Orbitales localisées pour les interactions intermoléculaires

We study in this thesis intermolecular interactions through a localized orbitals point of view. This concerns on one hand the intermolecular interactions generated by the occupied localized orbitals such as the electrostatic interaction, and on the other hand the intermolecular interactions like the dispersion interaction that involve virtual orbitals. We evaluate in a first part the electrostatic interactions on frozen monomer charge densities provided by multipolar distributions on occupied localized orbitals. These give chemically meaningful representations of molecular charge densities. We show that multipolar distributions on localized orbitals are suitable to describe intermolecular electrostatic interactions if the interaction is truncated to a suitable order, making localized orbitals potentially interesting to model electrostatic interactions in a force field. We use then the properties of a priori constructed localized orbitals on a complex in order to define a reference multipolar interaction for the electrostatic interaction of relaxed charge densities. We evaluate hence the capacity of multipolar distributions based on relaxed localized orbitals to decribe the relaxed electrostatic interaction. In a second part, localizing both occupied and virtual orbitals in an intermolecular framework allows us to attribute the orbitals of a noncovalent system to each of its fragments (and to divide the excitations by classes), and select in a further step only the most relevant excitations to the intermolecular post-Hartree-Fock correlation energy. We propose two different methods we developped in this work to select the excitations in the general framework of the range separated density functional theory (DFT) coupled to the random phase approximation (RPA). The first method is based on a simple energetic criterion while the other is based on a selection of only one class, namely the dispersion-type excitations. We show afterwards both the usefulness and the limits of those two methods of selection on complexes with various types of interaction.Nous réalisons dans cette thèse l'étude d'interactions intermoléculaires d'un point de vue d'orbitales localisées. Cela concerne d'une part les interactions intermoléculaires produites par des orbitales localisées occupées comme l'interaction électrostatique, et d'autre part les interactions intermoléculaires qui engagent aussi les orbitales localisées virtuelles comme l'interaction de dispersion. Nous évaluons dans un premier temps les interactions électrostatiques produites par des distributions multipolaires en orbitales localisées, qui donnent une représentation chimique intuitive d'une densité de charges moléculaire. Nous montrons que les distributions multipolaires en orbitales localisées sont raisonnables pour décrire les interactions électrostatiques des densités de charges gelées si l'interaction multipolaire est tronquée à un ordre bien choisi, ce qui rend les orbitales localisées potentiellement intéressantes pour modéliser les interactions électrostatiques dans un champ de force. Nous utilisons ensuite les propriétés des orbitales localisées a priori dans un complexe pour définir une référence multipolaire dans le cas de l'interaction électrostatique des densités de charges relaxées. Nous évaluons ensuite la capacité de distributions multipolaires issues d'orbitales localisées relaxées pour décrire l'interaction électrostatique relaxée. Dans un second temps, localiser les orbitales occupées et virtuelles dans un cadre intermoléculaire nous permet d'une part d'attribuer des orbitales à chaque fragment d'un système fragmenté non covalent, et donc de diviser les excitations en classes et sélectionner uniquement les excitations les plus importantes à l'énergie de corrélation intermoléculaire post-Hartree-Fock. Nous proposons deux méthodes différentes que nous avons développé dans cette thèse pour sélectionner des excitations dans le cadre général de la DFT à séparation de portée couplée à l'approximation des phases aléatoires (RPA). La première méthode de sélection est basée sur un simple critère énergetique tandis que la seconde est basée sur la sélection d'une seule classe d'excitation à savoir la classe de dispersion. Enfin, nous montrons l'intérêt et les limites de ces deux méthodes de sélection pour des complexes à interactions variées

Orbitales localisées pour les interactions intermoléculaires

Nous réalisons dans cette thèse l'étude d'interactions intermoléculaires d'un point de vue d'orbitales localisées. Cela concerne d'une part les interactions intermoléculaires produites par des orbitales localisées occupées comme l'interaction électrostatique, et d'autre part les interactions intermoléculaires qui engagent aussi les orbitales localisées virtuelles comme l'interaction de dispersion. Nous évaluons dans un premier temps les interactions électrostatiques produites par des distributions multipolaires en orbitales localisées, qui donnent une représentation chimique intuitive d'une densité de charges moléculaire. Nous montrons que les distributions multipolaires en orbitales localisées sont raisonnables pour décrire les interactions électrostatiques des densités de charges gelées si l'interaction multipolaire est tronquée à un ordre bien choisi, ce qui rend les orbitales localisées potentiellement intéressantes pour modéliser les interactions électrostatiques dans un champ de force. Nous utilisons ensuite les propriétés des orbitales localisées a priori dans un complexe pour définir une référence multipolaire dans le cas de l'interaction électrostatique des densités de charges relaxées. Nous évaluons ensuite la capacité de distributions multipolaires issues d'orbitales localisées relaxées pour décrire l'interaction électrostatique relaxée. Dans un second temps, localiser les orbitales occupées et virtuelles dans un cadre intermoléculaire nous permet d'une part d'attribuer des orbitales à chaque fragment d'un système fragmenté non covalent, et donc de diviser les excitations en classes et sélectionner uniquement les excitations les plus importantes à l'énergie de corrélation intermoléculaire post-Hartree-Fock. Nous proposons deux méthodes différentes que nous avons développé dans cette thèse pour sélectionner des excitations dans le cadre général de la DFT à séparation de portée couplée à l'approximation des phases aléatoires (RPA). La première méthode de sélection est basée sur un simple critère énergetique tandis que la seconde est basée sur la sélection d'une seule classe d'excitation à savoir la classe de dispersion. Enfin, nous montrons l'intérêt et les limites de ces deux méthodes de sélection pour des complexes à interactions variées.We study in this thesis intermolecular interactions through a localized orbitals' point of view. This concerns on one hand the intermolecular interactions generated by the occupied localized orbitals such as the electrostatic interaction, and on the other hand the intermolecular interactions like the dispersion interaction that involve virtual orbitals. We evaluate in a first part the electrostatic interactions on frozen monomer charge densities provided by multipolar distributions on occupied localized orbitals. These give chemically meaningful representations of molecular charge densities. We show that multipolar distributions on localized orbitals are suitable to describe intermolecular electrostatic interactions if the interaction is truncated to a suitable order, making localized orbitals potentially interesting to model electrostatic interactions in a force field. We use then the properties of a priori constructed localized orbitals on a complex in order to define a reference multipolar interaction for the electrostatic interaction of relaxed charge densities. We evaluate hence the capacity of multipolar distributions based on relaxed localized orbitals to decribe the relaxed electrostatic interaction. In a second part, localizing both occupied and virtual orbitals in an intermolecular framework allows us to attribute the orbitals of a noncovalent system to each of its fragments (and to divide the excitations by classes), and select in a further step only the most relevant excitations to the intermolecular post-Hartree-Fock correlation energy. We propose two different methods we developped in this work to select the excitations in the general framework of the range separated density functional theory (DFT) coupled to the random phase approximation (RPA). The first method is based on a simple energetic criterion while the other is based on a selection of only one class, namely the dispersion-type excitations. We show afterwards both the usefulness and the limits of those two methods of selection on complexes with various types of interaction.PARIS-BIUSJ-Biologie recherche (751052107) / SudocSudocFranceF

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes

Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet

We report a quantum chemical characterization of the non-natural (synthetic) H-bonded base pair formed by 6-amino-S-nitro-2(1H)-pyridone (Z) and 2-aminoimidazo [1,2-a]-1,3,5-triazin-4(8H)-one (P). The Z:P base pair, orthogonal to the classical G:C base pair, has been introduced into DNA molecules to expand the genetic code. Our results indicate that the Z:P base pair closely mimics the G:C base pair in terms of both structure and stability. To clarify the role of the NO2 group on the CS position of the Z base, we compared the stability of the Z:P base pair with that of base pairs having different functional groups at the CS position of Z. Our results indicate that the electron-donating/-withdrawing properties of the group on CS have a clear impact on the stability of the Z:P base pair, with the strong electron-withdrawing nitro group achieving the largest stabilizing effect on the H-bonding interaction and the strong electron-donating NH2 group destabilizing the Z:P pair by almost 4 kcal/mol. Finally, our gas-phase and in-water calculations confirm that the Z-nitro group reinforces the stacking interaction with its adjacent purine or pyrimidine ring

Occurrence and stability of lone pair-pi stacking interactions between ribose and nucleobases in functional RNAs

The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-pi stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes

Molecular dynamics characterization of five pathogenic Factor X mutants associated with decreased catalytic activity

Factor X (FX) is one of the major players in the blood coagulation cascade. Upon activation to FXa, it converts prothrombin to thrombin, which in turn converts fibrinogen into fibrin (blood clots). FXa deficiency causes hemostasis defects, such as intracranial bleeding, hemathrosis, and gastrointestinal blood loss. Herein, we have analyzed a pool of pathogenic mutations, located in the FXa catalytic domain and directly associated with defects in enzyme catalytic activity. Using chymotrypsinogen numbering, they correspond to D102N, T135M, V160A, G184S, and G197D. Molecular dynamics simulations were performed for 1.68 μs on the wild-type and mutated forms of FXa. Overall, our analysis shows that four of the five mutants considered, D102N, T135M, V160A, and G184S, have rigidities higher than those of the wild type, in terms of both overall protein motion and, specifically, subpocket S4 flexibility, while S1 is rather insensitive to the mutation. This acquired rigidity can clearly impact the substrate recognition of the mutants

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Accuracy of DLPNO-CCSD(T) Method for Noncovalent Bond Dissociation Enthalpies from Coinage Metal Cation Complexes

The performance of the domain based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) method has been tested to reproduce the experimental gas phase ligand dissociation enthalpy in a series of Cu+, Ag+, and Au+ complexes. For 33 Cu+-noncovalent ligand dissociation enthalpies, all-electron calculations with the same method result in MUE below 2.2 kcal/rnol, although a MSE of 1.4 kcal/mol indicates systematic underestimation of the experimental values. Inclusion of scalar relativistic effects for Cu either via effective core potential (ECP) or Douglass-Kroll-Hess Hamiltonian, reduces the MUE below 1.7 kcal/mol and the MSE to -1.0 kcal/mol. For 24 Ag+ noncovalent ligand dissociation enthalpies, the DLPNO-CCSD(T) method results in a mean unsigned error (MUE) below 2.1 kcal/mol and vanishing mean signed error (MSE). For 15 Au+ noncovalent ligand dissociation enthalpies, the DLPNO-CCSD(T) methods provides larger MUE and MSE, equal to 3.2 and 1.7 kcal/mol, which might be related to poor precision of the experimental measurements. Overall, for the combined data set of 72 coinage metal ion complexes, DLPNO CCSD(T) results in a MUE below 2.2 kcal/mol and an almost vanishing MSE. As for a comparison with computationally cheaper density functional theory (DFT) methods, the routinely used M06 functional results in MUE and MSE equal to 3.6 and -1.7 kcal/mol. Results converge already at CC-PVTZ quality basis set, making highly accurate DLPNO CCSD(T) estimates affordable for routine calculations (single-point) on large transition metal complexes of >100 atoms