Theoretical gas to liquid shift of 15 N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations

International audienceChemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We 10 propose here to combine ab initio Molecular Dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between-121.8 and-120.8 ppm. 1

Evaluation of Gas-to-Liquid 17 O Chemical Shift of Water: a Test Case for Molecular and Periodic Approaches

International audienceModelling liquid water features is a challenging and ongoing task that brings together a number of computational issues related to both the description of its electronic and geometrical structure. In order to go a step further in the understanding of this peculiar liquid, we present a thorough analysis of NMR gas-to-liquid 17 O and 1 H shifts of water using density functional theory based molecular dynamics. In order to be as consistent as possible, we consider the influence of basis sets, exchange-correlation functionals and structural models, in both molecular and periodic schemes to evaluate 17 O and 1 H nuclear shieldings. We show that strong error compensations between functional and basis-set expansion can be obtained in molecular approaches which artificially produces good 17 O gas-to-liquid shifts with relatively small basis sets. We also demonstrate that despite their ability to provide reliable liquid phase structures , generalized-gradient approximation based exchange-correlation functionals lead to strongly inconsistent values for 17 O gas-to-liquid shift. This latter property is shown to be strongly influenced by intra-molecular electronic delocalization, accentuated by the surrounded molecules. In contrast, 1 H is less sensitive to this effect. By including a Hartree-Fock exchange term, through the use of hybrid functionals which partially correct the self-interaction error, better agreement with experimental values is obtained. The present study provides a detailed guideline to properly evaluate gas-to-liquid shifts in hydrogen bonded systems and emphasizes that, for nuclear shieldings, an accurate electronic structure evaluation prevails over the description of the liquid structure

Recognition of the three-dimensional structure of small metal nanoparticles by a supervised artificial neural network

International audienceCatalytic characteristics of metal nanoparticles heavily depend on their global shapes and sizes as well as on the structure and environment of catalytic sites. On the computational chemistry side, calculations of thermodynamic and kinetic data involve a high calculation cost which can be significantly lowered by the use of a trained machine learning (ML) model. This paper outlines a preliminary approach that aims at classifying the shape of the metal core of nanoparticles. Four different supervised Artificial Neural Networks (ANN) were trained, tested and submitted to a challenging dataset. They are based on two different structural descriptors, Coulomb Matrices (CM) and Radial Distribution Functions (RDF). Each model is trained with hundreds of 3D models of nanoparticles that belong to eleven structural classes. The best model classifies a NP according to its discretized RDF profile and its first derivative. 100% accuracy is reached on the test stage and up to 70% accuracy is obtained on the challenging dataset. It is mainly made of compounds that have global shapes significantly different from the training set. But some non obvious structural patterns make then related to the eleven classes learned by the ANNs. Such strategy could easily be adapted to the recognition of NPs based on experimental neutron or X-ray diffraction data

Dynamique moléculaire ab initio en base locale (principes et applications)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Structures and NMR spectra of short amylose-lipid complexes. Insight using molecular dynamics and DFT quantum chemical calculations

International audienceIt is well established that amylose folds in a helix conformation in presence of lipids. Structural features of such molecular complexes are often analysed using 13C NMR spectroscopy. The large size of amylose used to make such analysis doesn't allow to unambiguously correlate structure of polymers and spectroscopic signals. We present structural analysis of small sized amyloses complexed to palmitic acid using classical molecular dynamics. 15 glucoses residues are necessary for the amylose to fold around the palmitic acid in a well-established helix conformation. Simulating 13C NMR spectra using quantum chemical DFT approach, we demonstrate that these spectra are affected by amylose size and specific intramolecular hydrogen bonds. By mean of theoretical NMR spectra of a 19-residues amylose, we precise the attribution of each characteristic resonances. One chemical shift that is usually attributed to a specific carbon may be related to the existence of different inter or intramolecular hydrogen bonds

Dynamique et orientation de peptides transmembranaires (étude couplant calculs quantiques et RMN du solide)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Relating circular dichroism to atomic structure by means of MD simulations and computed CD spectra with α-peptoids as an example

International audienceClassical molecular dynamics simulations have been combined to quantum calculations of CD spectra in order to fruitfully relate the experimental CD spectra, not only to the overall conformation of chiral a-peptoids, but also to its structure at the atomic scale, including the dihedral feature of the backbone (y,ϕ) and the orientation of the chiral side-chain (χ1). These simulations have been performed up to the hexamer Ac-(stbe)6-CO2tBu. We have shown that number of states has a significant impact on the shape of the spectrum below 215 nm. The number of states computed is also critical to simulate the spectra of long oligomer. While 10 to 20 states are sufficient to simulate the CD spectra of short oligomers, 100 states or more are mandatory to converge the CD spectrum shape for longer oligomers. The conformational sampling and the analysis of the intramolecular interactions responsible for the specific folding of the objects have been jointly explored by means of Replica Exchange MD and DFT calculations

Influence of Amylose Size on the Structure and NMR Spectrum of Amylose-Palmitic Acid Complexes. Insight from Classical Molecular Dynamics Simulations and DFT Quantum Chemical Computations.

We present, first, structural analysis of small sized amyloses complexed to palmitic acid studied using classical molecular dynamics. We show that even if amylose with a minimum of 11 residues exhibits transitional appearance of a V-type structure, 15 glucoses residues are necessary for the amylose to fold around the palmitic acid in a well-established helix conformation. Second, simulating 13C NMR spectrum using a strategy that combines molecular dynamics and quantum chemical DFT calculations, we demonstrate that part of the NMR spectrum is affected by the amylose size and by the presence of specific intramolecular hydrogen bonds. By mean of deconvolution procedure of NMR spectra of a 19-residues amylose calculated using a series of structures extracted from molecular dynamics, we have been able to precise the attribution of each characteristic resonances. In this context, we postulate that one chemical shift that is usually attributed to a specific carbon can, also, correspond to the presence of two different local conformations of amylose.</p

Understanding Sterol-Membrane Interactions Part I: Hartree-Fock versus DFT Calculations of 13 C and 1 H NMR Isotropic Chemical Shifts of Sterols in Solution and Analysis of Hydrogen-Bonding Effects

International audienc

Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case

International audienceDensity Functional Theory (B3LYP/6-31G(d,p)) calculations of 15 N amide and 13 C carbonyl NMR chemical shielding tensors have been performed on WALP23 trans-membrane -helix peptide and 10 compared to solid state NMR experiment performed on [ 13 C1-Ala13, 15 N-Leu14] specifically labelled peptide powder sample. Using either theoretical result obtained on the whole peptide or experimental data as reference, several simplest chemical models have been explored in order to reduce the computational cost while maintaining good theoretical accuracy. From this study, it appears that the hydrogen bond (N-H…O=C) network that exists in the -helix has a major 15 influence on the chemical shielding tensor and more specifically on the carbonyl 13 C 22 eigenvalue. We show that a small truncated WALP_7 model is not adequate for 13 C1 NMR description. The application of an external electric field in order to model the hydr ogen bond network allows calculating chemical shielding tensors with accurate eigenvalues while the associated eigenvectors are largely modified. Finally, a 23 residues polyglycine peptide that 20 includes the Alanine and Leucine residues for which NMR parameters must be calculated is proposed as the chemical model. This model is sufficient to mostly reproduce the calculation performed on WALP23 with major gain in computational time. Moreover, the application of an external electric field allows reaching the experimental accuracy for the determination of the eigenvalues. 2