Enhanced sampling of chemical and biochemical reactions with metadynamics

Role of Surface Features on the Initial Dissolution of CH3NH3PbI3 Perovskite in Liquid Water: An Ab Initio Molecular Dynamics Study

The degradation of CH3NH3PbI3 (MAPbI3) hybrid organic inorganic perovskite (HOIP) by water has been the major issue hampering its use in commercial perovskites solar cells (PSCs), as MAPbI3 HOIP has been known to easily degrade in the presence of water. Even though there have been numerous studies investigating this phenomenon, there is still no consensus on the mechanisms of the initial stages of dissolution. Here, we attempt to consolidate differing mechanistic interpretations previously reported in the literature through the use of the first-principles constrained ab initio molecular dynamics (AIMD) to study both the energetics and mechanisms that accompany the degradation of MAPbI3 HOIP in liquid water. By comparing the dissolution free energy barrier between surface species of different surficial types, we find that the dominant dissolution mechanisms of surface species vary widely based on the specific surface features. The high sensitivity of the dissolution mechanism to surface features has contributed to the many dissolution mechanisms proposed in the literature. In contrast, the dissolution free energy barriers are mainly determined by the dissolving species rather than the type of surfaces, and the type of surfaces the ions are dissolving from is inconsequential toward the dissolution free energy barrier. However, the presence of surface defects such as vacancy sites is found to significantly lower the dissolution free energy barriers. Based on the estimated dissolution free energy barriers, we propose that the dissolution of MAPbI3 HOIP in liquid water originates from surface defect sites that propagate laterally along the surface layer of the MAPbI3 HOIP crystal.

A Review of Laser-Induced Crystallization from Solution

Crystallization abounds in nature and industrial practice. A plethora of indispensable products ranging from agrochemicals and pharmaceuticals to battery materials are produced in crystalline form in industrial practice. Yet, our control over the crystallization process across scales, from molecular to macroscopic, is far from complete. This bottleneck not only hinders our ability to engineer the properties of crystalline products essential for maintaining our quality of life but also hampers progress toward a sustainable circular economy in resource recovery. In recent years, approaches leveraging light fields have emerged as promising alternatives to manipulate crystallization. In this review article, we classify laser-induced crystallization approaches where light-material interactions are utilized to influence crystallization phenomena according to proposed underlying mechanisms and experimental setups. We discuss nonphotochemical laser-induced nucleation, high-intensity laser-induced nucleation, laser trapping-induced crystallization, and indirect methods in detail. Throughout the review, we highlight connections among these separately evolving subfields to encourage the interdisciplinary exchange of ideas.

Reconstructing reactivity in dynamic host-guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage

Spatial confinement is widely employed by nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In an attempt to mimic natural catalytic systems, supramolecular metal-organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out of the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host-guest systems in dynamic regimes. In this way, we can characterize amide encapsulation/expulsion in/out of the cage cavity (thermodynamics and kinetics), coupling such host-guest dynamic equilibrium with characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host-guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled in such host-guest systems. This also provides us with a flexible computational framework, useful to build structure-dynamics-property relationships for a variety of reactive host-guest systems.

Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters

Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes andenhanced-sampling algorithms and the ASE module, which includes several ab initio electronic structure codes. The interface is validated with a Lennard-Jones cluster free-energy landscape calculation by averaging multiple short metadynamics trajectories. We use this interface and analysis to estimate the free-energy landscape of Ag5 and Ag6 clusters at 10, 100 and 300 K with the radius of gyration and coordination number as collective variables, finding at most tens of meV in error. Relative free-energy differences between the planar and non-planar isomers of both clusters decrease with temperature, in agreement with previously proposed stabilization of non-planar isomers. Interestingly, we find that Ag6 is the smallest silver cluster where entropic effects at room temperature boost the non planar isomer probability to a competing state. The new ASE-PLUMED interface enables simulating nanosystem electronic properties at more realistic temperature-dependent conditions.

Molecular Simulations to Elucidate Transport Phenomena in Polymeric Membranes

Despite decades of dominance in separation technology, progress in the design and development of high-performance polymer-based membranes has been incremental. Recent advances in materials science and chemical synthesis provide opportunities for molecular-level design of next-generation membrane materials. Such designs necessitate a fundamental understanding of transport and separation mechanisms at the molecular scale. Molecular simulations are important tools that could lead to the development of fundamental structure-property-performance relationships for advancing membrane design. In this Perspective, we assess the application and capability of molecular simulations to understand the mechanisms of ion and water transport across polymeric membranes. Additionally, we discuss the reliability of molecular models in mimicking the structure and chemistry of nanochannels and transport pathways in polymeric membranes. We conclude by providing research directions for resolving key knowledge gaps related to transport phenomena in polymeric membranes and for the construction of structure-property-performance relationships for the design of next-generation membranes.

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.

Unveiling the Synergistic Role of Oxygen Functional Groups in the Graphene-Mediated Oxidation of Glutathione

This is the first report of an atomic-scale direct oxidation mechanism of the thiol group in glutathione (GSH) by epoxides on graphene oxide (GO) at room temperature. The proposed reaction mechanism is determined using a coupled experimental and computational approach; active sites for the reaction are determined through examination of GO surface chemistry changes before and after exposure to GSH, and density functional theory (DFT) calculations determine the reaction barriers for the possible GO-GSH reaction schemes. The findings build on the previously established catalytic mechanism of GSH oxidation by graphenic nanocarbon surfaces and importantly identify the direct reaction mechanism which becomes important in low-oxygen environments. Experimental results suggest epoxides as the active sites for the reaction with GSH, which we confirm using DFT calculations of reaction barriers and further identify a synergism between the adjacent epoxide and hydroxyl groups on the GO surface. The direct oxidation mechanism at specific oxygen sites offers insight into controlling GO chemical reactivity through surface chemistry manipulations. This insight is critical for furthering our understanding of GO oxidative stress pathways in cytotoxicity as well as for providing rational material design for GO applications that can leverage this reaction.

Modeling of Hydrogen Storage Utilizing Silsesquioxane Cages: Adsorption and Quasi-Dynamic Simulations of Encapsulation of H2 Molecule into Silsesquioxane Cages

Solid-state hydrogen storage may be the only promising way for mobile applications of hydrogen energy since it is safe, quickly reversible, cost-efficient, and has a high volumetric energy density under standard conditions. Silsesquioxane and its derivatives seem well suited for solid-state hydrogen storage and have attracted many experimental and theoretical researchers. In the present work, we have systematically studied four cages of T8, T10, and T12 (D_2d and D_6h) for hydrogen storage including adsorption and encapsulation of hydrogen molecules. We find that silsesquioxane cages have up to about 4150 m²/g specific surface area (SSA) and 7.81 wt % for hydrogen storage. These calculated values are comparable to the highest hydrogen storage values of metal-organic frameworks, porous polymer networks, and covalent organic frameworks. In addition, we use the quasi-dynamic method to study the encapsulation of hydrogen molecules into these cages because of the timescale limitation of ab initio molecular dynamics. Thermodynamic parameters such as enthalpy and Gibbs free energy at different temperatures are calculated during the insertion processes. We find that the insertion process of a hydrogen molecule into the T12 (D_6h) cage is almost energy-conserved and its energy barriers of enthalpy and free energy are moderate under standard conditions.

Li diffusion in Si and LiSi: Nuclear quantum effects and anharmonicity

The diffusion of Li in bulk Si and crystalline LiSi is investigated over a wide range of temperatures employing first-principles calculations based on density functional theory, transition state theory, and the kinetic Monte Carlo method. Nuclear quantum effects are incorporated by computing the vibrational spectrum and its effect on the effective energy barrier. The Li diffusion coefficient in bulk Si calculated with such quantum effects is ∼33% lower than the classical limit near room temperature due to higher effective energy barrier and tends to the classical limit at a high temperature (>1000 K). The presence of anharmonicity, estimated by the quasiharmonic approximation and the cBΩ model, increases the diffusion coefficient by ∼60%. For Li diffusion in LiSi with multiple vacancy jumps, we obtain an effective diffusion barrier of 0.27 eV ± 0.01 eV. In the Li-Si system, the quantum mechanical effects are only marginally significant at room temperature.

Laplacian score and genetic algorithm based automatic feature selection for Markov State Models in adaptive sampling based molecular dynamics

Adaptive sampling molecular dynamics based on Markov State Models use short parallel MD simulations to accelerate simulations, and are proven to identify hidden conformers. The accuracy of the predictions provided by it depends on the features extracted from the simulated data that is used to construct it. The identification of the most important features in the trajectories of the simulated system has a considerable effect on the results.

Methods

In this study, we use a combination of Laplacian scoring and genetic algorithms to obtain an optimized feature subset for the construction of the MSM. The approach is validated on simulations of three protein folding complexes, and two protein ligand binding complexes.

Results

Our experiments show that this approach produces better results when the number of samples is significantly lesser than the number of features extracted. We also observed that this method mitigates over fitting that occurs due to high dimensionality of large biosystems with shorter simulation times.

Solvent oligomerization pathways facilitated by electrolyte additives during solid-electrolyte interphase formation

The solid-electrolyte interphase (SEI) layer formation is known to play an important role in determining the lifetime of lithium-ion batteries. A thin, stable SEI layer is linked to overall improved battery performance and longevity, however, the factors and mechanisms that lead to optimal SEI morphology and composition are not well understood. Inclusion of electrolyte additives (fluoroethylene carbonate, FEC; and vinylene carbonate, VC) is often necessary for improving SEI characteristics. To understand how these electrolyte additives impact SEI formation, molecular dynamics (MD) and density functional theory (DFT) simulations were employed to study the reaction networks and oligomerization pathways, respectively, for three systems containing ethylene carbonate (EC), a lithium ion, and FEC or VC. MD simulations suggest radical oligomerization pathways analogous to traditional oligomerization with nucleophilic alkoxide species via SN1 reaction mechanisms. Both SN1 and SN2 mechanisms were studied for all three systems using DFT. Oligomerization reactions were studied with both a standard alkoxide species and a ring-opened EC radical as the nucleophiles and EC, FEC, and VC as the electrophiles. For all cases, FEC and VC exhibited lower free energy barriers and more stable adducts when compared with EC. We conclude that one of the role of additives is to modify the oligomerization process of EC by introducing branching points (FEC) or termination points (VC).

Metadynamics to Enhance Sampling in Biomolecular Simulations

Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.

Origins of complex solvent effects on chemical reactivity and computational tools to investigate them: a review

Origins of solvent-induced enhancement in catalytic reactivity and product selectivity are discussed with computational methods to study them.

Towards operando computational modeling in heterogeneous catalysis

An increased synergy between experimental and theoretical investigations in heterogeneous catalysis has become apparent during the last decade. Experimental work has extended from ultra-high vacuum and low temperature towards operando conditions. These developments have motivated the computational community to move from standard descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concentrations (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodological developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodynamics, (iii) biased molecular dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the molecular level picture of catalytic sites and the associated reaction mechanisms changes when the chemical environment, pressure and temperature effects are correctly accounted for in molecular simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.

Reducing the number of mean-square deviation calculations with floating close structure in metadynamics

Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of collective coordinates to describe the studied molecular processes. Collective coordinates based on comparison with reference landmark structures can be used to enhance sampling in highly complex systems; however, they may slow down simulations due to high number of structure-structure distance (e.g., mean-square deviation) calculations. Here we introduce an approximation of root-mean-square or mean-square deviation that significantly reduces numbers of computationally expensive operations. We evaluate its accuracy and theoretical performance gain with metadynamics simulations on two molecular systems.

Real-time observation of cation exchange kinetics and dynamics at the muscovite-water interface

Ion exchange at charged solid–liquid interfaces is central to a broad range of chemical and transport phenomena. Real-time observations of adsorption/desorption at the molecular-scale elucidate exchange reaction pathways. Here we report temporal variation in the distribution of Rb⁺ species at the muscovite (001)–water interface during exchange with Na⁺. Time-resolved resonant anomalous X-ray reflectivity measurements at 25 °C reveal that Rb⁺ desorption occurs over several tens of seconds during which thermodynamically stable inner-sphere Rb⁺ slowly transforms to a less stable outer-sphere Rb⁺. In contrast, Rb⁺ adsorption is about twice as fast, proceeding from Rb⁺ in the bulk solution to the stable inner-sphere species. The Arrhenius plot of the adsorption/desorption rate constants measured from 9 to 55 °C shows that the pre-exponential factor for desorption is significantly smaller than that for adsorption, indicating that this reduced attempt frequency of cation detachment largely explains the slow cation exchange processes at the interface.

Ion exchange at charged mineral-water interfaces is an important geochemical process, but a molecular-level understanding is still required. Here, the authors probe real-time variations of the interfacial ion exchange dynamics at the muscovite-water interface, providing a general picture of adsorbed ion coverage and speciation.

An atomic-level insight into the basic mechanism responsible for the enhancement of the catalytic oxidation of carbon monoxide on a Cu/CeO2 surface

Reaction mechanism of CO molecules onto a Cu/CeO₂ surface and morphological changes.

The switching mechanism of the mitochondrial ADP/ATP carrier explored by free-energy landscapes

The ADP/ATP carrier (AAC) of mitochondria has been an early example for elucidating the transport mechanism alternating between the external (c-) and internal (m-) states (M. Klingenberg, Biochim. Biophys. Acta 1778 (2008) 1978-2021). An atomic resolution crystal structure of AAC is available only for the c-state featuring a three repeat transmembrane domain structure. Modeling of transport mechanism remained hypothetical for want of an atomic structure of the m-state. Previous molecular dynamics studies simulated the binding of ADP or ATP to the AAC remaining in the c-state. Here, a full description of the AAC switching from the c- to the m-state is reported using well-tempered metadynamics simulations. Free-energy landscapes of the entire translocation from the c- to the m-state, based on the gyration radii of the c- and m-gates and of the center of mass, were generated. The simulations revealed three free-energy basins attributed to the c-, intermediate- and m-states separated by activation barriers. These simulations were performed with the empty and with the ADP- and ATP-loaded AAC as well as with the poorly transported AMP and guanine nucleotides, showing in the free energy landscapes that ADP and ATP lowered the activation free-energy barriers more than the other substrates. Upon binding AMP and guanine nucleotides a deeper free-energy level stabilized the intermediate-state of the AAC2 hampering the transition to the m-state. The structures of the substrate binding sites in the different states are described producing a full picture of the translocation events in the AAC.

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

Towards molecular control of elementary reactions in zeolite catalysis by advanced molecular simulations mimicking operating conditions

Ingeniously selecting zeolite topology and acidity, reaction temperature and guest molecule loading enables tuning the reaction mechanism of zeolite-catalyzed methylation reactions.

Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics

Increasing attention has recently been devoted to allosteric modulators, as they can provide inherent advantages over classic receptor agonists. In the field of nicotinic receptors (nAChRs), the main advantage is that allosteric modulators can trigger pharmacological responses, limiting receptor desensitization. Most of the known allosteric ligands are "positive allosteric modulators" (PAMs), which increase both sensitivity to receptor agonists and current amplitude. Intriguingly, some allosteric modulators are also able to activate the α7 receptor (α7-nAChR) even in the absence of orthosteric agonists. These compounds have been named "ago-allosteric modulators" and GAT107 has been studied in depth because of its unique mechanism of action. We here investigate by molecular dynamics simulations, metadynamics, and essential dynamics the activation mechanism of α7-nAChR, in the presence of different nicotinic modulators. We determine the free energy profiles associated with the closed-to-open motion of the loop C, and we highlight mechanistic differences observed in the presence of different modulators. In particular, we demonstrate that GAT107 triggers conformational motions and cross-talk similar to those observed when the α7-nACh receptor is in complex with both an agonist and an allosteric modulator.

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method

The atomic mechanisms of isomerization of ATP-Mg(2+) in solution are characterized using the recently developed String Method with Optimal Molecular Alignment (SOMA) and molecular-dynamics simulations. Bias-Exchange Metadynamics simulations are first performed to identify the primary conformers of the ATP-Mg(2+) complex and their connectivity. SOMA is then used to elucidate the minimum free-energy path (MFEP) for each transition, in a 48-dimensional space. Analysis of the per-atom contributions to the global free-energy profiles reveals that the mechanism of these transitions is controlled by the Mg(2+) ion and its coordinating oxygen atoms in the triphosphate moiety, as well as by the ion-hydration shell. Metadynamics simulations in path collective variables based on the MFEP demonstrate these isomerizations proceed across a narrow channel of configurational space, thus validating the premise underlying SOMA. This study provides a roadmap for the examination of conformational changes in biomolecules, based on complementary enhanced-sampling techniques with different strengths. © 2015 Wiley Periodicals, Inc.