Ab Initio Metadynamics Research Articles

Ab initio metadynamics simulations on the formation of calcium silicate aqua complexes prior to the nuleation of calcium silicate hydrate

Although the calcium silicate hydrate (C-S-H) has been used for millennium, the structure and formation of C-S-H are still unclear at atomistic level. In this work, we find two kinds of calcium silicate aqua complexes, [Ca(H2O)n(SiO2(OH)2)] and [Ca(H2O)n(SiO(OH)3)]+, prior to the nuleation of C-S-H. The ab initio metadynamics simulations show that [Ca(H2O)n(SiO2(OH)2)] and [Ca(H2O)n(SiO(OH)3)]+ have six and five stable states on the free energy surface (FES), respectively. There are different ligand substitution mechanisms between the FES minima. The four- and six- coordinated [Ca(H2O)n(SiO2(OH)2)] only follow associative and dissociative mechanisms, respectively. While both dissociative and associative mechanisms apply to the six-coordinated [Ca(H2O)n(SiO(OH)3)]+ and no four-coordinated ligand substitution reaction is found. The most stable states in both systems show a distorted CaO octahedral feature. Our findings may promote a fundamental understanding for the calcium silicate based species in solution and pre-nucleation process of C-S-H.

Ab initio mechanism revealing for tricalcium silicate dissolution

Dissolution of minerals in water is ubiquitous in nature and industry, especially for the calcium silicate species. However, the behavior of such a complex chemical reaction is still unclear at atomic level. Here, we show that the ab initio molecular dynamics and metadynamics simulations enable quantitative analyses of reaction pathways, thermodynamics and kinetics of the calcium ion dissolution from the tricalcium silicate (Ca3SiO5) surface. The calcium sites with different coordination environments lead to different reaction pathways and free energy barriers. The low free energy barriers result in that the detachment of the calcium ion is a ligand exchange and auto-catalytic process. Moreover, the water adsorption, proton exchange and diffusion of water into the surface layer accelerate the leaching of the calcium ion from the surface step by step. The discovery in this work thus would be a landmark for revealing the mechanism of tricalcium silicate hydration.

Pyrophyllite dissolution at elevated pressure conditions: An ab initio study

The atomistic mechanism of dissolution reactions at mineral fluid interface is essential for understanding the reaction kinetics and the adsorption and thermodynamic equilibria at mineral surfaces. In this study we investigate the initial state of the dissolution process on (0 1 0) surface of pyrophyllite at elevated pressure by applying large-scale ab initio Meta-Dynamics simulations. The system setup provides a realistic representation of the clay mineral edge surface structure and takes into account explicit dynamics of solvent molecules. The model parameters follow the procedure recently tested for the simulation of the (1 1 0) pyrophyllite edge. The simulation reveals that dissolution of a single tetrahedral or an octahedral unit from the clay mineral edge is a complex multi-step process with several reaction intermediates. Typically, each reaction step changes the denticity of the reacting site in a step-by-step manner and leads, eventually, to the leaching of the ions forming the octahedral and tetrahedral sheets of the phyllosilicate. The solvent rearrangement and the proton transfer reactions in the first and second coordination shell of the dissolving unit play a critical role in the stabilization of reaction intermediates and the net progress of the dissolution reactions. In contrast to ambient conditions, the transition complexes formed during the dissolution at elevated conditions were found to have an increased coordination number. The simulation reveals new insight into the coordination environment of the dissolving complexes at the mineral fluid interface.

Reversible Hydration of α-Dicarbonyl Compounds from Ab Initio Metadynamics Simulations: Comparison between Pyruvic and Glyoxylic Acids in Aqueous Solutions.

Glyoxylic and pyruvic oxoacids are widely available in the atmosphere as gas-phase clusters and particles or in wet aerosols. In aqueous conditions, they undergo interconversion between the unhydrated oxo and gem-diol forms, where two hydroxyl groups replace the carbonyl group. We here examine the hydration equilibrium of glyoxylic and pyruvic acids with first-principles simulations in water at ambient conditions using ab initio metadynamics to reconstruct the corresponding free-energy landscapes. The main results are as follows: (i) our simulations reveal the high conformational diversity of these species in aqueous solutions. (ii) We show that gem-diol is strongly favored in water compared to its oxo counterpart by 29 and 16 kJ/mol for glyoxylic and pyruvic acids, respectively. (iii) From our atomic-scale simulations, we present new insights into the reaction mechanisms with a special focus on hydrogen-bond arrangements and the electronic structure of the transition state.

Recent Understanding of Low-Temperature Copper Dynamics in Cu-Chabazite NH3-SCR Catalysts

Dynamic motion of NH3-solvated Cu sites in Cu-chabazite (Cu-CHA) zeolites, which are the most promising and state-of-the-art catalysts for ammonia-assisted selective reduction of NOx (NH3-SCR) in the aftertreatment of diesel exhausts, represents a unique phenomenon linking heterogeneous and homogeneous catalysis. This review first summarizes recent advances in the theoretical understanding of such low-temperature Cu dynamics. Specifically, evidence of both intra-cage and inter-cage Cu motions, given by ab initio molecular dynamics (AIMD) or metadynamics simulations, will be highlighted. Then, we will show how, among others, synchrotron-based X-ray spectroscopy, vibrational and optical spectroscopy (diffuse reflection infrared Fourier transform spectroscopy (DRIFTS) and diffuse reflection ultraviolet-visible spectroscopy (DRUVS)), electron paramagnetic spectroscopy (EPR), and impedance spectroscopy (IS) can be combined and complement each other to follow the evolution of coordinative environment and the local structure of Cu centers during low-temperature NH3-SCR reactions. Furthermore, the essential role of Cu dynamics in the tuning of low-temperature Cu redox, in the preparation of highly dispersed Cu-CHA catalysts by solid-state ion exchange method, and in the direct monitoring of NH3 storage and conversion will be presented. Based on the achieved mechanistic insights, we will discuss briefly the new perspectives in manipulating Cu dynamics to improve low-temperature NH3-SCR efficiency as well as in the understanding of other important reactions, such as selective methane-to-methanol oxidation and ethene dimerization, catalyzed by metal ion-exchanged zeolites.

The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1.

Tyrosine sulfation alters the biological activity of many proteins involved in different physiological and pathophysiological conditions, such as non-specific immune reaction, response to inflammation and ischemia, targeting of leukocytes and stem cells, or the formation of cancer metastases. Tyrosine sulfation is catalyzed by the enzymes tyrosylprotein sulfotransferases (TPST). In this study, we used QM/MM Car-Parrinello metadynamics simulations together with QM/MM potential energy calculations to investigate the catalytic mechanism of isoform TPST-1. The structural changes along the reaction coordinate are analyzed and discussed. Furthermore, both the methods supported the SN2 type of catalytic mechanism. The reaction barrier obtained from CPMD metadynamics was 12.8 kcal mol-1, and the potential energy scan led to reaction barriers of 11.6 kcal mol-1 and 13.7 kcal mol-1 with the B3LYP and OPBE functional, respectively. The comparison of the two methods (metadynamics and potential energy scan) may be helpful for future mechanistic studies. The insight into the reaction mechanism of TPST-1 might help with the rational design of transition-state TPST inhibitors.

A dynamic picture of the halolactonization reaction through a combination of ab initio metadynamics and experimental investigations.

The halolactonization reaction is one of the most common electrophilic addition reactions to alkenes. The mechanism is generally viewed as a two-step pathway, which involves the formation of an ionic intermediate, in most cases a haliranium ion. Recently, an alternative concerted mechanism was proposed, in which the nucleophile of the reaction played a key role in the rate determining step by forming a pre-polarized complex with the alkene. This pathway was coined the nucleophile-assisted alkene activation (NAAA) mechanism. Metadynamics simulations on a series of model halolactonization reactions were used to obtain the full dynamic trajectory from reactant to product and investigate the explicit role of the halogen source and solvent molecules in the mechanism. The results in this work ratify the occasional preference of a concerted mechanism over the classic two-step transformation under specific reaction conditions. Nevertheless, as the stability of both the generated substrate cation and counter-anion increase, a transition towards the classic two-step mechanism was observed. NCI analyses on the transition states revealed that the activating role of the nucleophile is independent of the formation and stability of the intermediate. Additionally, the dynamic insights obtained from the metadynamics simulations and NCI analyses employed in this work, unveiled the presence of syn-directing noncovalent interactions, such as hydrogen bonding, between the alkenoic acid and the halogen source, which rationalized the experimentally observed diastereoselectivities. Explicit noncovalent interactions between the reactants and a protic solvent or basic additive are able to disrupt these syn-directing noncovalent interactions, affecting the diastereoselective outcome of the reaction.

Atomic scale mechanism of clay minerals dissolution revealed by ab initio simulations

Large-scale ab initio Meta-Dynamics simulations were applied to elucidate the molecular mechanism and reaction free energies of pyrophyllite dissolution at the (1 1 0) edge surface in pure water at close to neutral pH under far from equilibrium conditions. The simulation setup allows realistic representation of the clay mineral surface and explicit consideration of solvent dynamics at finite temperature. The simulation reveals that dissolution of a single tetrahedral or an octahedral unit from the clay mineral edge is a complex multi-step process with several reaction intermediates. Typically, each reaction step changes denticity of the reacting site in a step-by-step manner and leads, eventually, to the leaching of ions forming octahedral and tetrahedral sheets of the phyllosilicate. The solvent rearrangement and the proton transfer reactions in the first and the second coordination shell of the dissolving unit play a critical role in the stabilization of reaction intermediates and the net progress of the dissolution reactions. The overall reaction mechanism can be rationalized as sequence of concurrent and reversible elementary reaction events, which are:(1)the nucleophilic attack of H2O molecules or OH groups on the dissolving surface site.(2)ligand exchange reactions in the first coordination shell of the reacting sites leading to changes of its conformation and denticity at the mineral surface.(3)collective proton transfer reactions between the acidic and basic oxygen sites mediated via a chain of the hydrogen bonded molecules in the first and second coordination shell of the reacting site.The results obtained in this study are general and applicable to the group of 2:1 phyllosilicates in a wide range of chemical and thermodynamic conditions.

Theoretical insights into the activation of N2O by a model Frustrated Lewis Pair. An ab-initio metadynamics study

Frustrated Lewis Pairs (FLPs) are a prominent class of substances capable of activation of small molecules. Albeit several experimental and theoretical studies devoted to the activation of greenhouse gases were recently published, activation of N2O are yet scarce. In present study we employed Density Functional Theory based metadynamics to reconstruct the Free Energy Landscape of the activation of N2O by the model [t-Bu3P][B(C6F5)3] FLP. Similarly to the mechanism observed in the activation of CO2, Lewis acid promotes the thermodynamic requirements of the reaction by stabilizing key intermediates. Regioselectivity of the activation of N2O as well as the effect of phosphine basicity are also discussed.

Energy-entropy competition in cation-hydroxyl interactions at the liquid water-Pt(111) interface.

Electrochemical reaction rates are sensitive to interactions between electrolyte cations and adsorbed reaction intermediates, e.g., cation-*OH interactions in the oxygen reduction reaction on platinum. Here, we calculate the free energy interaction between adsorbed *OH and K+/Li+ situated at the liquid water-Pt(111) interface using ab initio molecular dynamics (AIMD) and metadynamics. Li+ stabilizes *OH by 0.1 ± 0.1 eV and K+ destabilizes *OH by 0.1 ± 0.1 eV, in qualitative agreement with experimental cyclic voltammogram (CV) measurements. In contrast, the internal energy of *OH is stabilized by 0.3 eV and 0.4 eV for Li+ and K+, respectively. This demonstrates that entropy significantly destabilizes cation-*OH interactions and is vital in order to understand even the relative influence of cations at interfaces.

Ab initio metadynamics calculations of dimethylamine for probing pKb variations in bulk vs. surface environments.

The basicity constant, or pKb, is an intrinsic physical property of bases that gives a measure of its proton affinity in macroscopic environments. While the pKb is typically defined in reference to the bulk aqueous phase, several studies have suggested that this value can differ significantly at the air-water interface (which can have significant ramifications for particle surface chemistry and aerosol growth modeling). To provide mechanistic insight into surface proton affinity, we carried out ab initio metadynamics calculations to (1) explore the free-energy profile of dimethylamine and (2) provide reasonable estimates of the pKb value in different solvent environments. We find that the free-energy profiles obtained with our metadynamics calculations show a dramatic variation, with interfacial aqueous dimethylamine pKb values being significantly lower than in the bulk aqueous environment. Furthermore, our metadynamics calculations indicate that these variations are due to reduced hydrogen bonding at the air-water surface. Taken together, our quantum mechanical metadynamics calculations show that the reactivity of dimethylamine is surprisingly complex, leading to pKb variations that critically depend on the different atomic interactions occurring at the microscopic molecular level.

Unraveling a New Chemical Mechanism of Missing Sulfate Formation in Aerosol Haze: Gaseous NO2 with Aqueous HSO3-/SO32.

A source of missing sulfate production associated with high-level fine-particle pollution in the megacities of China is believed to stem from the oxidation of a notable fraction of sulfur dioxide (SO2) by nitrogen dioxide (NO2) in aqueous aerosol environments, suggesting that an unknown reaction pathway exists for aqueous sulfur oxidation. At weakly acidic aerosols, the dissolved SO2 mainly exists in the form of HSO3-, whereas at neutral aerosols, SO32- becomes the main form. Herein, by using both ab initio molecular metadynamics simulations and high-level quantum mechanical calculations, we show a hitherto unreported chemical mechanism for the formation of sulfate through the reaction between HSO3-/SO32- anions at the surface/in the interior of a water nanodroplet and gas-phase NO2 molecules. For weakly acidic aerosols, contrary to the conventional high-barrier electron-transfer pathway in the gas phase, HSO3- at the water nanodroplet surface can transfer an electron to NO2 with a low free-energy barrier of 4.7 kcal/mol through a water bridge. For neutral aerosols, the electron-transfer pathway between SO32- in the interior of the water nanodroplet and NO2 needs to overcome a lower free-energy barrier of 3.6 kcal/mol to form SO3-, with the assistance of the hydrogen-bonding network of water molecules. This new reaction pathway for the sulfate formation from HSO3-/SO32- via water nanodroplets and gaseous NO2 provides a new perspective on the growth of haze particles from pre-existing aqueous aerosols and suggests that new control strategies are needed to address haze pollution.

Ion Pairing in HCl-Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development.

In the bulk, condensed-phase HCl exists as a dissociated Cl- ion and a proton that is delocalized over solvating water molecules. However, in the gas phase, HCl is covalent, and even on the introduction of hydrating water molecules, the HCl covalent state dominates small clusters and is relevant at larger clusters including 21 water molecules. Electronic structure calculations (at the MP2 level) and ab initio metadynamics simulations (at the DFT level) have been carried out on HCl-(H2O)n clusters with n = 2-22 to investigate distinct solvation environments in clusters from covalent HCl structure, to contact ion pairs and solvent-separated ion pairs. The data were further used to train and validate a multiconfigurational force-field for HCl-water clusters that incorporates covalent HCl states into the MS-EVB3.2 formalism. Additionally, the many-body interaction of the Cl- ion with water and the excess proton was modeled by the introduction of two geometric three-body terms that incorporates the dominant many-body interaction in an efficient noniterative manner.

Unsupervised Exploration of MoS2 Nanocluster Configurations: Structures, Energetics, and Electronic Properties

We propose an efficient method to explore the configuration space of nanoclusters by combining together ab initio molecular dynamics, metadynamics, and data clustering algorithms. On the one side, we employ collective variables sensitive to topological changes in the network of interatomic connections to map the configuration space; on the other side, we introduce an automatic approach to select, in such a space, representative structures to be optimized. In this way, we show that it is possible to sample thoroughly the set of relevant nanocluster geometries at a limited computational cost. We apply our method to explore MoS2 clusters that recently raised a sizable interest due to their remarkable electronic and catalytic properties. We demonstrate that the unsupervised algorithm is able to find a large number of low-energy structures at different cluster sizes, including both bulk-like geometries and very different topologies. We are thus able to recapitulate, in a single computational study on technologically relevant MoS2 clusters, the results of all previous works that employed distinct techniques like genetic algorithms or heuristic hypotheses. Furthermore, we found several new structures not previously reported. The ensemble of MoS2 cluster structures is deposited in a publicly accessible database.

Unraveling the Water Degradation Mechanism of CH3NH3PbI3

Instability of perovskite photovoltaics is still a topic which is currently under intense debate, especially the role of water environment. Unraveling the mechanism of this instability is urgent to enable practical application of perovskite solar cells. Here, ab initio metadynamics is employed to investigate the initial phase of a dissolution process of CH$_3$NH$_3$PbI$_3$ (MAPbI$_3$) in explicit water. It is found that the initial dissolution of MAPbI$_3$ is a complex multi-step process triggered by the departure of I$^-$ ion from the CH$_3$NH$_3$I-terminated surface. Reconstruction of the free energy landscape indicates a low energy barrier for water dissolution of MAPbI$_3$. In addition, we propose a two-step thermodynamic cycle for MAPbI$_3$ dissolution in water at a finite concentration that renders a spontaneity of the dissolution process. The low energy barrier for the initial dissolution step and the spontaneous nature of MAPbI$_3$ dissolution in water explain why the water immediately destroys pristine MAPbI$_3$. The dissolution thermodynamics of all-inorganic CsPbI$_3$ perovskite is also analyzed for comparison. Hydration enthalpies and entropies of aqueous ions play an important role for the dissolution process. Our findings provide a comprehensive understanding to the current debate on water instability of MAPbI$_3$.

The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study.

The discovery of effective hydrogen storage materials is fundamental for the progress of a clean energy economy. Ammonia borane (H3 BNH3 , AB) has attracted great interest as a promising candidate but the reaction path that leads from its solid phase to hydrogen release is not yet fully understood. To address the need for insights in the atomistic details of such a complex solid state process, in this work we use ab-initio molecular dynamics and metadynamics to study the early stages of AB dehydrogenation. We show that the formation of ammonia diborane (H3 NBH2 (μ-H)BH3 ) leads to the release of NH4 + , which in turn triggers an autocatalytic H2 production cycle. Our calculations provide a model for how complex solid state reactions can be theoretically investigated and rely upon the presence of multiple ammonia borane molecules, as substantiated by standard quantum-mechanical simulations on a cluster.

Structure and Dynamics of Polysulfide Clusters in a Nonaqueous Solvent Mixture of 1,3-Dioxolane and 1,2-Dimethoxyethane

Molecular clustering and associated dynamic processes of lithium polysulfide species were unraveled using classical molecular dynamics and ab initio metadynamics calculations. The spectroscopic signatures of polysulfide clusters were analyzed using a multimodal analysis including experimental and computational nuclear magnetic resonance (NMR) and X-ray absorption spectroscopies. Lithium polysulfide solutes (Li2S4, Li2S6, and Li2S8) and their mixtures in a 1,3-dioxolane and 1,2-dimethoxyethane (DOL/DME) solvent undergo aggregation driven by intramolecular lithium–sulfur (Li–S) interactions, leading to distributions of cluster sizes, which could critically influence the functioning of lithium–sulfur batteries. Representative polysulfide clusters with systematic increases in molecular size were extracted from the classical molecular dynamics trajectories for subsequent structural and spectroscopic property calculations using density functional theory analysis. Structural analysis of these clusters reveals pr...

On the issue of closed versus open forms of gamma-aminobutyric acid (GABA) in water: Ab initio molecular dynamics and metadynamics studies

Gamma-aminobutyric acid (GABA), a primary neurotransmitter, accomplishes its activities by binding to different receptor sites in different conformations. It is known to have two major conformers: the closed and open forms. Earlier studies on preferred conformation of GABA in water revealed differing results with some reporting the open form while others inferring the closed form to be more stable. We found the existence of many open forms and only one closed form of GABA in water through ab initio metadynamics simulation. Some of the open conformers are equally or more stable while others are less stable than the closed form. Free energy barriers reveal that different conformers are interconvertible at room temperature in typical experimental time scales. Ab initio molecular dynamics simulations are performed to further investigate the inter-conversion of various conformers of GABA in water and their dipole moments and also to make connections to experiments on the conformation of GABA in water.

Solvent and Autocatalytic Effects on the Stabilisation of the σ-Complex during Electrophilic Aromatic Chlorination.

The solvent and autocatalytic effects of the electrophilic aromatic chlorination of benzene are studied using a combined approach of static calculations and ab initio metadynamics simulations. Different possible reaction pathways are investigated and the influence of the solvents (CCl4 , acetonitrile and acetic acid) is thoroughly assessed. Our results show that the stability and lifetime of a charged σ-complex is increased by electrostatic stabilisation effects of the environment, which can originate from catalytic HCl, solvating effects of polar solvents (acetonitrile), or specific hydrogen bonding interactions with the solvent (acetic acid). Metadynamics simulations reveal a new chlorine addition mechanism explaining the autocatalytic effects of the reaction. The strength of combining static calculations and metadynamics simulations is highlighted, which provide complementary insight into chemical reactions in solvent.

Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field.

The formation of the first C-C bonds from formaldehyde represents the rate-limiting step of the formose reaction. However, the free-energy surface associated with such a process has never been determined in condensed phase. By means of ab initio molecular dynamics and metadynamics techniques here we report on the free-energy landscape underlying the synthesis of glycolaldehyde from a formaldehyde aqueous solution. Moreover, numerical samples of formaldehyde (both neat and in water solution) and of glycolaldehyde (both neat and in aqueous solution) have been exposed to intense electric fields. The application of electrostatic gradients strongly prevents the formaldehyde umpolung and catalyzes the formation of C-O-bonded polymers in formaldehyde-containing samples. However, when the field is applied on glycolaldehyde aqueous solutions, new C-C bonds are formed and (d)-erythrose is synthesized. This way, a numerical Miller-like experiment led to the formation of a prebiotically relevant (d)-tetrose from ubiquitarious molecules such as glycolaldehyde and water.