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Mast F, Hielscher MM, Wirtanen T, Erichsen M, Gauss J, Diezemann G, Waldvogel SR. Choice of the Right Supporting Electrolyte in Electrochemical Reductions: A Principal Component Analysis. J Am Chem Soc 2024. [PMID: 38785120 DOI: 10.1021/jacs.4c00910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
We present an analysis of a set of molecular, electrical, and electronic properties for a large number of the cations of quaternary ammonium salts usually employed as supporting electrolytes in cathodic reduction reactions. The goal of the present study is to define a measure for the quality of a supporting electrolyte in terms of the yield of the reaction considered. We performed a principal component analysis using the normalized values of the properties in order to lower the number of relevant reaction coordinates and find that the integral variance of 13 properties can well be represented by three principal components. The yield of the electrochemical hydrodimerization of acrylonitrile employing different quaternary ammonium salts as supporting electrolytes was determined in a series of experiments. We found only a very weak correlation between the yield and the values of the properties but a strong correlation between the yield and the values of the most important principal component. Very similar results are obtained for two further existing systematic experimental studies of the impact of the supporting electrolyte on the yield of cathodic reductions. For all three example reactions, a supervised regression using the two most important principal components as variables yields excellent values for the coefficients of determination. For comparison, we also applied our methodology to sets of purely structure-based features that are usually employed in cheminformatics and obtained results of almost similar quality. We therefore conjecture that our methodology in combination with a small number of experiments can be used to predict the yield of a given cathodic reduction on the basis of the properties of the supporting electrolyte.
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Affiliation(s)
- Florian Mast
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Maximilian M Hielscher
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Tom Wirtanen
- Chemical and Polymer Synthesis, VTT Technical Research Centre of Finland Ltd, Box 1000, FI-02044 Espoo, Finland
| | - Max Erichsen
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Siegfried R Waldvogel
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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2
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East NR, Naumann R, Förster C, Ramanan C, Diezemann G, Heinze K. Oxidative two-state photoreactivity of a manganese(IV) complex using near-infrared light. Nat Chem 2024; 16:827-834. [PMID: 38332331 DOI: 10.1038/s41557-024-01446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024]
Abstract
Highly reducing or oxidizing photocatalysts are a fundamental challenge in photochemistry. Only a few transition metal complexes with Earth-abundant metal ions have so far advanced to excited state oxidants. All these photocatalysts require high-energy light for excitation, and their oxidizing power has not been fully exploited due to energy dissipation before reaching the photoactive state. Here we demonstrate that the complex [Mn(dgpy)2]4+, based on Earth-abundant manganese and the tridentate 2,6-diguanidylpyridine ligand (dgpy), evolves to a luminescent doublet ligand-to-metal charge transfer (2LMCT) excited state (1,435 nm, 0.86 eV) with a lifetime of 1.6 ns after excitation with low-energy near-infrared light. This 2LMCT state oxidizes naphthalene to its radical cation. Substrates with extremely high oxidation potentials up to 2.4 V enable the [Mn(dgpy)2]4+ photoreduction via a high-energy quartet 4LMCT excited state with a lifetime of 0.78 ps, proceeding via static quenching by the solvent. This process minimizes free energy losses and harnesses the full photooxidizing power, and thus allows oxidation of nitriles and benzene using Earth-abundant elements and low-energy light.
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Affiliation(s)
- Nathan R East
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Robert Naumann
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Christoph Förster
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Charusheela Ramanan
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Max-Planck-Institute for Polymer Research, Mainz, Germany
| | - Gregor Diezemann
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Katja Heinze
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany.
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3
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Diezemann G. Nonlinear response theory for Markov processes. IV. The asymmetric double-well potential model revisited. Phys Rev E 2022; 106:064122. [PMID: 36671146 DOI: 10.1103/physreve.106.064122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The dielectric response of noninteracting dipoles is discussed in the framework of the classical model of stochastic reorientations in an asymmetric double-well potential (ADWP). In the nonlinear regime, this model exhibits some pecularities in the static response. We find that the saturation behavior of the symmetric double-well potential model does not follow the Langevin function and only in the linear regime are the standard results recovered. If a finite asymmetry is assumed, then the nonlinear susceptibilities are found to change the sign at a number of characteristic temperatures that depend on the magnitude of the asymmetry, as has been observed earlier for the third-order and fifth-order responses. If the kinetics of the barrier crossing in the ADWP model is described as a two-state model, then we can give analytical expressions for the values of the characteristic temperatures. The results for the response obtained from a (numerical) solution of the Fokker-Planck equation for the Brownian motion in a model ADWP behaves very similarly to the two-state model for high barriers. For small barriers no clear-cut timescale separation between the barrier crossing process and the intrawell relaxation exists and the model exhibits a number of timescales. In this case, the frequency-dependent linear susceptibility at low temperatures is dominated by the fast intrawell transitions and at higher temperatures by the barrier crossing kinetics. We find that for nonlinear susceptibilities the latter process appears to be more important and the intrawell transitions play only a role at the lowest temperatures.
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Affiliation(s)
- Gregor Diezemann
- Department Chemie, Johannes Gutenberg Universität Mainz, 55128 Mainz, Germany
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4
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Oestereich M, Gauss J, Diezemann G. Force probe simulations using an adaptive resolution scheme. J Phys Condens Matter 2021; 33:194005. [PMID: 33690183 DOI: 10.1088/1361-648x/abed18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute are described in a coarse-grained manner. We use the adaptive resolution scheme (AdResS) that has very successfully been applied to various examples of equilibrium simulations. We perform FPMD simulations using AdResS on a well studied system, a dimer formed from mechanically interlocked calixarene capsules. The results of the multiscale simulations are compared to all-atom simulations of the identical system and we observe that the size of the region in which atomistic resolution is required depends on the pulling velocity, i.e. the particular non-equilibrium situation. For large pulling velocities a larger all atom region is required. Our results show that multiscale simulations can be applied also in the strong non-equilibrium situations that the system experiences in FPMD simulations.
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Affiliation(s)
- Marco Oestereich
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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5
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Schäfer K, Diezemann G. Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1743886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ken Schäfer
- Institut für Physikalische Chemie, Universität Mainz, Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Mainz, Germany
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Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020; 59:18591-18598. [PMID: 32543728 PMCID: PMC7589243 DOI: 10.1002/anie.202004522] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/29/2020] [Indexed: 12/16/2022]
Abstract
The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.
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Affiliation(s)
- Ken Schäfer
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Hima Bindu Kolli
- Department of Physics and AstronomyThe University of SheffieldWestern BankSheffieldS10 2TNUK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Gregor Diezemann
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Jürgen Gauss
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Giuseppe Milano
- Department of Organic Materials ScienceYamagata University4-3-16 JonanYonezawaYamagata-ken992-8510Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
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7
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Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ken Schäfer
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Hima Bindu Kolli
- Department of Physics and Astronomy The University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Gregor Diezemann
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Jürgen Gauss
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Giuseppe Milano
- Department of Organic Materials Science Yamagata University 4-3-16 Jonan Yonezawa Yamagata-ken 992-8510 Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
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Kato T, Schäfer K, Jaschonek S, Gauss J, Diezemann G. Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations. J Chem Phys 2019; 151:045102. [DOI: 10.1063/1.5111717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Takashi Kato
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Stefan Jaschonek
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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9
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Jaschonek S, Schäfer K, Diezemann G. Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules. J Phys Chem B 2019; 123:4688-4694. [PMID: 31070922 DOI: 10.1021/acs.jpcb.9b02676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present force probe molecular dynamics simulations of dimers of interlocked calixarene nanocapsules and study the impact of structural details and solvent properties on the mechanical unfolding pathways. The system consists of two calixarene "cups" that form a catenane structure via interlocked aliphatic loops of tunable length. The dimer shows reversible rebinding, and the kinetics of the system can be understood in terms of a two-state model for shorter loops (≤14 CH2 units) and a three-state model for longer loops (≥15 CH2 units). The various conformational states of the dimer are stabilized by networks of hydrogen bonds, the mechanical susceptibility of which can be altered by changing the polarity and proticity of the solvent. The variation of the loop length and the solvent properties in combination with changes in the pulling protocol allows to tune the reversibility of the conformational transitions.
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Affiliation(s)
- Stefan Jaschonek
- Institut für Physikalische Chemie , Universität Mainz , Duesbergweg 10-14 , 55128 Mainz , Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie , Universität Mainz , Duesbergweg 10-14 , 55128 Mainz , Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie , Universität Mainz , Duesbergweg 10-14 , 55128 Mainz , Germany
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Kolli HB, de Nicola A, Bore SL, Schäfer K, Diezemann G, Gauss J, Kawakatsu T, Lu ZY, Zhu YL, Milano G, Cascella M. Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment. J Chem Theory Comput 2018; 14:4928-4937. [DOI: 10.1021/acs.jctc.8b00466] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
| | - Antonio de Nicola
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
| | - Ken Schäfer
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - You-Liang Zhu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
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Knoch F, Schäfer K, Diezemann G, Speck T. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding. J Chem Phys 2018; 148:044109. [PMID: 29390802 DOI: 10.1063/1.5010435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
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Affiliation(s)
- Fabian Knoch
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Thomas Speck
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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Jaschonek S, Cascella M, Gauss J, Diezemann G, Milano G. Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers. Biochem Biophys Res Commun 2018; 498:327-333. [PMID: 29101041 DOI: 10.1016/j.bbrc.2017.10.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/29/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
The capability of coarse-grained models based on the MARTINI mapping to reproduce the gel-liquid phase transition in saturated and unsaturated model lipids was investigated. We found that the model is able to reproduce a lower critical temperature for 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with respect to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Nonetheless, the appearance of a gel phase for DOPC is strictly dependent on the intramolecular parameters chosen to model its molecular structure. In particular, we show that the bending angle at the coarse-grained bead corresponding to the unsaturated carbon-carbon bond acts as an order parameter determining the temperature of the phase transition. Structural analysis of the molecular dynamics simulations runs evidences that in the gel phase, the packing of the lipophilic tails of DOPC assume a different conformation than in the liquid phase. In the latter phase, the DOPC geometry resembles that of the relaxed free molecule. DPPC:DOPC mixtures show a single phase transition temperature, indicating that the observation of a phase separation between the two lipids requires the simulation of systems with sizes much larger than the ones used here.
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Affiliation(s)
- Stefan Jaschonek
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Postboks 1033 Blindern, N-0315 Oslo, Norway.
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Italy.
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Uribe L, Diezemann G, Gauss J, Morth JP, Cascella M. Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations. Chemistry 2018; 24:5074-5077. [PMID: 29243856 DOI: 10.1002/chem.201705159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 01/15/2023]
Abstract
We performed quantum-chemical calculations, ab initio molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and enhanced sampling metadynamics simulations to investigate the origin of metal specificity in isatin hydrolase from Labrenzia aggregata. The peculiar octahedral binding geometry of the Mn2+ ion in the Michaelis complex includes both the isatin substrate and the catalytic water within the first coordination shell of the cation. Our calculations show that the same arrangement of the ligands cannot be efficiently achieved in the presence of other small divalent metal cations such as Zn2+ or Cu2+ . On the contrary, bulkier alkaline-earth cations such as Mg2+ , which allow octahedral coordination, are not able to activate the catalytic water into the stronger OH- nucleophile required to attack the stable N-aryl-amide moiety of isatin.
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Affiliation(s)
- Lalita Uribe
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Graduate School Materials Science in Mainz, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128, Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jens Preben Morth
- Norwegian Centre for Molecular Medicine, Nordic EMBL Partnership, University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital, Ullevål, PO Box 4965 Nydalen, 0424, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular, Sciences, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
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Abstract
Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method and the force matching procedure, and find that both methodologies give similar results. The results of the FPMD simulations are compared to all-atom simulations of the same system and we find that differences between these simulations and the ones using the hybrid scheme are in a similar range as the differences obtained when using different atomistic force fields. Thus, a hybrid scheme yields qualitatively correct results in the strong non-equilibrium situation the system is experiencing in FPMD simulations.
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Affiliation(s)
- Ken Schäfer
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Marco Oestereich
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Abstract
The nonlinear response of stochastic models obeying a master equation is calculated up to fifth order in the external field, thus extending the third-order results obtained earlier [G. Diezemann, Phys. Rev. E 85, 051502 (2012)PLEEE81539-375510.1103/PhysRevE.85.051502]. For sinusoidal fields the 5ω component of the susceptibility is computed for the model of dipole reorientations in an asymmetric double well potential and for a trap model with a Gaussian density of states. For most realizations of the models a hump is found in the higher-order susceptibilities. In particular, for the asymmetric double well potential model there are two characteristic temperature regimes showing the occurrence of such a hump as compared to a single characteristic regime in the case of the third-order response. In the case of the trap model the results strongly depend on the variable coupled to the field. As for the third-order response, the low-frequency limit of the susceptibility plays a crucial role with respect to the occurrence of a hump. The findings are discussed in light of recent experimental results obtained for supercooled liquids. The differences found for the third-order and the fifth-order response indicate that nonlinear response functions might serve as a powerful tool to discriminate among the large number of existing models for glassy relaxation.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Jaschonek S, Diezemann G. Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness. J Chem Phys 2017; 146:124901. [DOI: 10.1063/1.4978678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Stefan Jaschonek
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Affiliation(s)
- Lalita Uribe
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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18
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Affiliation(s)
- Lalita Uribe
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Graduate
School Materials Science in Mainz, Universität Mainz, Staudinger Weg
9, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Abstract
We calculate the effect of a linear electron-phonon coupling on vibronic transitions of dye molecules of arbitrary complexity. With the assumption of known vibronic frequencies (for instance from quantum-chemical calculations), we give expressions for the absorption or emission lineshapes in a second-order cumulant expansion. We show that the results coincide with those obtained from generalized Redfield theory if one uses the time-local version of the theory and applies the secular approximation. Furthermore, the theory allows to go beyond the Huang-Rhys approximation and can be used to incorporate Dushinsky effects in the treatment of the temperature dependence of optical spectra. We consider both, a pure electron-phonon coupling independent of the molecular vibrations and a coupling bilinear in the molecular vibrational modes and the phonon coordinates. We discuss the behavior of the vibronic density of states for various models for the spectral density representing the coupling of the vibronic system to the harmonic bath. We recover some of the results that have been derived earlier for the spin-boson model and we show that the behavior of the spectral density at low frequencies determines the dominant features of the spectra. In case of the bilinear coupling between the molecular vibrations and the phonons we give analytical expressions for different spectral densities. The spectra are reminiscent of those obtained from the well known Brownian oscillator model and one finds a zero-phonon line and phonon-side bands located at vibrational frequencies of the dye. The intensity of the phonon-side bands diminishes with increasing vibrational frequencies and with decreasing coupling strength (Huang-Rhys factor). It vanishes completely in the Markovian limit where only a Lorentzian zero-phonon line is observed.
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Affiliation(s)
- Claudia Roos
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Andreas Köhn
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Stöttinger S, Hinze G, Diezemann G, Oesterling I, Müllen K, Basché T. Impact of local compressive stress on the optical transitions of single organic dye molecules. Nat Nanotechnol 2014; 9:182-186. [PMID: 24463364 DOI: 10.1038/nnano.2013.303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
The ability to mechanically control the optical properties of individual molecules is a grand challenge in nanoscience and could enable the manipulation of chemical reactivity at the single-molecule level. In the past, light has been used to alter the emission wavelength of individual molecules or modulate the energy transfer quantum yield between them. Furthermore, tensile stress has been applied to study the force dependence of protein folding/unfolding and of the chemistry and photochemistry of single molecules, although in these mechanical experiments the strength of the weakest bond limits the amount of applicable force. Here, we show that compressive stress modifies the photophysical properties of individual dye molecules. We use an atomic force microscope tip to prod individual molecules adsorbed on a surface and follow the effect of the applied force on the electronic states of the molecule by fluorescence spectroscopy. Applying a localized compressive force on an isolated molecule induces a stress that is redistributed throughout the structure. Accordingly, we observe reversible spectral shifts and even shifts that persist after retracting the microscope tip, which we attribute to transitions to metastable states. Using quantum-mechanical calculations, we show that these photophysical changes can be associated with transitions among the different possible conformers of the adsorbed molecule.
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Affiliation(s)
- Sven Stöttinger
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Gerald Hinze
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Ingo Oesterling
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Thomas Basché
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
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Affiliation(s)
- Thomas Schlesier
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
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Diezemann G. Nonlinear response theory for Markov processes: simple models for glassy relaxation. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 85:051502. [PMID: 23004762 DOI: 10.1103/physreve.85.051502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Indexed: 06/01/2023]
Abstract
The theory of nonlinear response for Markov processes obeying a master equation is formulated in terms of time-dependent perturbation theory for the Green's functions and general expressions for the response functions up to third order in the external field are given. The nonlinear response is calculated for a model of dipole reorientations in an asymmetric double well potential, a standard model in the field of dielectric spectroscopy. The static nonlinear response is finite with the exception of a certain temperature T_{0} determined by the value of the asymmetry. In a narrow temperature range around T_{0}, the modulus of the frequency-dependent cubic response shows a peak at a frequency on the order of the relaxation rate and it vanishes for both low frequencies and high frequencies. At temperatures at which the static response is finite (lower and higher than T_{0}), the modulus is found to decay monotonously from the static limit to zero at high frequencies. In addition, results of calculations for a trap model with a Gaussian density of states are presented. In this case, the cubic response depends on the specific dynamical variable considered and also on the way the external field is coupled to the kinetics of the model. In particular, a set of different dynamical variables that gives rise to identical shapes of the linear susceptibility and only to different temperature dependencies of the relaxation times is considered. It is found that the frequency dependence of the nonlinear response functions, however, strongly depends on the particular choice of the variables. The results are discussed in the context of recent theoretical and experimental findings regarding the nonlinear response of supercooled liquids and glasses.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welder-Weg 11, 55128 Mainz, Germany
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Schlesier T, Metzroth T, Janshoff A, Gauss J, Diezemann G. Reversible Hydrogen Bond Network Dynamics: Molecular Dynamics Simulations of Calix[4]arene-Catenanes. J Phys Chem B 2011; 115:6445-54. [DOI: 10.1021/jp2025522] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Schlesier
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welder-Weg 11, 55128 Mainz, Germany
| | - Thorsten Metzroth
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welder-Weg 11, 55128 Mainz, Germany
| | - Andreas Janshoff
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welder-Weg 11, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welder-Weg 11, 55128 Mainz, Germany
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28
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Diezemann G, Heuer A. Memory effects in the relaxation of the Gaussian trap model. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 83:031505. [PMID: 21517505 DOI: 10.1103/physreve.83.031505] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Indexed: 05/30/2023]
Abstract
We investigate the memory effect in a simple model for glassy relaxation, a trap model with a Gaussian density of states. In this model, thermal equilibrium is reached at all finite temperatures and we therefore can consider jumps from low to high temperatures in addition to the quenches usually considered in aging studies. We show that the evolution of the energy following the Kovacs protocol can approximately be expressed as a difference of two monotonously decaying functions and thus show the existence of a so-called Kovacs hump whenever these functions are not single exponentials. It is well established that the Kovacs effect also occurs in the linear response regime, and we show that most of the gross features do not change dramatically when large temperature jumps are considered. However, there is one distinguishing feature that only exists beyond the linear regime, which we discuss in detail. For the memory experiment with inverted temperatures, i.e., jumping up and then down again, we find a very similar behavior apart from an opposite sign of the hump.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, DE-55099 Mainz, Federal Republic of Germany
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Diezemann G, Schlesier T, Geil B, Janshoff A. Statistics of reversible bond dynamics observed in force-clamp spectroscopy. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:051132. [PMID: 21230462 DOI: 10.1103/physreve.82.051132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 09/06/2010] [Indexed: 05/30/2023]
Abstract
We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance, the unfolding and refolding of biomolecules, over many orders of magnitude due to the force dependence of the respective rates. We discuss two different kinds of counting statistics, the event counting usually employed in the statistical analysis of two-state kinetics and additionally the so-called cycle counting. While in the former case all transitions are counted, cycle counting means that we focus on one type of transitions. This might be advantageous in particular if the equilibrium constant is much larger or much smaller than unity because in these situations the temporal resolution of the experimental setup might not allow to capture all transitions of an event-counting analysis. We discuss how an analysis of FCS data for complex systems exhibiting dynamic disorder might be performed yielding information about the detailed force dependence of the transition rates and about the time scale of the dynamic disorder. In addition, the question as to which extent the kinetic scheme can be viewed as a Markovian two-state model is discussed.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Germany
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Rehwald C, Gnan N, Heuer A, Schrøder T, Dyre JC, Diezemann G. Aging effects manifested in the potential-energy landscape of a model glass former. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:021503. [PMID: 20866814 DOI: 10.1103/physreve.82.021503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Indexed: 05/29/2023]
Abstract
We present molecular dynamics simulations of the binary Kob-Andersen Lennard-Jones model, a model glass former, and consider the distributions of inherent energies and metabasins during aging. In addition to the typical protocol of performing a temperature jump from a high temperature to a low destination temperature, we consider the temporal evolution of the energy distributions after an "up-jump," i.e., from a low to a high temperature. In this case, for times on the order of the relaxation time the distribution of metabasin energies exhibits a transient two-peak structure for a small system (65 particles). For a large system (1000 particles) no such two-peak structure appears because it is averaged out. The simulations show, however, that a clear signal of an intermediate two-peak structure survives in the thermodynamic limit, namely that the inherent energy distribution width goes through a maximum at intermediate times for temperature up jumps; no such maximum is found for temperature down jumps. These findings are qualitatively rationalized in terms of a simple trap model with a Gaussian distribution of energies, assuming that the liquid may be divided into non-interacting regions each of which is described by a trap model.
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Affiliation(s)
- Christian Rehwald
- Institut für Physikalische Chemie, Universität Münster, Federal Republic of Germany
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Diehl FP, Roos C, Jankowiak HC, Berger R, Köhn A, Diezemann G, Basché T. Combined Experimental and Theoretical Study of the Vibronic Spectra of Perylenecarboximides. J Phys Chem B 2010; 114:1638-47. [DOI: 10.1021/jp909862x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Florian P. Diehl
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Claudia Roos
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Hans-Christian Jankowiak
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Robert Berger
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Andreas Köhn
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Gregor Diezemann
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Thomas Basché
- Johannes Gutenberg-University, Institute of Physical Chemistry, Jakob-Welder-Weg 11, D-55099 Mainz, Germany, and Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
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Janke M, Rudzevich Y, Molokanova O, Metzroth T, Mey I, Diezemann G, Marszalek PE, Gauss J, Böhmer V, Janshoff A. Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force. Nat Nanotechnol 2009; 4:225-229. [PMID: 19350031 DOI: 10.1038/nnano.2008.416] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 12/19/2008] [Indexed: 05/27/2023]
Abstract
The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins. Here, we report a molecular design based on oligo calix[4]arene catenanes-calixarene dimers held together by 16 hydrogen bridges-in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual nanocapsules. Experimental evidence, supported by molecular dynamics simulations, reveals the presence of an intermediate state involving the concerted rupture of the 16 hydrogen bridges. Stochastic modelling using a three-well potential under external load allows reconstruction of the energy landscape.
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Affiliation(s)
- Matthias Janke
- University of Mainz, Institute of Physical Chemistry, Jakob-Welder-Weg 11, 55128 Mainz, Germany
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Abstract
The problem of diffusive bond dissociation in a double well potential under application of an external force is scrutinized. We compute the probability distribution of rupture forces and present a detailed discussion of the influence of finite rebinding probabilities on the dynamic force spectrum. In particular, we focus on barrier crossing upon extension, i.e., under linearly increased load, and upon relaxation starting from completely separated bonds. For large loading rates the rupture force and the rejoining force depend on the loading rate in the expected manner determined by the shape of the potential. For small loading rates the mean forces obtained from pull and relax modes approach each other as the system reaches equilibrium. We investigate the dependence of the rupture force distributions and mean rupture forces on external parameters such as cantilever stiffness and influence of a soft linker. We find that depending on the implementation of a soft linker the equilibrium rupture force is either unaffected by the presence of the linker or changes in a predictable way with the linker compliance. Additionally, we show that it is possible to extract the equilibrium constant of the on and off rates from the determination of the equilibrium rupture forces.
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Affiliation(s)
- Gregor Diezemann
- Institut fur Physikalische Chemie, Universitat Mainz, Welderweg 11, 55099 Mainz, Germany.
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Abstract
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the statistical properties of the unbinding/rebinding events and analyze their mean number and their variance in the framework of simple kinetic models. In the calculations, we explicitly exploit the analogy to single molecule fluorescence and particularly between unbinding/rebinding and photon emission events. Whereas for two-state behavior Poisson or sub-Poisson statistics of the events is found, we show that for more general kinetic schemes also super-Poisson statistics can occur. Temporal fluctuations of the transition rates, a hallmark for the presence of dynamic disorder, should become experimentally accessible via the determination of the second moment of the event-number distribution.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Germany.
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Geil B, Diezemann G, Böhmer R. Stimulated echoes and two-dimensional nuclear magnetic resonance spectra for solids with simple line shapes. J Chem Phys 2008; 128:114506. [DOI: 10.1063/1.2838623] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Fückel B, Köhn A, Harding ME, Diezemann G, Hinze G, Basché T, Gauss J. Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies. J Chem Phys 2008; 128:074505. [DOI: 10.1063/1.2829531] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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37
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Fückel B, Hinze G, Diezemann G, Nolde F, Müllen K, Gauss J, Basché T. Flexibility of phenylene oligomers revealed by single molecule spectroscopy. J Chem Phys 2006; 125:144903. [PMID: 17042646 DOI: 10.1063/1.2355488] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex. On average we find a 22 degrees deviation from the linear gas phase geometry (T = 0 K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes).
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Affiliation(s)
- Burkhard Fückel
- Institut für Physikalische Chemie, Universität Mainz, Jakob-Welderweg 11, D-55099 Mainz, Germany
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Geil B, Diezemann G, Böhmer R. Correlation of primary relaxations and high-frequency modes in supercooled liquids. I. Theoretical background of a nuclear magnetic resonance experiment. Phys Rev E Stat Nonlin Soft Matter Phys 2006; 74:041504. [PMID: 17155062 DOI: 10.1103/physreve.74.041504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Indexed: 05/12/2023]
Abstract
The question regarding a possible correlation of the time scales of primary and secondary relaxations in supercooled liquids is formulated quantitatively. It is shown how this question can be answered using spin-lattice relaxation weighted stimulated-echo experiments, which are presented in an accompanying paper [A. Nowaczyk, B. Geil, G. Hinze, and R. Böhmer, Phys. Rev. E 74, 041505 (2006)]. General theoretical expressions relevant for the description of such experiments in the presence of correlation effects are derived. These expressions are analyzed by Monte Carlo integration for various correlation scenarios also including exchange processes, which are the hallmark of dynamical heterogeneity. The results of these numerical simulations provide clear signatures that allow one to distinguish uncorrelated from differently correlated cases. Since modified spin-lattice relaxation effects occur in the presence of nonexponential magnetization recovery, it is shown how to correct for them to a good approximation.
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Affiliation(s)
- B Geil
- Experimentelle Physik III and Interdisziplinäres Zentrum für Magnetische Resonanz, Universität Dortmund, 44221 Dortmund, Germany
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Böhmer R, Diezemann G, Geil B, Hinze G, Nowaczyk A, Winterlich M. Correlation of primary and secondary relaxations in a supercooled liquid. Phys Rev Lett 2006; 97:135701. [PMID: 17026046 DOI: 10.1103/physrevlett.97.135701] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Indexed: 05/12/2023]
Abstract
The widespread assumption that primary and secondary relaxations in glass-forming materials are independent processes is scrutinized using spin-lattice relaxation weighted stimulated-echo spectroscopy. This nuclear magnetic resonance (NMR) technique is simultaneously sensitive to the dynamics on well-separated time scales. For the deeply supercooled liquid sorbitol, which exhibits a strong secondary relaxation, the primary relaxation (that is observable using NMR) can be modified by suppressing the contributions of those subensembles which are characterized by relatively slow secondary relaxations. This is clear evidence for a correlation between primary and secondary relaxation times. In the disordered crystal orthocarborane high-frequency processes are absent and consequently no such modifications could be achieved.
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Affiliation(s)
- R Böhmer
- Experimentelle Physik III and Interdisziplinäres Zentrum für Magnetische Resonanz, Universität Dortmund, 44221 Dortmund, Germany
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Abstract
Several fluctuation-dissipation relations are investigated for a simple free-energy landscape model designed to describe the primary relaxation in supercooled liquids. The calculations of the response and of the correlation functions are performed for a quench from a high temperature to a low temperature. In the model, all dynamical quantities reach equilibrium after long times, but for times shorter than the re-equilibration time they do not exhibit time-translational invariance and the fluctuation-dissipation theorem is violated. Two measures for these violations are considered. One such measure is given by the slope in a plot of the integrated response versus the correlation function and another one by the so-called fluctuation-dissipation ratio. It is found that these measures do not coincide and furthermore are not independent of the dynamical variable considered in the calculation. We propose to determine the fluctuation-dissipation ratio experimentally via measurements of the deuteron spin-lattice relaxation rate and the dielectric loss.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, 55099 Mainz, Federal Republic of Germany.
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41
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Abstract
We propose a dynamic Kerr effect experiment for the distinction between dynamic heterogeneous and homogeneous relaxations in glassy systems. The possibility of this distinction is due to the inherent nonlinearity of the Kerr effect signal. We model the slow reorientational molecular motion in supercooled liquids in terms of noninertial rotational diffusion. The Kerr effect response, consisting of two terms, is calculated for heterogeneous and for homogeneous variants of the stochastic model. It turns out that the experiment is able to distinguish between the two scenarios. We furthermore show that exchange between relatively "slow" and "fast" environments does not affect the possibility of frequency-selective modifications. It is demonstrated how information about changes in the width of the relaxation-time distribution can be obtained from experimental results.
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Affiliation(s)
- Uli Häberle
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Germany
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42
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Abstract
The aging properties of a simple free-energy landscape model for the primary relaxation in supercooled liquids are investigated. The intermediate scattering function and the rotational correlation functions are calculated for the generic situation of a quench from a high temperature to below the glass transition temperature. It is found that the reequilibration of molecular orientations takes longer than for translational degrees of freedom. The time scale for reequilibration is determined by that of the primary relaxation as an intrinsic property of the model.
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Affiliation(s)
- Gregor Diezemann
- Institute für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Federal Republic of Germany.
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43
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Winterlich M, Böhmer R, Diezemann G, Zimmermann H. Rotational motion in the molecular crystalsmeta- andortho-carborane studied by deuteron nuclear magnetic resonance. J Chem Phys 2005; 123:94504. [PMID: 16164350 DOI: 10.1063/1.2013254] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spin-lattice and spin-spin-relaxation times, one- and two-dimensional spectra as well as two- and four-time correlation functions were measured for the molecular crystals ortho- and meta-carborane using deuteron nuclear magnetic resonance. It is found that in their noncubic phases these crystals exhibit highly anisotropic motions. In order to allow for a quantitative description of the motional geometry of the carboranes several stochastic models are formulated. By comparison of the model calculations with the experimental results it is found that the dynamics of these quasi-icosahedrally shaped molecules is governed by a composite reorientation process. Here the molecules perform threefold jumps around a molecule-fixed axis which itself can be tilted in four different directions with respect to a crystal-fixed axis. The tilt angle increases significantly with increasing temperature. On the basis of measurements of four-time stimulated-echo functions, implications for dynamic heterogeneity also in comparison with that of supercooled liquids are discussed.
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Affiliation(s)
- Manfred Winterlich
- Experimentelle Physik III and Interdisziplinäres Zentrum für Magnetische Resonanz, Universität Dortmund, 44221 Dortmund, Germany
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44
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Abstract
The fluctuation-dissipation relation is calculated for stochastic models obeying a master equation with continuous time. In the general case of a nonstationary process, there appears to be no simple relation between the response and the correlation. Also, if one considers stationary processes, the linear response cannot be expressed via time-derivatives of the correlation function alone. In this case, an additional function, which has rarely been discussed previously, is required. This so-called asymmetry depends on the two times also relevant for the response and the correlation and it vanishes under equilibrium conditions. The asymmetry can be expressed in terms of the propagators and the transition rates of the master equation but it is not related to any physical observable in an obvious way. It is found that the behavior of the asymmetry strongly depends on the nature of the dynamical variable considered in the calculation of the correlation and the response. If one is concerned with a variable which randomizes with any transition among the states of the system, the asymmetry vanishes in most cases. This is in contrast to the situation for other classes of variables. In particular, for trap models of glassy relaxation, the fluctuation-dissipation ratio strongly depends on the observable and the asymmetry plays a dominant role in the determination of this ratio also if only neutral variables are considered. Some implications of a nonvanishing asymmetry with regard to the definition of an effective temperature are discussed.
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45
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Abstract
Dynamic Kerr effect measurements provide a simple realization of a nonlinear experiment. We propose a field-off experiment where an electric field of one or several sinusoidal cycles with frequency omega is applied to a sample in thermal equilibrium. Afterwards, the evolution of the polarizability is measured. If such an experiment is performed in the terahertz range it might provide valuable information about the low-frequency dynamics in disordered systems. We treat these dynamics in terms of a Brownian oscillator model and calculate the Kerr effect response. It is shown that frequency-selective behavior can be expected. In the interesting case of underdamped vibrational motion we find that the frequency dependence of the phonon damping can be determined from the experiment. Also the behavior of overdamped relaxational modes is discussed. For typical glassy materials we estimate the magnitude of all relevant quantities, which we believe will be helpful in experimental realizations.
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Affiliation(s)
- Uli Häberle
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Germany
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46
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Abstract
Single molecule rotational correlation functions are analyzed for several reorientation geometries. Even for the simplest model of isotropic rotational diffusion our findings predict nonexponential correlation functions to be observed by polarization sensitive single molecule fluorescence microscopy. This may have a deep impact on interpreting the results of molecular reorientation measurements in heterogeneous environments.
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Affiliation(s)
- G Hinze
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität, D-55099 Mainz, Germany.
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47
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Qi F, Diezemann G, Böhm H, Lambert J, Böhmer R. Simple modeling of dipolar coupled 7Li spins and stimulated-echo spectroscopy of single-crystalline beta-eucryptite. J Magn Reson 2004; 169:225-39. [PMID: 15261617 DOI: 10.1016/j.jmr.2004.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Revised: 04/21/2004] [Indexed: 05/20/2023]
Abstract
Stimulated-echo spectroscopy has recently been applied to study the ultra-slow dynamics of nuclear spin-3/2 probes such as 7Li and 9Be in solids. Apart from the dominant first-order quadrupolar interaction in the present article also the impact of the homonuclear dipolar interactions is considered in a simple way: the time evolution of a dipole coupled pair of spins with I = 3/2 is calculated in an approximation, which takes into account that the satellite transitions usually do not overlap. Explicit analytical expressions describing various aspects of a coupled quadrupolar pair subjected to a Jeener-Broekaert pulse sequence are derived. Extensions to larger spin systems are also briefly discussed. These results are compared with experimental data on a single-crystalline Li ion conductor.
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Affiliation(s)
- F Qi
- Experimentelle Physik III, Universität Dortmund, Germany
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48
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Abstract
The response to the field sequence of nonresonant hole burning, a pump-wait-probe experiment originally designed to investigate slow relaxation in complex systems, is calculated for a model of Brownian oscillators, thus including inertial effects. In the overdamped regime the model predictions are very similar to those of the purely dissipative stochastic models investigated earlier, including the possibility to discriminate between dynamic homogeneous and heterogeneous relaxation. The case of underdamped oscillations is of particular interest when low-frequency excitations in glassy systems are considered. We show that also in this situation a frequency selective modification of the response should be feasable. This means that it is possible to specifically address various parts of the spectrum. An experimental realization of nonresonant holeburning in the Terahertz regime therefore is expected to shed further light on the nature of the vibrations around the so-called boson peak.
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Affiliation(s)
- Uli Haberle
- Institut fur Physikalische Chemie, Universitat Mainz, Welderweg 11, 55099 Mainz, Germany
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49
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Winterlich M, Diezemann G, Zimmermann H, Böhmer R. Microscopic origin of the nonexponential dynamics in a glassy crystal. Phys Rev Lett 2003; 91:235504. [PMID: 14683195 DOI: 10.1103/physrevlett.91.235504] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Indexed: 05/24/2023]
Abstract
The origin of the slow relaxation and of the dynamic heterogeneity is studied for an orientation-ally disordered crystal, orthocarborane, composed of quasi-icosahedrally shaped molecules. Multidimensional deuteron magnetic resonance reveals that large jump angles dominate their complex, anisotropic reorientational motion. It involves a sequence of small-angle tilts about locally preferred axes as well as symmetry adapted threefold jumps. The intrinsic dynamics of this glassy crystal is nonexponential and can be fully accounted for in terms of the tilt and jump motion.
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Affiliation(s)
- M Winterlich
- Experimentelle Physik III, Universität Dortmund, 44221 Dortmund, Germany
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50
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Diezemann G. Dynamic heterogeneities in the out-of-equilibrium dynamics of simple spherical spin models. Phys Rev E Stat Nonlin Soft Matter Phys 2003; 68:021105. [PMID: 14524951 DOI: 10.1103/physreve.68.021105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2003] [Indexed: 05/24/2023]
Abstract
The response of spherical two-spin interaction models, the spherical ferromagnet (s-FM) and the spherical Sherrington-Kirkpatrick (s-SK) model, is calculated for the protocol of the so-called nonresonant hole burning (NHB) experiment for temperatures below the respective critical temperatures. It is shown that it is possible to select dynamic features in the out-of-equilibrium dynamics of both models, one of the hallmarks of dynamic heterogeneities. The behavior of the s-SK model and the s-FM model in three dimensions is very similar, showing dynamic heterogeneities in the long-time behavior, i.e., in the aging regime. The appearance of dynamic heterogeneities in the s-SK model explicitly demonstrates that these are not necessarily related to spatial heterogeneities. For the s-FM model, it is shown that the nature of the dynamic heterogeneities changes as a function of dimensionality. With the increasing dimension, the frequency selectivity of the NHB diminishes and the dynamics in the mean-field limit of the s-FM model becomes homogeneous.
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Affiliation(s)
- Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Welderweg 11, 55099 Mainz, Germany
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