Conformational Mobility in Monolayer-Protected Nanoparticles: From Torsional Free Energy Profiles to NMR Relaxation

Piserchia, Andrea; Zerbetto, Mirco; Salvia, Marie‐Virginie; Salassa, Giovanni; Gabrielli, Luca; Mancin, Fabrizio; Rastrelli, Federico; Frezzato, Diego

doi:10.1021/acs.jpcc.5b04884

Cited by 18 publications

(27 citation statements)

References 40 publications

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“…Although this model does not account for size dispersion, it is responsible for most of the effect observed in our experiments (see Results and Supplemental Information, Section S7). We have already shown that simulations performed with this model nicely reproduce the behavior of nanoparticles samples with an average diameter of 1.6–1.8 nm 36 . The coating groups, as well as salicylate and 4-hydroxybenzoate ( 3 and 5 in Scheme 1), were parametrized with GAFF 49 and the atomic charges were derived by the RESP fitting procedure 50 by a force-field topology database-building approach as developed in RedServer 51 .…”

Section: Methodsmentioning

confidence: 99%

Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition

Riccardi

Gabrielli

Sun

et al. 2017

Chem

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SummaryThe self-assembly of a monolayer of ligands on the surface of noble-metal nanoparticles dictates the fundamental nanoparticle's behavior and its functionality. In this combined computational-experimental study, we analyze the structure, organization, and dynamics of functionalized coating thiols in monolayer-protected gold nanoparticles (AuNPs). We explain how functionalized coating thiols self-organize through a delicate and somehow counterintuitive balance of interactions within the monolayer itself and with the solvent. We further describe how the nature and plasticity of these interactions modulate nanoparticle-based chemosensing. Importantly, we found that self-organization of coating thiols can induce the formation of binding pockets in AuNPs. These transient cavities can accommodate small molecules, mimicking protein-ligand recognition, which could explain the selectivity and sensitivity observed for different organic analytes in NMR chemosensing experiments. Thus, our findings advocate for the rational design of tailored coating groups to form specific recognition binding sites on monolayer-protected AuNPs.

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Section: Methodsmentioning

confidence: 99%

Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition

Riccardi

Gabrielli

Sun

et al. 2017

Chem

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“…Moreover, using internal coordinates can represent a way to apply a further, important complexity reduction. As an example, in the work of Piserchia et al authors can access long‐time dynamics of a decanethiols coated Au nanoparticle and simulate nuclear magnetic resonance (NMR) relaxation data of 13 C 1 H probes along the alkyl chains just using the minimal set of internal coordinates.…”

Section: Introductionmentioning

confidence: 99%

DiTe2: Calculating the diffusion tensor for flexible molecules

2018

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We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z‐Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all‐atom and coarse‐grained levels. © 2018 Wiley Periodicals, Inc.

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“…Also, since the details of the internal energy

U (x, θ)

grow smoothly, the morphing route allows the system to more efficiently sample the whole space of conformations, allowing a good estimation of POMF profiles even if the latter presents high (free) energy barriers. Such a strategy has been recently successfully applied in a study on clusters of 1‐decanethiol chains tethered to a planar gold surface, and on a gold nanoparticle . JEFREE is distributed within the GPL v2.0 license, and can be downloaded from our website (http://www.chimica.unipd.it/licc/software.html).…”

Section: Computational Aspectsmentioning

confidence: 99%

“…The second case study that we want to propose as an example of the application of the integrated computational approach to NMR spectroscopy of flexible molecules is the interpretation of the 13 C 1 H T 1 relaxation data along the carbon atoms of a 1‐decanethiol chain tethered to an Au nanoparticle . Data has been acquired in CD 2 Cl 2 at 298.15 K and 500.13 MHz 1 H frequency.…”

Section: Examplesmentioning

confidence: 99%

“…(C) Coarse‐grained model used for the calculation of the POMF. The 1‐decanethiol chains are treated within the united‐atoms description with fixed bond lengths and angles; the Au nanoparticle is approximated to a sphere which interacts with the chains constituting the chains by means of a modified Lennard‐Jones potential . (D) View of the probe chain selected degrees of freedom.…”

Section: Examplesmentioning

confidence: 99%

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Multiscale modeling for interpreting nuclear magnetic resonance relaxation in flexible molecules

Zerbetto

Polimeno

2016

Int J of Quantum Chemistry

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In this tutorial review, we provide a comprehensive description of a multiscale methodology tailored to the calculation of nuclear magnetic resonance (NMR) relaxation data of flexible molecules, based on the definition, parametrization, and solution of a Smoluchowski equation defined for a set of relevant molecular coordinates. While the method is applicable in principle to any collection of internal degrees of freedom, here we focus on flexibility described in terms of torsion angles under the paradigm of what we call the diffusive chain model. The theoretical basis of the multiscale stochastic approach to NMR spectroscopy is provided in detail. Computational aspects are discussed, pointing at a suggested set of specific software packages. To give to this contribution a hands-on component, a self-contained tutorial is made available as Supporting Information with the discussion of some examples taken from recently published studies.diffusive chain model, integrated computational approach, nuclear magnetic resonance, stochastic methods | I N T R O D U C T I O NIn this contribution, we present a general overview of a multiscale modeling approach to the interpretation of spectroscopic observables that are highly sensitive to molecular flexibility. In particular, we discuss a stochastic approach for the calculation of nuclear magnetic resonance (NMR) relaxation data of flexible molecules. In a multiscale spirit, all parameters entering the basic stochastic equation are calculated (or evaluated) using a proper level of description of the molecule, which can be quantum mechanical (QM), classical, or hybrid quantumclassical, depending on the type of the required parameter. After a short general review of the connection between molecular dynamics (MD) and spectroscopic observables, the discussion will be focused on NMR studies of molecules in solution, where the fast motional regime can be invoked.Our target is the description of the structural dynamics of a given flexible molecular system. MD is a fundamental ingredient, together with structural properties, that needs to be taken into account when interpreting, understanding, and predicting both single-molecule and bulk properties of matter. Just to mention a few important examples, dynamics affects proteins properties in a number of different ways, from tuning the binding properties of folded proteins to regulating pathways of folding and binding, from modulating allosteric regulation to controlling function in disordered/unstructured proteins or domains. [1,2] MD is also at the basis of function of molecular machines [3] and it can modulate charge transfer in molecular electronic devices. [4] Having access to molecular motions is, thus, of primary importance and a number of experimental (spectroscopic) techniques are at present available, which are split in two main branches: bulk and single-molecule experiments.NMR is the selected bulk technique to be described in this tutorial review. It is widely used in studying structure and dynamics of biomolecules, es...

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Conformational Mobility in Monolayer-Protected Nanoparticles: From Torsional Free Energy Profiles to NMR Relaxation

Cited by 18 publications

References 40 publications

Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition

Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition

DiTe2: Calculating the diffusion tensor for flexible molecules

Multiscale modeling for interpreting nuclear magnetic resonance relaxation in flexible molecules

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