Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory.

Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme's semi-classical models (DFT-D), to different Kohn-Sham exchange-correlation functionals sometimes leads to variable and inconsistent results, which recommend a careful prior evaluation. In a recent study, we proposed a simple optimization protocol for enhancing the accuracy of these DFT-D methods by following an alternative and system-specific approach. Here, adopting the same computational strategy, we show how the accurate MC intermolecular interactions of a large set of water clusters of variable sizes (i.e., 300 (H2O)n structures, n = 9, 15, 27) can be reproduced remarkably well by dispersion-corrected DFT models (i.e., B3LYP-D4, PBE-D4, revPBE(0)-D4) upon re-optimization, reaching a mean absolute error per monomer of ~0.1 kcal/mol. Hence, the obtained results support the use of this procedure for fine-tuning tailored DFT-D models for the accurate description of targeted molecular systems.

One-step functionalization of mildly and strongly reduced graphene oxide with maleimide: an experimental and theoretical investigation of the Diels-Alder [4+2] cycloaddition reaction.

For large-scale graphene applications, such as the production of polymer-graphene nanocomposites, exfoliated graphene oxide (GO) and its reduced form (rGO) are presently considered to be very suitable starting materials, showing enhanced chemical reactivity with respect to pristine graphene, in addition to suitable electronic properties (i.e., tunable band gap). Among other chemical processes, a suitable way to obtain surface decoration of graphene is through a direct one-step Diels-Alder (DA) reaction, e.g. through the use of dienophile or diene moieties. However, the feasibility and extent of decoration largely depends on the specific graphene microstructure that in the case of rGO sheets is not easy to control and generally presents a high degree of inhomogeneity owing to various on-plane functionalization (e.g., epoxide and hydroxyl groups) or in-plane lattice defects. In an effort to gain some insights into the covalent functionalization of variably reduced GO samples, we present a combined experimental and theoretical study on the DA cycloaddition reaction of maleimide, a dienophile functional unit well-suited for chemical conjugation of polymers and macromolecules. In particular, we considered both mildly and strongly reduced GOs. Using thermogravimetry, Raman and X-Ray photoelectron spectroscopy, and elemental analysis we show evidence of variable chemical reactivity of rGO as a function of the residual oxygen content. Moreover, from quantum mechanical calculations carried out at the DFT level on different graphene reaction sites, we provide a more detailed molecular view to interpret experimental findings and to assess the reactivity series of different graphene modifications.

Expanding the Chemical Space of Tetracyanobuta-1,3-diene (TCBD) through a Cyano-Diels-Alder Reaction: Synthesis, Structure, and Physicochemical Properties of an Anthryl-fused-TCBD Derivative.

Tetracyanobuta-1,3-diene (TCBD) is a powerful and versatile electron-acceptor moiety widely used for the preparation of electroactive conjugates. While many reports addressing its electron-accepting capability have appeared in the literature, significantly scarcer are those dealing with its chemical modification, a relevant topic which allows to broaden the chemical space of this interesting functional unit. Here, we report on the first example of a high-yielding cyano-Diels-Alder (CDA) reaction between TCBD, that is, where a nitrile group acts as a dienophile, and an anthryl moiety, that is, acting as a diene. The resulting anthryl-fused-TCBD derivative, which structure was unambiguously identified by X-ray diffraction, shows high thermal stability, remarkable electron-accepting capability, and interesting electronic ground- and excited-state features, as characterized by a thorough theoretical, electrochemical, and photophysical investigation. Moreover, a detailed kinetic analysis of the intramolecular CDA reaction transforming the anthryl-TCBD-based reactant into the anthryl-fused-TCBD product was carried out at different temperatures.

Photoinduced azobenzene-modified DNA dehybridization: insights into local and cooperativity effects from a molecular dynamics study.

Photoresponsive azobenzene-modified DNA (RNA) has become a very fruitful material for nanotechnology due to the capability of switching on and off hybridization (i.e., duplex formation) in smart nanostructures. This nanomaterial exploits the well-known azobenzene trans/cis photo-isomerization. In fact, it has been found that DNA tethered with trans-azobenzene shows normal nucleic acid recognition and hybridization, while the cis form destabilizes the duplex configuration, eventually leading to DNA unzipping. However, while the working principle of the light-triggered DNA dehybridization is apparent, specific details of this mechanism still remain elusive to experiments. Previous in silico studies successfully addressed some aspects (e.g., local structural effects, thermal stability, and early events of azobenzene photoisomerization) of this challenging molecular process characterized by timescales spanning several orders of magnitude, from picoseconds (i.e., azobenzene photoisomerization) to micro- and milli-seconds (i.e., complete strand detachment). In this work, inspired by a recent report by Asanuma and coworkers, we focus on the local and cooperativity effects played by multiple azobenzene units on a 10-mer azobenzene-modified DNA duplex. Using molecular dynamics (MD) simulations, we investigated nine systems equipped with a variable number (from 1 to 7) of photoswitch units and different configurations, focusing our analysis on the initial events (from few ps to hundreds of ns) characterizing DNA destabilization upon trans-to-cis isomerization, such as hydrogen bonding breakage and base pair misalignment. Results highlight, on one hand, the local effects of single azobenzene units on DNA duplex structure and, on the other hand, the cooperative role that multiple photoswitches show in enhancing and accelerating DNA dehybridization following trans-to-cis conversion, in agreement with previously reported data and observations.

Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case.

Grimme's dispersion-corrected density functional theory (DFT-D) methods have emerged among the most practical approaches to perform accurate quantum mechanical calculations on molecular systems ranging from small clusters to microscopic and mesoscopic samples, i.e., including hundreds or thousands of molecules. Moreover, DFT-D functionals can be easily integrated into popular ab initio molecular dynamics (MD) software packages to carry out first-principles condensed-phase simulations at an affordable computational cost. Here, starting from the well-established D3 version of the dispersion-correction term, we present a simple protocol to improve the accurate description of the intermolecular interactions of molecular clusters of growing size, considering acetonitrile as a test case. Optimization of the interaction energy was performed with reference to diffusion quantum Monte Carlo calculations, successfully reaching the same inherent accuracy of the latter (statistical error of ∼0.1 kcal/mol per molecule). The refined DFT-D3 model was then used to perform ab initio MD simulations of liquid acetonitrile, again showing significant improvements toward available experimental data with respect to the default correction.

Enabling Racemization of Axially Chiral Subphthalocyanine-Tetracyanobutadiene-Aniline Enantiomers by Triplet State Photogeneration.

In recent years, several tetracyanobuta-1,3-diene (TCBD) conjugates have been prepared by linking the tetracyano unit to various electroactive moieties. These push-pull conjugates, besides showing interesting physicochemical properties, are axially chiral, a feature arising from the restricted rotation around the central bond of the butadiene. Yet, only in a few cases, separation and isolation of the enantiomers have been successfully achieved, owing to the configurational lability of the corresponding enantiopure species. Herein, we report the first example of photo- and electroactive TCBD-based derivatives showing unprecedented configurational stability and a peculiar light-triggered enantiomer conversion mechanism enabled by triple-state photogeneration. These systems represent a nice addition to the fast-increasing arsenal of artificial, light-controllable molecular switches.

Temperature Dependence of the Structure and Dynamics of a Dye-Labeled Lipid in a Planar Phospholipid Bilayer: A Computational Study.

Fluorescent probes are widely employed to label lipids for the investigation of structural and dynamic properties of model and cell membranes through optical microscopy techniques. Although the effect of tagging a lipid with an organic dye is generally assumed to be negligible, optically modified lipids can nonetheless affect the local lipid structure and, in turn, the lipid lateral mobility. To better assess this potential issue, all-atom (MD) molecular dynamics simulations have been performed to study structural and dynamic effects in a model DOPC membrane in the presence of a standard Rhodamine B-labeled DOPE lipid (RHB) as a function of temperature, i.e., 293 K, 303 K, and 320 K. As the temperature is increased, we observe similar changes in the structural properties of both pure DOPC and RHB-DOPC lipid bilayers: an increase of the area per lipid, a reduction of the membrane thickness and a decrease of lipid order parameters. The partial density profile of the RHB headgroups and their orientation within the lipid bilayer confirm the amphiphilic nature of the RHB fluorescent moiety, which mainly partitions in the DOPC glycerol backbone region at each temperature. Moreover, at all temperatures, our results on lipid lateral diffusion support a non-neutral role of the dye with respect to the unlabeled lipid mobility, thus suggesting important implications for optical microscopy studies of lipid membranes.

In silico investigation of the interaction between the voltage-gated potassium channel Kv4.3 and its auxiliary protein KChIP1.

The voltage-gated potassium channel Kv4.3 plays a vital role in shaping the timing, frequency, and backpropagation of electrical signals in the brain and heart by generating fast transient currents at subthreshold membrane potentials in repetitive firing neurons. To achieve its physiological function, Kv4.3 is assisted by auxiliary ß-subunits that become integral parts of the native A-type potassium channels, among which there are the Kv channel-interacting proteins (KChIPs). KChIPs are a family of cytosolic proteins that, when coexpressed with Kv4, lead to higher current density, modulation of channel inactivation and faster recovery from inactivation, while the loss of KChIP function may lead to severe pathological states. Recently, the structural basis of the KChIP1-Kv4.3 interaction was reported by using two similar X-ray crystallographic structures, which supported a crucial role for KChIP1 in enhancing the stability of the Kv4.3 tetrameric assembly, thus helping the trafficking of the channel to the plasma membrane. Here, we investigate through fully atomistic simulations the structure and stability of the human Kv4.3 tetramerization (T1) domain in complex with KChIP1 upon specific mutations located in the first and second interfaces of the complex, as compared to the wild-type (WT). Our results nicely complement the available structural and biophysical information collected so far on these complex variants. In particular, the degree of structural deviations and energetic instability, from small to substantial, observed in these variants with respect to the WT model seems to parallel well the level of channel dysfunction known from electrophysiology data. Our simulations provide an octameric structure of the WT KChIP1-Kv4.3 assembly very similar to the known crystal structures, and, at the same time, highlight the importance of a previously overlooked site of interaction between KChIP1 and the Kv4.3 T1 domain.

Electrostatic and Structural Bases of Fe2+ Translocation through Ferritin Channels.

Ferritin molecular cages are marvelous 24-mer supramolecular architectures that enable massive iron storage (>2000 iron atoms) within their inner cavity. This cavity is connected to the outer environment by two channels at C3 and C4 symmetry axes of the assembly. Ferritins can also be exploited as carriers for in vivo imaging and therapeutic applications, owing to their capability to effectively protect synthetic non-endogenous agents within the cage cavity and deliver them to targeted tissue cells without stimulating adverse immune responses. Recently, X-ray crystal structures of Fe2+-loaded ferritins provided important information on the pathways followed by iron ions toward the ferritin cavity and the catalytic centers within the protein. However, the specific mechanisms enabling Fe2+ uptake through wild-type and mutant ferritin channels is largely unknown. To shed light on this question, we report extensive molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements that characterize the transport properties and translocation mechanism of Fe2+ through the two ferritin channels, using the wild-type bullfrog Rana catesbeiana H' protein and some of its variants as case studies. We describe the structural features that determine Fe2+ translocation with atomistic detail, and we propose a putative mechanism for Fe2+ transport through the channel at the C3 symmetry axis, which is the only iron-permeable channel in vertebrate ferritins. Our findings have important implications for understanding how ion permeation occurs, and further how it may be controlled via purposely engineered channels for novel biomedical applications based on ferritin.

Introducing an artificial photo-switch into a biological pore: A model study of an engineered α-hemolysin.

In recent years, engineered biological pores responsive to external stimuli have been fruitfully used for various biotechnological applications. Moreover, the strategy of tethering photo-switchable moieties into biomolecules has provided an unprecedented temporal control of purposely designed nanodevices, as demonstrated, for example, by the light-mediated regulation of the activity of enzymes and biochannels. Inspired by these advancements, we propose here a de novo designed nanodevice featuring the α-hemolysin (αHL) membrane channel purposely functionalized by an artificial "on/off" molecular switch. The switch, which is based on the photo-isomerization of the azobenzene moiety, introduces a smart nano-valve into the natural non-gated pore to confer tunable transport properties. We validated through molecular dynamics simulations and free energy calculations the effective inter-conversion of the engineered αHL pore between two configurations corresponding to an "open" and a "closed" form. The reported switchable translocation of a single-stranded DNA fragment under applied voltage supports the promising capabilities of this nanopore prototype in view of molecular sensing, detection and delivery applications at single-molecule level.

Understanding the role of dynamics in the iron sulfur cluster molecular machine.

BACKGROUND: The bacterial proteins IscS, IscU and CyaY, the bacterial orthologue of frataxin, play an essential role in the biological machine that assembles the prosthetic FeS cluster groups on proteins. They form functionally binary and ternary complexes both in vivo and in vitro. Yet, the mechanism by which they work remains unclear. METHODS: We carried out extensive molecular dynamics simulations to understand the nature of their interactions and the role of dynamics starting from the crystal structure of a IscS-IscU complex and the experimentally-based model of a ternary IscS-IscU-CyaY complex and used nuclear magnetic resonance to experimentally test the interface. RESULTS: We show that, while being firmly anchored to IscS, IscU has a pivotal motion around the interface. Our results also describe how the catalytic loop of IscS can flip conformation to allow FeS cluster assembly. This motion is hampered in the ternary complex explaining its inhibitory properties in cluster formation. CONCLUSIONS: We conclude that the observed 'fluid' IscS-IscU interface provides the binary complex with a functional adaptability exploited in partner recognition and unravels the molecular determinants of the reported inhibitory action of CyaY in the IscS-IscU-CyaY complex explained in terms of the hampering effect on specific IscU-IscS movements. GENERAL SIGNIFICANCE: Our study provides the first mechanistic basis to explain how the IscS-IscU complex selects its binding partners and supports the inhibitory role of CyaY in the ternary complex.

The role of Tat peptide self-aggregation in membrane pore stabilization: insights from a computational study.

It is widely accepted that endocytosis mediates the uptake of cationic cell penetrating peptides (CPPs) at relatively low concentrations (i.e. nano- to micromolar), while direct transduction across the plasma membrane comes into play at higher concentrations (i.e. micro- to millimolar). This latter process appears to depend on peptide-driven cellular processes, which in turn may induce local perturbations of plasma-membrane composition and/or integrity, and to be favored by peptide aggregation, especially into dimers. Besides, in most studies CPPs are tethered to fluorescent dyes in order to track peptide transduction events under the microscope, although often overlooking the possible role played by the dyes in assisting translocation. In an effort to provide some insights into the transduction process, here we report on a molecular dynamics (MD) simulation study of a prototype of the CPP family, namely the Tat11 arginine-rich motif. To be specific, the translocation of Tat11 across a purposely-created membrane pore, either or not covalently-linked to the tetramethylrhodamine-5-maleimide (TAMRA) dye and in both its monomeric and dimeric form, is analyzed in some detail. Results from several unconstrained and steered MD simulations, as well as energy decomposition analysis, nicely support the latest experimental evidence and help to shed light on key factors enabling peptide transduction. In particular, our study highlights the much slower translocation kinetics of Tat11 dimer in comparison to the single peptide, and therefore its enhanced capability to stabilize membrane pores. Notably, it also shows how TAMRA has overall negligible kinetic and energetic effects on peptide transduction, yet it promotes this process indirectly by favoring peptide aggregation.

Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations.

Fluorescent molecular rotors (FMRs) belong to an important class of environment-sensitive dyes capable of acting as nanoprobes in the measurement of viscosity and polarity of their micro-environment. FMRs have found widespread applications in various research fields, ranging from analytical to biochemical sciences, for example in intracellular imaging studies or in volatile organic compound detection. Here, a computational investigation of a recently proposed FMR, namely 4-(diphenylamino)phthalonitrile (DPAP), in various chemical environments is presented. A purposely developed molecular mechanics force field is proposed and then applied to simulate the rotor in a high- and low-polar solvent (i.e., acetonitrile, tetrahydrofuran, o-xylene and cyclohexane), a polymer matrix and a lipid membrane. Subtle effects of the molecular interactions with the embedding medium, the structural fluctuations of the rotor and its rotational dynamics are analyzed in some detail. The results correlate with a previous work, thus supporting the reliability of the model, and provide further insights into the environment-specific properties of the dye. In particular, it is shown how molecular diffusion and rotational correlation times of the FMR are affected by the surrounding medium and how the molecular orientation of the dye becomes anisotropic once immersed in the lipid bilayer. Moreover, a qualitative correlation between the FMR rotational dynamics and the fluorescence lifetime is detected, a result in line with the observed viscosity dependence of its emission. Finally, optical absorption spectra are computed and successfully compared with their experimental counterparts.

Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides.

Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.

Boundary condition effects on the dynamic and electric properties of hydration layers.

Water solvation has a central role in several biochemical processes ranging from protein folding to biomolecular recognition and enzyme catalysis. Because of its importance, the structure and dynamics of hydration layers around biological macromolecules have been the targets of a great number of experimental and computational studies. In the present contribution, we have investigated the effects of periodic boundary conditions (PBCs), as used in conjunction with molecular dynamics (MD) simulations, on the dynamic and electric properties of water layers. In particular, we have systematically performed MD simulations of neat water and biomolecules in aqueous solutions by imposing a different external dielectric constant, a generally overlooked parameter in PBC simulations. The effect of the system size has also been addressed. Overall, our results consistently indicate that the dipole moment properties of water layers, and specifically the dipole moment fluctuations and the reorientational correlation functions, can be sensitive to the choice of the external boundary conditions, whereas other molecular properties, such as the self-diffusion coefficient and the reorientational relaxation times, are not affected. We think that our investigation may help to assess appropriate simulation conditions for modeling the aqueous environment of relevant biochemical systems and processes.

Thermodynamics of Metal-Acetate Interactions.

Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C4 parameters for the 12-6-4 LJ nonbonded model to be used with three widely employed water models (Transferable Intermolecular Potential with 3 Points (TIP3P), Simple Point Charge Extended (SPC/E), and Optimal Point Charge (OPC) water models). These parameters can accurately match the experimental binding free energy between 11 metal ions and acetate. These parameters can be applied to the study of metalloproteins and transition metal ion channels and transporters, as acetate serves as a representative of the negatively charged amino acid side chains from aspartate and glutamate.

An improved AMBER force field for α,α-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems.

α,α-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely Aib (α-aminoisobutyric acid), appears to play a dominant role in determining the preferred conformations of host proteins. We have recently introduced into the standard AMBER force field some new parameters, fitted against high-level quantum mechanical (QM) data, for simulating peptides containing α,α-dialkylated residues with cyclic side chains, such as TOAC (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) and Ac6c (Ac6c = 1-aminocyclohexaneacetic acid). Here, we show that in order to accurately reproduce the observed conformational geometries and structural fluctuations of linear α,α-dialkylated peptides based on Aib, further improvements of the non-bonding and side chain torsion potential parameters have to be considered, due to the expected larger structural flexibility of linear residues with respect to cyclic ones. To this end, we present an extended set of parameters, which have been optimized by fitting the energies of multiple conformations of the Aib dipeptide analogue to corresponding QM calculations that properly account for dispersion interactions (B3LYP-D3). The quality, transferability and size-consistency of the proposed force field have been assessed both by considering a series of poly-Aib peptides, modeled at the same QM level, and by performing molecular dynamics simulations in solvents with high and low polarity. As a result, the present parameters allow one to reproduce with good reliability the available QM and experimental data, thus representing a notable improvement over current force field especially in the description of the α/310-helix conformational equilibria of α,α-dialkylated peptides with linear and cyclic side chains.

Extension of the AMBER force field to cyclic α,α dialkylated peptides.

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing α,α dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and α-helical structures is established in aqueous solution, in agreement with EPR data.

Stochastic Model of Solvent Exchange in the First Coordination Shell of Aqua Ions.

Ion microsolvation is a basic, yet fundamental, process of ionic solutions underlying many relevant phenomena in either biological or nanotechnological applications, such as solvent reorganization energy, ion transport, catalytic activity, and so on. As a consequence, it is a topic of extensive investigations by various experimental techniques, ranging from X-ray diffraction to NMR relaxation and from calorimetry to vibrational spectroscopy, and theoretical approaches, especially those based on molecular dynamics (MD) simulations. The conventional microscopic view of ion solvation is usually provided by a "static" cluster model representing the first ion-solvent coordination shell. Despite the merits of such a simple model, however, ion coordination in solution should be better regarded as a complex population of dynamically interchanging molecular configurations. Such a more comprehensive view is more subtle to characterize and often elusive to standard approaches. In this work, we report on an effective computational strategy aiming at providing a detailed picture of solvent coordination and exchange around aqua ions, thus including the main structural, thermodynamic, and dynamic properties of ion microsolvation, such as the most probable first-shell complex structures, the corresponding free energies, the interchanging energy barriers, and the solvent-exchange rates. Assuming the solvent coordination number as an effective reaction coordinate and combining MD simulations with enhanced sampling and master-equation approaches, we propose a stochastic model suitable for properly describing, at the same time, the thermodynamics and kinetics of ion-water coordination. The model is successfully tested toward various divalent ions (Ca2+, Zn2+, Hg2+, and Cd2+) in aqueous solution, considering also the case of a high ionic concentration. Results show a very good agreement with those issuing from brute-force MD simulations, when available, and support the reliable prediction of rare ion-water complexes and slow water exchange rates not easily accessible to usual computational methods.

Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics.

Morphological analysis of protein channels is a key step for a thorough understanding of their biological function and mechanism. In this respect, molecular dynamics (MD) is a very powerful tool, enabling the description of relevant biological events at the atomic level, which might elude experimental observations, and pointing to the molecular determinants thereof. In this work, we present a computational geometry-based approach for the characterization of the shape and dynamics of biological ion channels or pores to be used in combination with MD trajectories. This technique relies on the earliest works of Edelsbrunner and on the NanoShaper software, which makes use of the alpha shape theory to build the solvent-excluded surface of a molecular system in an aqueous solution. In this framework, a channel can be simply defined as a cavity with two entrances on the opposite sides of a molecule. Morphological characterization, which includes identification of the main axis, the corresponding local radius, and the detailed description of the global shape of the cavity, is integrated with a physico-chemical description of the surface facing the pore lumen. Remarkably, the possible existence or temporary appearance of fenestrations from the channel interior towards the outer lipid matrix is also accounted for. As a test case, we applied the present approach to the analysis of an engineered protein channel, the mechanosensitive channel of large conductance.