A many-body model to study proteins. I. Applications to MLnm+ complexes, Mm+=Li+, Na+, K+, Mg2+, Ca2+, and Zn2+, L=H2O, CH3OH, HCONH2, n=1–6, and to small hydrogen bonded systems

Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation

Hybrid modeling approaches based on all-atom force fields to handle a solute and coarse-grained models to account for the solvent are promising numerical tools that can be used to understand the properties of large and multi-components solutions and thus to speed up the development of new industrial products that obey the standard of green and sustainable chemistry. Here, we discuss the ability of a full polarizable hybrid approach coupled to a standard molecular dynamics scheme to model the behavior in the aqueous phase and at infinite dilution conditions of a standard hydrophobic polyelectrolyte polymer whose charge is neutralized by explicit counterions. Beyond the standard picture of a polyelectrolyte behavior governed by an interplay between opposite intra-polyelectrolyte and inter-polyelectrolyte/counterion Coulombic effects, our simulations show the key role played by both intra-solute polarization effects and long range solute/solvent electrostatics to stabilize compact globular conformations of that polyelectrolyte. Our full polarizable hybrid modeling approach is thus a new theoretical tool well suited to be used in digital strategies for accelerating innovation for green science, for instance.

Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution

We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor

The dynamic coupling between a polarizable protein force field and a particle-based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones pseudo-particles. The solvent-induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent-solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self-consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson-Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction.

Electronic basis of the comparable hydrogen bond properties of small H2CO/(H2O)n and H2NO/(H2O)n systems (n = 1, 2)

The electronic and structural properties of dihydronitroxide/water clusters are investigated and compared to the properties of formaldehyde/water clusters. Exploring the stationary points of their potential energy surfaces (structurally, vibrationally, and energetically) and characterizing their hydrogen bonds (by both atoms in molecules and natural bond orbitals methods) clearly reveal the strong similarity between these two kind of molecular systems. The main difference involves the nature of the hydrogen bond taking place between the X-H bond and the oxygen atom of a water molecule. All the properties of the hydrogen bonds occurring in both kind of clusters can be easily interpreted in terms of competition between intermolecular and intramolecular hyperconjugative interactions.

Structural studies of human alkaline phosphatase in complex with strontium: implication for its secondary effect in bones

Strontium is used in the treatment of osteoporosis as a ranelate compound, and in the treatment of painful scattered bone metastases as isotope. At very high doses and in certain conditions, it can lead to osteomalacia characterized by impairment of bone mineralization. The osteomalacia symptoms resemble those of hypophosphatasia, a rare inherited disorder associated with mutations in the gene encoding for tissue-nonspecific alkaline phosphatase (TNAP). Human alkaline phosphatases have four metal binding sites--two for zinc, one for magnesium, and one for calcium ion--that can be substituted by strontium. Here we present the crystal structure of strontium-substituted human placental alkaline phosphatase (PLAP), a related isozyme of TNAP, in which such replacement can have important physiological implications. The structure shows that strontium substitutes the calcium ion with concomitant modification of the metal coordination. The use of the flexible and polarizable force-field TCPEp (topological and classical polarization effects for proteins) predicts that calcium or strontium has similar interaction energies at the calcium-binding site of PLAP. Since calcium helps stabilize a large area that includes loops 210-228 and 250-297, its substitution by strontium could affect the stability of this region. Energy calculations suggest that only at high doses of strontium, comparable to those found for calcium, can strontium substitute for calcium. Since osteomalacia is observed after ingestion of high doses of strontium, alkaline phosphatase is likely to be one of the targets of strontium, and thus this enzyme might be involved in this disease.

Aplicaciones de los métodos computacionales al estudio de la estructura y propiedades de polímeros

En este trabajo se revisan las técnicas de simulación molecular más habituales y potentes para la descripción de los polímeros a escala atómica y molecular, las cuales se han clasificado en cuánticas o clásicas dependiendo de cómo se describen las interacciones entre las partículas. Se presentan asimismo diversas aplicaciones de dichas metodologías, realizadas en nuestro laboratorio, en el contexto del estudio de la estructura y propiedades de polímeros. En particular, se muestran aplicaciones de las técnicas clásicas a la determinación de estructuras cristalinas, a estudio del plegamiento lamelar de los nylons, a la estabilidad de las estructuras supramoleculares observadas en algunos complejos tensioactivo·polielectrolito y a la difusión de gases en matrices poliméricas, mientras que el uso de técnicas cuánticas se ha ilustrado presentando estudios dedicados a la predicción de efectos cooperativos, interacciones específicas y parámetros espectroscópicos.