peddis, Davide and Baskin, Artem and Leitus, Gregory and Král, Petr and Klajn, Rafal}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, pages = {403--421}, publisher = {Royal Society of Chemistry}, title = {{Magnetic field-induced self-assembly of iron oxide nanocubes}}, doi = {10.1039/c4fd00265b}, volume = {181}, year = {2015}, } @article{13398, author = {Sun, Yugang and Scarabelli, Leonardo and Kotov, Nicholas and Tebbe, Moritz and Lin, Xiao-Min and Brullot, Ward and Isa, Lucio and Schurtenberger, Peter and Moehwald, Helmuth and Fedin, Igor and Velev, Orlin and Faivre, Damien and Sorensen, Christopher and Perzynski, Régine and Chanana, Munish and Li, Zhihai and Bresme, Fernando and Král, Petr and Firlar, Emre and Schiffrin, David and Souza Junior, Joao Batista and Fery, Andreas and Shevchenko, Elena and Tarhan, Ozgur and Alivisatos, Armand Paul and Disch, Sabrina and Klajn, Rafal and Ghosh, Suvojit}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, pages = {463--479}, publisher = {Royal Society of Chemistry}, title = {{Field-assisted self-assembly process: General discussion}}, doi = {10.1039/c5fd90041g}, volume = {181}, year = {2015}, } @article{14018, abstract = {The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations.}, author = {Baykusheva, Denitsa Rangelova and Kraus, Peter M. and Zhang, Song Bin and Rohringer, Nina and Wörner, Hans Jakob}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, pages = {113--132}, publisher = {Royal Society of Chemistry}, title = {{The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics}}, doi = {10.1039/c4fd00018h}, volume = {171}, year = {2014}, } @article{14019, abstract = {The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.}, author = {Vasilatou, K. and Michaud, J. M. and Baykusheva, Denitsa Rangelova and Grassi, G. and Merkt, F.}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {6}, publisher = {AIP Publishing}, title = {{The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra}}, doi = {10.1063/1.4890744}, volume = {141}, year = {2014}, } @article{8470, abstract = {Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).}, author = {Huber, Matthias and Hiller, Sebastian and Schanda, Paul and Ernst, Matthias and Böckmann, Anja and Verel, René and Meier, Beat H.}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {5}, pages = {915--918}, publisher = {Wiley}, title = {{A proton-detected 4D solid-state NMR experiment for protein structure determination}}, doi = {10.1002/cphc.201100062}, volume = {12}, year = {2011}, } @article{10128, abstract = {An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand.}, author = {Šarić, Anđela and Hrenar, T. and Mališ, M. and Došlić, N.}, issn = {1463-9076}, journal = {Physical Chemistry Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {18}, pages = {4678--4685}, publisher = {Royal Society of Chemistry }, title = {{Quantum mechanical study of secondary structure formation in protected dipeptides}}, doi = {10.1039/b923041f}, volume = {12}, year = {2010}, } @article{10392, abstract = {Protonated formylmetallocenes [M(C5H5)(C5H4-CHOH)]+ (M = Fe, Ru) and their isomers have been studied at the BP86 and B3LYP levels of density functional theory. Oxygen-protonated isomers are the most stable forms in each case, with a plethora of ring- or metal-protonated species at least ca. 14 and 10 kcal/mol higher in energy for M = Fe and Ru, respectively. The computed rotational barriers around the C−C bond connecting the cyclopentadienyl and protonated formyl moieties, ca. 18 kcal/mol, are indicative of substantial conjugation between these moieties. Some of the ring- and iron-protonated species are models for possible intermediates in Friedel–Crafts acylation of ferrocene, and the computations provide further evidence that exo attack is clearly favored over endo attack of the electrophile in this reaction. The structures of the most stable mono- and diprotonated formylferrocenes are corroborated by the good agreement between GIAO-B3LYP-computed and experimental NMR chemical shifts.}, author = {Šarić, Anđela and Vrček, Valerije and Bühl, Michael}, issn = {1520-6041}, journal = {Organometallics}, keywords = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry}, number = {3}, pages = {394--401}, publisher = {American Chemical Society}, title = {{Density functional study of protonated formylmetallocenes}}, doi = {10.1021/om700916f}, volume = {27}, year = {2008}, } @article{13430, abstract = {Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.}, author = {Fialkowski, Marcin and Bishop, Kyle J. M. and Klajn, Rafal and Smoukov, Stoyan K. and Campbell, Christopher J. and Grzybowski, Bartosz A.}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, keywords = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry}, number = {6}, pages = {2482--2496}, publisher = {American Chemical Society}, title = {{Principles and implementations of dissipative (dynamic) self-assembly}}, doi = {10.1021/jp054153q}, volume = {110}, year = {2006}, }