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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.

The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance (SPR) measurements, and X-ray crystallography experiments. Our analysis shows that the protein-ligand association rate (kon) dramatically increases with the ligand's hydrophobicity, pointing to the existence of a prebinding stage largely stabilized by a favorable packing of the ligand's apolar moieties with the hCAII "hydrophobic wall". The characterization of the binding pathway allows an unprecedented understanding of the structure-kinetic relationship in hCAII/benzenesulfonamide complexes, depicting a paradigmatic scenario for the multistep binding process in protein-ligand systems.

Colloidal CuFeS2 Nanocrystals: Intermediate Fe d-Band Leads to High Photothermal Conversion Efficiency.

We describe the colloidal hot-injection synthesis of phase-pure nanocrystals (NCs) of a highly abundant mineral, chalcopyrite (CuFeS2). Absorption bands centered at around 480 and 950 nm, spanning almost the entire visible and near-infrared regions, encompass their optical extinction characteristics. These peaks are ascribable to electronic transitions from the valence band (VB) to the empty intermediate band (IB), located in the fundamental gap and mainly composed of Fe 3d orbitals. Laser-irradiation (at 808 nm) of an aqueous suspension of CuFeS2 NCs exhibited significant heating, with a photothermal conversion efficiency of 49%. Such efficient heating is ascribable to the carrier relaxation within the broad IB band (owing to the indirect VB-IB gap), as corroborated by transient absorption measurements. The intense absorption and high photothermal transduction efficiency (PTE) of these NCs in the so-called biological window (650-900 nm) make them suitable for photothermal therapy as demonstrated by tumor cell annihilation upon laser irradiation. The otherwise harmless nature of these NCs in dark conditions was confirmed by in vitro toxicity tests on two different cell lines. The presence of the deep Fe levels constituting the IB is the origin of such enhanced PTE, which can be used to design other high performing NC photothermal agents.

Pyramid-Shaped Wurtzite CdSe Nanocrystals with Inverted Polarity.

We report on pyramid-shaped wurtzite cadmium selenide (CdSe) nanocrystals (NCs), synthesized by hot injection in the presence of chloride ions as shape-directing agents, exhibiting reversed crystal polarity compared to former reports. Advanced transmission electron microscopy (TEM) techniques (image-corrected high-resolution TEM with exit wave reconstruction and probe-corrected high-angle annular dark field-scanning TEM) unequivocally indicate that the triangular base of the pyramids is the polar (0001̅) facet and their apex points toward the [0001] direction. Density functional theory calculations, based on a simple model of binding of Cl(-) ions to surface Cd atoms, support the experimentally evident higher thermodynamic stability of the (0001̅) facet over the (0001) one conferred by Cl(-) ions. The relative stability of the two polar facets of wurtzite CdSe is reversed compared to previous experimental and computational studies on Cd chalcogenide NCs, in which no Cl-based chemicals were deliberately used in the synthesis or no Cl(-) ions were considered in the binding models. Self-assembly of these pyramids in a peculiar clover-like geometry, triggered by the addition of oleic acid, suggests that the basal (polar) facet has a density and perhaps type of ligands significantly different from the other three facets, since the pyramids interact with each other exclusively via their lateral facets. A superstructure, however with no long-range order, is observed for clovers with their (0001̅) facets roughly facing each other. The CdSe pyramids were also exploited as seeds for CdS pods growth, and the peculiar shape of the derived branched nanostructures clearly arises from the inverted polarity of the seeds.

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.

Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance.

Cu3-x P Nanocrystals as a Material Platform for Near-Infrared Plasmonics and Cation Exchange Reactions.

Synthesis approaches to colloidal Cu3P nanocrystals (NCs) have been recently developed, and their optical absorption features in the near-infrared (NIR) have been interpreted as arising from a localized surface plasmon resonance (LSPR). Our pump-probe measurements on platelet-shaped Cu3-x P NCs corroborate the plasmonic character of this absorption. In accordance with studies on crystal structure analysis of Cu3P dating back to the 1970s, our density functional calculations indicate that this material is substoichiometric in copper, since the energy of formation of Cu vacancies in certain crystallographic sites is negative, that is, they are thermodynamically favored. Also, thermoelectric measurements point to a p-type behavior of the majority carriers from films of Cu3-x P NCs. It is likely that both the LSPR and the p-type character of our Cu3-x P NCs arise from the presence of a large number of Cu vacancies in such NCs. Motivated by the presence of Cu vacancies that facilitate the ion diffusion, we have additionally exploited Cu3-x P NCs as a starting material on which to probe cation exchange reactions. We demonstrate here that Cu3-x P NCs can be easily cation-exchanged to hexagonal wurtzite InP NCs, with preservation of the anion framework (the anion framework in Cu3-x P is very close to that of wurtzite InP). Intermediate steps in this reaction are represented by Cu3-x P/InP heterostructures, as a consequence of the fact that the exchange between Cu+ and In3+ ions starts from the peripheral corners of each NC and gradually evolves toward the center. The feasibility of this transformation makes Cu3-x P NCs an interesting material platform from which to access other metal phosphides by cation exchange.