Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations.

Dynamical properties are of great importance in determining the behavior of synthetic and natural molecules, but capturing them by computational methods is a nontrivial task. Very often the time scales of the relevant phenomena are far beyond the typical time windows accessible by classical Molecular Dynamics (MD) simulations, currently limited to the order of microseconds on standard laboratory workstations. On the other hand, biased and accelerated simulations allow for fast and thorough exploration of the molecular conformational space, but they lose the dynamic information. The problem of recovering dynamics from biased/accelerated simulations is a very active field of research, but no totally robust/reliable solutions have been given yet. In this paper it is shown how the Smoluchowski equation, in the framework of Diffusion Theory (DT), can be used to bridge this gap, and dynamical properties, in the form of time correlation functions (TCFs), can be extracted also from such kind of simulations. DT is first extended (EDT) to express the mobility tensors entering the Smoluchowski operator in terms of a recently introduced unified and regularized Rotne-Prager-Yamakawa approximation, [P. J. Zuk, E. Wajnryb, K. A. Mizerski, P. Szymczak, J. Fluid. Mech. 2014, 741, R5, 1-13] also involving mixed rotation-translation contributions, and rotation-rotation terms beside the classical translation-translation ones, so far used in DT. Then, the method is applied to recover the dynamics of a nontrivial example of a peptide in explicit water from the first 200 ns of a Replica Exchange Molecular Dynamics simulation, which is a popular computational method that destroys the long time dynamics. EDT dynamics were found to favorably compare against those coming from a standard MD simulation of the same system, requiring a time window of 30 µs to converge. This result shows that EDT is a tool of practical value to recover the long time dynamics of systems in diffusive regimes from biased/accelerated simulations, to be exploited in those cases when direct evaluation by standard MD is unfeasible.

Ab Initio Structure Determination of Cu2- xTe Plasmonic Nanocrystals by Precession-Assisted Electron Diffraction Tomography and HAADF-STEM Imaging.

We investigated pseudo-cubic Cu2- xTe nanosheets using electron diffraction tomography and high-resolution HAADF-STEM imaging. The structure of this metastable nanomaterial, which has a strong localized surface plasmon resonance in the near-infrared region, was determined ab initio by 3D electron diffraction data recorded in low-dose nanobeam precession mode, using a new generation background-free single-electron detector. The presence of two different, crystallographically defined modulations creates a 3D connected vacancy channel system, which may account for the strong plasmonic response of this material. Moreover, a pervasive rotational twinning is observed for nanosheets as thin as 40 nm, resulting in a tetragonal pseudo-symmetry.

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.

Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.

Dioxygen, an unexpected carbonic anhydrase ligand.

Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous metalloenzymes, grouped into seven different classes, which catalyze the reaction of CO2 hydration to bicarbonate and protons. All of the fifteen human isoforms reported to date belong to the α-class and contain zinc as a cofactor. The structure of human Zn,Cu-CA II has been solved which contains a copper ion bound at its N-terminal, coordinated to His4 and His64. In the active site a dioxygen molecule is coordinated to the zinc ion. Since dioxygen is a rather unexpected CA ligand, molecular dynamics (MD) simulations were performed which suggested a superoxide character of the zinc bound O2.

Quasi-Static Resonances in the Visible Spectrum from All-Dielectric Intermediate Band Semiconductor Nanocrystals.

The quest for materials with metal-like properties as alternatives to noble metals is an intense area of research that is set to lead to dramatic improvements in technologies based on plasmonics. Here, we present intermediate band (IB) semiconductor nanocrystals (NCs) as a class of all-dielectric nanomaterials providing quasi-static optical resonances. We show that IB NCs can display a negative permittivity in a broad range of visible wavelengths, enabling a metal-like optical response despite the absence of free carriers in the NC ground state. Using a combination of spectroscopy measurements and ab initio calculations, we hereby provide a theoretical model for both the linear and nonlinear optical properties of chalcopyrite CuFeS2 NCs, as a case study of IB semiconductor nanomaterials. Our results rationalize the high performance of IB nanomaterials as photothermal agents and suggest the use of IB semiconductors as alternatives to noble metals for technologies based on plasmonic materials.

Colloidal Monolayer ß-In2Se3 Nanosheets with High Photoresponsivity.

We report a low-temperature colloidal synthesis of single-layer, five-atom-thick, ß-In2Se3 nanosheets with lateral sizes tunable from ∼300 to ∼900 nm, using short aminonitriles (dicyandiamide or cyanamide) as shape controlling agents. The phase and the monolayer nature of the nanosheets were ascertained by analyzing the intensity ratio between two diffraction peaks from two-dimensional slabs of the various phases, determined by diffraction simulations. These findings were further backed-up by comparing and fitting the experimental X-ray diffraction pattern with Debye formula simulated patterns and with side-view high-resolution transmission electron microscopy imaging and simulation. The ß-In2Se3 nanosheets were found to be indirect band gap semiconductors (Eg = 1.55 eV), and single nanosheet photodetectors demonstrated high photoresponsivity and fast response times.

Role of the Crystal Structure in Cation Exchange Reactions Involving Colloidal Cu2Se Nanocrystals.

Stoichiometric Cu2Se nanocrystals were synthesized in either cubic or hexagonal (metastable) crystal structures and used as the host material in cation exchange reactions with Pb2+ ions. Even if the final product of the exchange, in both cases, was rock-salt PbSe nanocrystals, we show here that the crystal structure of the starting nanocrystals has a strong influence on the exchange pathway. The exposure of cubic Cu2Se nanocrystals to Pb2+ cations led to the initial formation of PbSe unselectively on the overall surface of the host nanocrystals, generating Cu2Se@PbSe core@shell nanoheterostructures. The formation of such intermediates was attributed to the low diffusivity of Pb2+ ions inside the host lattice and to the absence of preferred entry points in cubic Cu2Se. On the other hand, in hexagonal Cu2Se nanocrystals, the entrance of Pb2+ ions generated PbSe stripes "sandwiched" in between hexagonal Cu2Se domains. These peculiar heterostructures formed as a consequence of the preferential diffusion of Pb2+ ions through specific (a, b) planes of the hexagonal Cu2Se structure, which are characterized by almost empty octahedral sites. Our findings suggest that the morphology of the nanoheterostructures, formed upon partial cation exchange reactions, is intimately connected not only to the NC host material, but also to its crystal structure.

Colloidal Synthesis of Bipolar Off-Stoichiometric Gallium Iron Oxide Spinel-Type Nanocrystals with Near-IR Plasmon Resonance.

We report the colloidal synthesis of ∼5.5 nm inverse spinel-type oxide Ga2FeO4 (GFO) nanocrystals (NCs) with control over the gallium and iron content. As recently theoretically predicted, some classes of spinel-type oxide materials can be intrinsically doped by means of structural disorder and/or change in stoichiometry. Here we show that, indeed, while stoichiometric Ga2FeO4 NCs are intrinsic small bandgap semiconductors, off-stoichiometric GFO NCs, produced under either Fe-rich or Ga-rich conditions, behave as degenerately doped semiconductors. As a consequence of the generation of free carriers, both Fe-rich and Ga-rich GFO NCs exhibit a localized surface plasmon resonance in the near-infrared at ∼1000 nm, as confirmed by our pump-probe absorption measurements. Noteworthy, the photoelectrochemical characterization of our GFO NCs reveal that the majority carriers are holes in Fe-rich samples, and electrons in Ga-rich ones, highlighting the bipolar nature of this material. The behavior of such off-stoichiometric NCs was explained by our density functional theory calculations as follows: the substitution of Ga3+ by Fe2+ ions, occurring in Fe-rich conditions, can generate free holes (p-type doping), while the replacement of Fe2+ by Ga3+ cations, taking place in Ga-rich samples, produces free electrons (n-type doping). These findings underscore the potential relevance of spinel-type oxides as p-type transparent conductive oxides and as plasmonic semiconductors.

Thermal Stability and Anisotropic Sublimation of Two-Dimensional Colloidal Bi2Te3 and Bi2Se3 Nanocrystals.

The structural and compositional stabilities of two-dimensional (2D) Bi2Te3 and Bi2Se3 nanocrystals, produced by both colloidal synthesis and by liquid phase exfoliation, were studied by in situ transmission electron microscopy (TEM) during annealing at temperatures between 350 and 500 °C. The sublimation process induced by annealing is structurally and chemically anisotropic and takes place through the preferential dismantling of the prismatic {011̅0} type planes, and through the preferential sublimation of Te (or Se). The observed anisotropic sublimation is independent of the method of nanocrystal's synthesis, their morphology, or the presence of surfactant molecules on the nanocrystals surface. A thickness-dependent depression in the sublimation point has been observed with nanocrystals thinner than about 15 nm. The Bi2Se3 nanocrystals were found to sublimate below 280 °C, while the Bi2Te3 ones sublimated at temperatures between 350 and 450 °C, depending on their thickness, under the vacuum conditions in the TEM column. Density functional theory calculations confirm that the sublimation of the prismatic {011̅0} facets is more energetically favorable. Within the level of modeling employed, the sublimation occurs at a rate about 700 times faster than the sublimation of the {0001} planes at the annealing temperatures used in this work. This supports the distinctly anisotropic mechanisms of both sublimation and growth of Bi2Te3 and Bi2Se3 nanocrystals, known to preferentially adopt a 2D morphology. The anisotropic sublimation behavior is in agreement with the intrinsic anisotropy in the surface free energy brought about by the crystal structure of Bi2Te3 or Bi2Se3.

Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.

Hydrogen atoms play a key role in protein-ligand recognition. They determine the quality of established H-bonding networks and define the protonation of bound ligands. Structural visualization of H atoms by X-ray crystallography is rarely possible. We used neutron diffraction to determine the positions of the hydrogen atoms in the ligands aniline and 2-aminopyridine bound to the archetypical serine protease trypsin. The resulting structures show the best resolution so far achieved for proteins larger than 100 residues and allow an accurate description of the protonation states and interactions with nearby water molecules. Despite its low pKa of 4.6 and a large distance of 3.6 Što the charged Asp189 at the bottom of the S1 pocket, the amino group of aniline becomes protonated, whereas in 2-aminopyridine, the pyridine nitrogen picks up the proton although its amino group is 1.6 Šcloser to Asp189. Therefore, apart from charge-charge distances, tautomer stability is decisive for the resulting binding poses, an aspect that is pivotal for predicting correct binding.

Influence of the Ion Coordination Number on Cation Exchange Reactions with Copper Telluride Nanocrystals.

Cu2-xTe nanocubes were used as starting seeds to access metal telluride nanocrystals by cation exchanges at room temperature. The coordination number of the entering cations was found to play an important role in dictating the reaction pathways. The exchanges with tetrahedrally coordinated cations (i.e., with coordination number 4), such as Cd(2+) or Hg(2+), yielded monocrystalline CdTe or HgTe nanocrystals with Cu2-xTe/CdTe or Cu2-xTe/HgTe Janus-like heterostructures as intermediates. The formation of Janus-like architectures was attributed to the high diffusion rate of the relatively small tetrahedrally coordinated cations, which could rapidly diffuse in the Cu2-xTe NCs and nucleate the CdTe (or HgTe) phase in a preferred region of the host structure. Also, with both Cd(2+) and Hg(2+) ions the exchange led to wurtzite CdTe and HgTe phases rather than the more stable zinc-blende ones, indicating that the anion framework of the starting Cu2-xTe particles could be more easily deformed to match the anion framework of the metastable wurtzite structures. As hexagonal HgTe had never been reported to date, this represents another case of metastable new phases that can only be accessed by cation exchange. On the other hand, the exchanges involving octahedrally coordinated ions (i.e., with coordination number 6), such as Pb(2+) or Sn(2+), yielded rock-salt polycrystalline PbTe or SnTe nanocrystals with Cu2-xTe@PbTe or Cu2-xTe@SnTe core@shell architectures at the early stages of the exchange process. In this case, the octahedrally coordinated ions are probably too large to diffuse easily through the Cu2-xTe structure: their limited diffusion rate restricts their initial reaction to the surface of the nanocrystals, where cation exchange is initiated unselectively, leading to core@shell architectures. Interestingly, these heterostructures were found to be metastable as they evolved to stable Janus-like architectures if annealed at 200 °C under vacuum.

A theoretical investigation of the (0001) covellite surfaces.

We report on the properties of the (0001) covellites surfaces, which we investigate by periodic slab density functional theory calculations. The absolute surface energies have been computed for all bulk terminations, showing that surfaces terminated by the flat CuS layer are associated with the lowest surface energy. Cleavage is predicted to occur across the [0001] interlayer Cu-S bond. The surfaces obtained by lowest energy cleavage are analyzed in terms of the atomic vertical relaxation, workfunction, and surface band structure. Our study predicts the presence of a shallow pz-derived surface state located 0.26 eV below the Fermi level, which is set to play an important role in the surface reactivity of covellite.

Adsorption and friction behavior of amphiphilic polymers on hydrophobic surfaces.

The ability of amphiphilic polymers to self-assemble and form a gel or gel-like layer has been investigated by means of both experimental and theoretical studies on alkylated derivatives of poly(acrylic acid). Experiments were performed to determine the relationship between amphiphilic polymer chemistry, structure, water retention, and friction in the presence of hydrophobic substrates. The results indicate that the amphiphilic polymer forms a water-enriched, friction-reducing adsorbed layer on hydrophobic surfaces. The shear moduli and viscosities of the adsorbed layers, as determined by fitting the Voigt model to QCM-D data, were consistent with the presence of a gel. Computational studies on HPAA-12 were performed and are consistent with the presence of adsorbed conformations, in which the lowest free energy in the model corresponded to a partially adsorbed molecule, with a small fraction of hydrophobic side chains being compelled, for configurational reasons, to point into the bulk water. This would support the possibility of the formation of either a gel-like layer or surface aggregation. However, because the adsorption experiments showed no evidence of aggregation, this strongly suggests the formation of a gel.

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions.

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600 K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation.

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.

Docking algorithms for computer-aided drug discovery and design often ignore or restrain the flexibility of the receptor, which may lead to a loss of accuracy of the relative free enthalpies of binding. In order to evaluate the contribution of receptor flexibility to relative binding free enthalpies, two host-guest systems have been examined: inclusion complexes of α-cyclodextrin (αCD) with 1-chlorobenzene (ClBn), 1-bromobenzene (BrBn) and toluene (MeBn), and complexes of DNA with the minor-groove binding ligands netropsin (Net) and distamycin (Dist). Molecular dynamics simulations and free energy calculations reveal that restraining of the flexibility of the receptor can have a significant influence on the estimated relative ligand-receptor binding affinities as well as on the predicted structures of the biomolecular complexes. The influence is particularly pronounced in the case of flexible receptors such as DNA, where a 50% contribution of DNA flexibility towards the relative ligand-DNA binding affinities is observed. The differences in the free enthalpy of binding do not arise only from the changes in ligand-DNA interactions but also from changes in ligand-solvent interactions as well as from the loss of DNA configurational entropy upon restraining.

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum trajectory, with great savings in computational time required. This offers a theoretical bridge between the experimental static and dynamical properties of polymers.

Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.

Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 Å in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.

Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor.

Herein, we present a new computational approach for analyzing hydration patterns in biomolecular systems. This protocol aims to efficiently identify regions where structural waters may be located and, in the case of protein-ligand binding, where displacing one or more water molecules could be advantageous in terms of affinity and/or residence time. We validated our approach on the adenosine A2A receptor, a target of significant pharmaceutical relevance. The results of the approach are enriched with an extensive analysis of hydration in A2A and other members of the A-family of GPCRs using available crystallographic evidence and reviewing existing literature. As per the protein-ligand complex case, we conducted a more detailed study of a series of triazine analogues inhibiting A2A. The proposed approach provides results in good agreement with existing data and offers interpretability and simple and fast applicability.

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase.

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.