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Cerezo J, Gierschner J, Santoro F, Prampolini G. Explicit Modelling of Spectral Bandshapes by a Mixed Quantum-Classical Approach: Solvent Order and Temperature Effects in the Optical Spectra of Distyrylbenzene. Chemphyschem 2024:e202400307. [PMID: 38728539 DOI: 10.1002/cphc.202400307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/12/2024]
Abstract
The absorption and emission spectral shapes of a flexible organic probe, the distyrylbenzene (DSB) dye, are simulated accounting for the effect of different environments of increasing complexity, ranging from a homogeneous, low-molecular- weight solvent, to a long-chain alkane, and, eventually, a channel-forming organic matrix. Each embedding is treated explicitly, adopting a mixed quantum-classical approach, the Adiabatic Molecular Dynamics - generalized vertical Hessian (Ad-MD|gVH) model, which allows a direct simulation of the environment-induced constraining effects on the vibronic spectral shapes. In such a theoretical framework, the stiff modes of the dye are described at a quantum level within the harmonic approximation, including Duschinsky mixing effects, while flexible degrees of freedom of the solute (e. g. torsions) and those of the solvent are treated classically by means of molecular dynamics sampling. Such a setup is shown to reproduce the distinct effects exerted by the different environments in varied thermodynamic conditions. Besides allowing for a first-principles rationale on the supramolecular mechanism leading to the experimental spectral features, this result represents the first successful application of the Ad-MD|gVH method to complex embeddings and supports its potential application to other heterogeneous environments, such as for instance, pigment-protein complexes or organic dyes adsorbed into metal-organic frameworks.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM), Consiglio Nazionale delle Ricerche (CNR), 50019, Sesto Fiorentino, Italien
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies, IMDEA Nanoscience, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM), Consiglio Nazionale delle Ricerche (CNR), 50019, Sesto Fiorentino, Italien
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM), Consiglio Nazionale delle Ricerche (CNR), 50019, Sesto Fiorentino, Italien
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2
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Dellai A, Naim C, Cerezo J, Prampolini G, Castet F. Dynamic effects on the nonlinear optical properties of donor acceptor stenhouse adducts: insights from combined MD + QM simulations. Phys Chem Chem Phys 2024; 26:13639-13654. [PMID: 38511505 DOI: 10.1039/d4cp00310a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The second-order nonlinear optical (NLO) responses of a donor-acceptor stenhouse adduct (DASA) are investigated by using a computational approach combining molecular dynamics simulations and density functional theory (DFT) calculations. Specific force fields for the open and closed photoswitching forms are first parameterized and validated according to the Joyce protocol, in order to finely reproduce the geometrical features and potential energy surfaces of both isomers in chloroform solution. Then, DFT calculations are performed on structural snapshots extracted at regular time steps of the MD trajectories to address the influence of the thermalized conformational dynamics on the NLO responses related to hyper-Rayleigh scattering (HRS) experiments. We show that accounting for the structural dynamics largely enhances the HRS hyperpolarizability (βHRS) compared to DFT calculations considering solely equilibrium geometries, and greatly improves the agreement with experimental measurements. Furthermore, we show that the NLO responses of the NLO-active open form are correlated with the bond order alternation along the triene bridge connecting the donor and acceptor moieties, which is rationalized using simple essential state models.
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Affiliation(s)
- Angela Dellai
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
| | - Carmelo Naim
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain
| | - Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Frédéric Castet
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
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3
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Bhuiyan FH, Li YS, Kim SH, Martini A. Shear-activation of mechanochemical reactions through molecular deformation. Sci Rep 2024; 14:2992. [PMID: 38316829 PMCID: PMC10844542 DOI: 10.1038/s41598-024-53254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024] Open
Abstract
Mechanical stress can directly activate chemical reactions by reducing the reaction energy barrier. A possible mechanism of such mechanochemical activation is structural deformation of the reactant species. However, the effect of deformation on the reaction energetics is unclear, especially, for shear stress-driven reactions. Here, we investigated shear stress-driven oligomerization reactions of cyclohexene on silica using a combination of reactive molecular dynamics simulations and ball-on-flat tribometer experiments. Both simulations and experiments captured an exponential increase in reaction yield with shear stress. Elemental analysis of ball-on-flat reaction products revealed the presence of oxygen in the polymers, a trend corroborated by the simulations, highlighting the critical role of surface oxygen atoms in oligomerization reactions. Structural analysis of the reacting molecules in simulations indicated the reactants were deformed just before a reaction occurred. Quantitative evidence of shear-induced deformation was established by comparing bond lengths in cyclohexene molecules in equilibrium and prior to reactions. Nudged elastic band calculations showed that the deformation had a small effect on the transition state energy but notably increased the reactant state energy, ultimately leading to a reduction in the energy barrier. Finally, a quantitative relationship was developed between molecular deformation and energy barrier reduction by mechanical stress.
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Affiliation(s)
- Fakhrul H Bhuiyan
- Department of Mechanical Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA, 95343, USA
| | - Yu-Sheng Li
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ashlie Martini
- Department of Mechanical Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA, 95343, USA.
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Greff da Silveira L, Livotto PR, Padula D, Vilhena JG, Prampolini G. Accurate Quantum-Mechanically Derived Force-Fields through a Fragment-Based Approach: Balancing Specificity and Transferability in the Prediction of Self-Assembly in Soft Matter. J Chem Theory Comput 2022; 18:6905-6919. [PMID: 36260420 DOI: 10.1021/acs.jctc.2c00747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The wide range of time/length scales covered by self-assembly in soft matter makes molecular dynamics (MD) the ideal candidate for simulating such a supramolecular phenomenon at an atomistic level. However, the reliability of MD outcomes heavily relies on the accuracy of the adopted force-field (FF). The spontaneous re-ordering in liquid crystalline materials stands as a clear example of such collective self-assembling processes, driven by a subtle and delicate balance between supramolecular interactions and single-molecule flexibility. General-purpose transferable FFs often dramatically fail to reproduce such complex phenomena, for example, the error on the transition temperatures being larger than 100 K. Conversely, quantum-mechanically derived force-fields (QMD-FFs), specifically tailored for the target system, were recently shown (J. Phys. Chem. Lett.2022,13, 243) to allow for the required accuracy as they not only well reproduced transition temperatures but also yielded a quantitative agreement with the experiment on a wealth of structural, dynamic, and thermodynamic properties. The main drawback of this strategy stands in the computational burden connected to the numerous quantum mechanical (QM) calculations usually required for a target-specific parameterization, which has undoubtedly hampered the routine application of QMD-FFs. In this work, we propose a fragment-based strategy to extend the applicability of QMD-FFs, in which the amount of QM calculations is significantly reduced, being a single-molecule-optimized geometry and its Hessian matrix the only QM information required. To validate this route, a new FF is assembled for a large mesogen, exploiting the parameters obtained for two smaller liquid crystalline molecules, in this and previous work. Lengthy MD simulations are carried out with the new transferred QMD-FF, observing again a spontaneous re-orientation in the correct range of temperatures, with good agreement with the available experimental measures. The present results strongly suggest that a partial transfer of QMD-FF parameters can be invoked without a significant loss of accuracy, thus paving the way to exploit the method's intrinsic predictive capabilities in the simulation of novel soft materials.
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Affiliation(s)
- Leandro Greff da Silveira
- Instituto de Química (Universidade Federal do Rio Grande do Sul), Avenida Bento Gonçalves 9500, CEP 91501-970Porto Alegre, Brazil
| | - Paolo Roberto Livotto
- Instituto de Química (Universidade Federal do Rio Grande do Sul), Avenida Bento Gonçalves 9500, CEP 91501-970Porto Alegre, Brazil
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia (Università di Siena), via Aldo Moro 2, 53100Siena, SI, Italy
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada (Universidad Autónoma de Madrid), E-28049Madrid, Spain.,Condensed Matter Physics Center (IFIMAC) (Universidad Autónoma de Madrid), E-28049Madrid, Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
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Vilhena JG, Pawlak R, D'Astolfo P, Liu X, Gnecco E, Kisiel M, Glatzel T, Pérez R, Häner R, Decurtins S, Baratoff A, Prampolini G, Liu SX, Meyer E. Flexible Superlubricity Unveiled in Sidewinding Motion of Individual Polymeric Chains. PHYSICAL REVIEW LETTERS 2022; 128:216102. [PMID: 35687435 DOI: 10.1103/physrevlett.128.216102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
A combination of low temperature atomic force microcopy and molecular dynamic simulations is used to demonstrate that soft designer molecules realize a sidewinding motion when dragged over a gold surface. Exploiting their longitudinal flexibility, pyrenylene chains are indeed able to lower diffusion energy barriers via on-surface directional locking and molecular strain. The resulting ultralow friction reaches values on the order of tens of pN reported so far only for rigid chains sliding on an incommensurate surface. Therefore, we demonstrate how molecular flexibility can be harnessed to realize complex nanomotion while retaining a superlubric character. This is in contrast with the paradigm guiding the design of most superlubric nanocontacts (mismatched rigid contacting surfaces).
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Affiliation(s)
- J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Philipp D'Astolfo
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Xunshan Liu
- Department of Chemistry, Zhejiang Sci-tech University, 314423 Hangzhou, China
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Enrico Gnecco
- Marian Smoluchowski Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Marcin Kisiel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Rúben Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Silvio Decurtins
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Alexis Baratoff
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche (ICCOM-CNR), 56124 Pisa, Italy
| | - Shi-Xia Liu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
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Silva A, Tosatti E, Vanossi A. Critical peeling of tethered nanoribbons. NANOSCALE 2022; 14:6384-6391. [PMID: 35412551 DOI: 10.1039/d2nr00214k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The peeling of an immobile adsorbed membrane is a well-known problem in engineering and macroscopic tribology. In the classic setup, picking up at one extreme and pulling off result in a peeling force that is a decreasing function of the pickup angle. As one end is lifted, the detachment front retracts to meet the immobile tail. At the nanoscale, interesting situations arise with the peeling of graphene nanoribbons (GNRs) on gold, as realized, e.g., by atomic force microscopy. The nanosized system shows a constant-force steady peeling regime, where the tip lifting h produces no retraction of the ribbon detachment point, and just an advancement h of the free tail end. This is opposite to the classic case, where the detachment point retracts and the tail end stands still. Here we characterise, by analytical modeling and numerical simulations, a third, experimentally relevant setup where the nanoribbon, albeit structurally lubric, does not have a freely moving tail end, which is instead elastically tethered. Surprisingly, novel nontrivial scaling exponents appear that regulate the peeling evolution. As the detachment front retracts and the tethered tail is stretched, power laws of h characterize the shrinking of the adhered length, the growth of peeling force and the peeling angle. These exponents precede the final total detachment as a critical point, where the entire ribbon eventually hangs suspended between the tip and the tethering spring. These analytical predictions are confirmed by realistic MD simulations, retaining the full atomistic description, also confirming their survival at finite experimental temperatures.
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Affiliation(s)
- Andrea Silva
- CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, c/o SISSA Via Bonomea 265, 34136 Trieste, Italy.
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Erio Tosatti
- CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, c/o SISSA Via Bonomea 265, 34136 Trieste, Italy.
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy
| | - Andrea Vanossi
- CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, c/o SISSA Via Bonomea 265, 34136 Trieste, Italy.
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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7
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Drechsel C, D’Astolfo P, Liu JC, Glatzel T, Pawlak R, Meyer E. Topographic signatures and manipulations of Fe atoms, CO molecules and NaCl islands on superconducting Pb(111). BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2022; 13:1-9. [PMID: 35059274 PMCID: PMC8744454 DOI: 10.3762/bjnano.13.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Topological superconductivity emerging in one- or two-dimensional hybrid materials is predicted as a key ingredient for quantum computing. However, not only the design of complex heterostructures is primordial for future applications but also the characterization of their electronic and structural properties at the atomic scale using the most advanced scanning probe microscopy techniques with functionalized tips. We report on the topographic signatures observed by scanning tunneling microscopy (STM) of carbon monoxide (CO) molecules, iron (Fe) atoms and sodium chloride (NaCl) islands deposited on superconducting Pb(111). For the CO adsorption a comparison with the Pb(110) substrate is demonstrated. We show a general propensity of these adsorbates to diffuse at low temperature under gentle scanning conditions. Our findings provide new insights into high-resolution probe microscopy imaging with terminated tips, decoupling atoms and molecules by NaCl islands or tip-induced lateral manipulation of iron atoms on top of the prototypical Pb(111) superconducting surface.
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Affiliation(s)
- Carl Drechsel
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Philipp D’Astolfo
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Jung-Ching Liu
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Rémy Pawlak
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Ernst Meyer
- Department of Physics, Universität Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
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Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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9
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Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
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Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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