Following nature's example, there is currently strong interest in using adenosine 5′-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC16 TACN]2+) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn2+ and with methyl-1,4,7-triazacyclononane ([ZnCH3 TACN]2+), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn2+ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH3 TACN which, however, may be important for the build-up of supramolecular assemblies. © 2023 The Royal Society of Chemistry.

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration. © 2023 American Chemical Society. All rights reserved.

The water/fluorite interface is of relevance to diverse industrial, environmental, and medical applications. In this contribution we review some of our recent results on the dynamics of water in contact with the solid calcium fluoride at low pH, where localised charge can develop upon fluorite dissolution. We use ab initio molecular dynamics simulations, including the full electronic structure, to simulate the vibrational energy relaxation and to quantify the heterogeneity of the interfacial water molecules. We find that strongly hydrogen-bonded OH groups display very rapid spectral diffusion and vibrational relaxation; for weakly H-bonded OD groups, the dynamics is instead much slower. Detailed analysis of the simulations reveals the molecular origin of energy transport through the local hydrogen-bond network. In particular, we find that the water molecules in the adsorbed layer, whose orientation is pinned by the localised charge defects, can exchange vibrational energy using just half a solvation shell, thanks to the strong dipole-dipole alignment between H-bond donor and acceptor. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2021.

The charge state of dielectric surfaces in aqueous environments is of fundamental and technological importance. Here, we study the influence of dissolved molecular CO2on the charging of three chemically different surfaces (SiO2, Polystyrene, Perfluorooctadecyltrichlorosilane). We determine their charge state from electrokinetic experiments. We compare an ideal, CO2-free reference system to a system equilibrated against ambient CO2conditions. In the reference system, the salt-dependent decrease of the magnitudes of ζ-potentials follows the expectations for a constant charge scenario. In the presence of CO2, the starting potential is lower by some 50%. The following salt-dependent decrease is weakened for SiO2and inverted for the organic surfaces. We show that screening and pH-driven charge regulation alone cannot explain the observed effects. As an additional cause, we tentatively suggest dielectric regulation of surface charges due to a diffusively adsorbed thin layer of molecular CO2. The formation of such a dynamic layer, even at the hydrophilic and partially ionized silica surfaces, is supported by a minimal theoretical model and results from molecular simulations. © 2022 American Chemical Society. All rights reserved.

Understanding the acid/base behavior of environmentally relevant organic acids is of key relevance for accurate climate modelling. Here we investigate the effect of pH on the (de)protonation state of pyruvic acid at the air-water interface and in bulk by using the analytical techniques surface-specific vibrational sum frequency generation and attenuated total reflection spectroscopy. To provide a molecular interpretation of the observed behavior, simulations are carried out using a free energy perturbation approach in combination with electronic structure-based molecular dynamics. In both the experimental and theoretical results we observe that the protonated form of pyruvic acid is preferred at the air-water interface. The increased proton affinity is the result of the specific microsolvation at the interface. © 2022 The Royal Society of Chemistry

It has been shown that a weak shear can induce crystallisation in a disordered, glassy state. In this study, we use molecular dynamics simulations in order to investigate the out-of-equilibrium properties of [BMIM][BF4] confined between metal slabs. In particular, we want to understand the extent to which the shear flow modifies the interfacial properties. In particular, the questions we address here are (i) is the shear able to promote the crystalline phase in [BMIM][BF4]? (ii) Can, as a consequence of shear flow, a solid-like layer develop at the interface with a metallic surface? (iii) What are the tribological properties of nanoconfined [BMIM][BF4]? We find that the system behaves quite differently from the ideal linear Couette flow. Indeed, the portion of fluid closer to the shearing slabs behaves as a disordered, solid-like layer, which, under the investigated conditions extends to a few nanometres. The linear velocity regime is only recovered in the central region of the ionic liquid slab. The formation of such a solid-like glassy rather than crystalline layer is in agreement with recent mechanical impedance measurements performed on nano-confined ionic liquids. © the Owner Societies 2021.

We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages that stabilize their formation and leading to narrower inter-micelles channels that smooth down their anisotropic growth. Absorption spectroscopy and scanning electron microscopy confirmed the formation of nanograins and demonstrated the importance of surfactant concentration on driving the growth towards nano-bipyramids rather than nanorods. The outcome explains the formation of the monodisperse bipyramidal nano-objects, the origin of their controlled shapes and sizes along with their remarkable stability. © The Royal Society of Chemistry.

The use of biomolecules as capping and reducing agents in the synthesis of metallic nanoparticles constitutes a promising framework to achieve desired functional properties with minimal toxicity. The system's complexity and the large number of variables involved represent a challenge for theoretical and experimental investigations aiming at devising precise synthesis protocols. In this work, we use L-asparagine (Asn), an amino acid building block of large biomolecular systems, to synthesise gold nanoparticles (AuNPs) in aqueous solution at controlled pH. The use of Asn offers a primary system that allows us to understand the role of biomolecules in synthesising metallic nanoparticles. Our results indicate that AuNPs synthesised in acidic (pH 6) and basic (pH 9) environments exhibit somewhat different morphologies.We investigate these AuNPs via Raman scattering experiments and classical molecular dynamics simulations of zwitterionic and anionic Asn states adsorbing on (111)-, (100)-, (110)-, and (311)-oriented gold surfaces. A combined analysis suggests that the underlying mechanism controlling AuNPs geometry correlates with amine's preferential adsorption over ammonium groups, enhanced upon increasing pH. Our simulations reveal that Asn (both zwitterionic and anionic) adsorption on gold (111) is essentially different from adsorption on more open surfaces. Water molecules strongly interact with the gold face-centred-cubic lattice and create traps, on the more open surfaces, that prevent the Asn from diffusing. These results indicate that pH is a relevant parameter in green-synthesis protocols with the capability to control the nanoparticle's geometry, and pave the way to computational studies exploring the effect of water monolayers on the adsorption of small molecules on wet gold surfaces. © 2021 The Author(s).

Atomistic mass and charge distribution at electrified interfaces play a key role in electrochemical phenomena of huge technological relevance for energy production and conversion. However, in spite of its importance, the structure of the double layer at the nanoscale is still to a large extent unknown, even for Pt-water, the most fundamental electrochemical interface. Using a new, general ab initio methodology to model charged electrodes, we simulate the atomistic structure of the Pt-water double layer and its response to an applied potential, in realistic solution conditions. We evaluate the interface capacitance and the absolute electrode potential for three states of charge of the electrode. We reveal that electrode polarisation induces interfacial electronic charge spillover and oscillation, and changes the surface coverage of the first adsorbed water layer. Since the molecules in this layer are all found to be equally charged, the interface dipole is strongly affected by such change of coverage, while water reorientation becomes relevant only from the second water layer. Our findings will be essential to develop highly realistic models for catalytic processes at the Pt-water interface. © 2021

The peculiar properties of ionic liquids in confinement have not only become essential for energy storage, catalysis and tribology, but still pose fundamental questions. Recently, an anomalous liquid-solid phase transition has been observed in atomic force microscopy experiments for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), the transition being more pronounced for metallic surfaces. Image charges have been suggested as the key element driving the anomalous freezing. Using atomistic molecular dynamics simulations, we investigate the impact of image charges on structure, dynamics and thermodynamics of [BMIM][BF4] confined between gold electrodes. Our results not only unveil a minor role played by the metal polarisation, but also provide a novel description of the interfacial layer. Although no diffuse layer can be defined in terms of the electrostatic potential, long range effects are clearly visible in the dynamical properties up to 10 nanometers away from the surface, and are expected to influence viscous forces in the experiments. This journal is © the Owner Societies.

This chapter specifically focuses on oxide/liquid water interfaces and in particular on the silica/water and silica/water/electrolyte interfaces, and on the calcium fluorite/water interfaces. Because of their original properties, distinct from the individual bulk media, solid/liquid interfaces and in particular solid/water interfaces play crucial roles in various fields of modern chemistry. The chapter looks at the structural arrangement of interfacial water molecules at the interface with the crystalline α-quartz oxide surface from a more chemical point of view. It reviews ab initio molecular dynamics in the framework of density functional theory (DFT) and its implementations in terms of Born-Oppenheimer molecular dynamics, as well as the theoretical approaches to nonlinear vibrational sum frequency generation theoretical spectroscopy and acidity constant calculations. One ingenious approach to the solution of the electronic structure problem is represented by DFT. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA.

We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface-specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D2O) molecules and provide information about the sub-picosecond vibrational-energy-relaxation dynamics at the buried solid/liquid interface. We find that strongly H-bonded OD groups, with a vibrational frequency below 2500 cm−1, display very rapid spectral diffusion and vibrational relaxation; for weakly H-bonded OD groups, above 2500 cm−1, the dynamics slows down substantially. Atomistic simulations based on electronic-structure theory reveal the molecular origin of energy transport through the local H-bond network. We conclude that strongly oriented H-bonded water molecules in the adsorbed layer, whose orientation is pinned by the localized charge defects, can exchange vibrational energy very rapidly due to the strong collective dipole, compensating for a partially missing solvation shell. © 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

The adsorption of gas-phase pyruvic acid (CH 3 COCOOH) on hydroxylated silica particles has been investigated at 296 K using transmission Fourier transform infrared (FTIR) spectroscopy and theoretical simulations. Under dry conditions (<1% relative humidity, RH), both the trans-cis (Tc) and trans-trans (Tt) pyruvic acid conformers are observed on the surface as well as the (hydrogen bonded) pyruvic acid dimer. The detailed surface interactions were further understood through ab initio molecular dynamics simulations. Under higher relative humidity conditions (above 10% RH), adsorbed water competes for surface adsorption sites. Adsorbed water is also observed to change the relative populations of the different adsorbed pyruvic acid configurations. Overall, this study provides valuable insights into the interaction of pyruvic acid with hydroxylated silica surfaces on the molecular level from both experimental and theoretical analyses. Furthermore, these results highlight the importance of the environment (relative humidity and coadsorbed water) in the adsorption, partitioning, and configurations of pyruvic acid at the surface. Copyright © 2019 American Chemical Society.

Background: Silica continues to represent an intriguing topic of fundamental and applied research across various scientific fields, from geology to physics, chemistry, cell biology, and particle toxicology. The pathogenic activity of silica is variable, depending on the physico-chemical features of the particles. In the last 50 years, crystallinity and capacity to generate free radicals have been recognized as relevant features for silica toxicity. The 'surface' also plays an important role in silica toxicity, but this term has often been used in a very general way, without defining which properties of the surface are actually driving toxicity. How the chemical features (e.g., silanols and siloxanes) and configuration of the silica surface can trigger toxic responses remains incompletely understood. Main body: Recent developments in surface chemistry, cell biology and toxicology provide new avenues to improve our understanding of the molecular mechanisms of the adverse responses to silica particles. New physico-chemical methods can finely characterize and quantify silanols at the surface of silica particles. Advanced computational modelling and atomic force microscopy offer unique opportunities to explore the intimate interactions between silica surface and membrane models or cells. In recent years, interdisciplinary research, using these tools, has built increasing evidence that surface silanols are critical determinants of the interaction between silica particles and biomolecules, membranes, cell systems, or animal models. It also has become clear that silanol configuration, and eventually biological responses, can be affected by impurities within the crystal structure, or coatings covering the particle surface. The discovery of new molecular targets of crystalline as well as amorphous silica particles in the immune system and in epithelial lung cells represents new possible toxicity pathways. Cellular recognition systems that detect specific features of the surface of silica particles have been identified. Conclusions: Interdisciplinary research bridging surface chemistry to toxicology is progressively solving the puzzling issue of the variable toxicity of silica. Further interdisciplinary research is ongoing to elucidate the intimate mechanisms of silica pathogenicity, to possibly mitigate or reduce surface reactivity. © 2019 The Author(s).

Amorphous silica is an intrinsic challenging system to study. In the last decades, some particular chemical properties have been discovered and described, but their description and understanding at the molecular level are experimentally difficult. Therefore, theoretical quantum chemical methods and descriptors, combined with experimental input, are a very appropriate set up to tackle this topic. In this study, the acidity of silanol groups of amorphous silica in hydrated conditions is investigated. Special attention has been drawn to the chemical shift, but also Bader charges, and vibrational frequencies with their intensities. The known bimodal acidity behavior was recovered and rationalized. The findings support that the chemistry of the silica surface is not determined by a single site or a family of sites but by a broad distribution of very different geometries of silanol groups in a H-bond network that can eventually show very acidic and at the same time very basic properties. © 2019 American Chemical Society.

What happens when extra vibrational energy is added to water? Using nonequilibrium molecular dynamics simulations, also including the full electronic structure, and novel descriptors, based on projected vibrational density of states, we are able to follow the flow of excess vibrational energy from the excited stretching and bending modes. We find that the energy relaxation, mostly mediated by a stretching-stretching coupling in the first solvation shell, is highly heterogeneous and strongly depends on the local environment, where a strong hydrogen bond network can transport energy with a time scale of 200 fs, whereas a weaker network can slow down the transport by a factor 2-3. Copyright © 2018 American Chemical Society.

We present a measurement cell that allows simultaneous measurement of second harmonic generation (SHG) and streaming potential (SP) at mineral-water interfaces with flat specimen that are suitable for non-linear optical (NLO) studies. The set-up directly yields SHG data for the interface of interest and can also be used to obtain information concerning the influence of flow on NLO signals from that interface. The streaming potential is at present measured against a reference substrate (PTFE). The properties of this inert reference can be independently determined for the same conditions. With the new cell, for the first time the SHG signal and the SP for flat surfaces have been simultaneously measured on the same surface. This can in turn be used to unambiguously relate the two observations for identical solution composition. The SHG test of the cell with a fluorite sample confirmed previously observed differences in NLO signal under flow vs. no flow conditions in sum frequency generation (SFG) investigations. As a second test surface, an inert (“hydrophobic”) OTS covered sapphire-c electrolyte interface was studied to verify the zeta-potential measurements with the new cell. For this system we obtained combined zeta-potential/SHG data in the vicinity of the point of zero charge, which were found to be proportional to each other as expected. Furthermore, on the accessible time scales of the SHG measurements no effects of flow, flow velocity and stopped flow occurred on the interfacial water structure. This insensitivity to flow for the inert surface was corroborated by concomitant molecular dynamics simulations. Finally, the set-up was used for simultaneous measurements of the two properties as a function of pH in automated titrations with an oxidic surface. Different polarization combinations obtained in two separate titrations, yielded clearly different SHG data, while under identical conditions zeta-potentials were exactly reproduced. The polarization combination that is characteristic for dipoles perpendicular to the surface scaled with the zeta-potentials over the pH-range studied, while the other did not. The work provides an advanced approach for investigating liquid/surface interactions which play a major role in our environment. The set-up can be upgraded for SFG studies, which will allow more detailed studies on the chemistry and the water structure at a given interface, but also the combined study of specific adsorption including kinetics in combination with electrokinetics. Such investigations are crucial for the basic understanding of many environmental processes from aquatic to atmospheric systems. © 2018 Elsevier Inc.

Although they have been widely used as models for oxide surfaces, the deprotonation behaviors of the Keggin-ions (MeAl127+) and typical oxide surfaces are very different. On Keggin-ions, the deprotonation occurs over a very narrow pH range at odds with the broad charging curve of larger oxide surfaces. Depending on the Me concentration, the deprotonation curve levels off sooner (high Me concentration) or later (for low Me concentration). The leveling off shows the onset of aggregation before which the Keggin-ions are present as individual units. We show that the atypical titration data previously observed for some GaAl12 solutions in comparison to the originally reported data can be explained by the presence of Ga2Al11 ions. The pKa value of aquo-groups bound to octahedral Ga was determined from ab initio molecular dynamics simulations relative to the pure GaAl12 ions. Using these results within a surface complexation model, the onset of deprotonation of the crude solution is surprisingly well predicted and the ratio between the different species is estimated to be in the proportion 20 (Ga2Al11): 20 (Al13): 60 (GaAl12). © 2018 Author(s).

Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ∼picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead-H group and the hydrophobic Ctail-H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead-H group is slower because of the strong coulombic interaction with the nitrate counter-ionic anions, while the dynamics of the Ctail-H group is faster because of the weaker van der Waals interaction with the surrounding atoms. In particular, the rotation of the Nhead-H group slows down with increasing cationic chain length, while the rotation of the Ctail-H group shows little dependence on the cationic chain length, manifesting that the dynamical heterogeneity is enhanced with a longer cationic chain. The slowdown of the Nhead-H group with increasing cationic chain length is associated with a lower number of nitrate anions near the Nhead-H group, which presumably results in the increase of the energy barrier for the rotation. The sensitivity of the Nhead-H rotation to the number of surrounding nitrate anions, in conjunction with the varying number of nitrate anions, gives rise to a broad distribution of Nhead-H reorientation times. Our results suggest that the asymmetry of the cations and the larger excluded volume for longer cationic chain are important for both the structural heterogeneity and the dynamical heterogeneities. The observed dynamical heterogeneities may affect the rates of chemical reactions depending on where the reactants are solvated in ionic liquids and provide an additional guideline for the design of RTILs as solvents. © 2018 Author(s).

As shown by a quite significant amount of literature, acids at the water surface tend to be "less" acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units. Such increased acidity is the result of the specific microsolvation at the interface and, in particular, of the stabilization of the deprotonated form by the silanols on the quartz surface and the special interfacial water layer. © 2018 American Chemical Society.

Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals. © 2018 The Author(s).

At the interface, the properties of water can be rather different from those observed in the bulk. In this chapter we present an overview of our computational approach to understand water structure and dynamics at the interface including atomistic and electronic structure details. In particular we show how Density Functional Theory-based molecular dynamics simulations (DFT-MD) of water interfaces can provide a microscopic interpretation of recent experimental results from surface sensitive vibrational Sum Frequency Generation spectroscopy (SFG). In our recent work we developed an expression for the calculation of the SFG spectra of water interfaces which is based on the projection of the atomic velocities on the local normal modes. Our approach permits to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated to the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region. The results for the water-air interface, obtained using extensive ab initio molecular dynamics simulations over 400 ns, are discussed in connection to recent phase resolved experimental data. © Springer International Publishing AG 2018.

The adsorption of GLY-PRO-GLU tripeptide on Au(110) is investigated within the frame of all atom classical mechanics simulations and Density Functional Theory, focusing on the surface reconstruction. It is shown that the tripeptide adsorption reorganizes and restructures the Au(110) surface. A mechanism for the surface restructuration is proposed for both the neutral and zwitterionic form of the peptide at room temperature in Ultra High Vacuum. Diverse residues may be involved in the Au atoms displacement, and in particular glutamic acid, triggering a double proton transfer and the formation of a zwitter ionic state, is found to be responsible for the triggering of the surface reconstruction. © 2018 Elsevier B.V.

Water/mineral interfaces are central to a wide range of environmental and technological processes. In this report we provide a quantitative, molecular-level understanding of the CaF2/water interface using Density Functional Theory-based molecular dynamics simulations. In particular through the comparison of calculated Vibrational Sum Frequency Generation spectra to the experimental ones, we give a structural characterisation of the interface at different pH. At low pH, the surface is positively charged, causing a substantial degree of water ordering. Our results suggest that the surface charge originates from the dissolution of fluoride ions of the topmost layer, rather than from proton adsorption to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. Such OH groups do not establish hydrogen bonds with the surrounding water, and are therefore responsible for the “free OH�? signature which is recorded in the Vibrational Sum Frequency Generation spectrum. © Springer International Publishing AG 2016. All rights reserved.

Nanophase segregation of a bicomponent thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of interchain hydrogen bonds. The predicted phase segregation is experimentally confirmed by the synthesis of 35 and 15 nm gold nanoparticles functionalized with several binary mixtures of ligands. An extensive study by transmission electron microscopy and electron tomography, using silica selective heterogeneous nucleation on acid-rich domains to provide electron contrast, supports simulations and highlights patchy nanoparticles with a trend toward Janus nano-objects depending on the nature of the ligands and the particle size. These results validate our computational platform as an effective tool to predict nanophase separation in organic mixtures on a surface and drive further exploration of advanced nanoparticle functionalization. © 2017 American Chemical Society.

We developed an expression for the calculation of the sum frequency generation spectra (SFG) of water interfaces that is based on the projection of the atomic velocities on the local normal modes. Our approach permits one to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated with the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region. The results for the water-air interface, obtained using ab initio molecular dynamics simulations, are discussed in connection to recent phase resolved experimental data. © 2017 American Chemical Society.

We report the potential-dependent interactions of trimesic acid with Cu surfaces in EtOH. CV experiments and electrochemical surface-enhanced Raman spectroscopy show the presence of an adsorbed trimesic acid layer on Cu at potentials lower than 0 V vs Cu. The BTC coverage increases as the potential increases, reaching a maximum at 0 V. Based on molecular dynamics simulations, we report adsorption geometries and possible structures of the organic adlayer. We find that, depending on the crystal facet, trimesic acid adsorbs either flat or with one or two of the carboxyl groups facing the metal surface. At higher coverages, a multi-layer forms that is composed mostly of flat-lying trimesic acid molecules. Increasing the potential beyond 0 V activates the Cu-adsorbate interface in such a way that under oxidation of Cu to Cu2 +, a 3-D metal-organic framework forms directly on the electrode surface. © 2017 Elsevier B.V.

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions. © 2016 Author(s).

Directly manipulating and controlling the size and shape of metal nanoparticles is a key step for their tailored applications. In this work, molecular dynamics simulations were applied to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. Different factors influencing the growth were selectively included in the models to unravel the role of the surfactants and ions. In the early stage of the growth, when the seed is only a few nanometers large, a dramatic symmetry breaking occurs as the surfactant layer preferentially covers the (100) and (110) facets, leaving the (111) facets unprotected. This anisotropic surfactant layer in turn promotes anisotropic growth with the less protected tips growing faster. When silver salt is added to the growth solution, the asymmetry of the facets is preserved, but the Br−concentration at the interface increases, resulting in increased surface passivation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

At the water-air interface, the hydrogen-bond network of water molecules is interrupted, and accordingly, the structure and dynamics of the interfacial water molecules are altered considerably compared with the bulk. Such interfacial water molecules have been studied by surface-specific vibrational sum-frequency generation (SFG) spectroscopy probing high-frequency O-H stretch and H-O-H bending modes. In contrast, the low-frequency librational mode has been much less studied with SFG. Because this mode is sensitive to the hydrogen-bond connectivity, understanding the librational mode of the interfacial water is crucial for unveiling a microscopic view of the interfacial water. Here, we compute the SFG librational mode spectra at the water-air interface by using molecular dynamics simulation. We show that the modeling of the polarizability has a drastic effect on the simulated librational mode spectra, whereas the spectra are less sensitive to the force field models and the modeling of the dipole moment. The simulated librational spectra display a peak centered at ∼700 cm-1, which is close to the infrared peak frequency of the liquid water librational mode of 670 cm-1. This indicates that the librational mode of the interfacial water at the water-air interface closely resembles that of bulk liquid water. © 2016 American Chemical Society.

Understanding the molecular mechanisms which nature uses to control biomineral growth is a fundamental science goal with profound medical implication. In the case of calcium oxalate, a microscopic understanding of the interactions which regulate the growth and stabilization of metastable phases would permit to inhibit the growth of the crystals which are the main components of kidney stones. Here we use ab initio molecular dynamics simulations to unravel how specific molecular interactions occurring on calcium oxalate dihydrate surface can promote an anisotropic crystal growth. We find that the calcium oxalate dihydrate (100) and (101) surfaces are both hydrophilic and solvated by a strongly bound layer of water; however, they exhibit important differences in their ability to bind water and small molecules such as acetate. In particular, on the (100) surface, the more exposed Ca2+ ions can more strongly bind to negatively charged groups, exerting a protecting action on the surface and preventing its further growth. This mechanism in turn would favor an anisotropic growth of the calcium oxalate dihydrate crystals in the [100] direction, as observed in experiments. © 2016 American Chemical Society.

Acidity of silanol sites at the crystalline quartz/aqueous electrolyte (NaCl, NaI, KCl) interfaces are calculated from ab initio molecular dynamics simulations. pKa's are found to follow a combination of the cationic and anionic Hofmeister series in the order pKa(neat solution) < pKa(NaCl) < pKa(NaI) < pKa(KCl), in agreement with experimental measurements. Rationalization of this ranking is achieved in terms of the microscopic local solvation of the protonated silanols and their conjugated bases, the silanolates SiO-. The change in the pKa is the result of both water destructuring by alkali halides, as well as of the specific cation/SiO- interaction, depending on the electrolyte. Molecular modeling at the atomistic level is required to achieve such comprehension, with ab initio molecular dynamics being able to model complex inhomogeneous charged interfaces and the associated interfacial chemical reactivity. © 2016 American Chemical Society.

We provide a microscopic view of the role of halides in controlling the anisotropic growth of gold nanorods through a combined computational and experimental study. Atomistic molecular dynamics simulations unveil that Br- adsorption is not only responsible for surface passivation, but also acts as the driving force for CTAB micelle adsorption and stabilization on the gold surface in a facet-dependent way. The partial replacement of Br- by Cl- decreases the difference between facets and the surfactant density. Finally, in the CTAC solution, no halides or micellar structures protect the gold surface and further gold reduction should be uniformly possible. Experimentally observed nanoparticle's growth in different CTAB/CTAC mixtures is more uniform and faster as the amount of Cl- increases, confirming the picture from the simulations. In addition, the surfactant layer thickness measured on nanorods exposed to CTAB and CTAC quantitatively agrees with the simulation results. © the Owner Societies 2016.

Water in contact with mineral interfaces is important for a variety of different processes. Here, we present a combined theoretical/experimental study which provides a quantitative, molecular-level understanding of the ubiquitous and important CaF 2 /water interface. Our results show that, at low pH, the surface is positively charged, causing a substantial degree of water ordering. The surface charge originates primarily from the dissolution of fluoride ions, rather than from adsorption of protons to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. These OH groups interact remarkably weakly with the surrounding water, and are responsible for the free OH signature in the VSFG spectrum, which can be explained from local electronic structure effects. The quantification of the surface termination, near-surface ion distribution and water arrangement is enabled by a combination of advanced phase-resolved Vibrational Sum Frequency Generation spectra of CaF 2 /water interfaces and state-of-the-art ab initio molecular dynamics simulations which include electronic structure effects.

Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (OTMAO) atom, due to the O-D···OTMAO hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···OTMAO hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O-D···OTMAO hydrogen-bond has a strong directionality through the sp3 orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics. © 2015 American Chemical Society.

Understanding the microscopic origin of the acid-base behavior of mineral surfaces in contact with water is still a challenging task, for both the experimental and the theoretical communities. Even for a relatively simple material, such as silica, the origin of the bimodal acidity behavior is still a debated topic. In this contribution we calculate the acidity of single sites on the humid silica surface represented by a model for the hydroxylated amorphous surface. Using a thermodynamic integration approach based on ab initio molecular dynamics, we identify two different acidity values. In particular, some convex geminals and some type of vicinals are very acidic (pKa = 2.9 and 2.1, respectively) thanks to a special stabilization of their deprotonated forms. This recalls the behavior of the out-of-plane silanols on the crystalline (0001) α-quartz surface, although the acidity here is even stronger. On the contrary, the concave geminals and the isolated groups present a quite high pKa (8.9 and 10.3, respectively), similar to the one of silicic acid in liquid water. © 2015 American Chemical Society.

We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the water hydrogen bond network to reach, with its (up-oriented) O-H groups, into the headgroup of the lipid, a mechanism not available for water underneath the AO surfactant. This highlights the role of the lipid carbonyl group in the interfacial water structure at the membrane interface, namely, stabilizing the water hydrogen bond network. © 2015 American Chemical Society.

Despite its relevance to industrial, environmental and medical application, the fluorite/water interface still lacks a microscopic/atomistic characterization. In this contribution we provide the first atomistic description of such interface using first principles molecular dynamics simulations. Our models, which explore a wide range of pH, are able to provide a rational of the recent vibrational spectroscopy experiments. In particular we find that at neutral pH the water at the interface is disordered, in agreement with the experimental data, and explaining why no Vibrational Sum Frequency Generation (VSFG) signal is recorded. At high pH, OH groups which localize at the interface are responsible for the “free OH signal” recorded in the vibrational spectroscopy experiments. Finally we propose one possible model for the low pH condition where the F vacancies induce a strong layering of the interfacial water. © Springer International Publishing Switzerland 2015.

Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing. © 2014 American Chemical Society.

Calcium Silicate Hydrates (C-S-H) are the major hydration products of portland cement paste. The accurate description of acid-base reactions at the surface of C-S-H particles is essential for both understanding the ion sorption equilibrium in cement and prediction of mechanical properties of the hardened cement paste. Ab initio molecular dynamics simulations at the density functional level of theory were applied to calculate intrinsic acidity constants (pK a's) of the relevant -SiOH and -CaOH2 groups on the C-S-H surfaces using a thermodynamic integration technique. Ion sorption equilibrium in C-S-H was modeled applying ab initio calculated pKa's in titrating Grand Canonical Monte Carlo simulations using a coarse-grained model for C-S-H/solution interface in the framework of the Primitive Model for electrolytes. The modeling results were compared with available data from electrophoretic measurements. The model predictions were found to satisfactorily reproduce available experimental data. © 2014 American Chemical Society.

All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods. The key computational tool is a FEP based method for reversible insertion of a proton or electron in a periodic DFTMD model system. The free energy of insertion (work function) is computed by thermodynamic integration of vertical energy gaps obtained from total energy differences. The problem of the loss of a physical reference for ionization energies under periodic boundary conditions is solved by comparing with the proton work function computed for the same supercell. The scheme acts as a computational hydrogen electrode, and the DFTMD redox energies can be directly compared with experimental redox potentials. Consistent with the closed shell nature of acid dissociation, pKa estimates computed using the proton insertion/removal scheme are found to be significantly more accurate than the redox potential calculations. This enables us to separate the DFT error from other sources of uncertainty such as finite system size and sampling errors. Drawing an analogy with charged defects in solids, we trace the error in redox potentials back to underestimation of the energy gap of the extended states of the solvent. Accordingly the improvement in the redox potential as calculated by hybrid functionals is explained as a consequence of the opening up of the bandgap by the Hartree-Fock exchange component in hybrids. Test calculations for a number of small inorganic and organic molecules show that the hybrid functional implementation of our method can reproduce acidity constants with an uncertainty of 1-2 pKa units (0.1 eV). The error for redox potentials is in the order of 0.2 V. (Figure Presented). © 2014 American Chemical Society.

The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface. © 2014 IOP Publishing Ltd.

We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular, we show how AuCl2- ions, which are found in the growth solution, can freely diffuse from the bulk solution to the gold surface. We also find that the (111) surface exhibits a higher CTAB packing density and a higher electrostatic potential. Both elements would favor the growth of gold nanoparticles along the (111) direction. These findings are in agreement with the growth mechanisms proposed by the experimental groups of Murphy and Mulvaney. © 2013 American Chemical Society.

The vibrational sum frequency generation (VSFG) spectrum of the water liquid-vapor (LV) interface is calculated using density functional theory-based molecular dynamics simulations. The real and imaginary parts of the spectrum are in good agreement with the experimental data, and we provide an assignment of the SFG bands according to the dipole orientation of the interfacial water molecules. We use an instantaneous definition of the surface, which is more adapted to the study of interfacial phenomena than the Gibbs dividing surface. By calculating the vibrational (infrared, Raman) properties for interfaces of varying thickness, we show that the bulk spectra signatures appear after a thin layer of 2-3 Å only. We therefore use this value as a criterion for calculating the VSFG spectrum. © 2012 American Chemical Society.

We provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (010) face of pyrophyllite. Such information cannot be inferred directly from titration experiments, which do not discriminate between different sites and whose interpretation resorts to macroscopic models. The determination of the corresponding pK a then usually relies on bond valence models, sometimes improved by incorporating some structural information from ab-initio simulations. Here we use density functional theory based molecular dynamics simulations, combined with thermodynamic integration, to compute the free energy of the reactions of water with the different surface groups, leading to a deprotonated site and an aqueous hydronium ion. Our approach consistently describes the clay and water sides of the interface and includes naturally electronic polarization effects. It also allows to investigate the structure and solvation of all sites separately. We find that the most acidic group is SiOH, due to its ability to establish strong hydrogen bonds with adsorbed water, as it also happens on the quartz and amorphous silica surfaces. The acidity constant of AlOH 2 is only 1 pK a unit larger. Finally, the pK a of AlOH is outside the possible range in water and this site should not deprotonate in aqueous solution. We show that the solvation of surface sites and hence their acidity is strongly affected by the proximity of other sites, in particular for AlOH and AlOH 2 which share the same Al. We discuss the implications of our findings on the applicability of bond valence models to predict the acidity of edge sites of clays. © 2012 Elsevier Ltd.

The electronic states of aqueous species can mix with the extended states of the solvent if they are close in energy to the band edges of water. Using density functional theory-based molecular dynamics simulation, we show that this is the case for OH- and Cl-. The effect is, however, badly exaggerated by the generalized gradient approximation leading to systematic underestimation of redox potentials and spurious nonlinearity in the solvent reorganization. Drawing a parallel to charged defects in wide gap solid oxides, we conclude that misalignment of the valence band of water is the main source of error turning the redox levels of OH- and Cl- in resonant impurity states. On the other hand, the accuracy of energies of levels corresponding to strongly negative redox potentials is acceptable. We therefore predict that mixing of the vertical attachment level of CO2 and the unoccupied states of water is a real effect. © 2012 American Chemical Society.

The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, ice-like and liquid-like features in these spectra are interpreted as the result of hydrogen bonds of different strengths between surface silanols/aluminols and water. © 2012 IOP Publishing Ltd.

Silica is the most abundant metal oxide and the main component of the Earth's crust. Its behavior in contact with water plays a critical role in a variety of geochemical and environmental processes. Despite its key role, the details of the aqueous silica interface at the microscopic molecular level are still elusive. Here we provide such a detailed understanding of the molecular behavior of the silica-water interface, using density functional theory based molecular dynamics (DFTMD) simulations, where a consistent treatment of the electronic structure of solvent and surface is provided. We have calculated the acidity of the silanol groups at the interface directly from the DFTMD simulations, without any fitting of parameters to the experimental data. We find two types of silanol groups at the surface of quartz: out-of-plane silanols with a strong acidic character (pK a = 5.6), which consequently results in the formation of strong and short hydrogen bonds with water molecules at the interface, and in-plane silanols with a pK a of 8.5, forming weak hydrogen bonds with the interfacial water molecules. Our estimate of the quartz point of zero charge (1.0) is found in good agreement with the experimental value of 1.9. We have also shown how the silanols orientation and their hydrogen bond properties are responsible for an amphoteric behavior of the surface. A detailed analysis has identified two species of adsorbed water molecules at the solid-liquid interface, which using the language of vibrational spectroscopy can be identified as "liquid-like" and "ice-like" water or, in other words, water molecules forming respectively weak and strong H-bonds with the oxide surface. These two populations of water are in turn responsible for two distinct peaks in the infrared spectrum of interfacial water and thus provide a molecular explanation of the experimental sum frequency generation spectrum recorded in the literature. In the specific case of quartz, we show that the liquid-/ice-like behavior is the result of the silanol groups ability to donate or accept hydrogen bonds with different strengths, which consequently modulates the vibrational properties of the adsorbed water layer. © 2012 American Chemical Society.

Absolute pKa values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [Cheng, J.; Sulpizi, M.; Sprik, M.J. Chem. Phys. 2009, 131, 154504 ]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed solvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pKa units with a maximum error of 4.0 pKa units. The estimated mean statistical uncertainty due to the finite length of the trajectories is ±1.1 pK a units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments. © 2011 American Chemical Society.

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3O+). Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pKa and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]10.1063/1.3250438. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pKa, NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent. © 2011 American Institute of Physics.

In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Brønsted pKa when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pKa values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail. © 2010 IOP Publishing Ltd.