Search

Peptoids are peptide-mimetic biopolymers that are easy to synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semiempirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids toward these conformations. [ABSTRACT FROM AUTHOR]

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. [ABSTRACT FROM AUTHOR]

The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2+...Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements that probe the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for both coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. [ABSTRACT FROM AUTHOR]

We present an analysis of the dynamics of ion-pairing of lithium fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a generalized Langevin equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response to ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short-time anharmonic response is recovered with a GLE parametrization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straightforward application of variational transition state theory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. [ABSTRACT FROM AUTHOR]

Thepropensities of the water self-ions, H3O+andOH–, for the air–water interface haveimplications for interfacial acid–base chemistry. Despite numerousexperimental and computational studies, no consensus has been reachedon the question of whether or not H3O+and/orOH–prefer to be at the water surface or in thebulk. Here we report a molecular dynamics simulation study of thebulk vs interfacial behavior of H3O+and OH–that employs forces derived from density functionaltheory with a generalized gradient approximation exchange-correlationfunctional (specifically, BLYP) and empirical dispersion corrections.We computed the potential of mean force (PMF) for H3O+as a function of the position of the ion in the vicinityof an air–water interface. The PMF suggests that H3O+has equal propensity for the interface and the bulk.We compare the PMF for H3O+to our previouslycomputed PMF for OH–adsorption, which containsa shallow minimum at the interface, and we explore how differencesin solvation of each ion at the interface vs in the bulk are connectedwith interfacial propensity. We find that the solvation shell of H3O+is only slightly dependent on its position inthe water slab, while OH–partially desolvates asit approaches the interface, and we examine how this difference insolvation behavior is manifested in the electronic structure and chemistryof the two ions. [ABSTRACT FROM AUTHOR]

For strong acids, like hydrochloricacid, the complete dissociationinto an excess proton and conjugated base as well as the formationof independent solvated charged fragments is assumed. The existenceof chloride–hydronium (Cl–···H3O+) contact ion pairs even in moderate concentrationhydrochloric acid (2.5 m) demonstrates that the counterions do notbehave merely as spectators. Through comparison of recent extendedX-ray absorption fine structure (EXAFS) measurements to state-of-the-artdensity functional theory (DFT) simulations, we are able to obtaina unique view into the molecular structure of medium-to-high concentratedelectrolytes. Here we report that the Cl–···H3O+contact ion pair structure persists throughoutthe entire concentration range studied and that these structures differsignificantly from moieties studied in microsolvated hydrochloricacid gas phase clusters. Characterizing distinct populations of theseion pairs gives rise to a novel molecular level description of howto view the reaction network for acid dissociation and how it relatesto our picture of acid–base equilibria. [ABSTRACT FROM AUTHOR]

In recent years, theoretical as well as experimental studies have presented a novel view of the aqueous interface, wherein hard and/or multiply charged ions are excluded from the interface but large polarizable anions show interfacial enhancement relative to the bulk. The observed trend in the propensity of anions to adsorb at the air/water interface appears to follow an inverse order of the Hofmeister series for anions. This study focuses on experimental and theoretical examination of the partitioning behavior of perchlorate (ClO4−) and chloride (Cl−) ions at the air/water interface. We have used ambient pressure X-ray photoelectron spectroscopy to directly probe the interfacial concentrations of ClO4−and Cl−ions in sodium perchlorate and sodium chloride solutions, respectively. In the case of ClO4−ion, experimental observations are compared with molecular dynamics simulations utilizing both first principles based interaction potentials as well as polarizable classical force fields. Both the experimental and the theoretical results show enhancement of ClO4−ion at the interface, compared with the absence of such enhancement in the case of the Cl−ion. Our observations are in agreement with the expected trend in the interfacial propensity of anions based on the Hofmeister series. [ABSTRACT FROM AUTHOR]

Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. In this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.

When hydrolyzable cations such as aluminum interact with solid-water interfaces, macroscopic interfacial properties ( e.g ., surface charge and potential) and interfacial phenomena ( e.g ., particle adhesion) become tightly linked with the microscopic details of ion adsorption and speciation. We use in situ atomic force microscopy to directly image individual aluminum ions at a mica-water interface and show how adsorbate populations change with pH and aluminum activity. Complementary streaming potential measurements then allow us to build a triple layer model (TLM) that links surface potentials to adsorbate populations, via equilibrium binding constants. Our model predicts that hydrolyzed species dominate the mica-water interface, even when unhydrolyzed species dominate the solution. Ab initio molecular dynamics (AIMD) simulations confirm that aluminum hydrolysis is strongly promoted at the interface. The TLM indicates that hydrolyzed adsorbates are responsible for surface-potential inversions, and we find strong correlations between hydrolyzed adsorbates and particle-adhesion forces, suggesting that these species mediate adhesion by chemical bridging.

Muscovite mica (001) is a widely used model surface for controlling molecular assembly and a common substrate for environmental adsorption processes. The mica (001) surface displays near-trigonal symmetry, but many molecular adsorbates-including water-exhibit unequal probabilities of alignment along its three nominally equivalent lattice directions. Buried hydroxyl groups within the muscovite structure are speculated to be responsible, but direct evidence is lacking. Here, we utilize vibrational sum frequency generation spectroscopy (vSFG) to characterize the orientation and hydrogen-bonding environment of near-surface hydroxyls inside mica. Multiple distinct peaks are detected in the O-H stretch region, which we attribute to Si/Al substitution in the SiO 4 tetrahedron and K + ion adsorption above the hydroxyls based on density functional theory simulations. Our findings demonstrate that vSFG can identify the absolute orientation of -OH groups and, hence, the surface termination at a mica surface, providing a means to investigate how -OH groups influence molecular adsorption and better understand mica stacking-sequences and physical behavior.

We present a theory for ion pair dissociation and association, motivated by the concepts of Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water. The potential of mean force on these 2D surfaces computed from molecular dynamics simulations of different monovalent ion pairs reveal a Marcus-like mechanism for ion-pairing: Water molecules rearrange forming an activated coordination state prior to ion pair dissociation or association, followed by relaxation of the coordination state due to further water rearrangement. Like Marcus theory, we find the existence of an inverted region where the transition rates are slower with increasing exergonicity. This study provides a new perspective for the future investigations of ion-pairing and transport.

The molecular details of single ion solvation around Ca(2+) and ion-pairing of Ca(2+)···Cl(-) are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements that probe the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for both coordination number of Ca(2+) and its ion-pairing with Cl(-) depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment.

Insertion of a hard sphere cavity in liquid water breaks translational symmetry and generates an electrostatic potential difference between the region near the cavity and the bulk. Here, we clarify the physical interpretation of this potential and its calculation. We also show that the electrostatic potential in the center of small, medium, and large cavities depends very sensitively on the form of the assumed molecular interactions for different classical simple point-charge models and quantum mechanical DFT-based interaction potentials, as reflected in their description of donor and acceptor hydrogen bonds near the cavity. These differences can significantly affect the magnitude of the scalar electrostatic potential. We argue that the result of these studies will have direct consequences toward our understanding of the thermodynamics of ion solvation through the cavity charging process.

Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (IR) shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Because sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water.

We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H2O/SO3(-) corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3(-)-H3O(+) contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10(-5) cm(2)/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations.

We demonstrate that the driving forces for ion adsorption to the air-water interface for point charge models result from both cavitation and a term that is of the form of a negative electrochemical surface potential. We carefully characterize the role of the free energy due to the electrochemical surface potential computed from simple empirical models and its role in ionic adsorption within the context of dielectric continuum theory. Our research suggests that the electrochemical surface potential due to point charge models provides anions with a significant driving force for adsoprtion to the air-water interface. This is contrary to the results of ab initio simulations that indicate that the average electrostatic surface potential should favor the desorption of anions at the air-water interface. The results have profound implications for the studies of ionic distributions in the vicinity of hydrophobic surfaces and proteins.

Molecular-level insight into the dissociation of nitric acid in water is obtained from X-ray photoelectron spectroscopy and first-principles molecular dynamics (MD) simulations. Our combined studies reveal surprisingly abrupt changes in solvation configurations of undissociated nitric acid at approximately 4 M concentration. Experimentally, this is inferred from shifts of the N1s binding energy of HNO(3)(aq) as a function of concentration and is associated with variations in the local electronic structure of the nitrogen atom. It also shows up as a discontinuity in the degree of dissociation as a function of concentration, determined here from the N1s photoelectron signal intensity, which can be separately quantified for undissociated HNO(3)(aq) and dissociated NO(3)(-)(aq). Intermolecular interactions within the nitric acid solution are discussed on the basis of MD simulations, which reveal that molecular HNO(3) interacts remarkably weakly with solvating water molecules at low concentration; around 4 M there is a turnover to a more structured solvation shell, accompanied by an increase in hydrogen bonding between HNO(3) and water. We suggest that the driving force behind the more structured solvent configuration of HNO(3) is the overlap of nitric acid solvent shells that sets in around 4 M concentration.

The computation of vibrational spectra via molecular dynamics (MD) simulations has made lively progress in recent years. In particular, infrared spectra are accessible employing ab initio MD, for which only the total dipole moment has to be computed "on the fly" from the electronic structure along the trajectory. The analysis of such spectra in terms of the normal modes of intramolecular motion, however, still poses a challenge to theory. Here, we present an algorithm to extract such normal modes from MD trajectories by combining several ideas available in the literature. The algorithm allows one to compute both the normal modes and their vibrational bands without having to rely on an equipartition assumption, which hampered previous methods. Our analysis is based on a tensorial definition of the vibrational density of states, which spans both the frequency resolved cross- and auto-correlations of the molecular degrees of freedom. Generalized normal coordinates are introduced as orthonormal transforms of mass-weighted coordinates, which minimize their mutual cross-correlations. The generalized normal coordinates and their associated normal modes are iteratively constructed by a minimization scheme based on the Jacobi diagonalization. Furthermore, the analysis furnishes mode local temperatures, which provide not only a measure for the convergence of the computed intensities but also permits one to correct these intensities a posteriori toward the ensemble limit. As a first non-trivial test application we analyze the infrared spectrum of isoprene based on ab initio MD, which is an important building block of various dye molecules in molecular biology.