An interpretation of the enhancement of the water dipole moment due to the presence of other water molecules

Biomolecular condensates can function as inherent catalysts

We report the discovery that chemical reactions such as ATP hydrolysis can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs), which themselves lack any intrinsic ability to function as enzymes. This inherent catalytic feature of condensates derives from the electrochemical environments and the electric fields at interfaces that are direct consequences of phase separation. The condensates we studied were capable of catalyzing diverse hydrolysis reactions, including hydrolysis and radical-dependent breakdown of ATP whereby ATP fully decomposes to adenine and multiple carbohydrates. This distinguishes condensates from naturally occurring ATPases, which can only catalyze the dephosphorylation of ATP. Interphase and interfacial properties of condensates can be tuned via sequence design, thus enabling control over catalysis through sequence-dependent electrochemical features of condensates. Incorporation of hydrolase-like synthetic condensates into live cells enables activation of transcriptional circuits that depend on products of hydrolysis reactions. Inherent catalytic functions of condensates, which are emergent consequences of phase separation, are likely to affect metabolic regulation in cells.

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables

The development of accurate water models is of primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid water models are still ubiquitously used to simulate a variety of molecular systems. Automatic optimization approaches have been recently used to iteratively refine three-site water models to fit macroscopic (average) thermodynamic properties, providing state-of-the-art three-site models that still present some deviations from the liquid water properties. Here, we show the results obtained by automatically optimizing three-site rigid water models to fit a combination of microscopic and macroscopic experimental observables. We use Swarm-CG, a multiobjective particle-swarm-optimization algorithm, for training the models to reproduce the experimental radial distribution functions of liquid water at various temperatures (rich in microscopic-level information on, e.g., the local orientation and interactions of the water molecules). We systematically analyze the agreement of these models with experimental observables and the effect of adding macroscopic information to the training set. Our results demonstrate how adding microscopic-rich information in the training of water models allows one to achieve state-of-the-art accuracy in an efficient way. Limitations in the approach and in the approximated description of water in these three-site models are also discussed, providing a demonstrative case useful for the optimization of approximated molecular models, in general.

An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2-25

We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2-11, 16-17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (D_e's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2-25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83-119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (D_e's) throughout the entire cluster range (n = 2-25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ∼4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6-3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.

Decomposed Mean-Field Simulations of Local Properties in Condensed Phases

The present work demonstrates a robust protocol for probing localized electronic structure in condensed-phase systems, operating in terms of a recently proposed theory for decomposing the results of Kohn-Sham density functional theory in a basis of spatially localized molecular orbitals. In an initial application to liquid, ambient water and the assessment of the solvation energy and the embedded dipole moment of H₂O in solution, we find that both properties are amplified on average-in accordance with expectation-and that correlations are indeed observed to exist between them. However, the simulated solvent-induced shift to the dipole moment of water is found to be significantly dampened with respect to typical literature values. The local nature of our methodology has further allowed us to evaluate the convergence of bulk properties with respect to the extent of the underlying one-electron basis set, ranging from single-ζ to full (augmented) quadruple-ζ quality. Albeit a pilot example, our work paves the way toward future studies of local effects and defects in more complex phases, e.g., liquid mixtures and even solid-state crystals.

Structure, Molecular Interactions, and Dynamics of Aqueous [BMIM][BF4] Mixtures: A Molecular Dynamics Study

Molecular dynamics simulations with many-body polarizable force fields were carried out to investigate the thermodynamic, structural, and dynamic properties of aqueous solutions of 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF₄]). The radial distribution functions exhibit well-defined features, revealing favored structural correlations between [bmim]⁺, [BF₄]^-, and H₂O. The addition of water is shown to alter ionic liquid structural organizations by replacing counterions in the coordination shells and disrupt the cation-anion network. At low water concentration, the majority of water molecules are isolated from each other and have lower average dipole moment than that in pure water. With increasing hydration level, while [bmim][BF₄] ionic network breaks up and becomes isolated ion pairs or free ions in the dilute limit, water begins to form clusters of increasing sizes and eventually forms a percolating network. As a result, the average water dipole moment increases and approaches its bulk value. Water is also observed to have a substantial influence on the dynamics of ionic liquids. At low water content, the cation and anion have similar diffusion coefficients due to the correlated ionic motion of long-lived ion pairs. As the water concentration increases, both ions exhibit greater mobility and faster rotations from the breakup of ionic network. Consequently, the ionic conductivity of [bmim][BF₄] aqueous solutions rises with increasing water composition.

Understanding the Dipole Moment of Liquid Water from a Self-Attractive Hartree Decomposition

The dipole moment of a single water molecule in liquid water has been a critical concept for understanding water's dielectric properties. In this work, we investigate the dipole moment of liquid water through a self-attractive Hartree (SAH) decomposition of total electron density computed by density functional theory, on water clusters sampled from ab initio molecular dynamics simulation of bulk water. By adjusting one parameter that controls the degree of density localization, we reveal two distinct pictures of water dipoles that are consistent with bulk dielectric properties: a localized picture with smaller and less polarizable monomer dipoles and a delocalized picture with larger and more polarizable monomer dipoles. We further uncover that the collective dipole-dipole correlation is stronger in the localized picture and is key to connecting individual dipoles with bulk dielectric properties. On the basis of these findings, we suggest considering both individual and collective dipole behaviors when studying the dipole moment of liquid water and propose new design strategies for developing water models.

Does Oxygen Feature Chalcogen Bonding?

Using the second-order Møller-Plesset perturbation theory (MP2), together with Dunning's all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R-M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.

Water in protein hydration and ligand recognition

This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.

Cell theory, intrinsically disordered proteins, and the physics of the origin of life

Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.

Hydrogen-bond pattern to characterize water network

Hydrogen-bond (HB) patterns correspond to topologically distinct isomers of water clusters, and can be expressed by digraphs. The HB pattern is used to divide the configuration space of water cluster at a finite temperature. The populations of the HB patterns are transformed into the relative Helmholtz energies. The method is based on the combination of molecular simulation with graph theory. At a finite temperature it can be observed that other isomers than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced depending on the local HB network around the water molecule. Rooted digraph is used to represent topologically distinct isomers of protonated water (PW) clusters. O–H bonds of PW clusters are classified into 10 topological types based on the combination of the local HB types of the contributing water molecules to the O–H bond. If the topological type is the same, vibrational frequencies of those O–H bonds of PW clusters are similar even in different isomers; i.e. vibrational frequency of O–H bond is transferable, and can be used as a vibrational spectral signature of PW clusters.

Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures

The nature of the dynamical hydrogen-bond network of liquid water under ambient conditions has challenged both experimental and theoretical researchers for decades and remains a topic of intense debate. In this work, we addressed the structural issue of the hydrogen-bond network of liquid water based on an accurate ab initio molecular dynamics simulation. The present work showed clearly that liquid water is neither accurately described by a static picture of mostly tetrahedral water molecules nor dominated by "ring-and-chain" like structures. Instead, the structure of water is a dynamical mixture of tetrahedral and 'ring-and-chain' like structures with a slight bias toward the former. On average, each water molecule forms about three hydrogen bonds with the surrounding water molecules. The present accurate ab initio molecular dynamics simulation of liquid water was made possible by using a fragment-based second-order Møller-Plesset perturbation theory (MP2) with a large basis set to treat a large body of water molecules. This level of ab initio theory is sufficiently accurate for describing water interactions, and the simulated structural and dynamical properties of liquid water, including radial distribution functions, diffusion coefficient, dipole moment, etc., are uniformly in excellent agreement with experimental observations.

The long-range convergence of the energetic properties of the water monomer in bulk water at room temperature

The Interacting Quantum Atoms (IQA) energy partitioning scheme has been applied to a set of liquid water largely spherical clusters (henceforth called spheres) of up to 9 Å radius, with a maximum cluster size of 113 molecules. This constitutes half of the commonly used 216 molecules in a typical simulation box of a liquid water box, and to our knowledge is the largest analysis of this kind ever undertaken. As well as demonstrating the topological analysis of large systems, which has only recently become computationally feasible, important long range properties of liquid water are obtained. The full topological partitioning of each sphere into atomic basins is used to consider the long-range convergence of the energetic and multipolar properties of the water molecule at the centre of each sphere. It is found that the total molecular energy converges to its 9 Å value after 7 Å, which corresponds to approximately the first three solvation shells, while the molecular dipole and quadrupole moments approximately converge after 5.5 Å, which corresponds to approximately the first two solvation shells. The effect of water molecule flexibility is also considered.

Microwave dielectric spectroscopy study of water dynamics in normal and contaminated raw bovine milk

The role of water in bovine milk is more complicated than that of a background solvent. To understand the interaction between water and the constituents of milk, an extensive dielectric study of the γ-dispersion of raw bovine milk was carried out over the frequency range 0.1-50GHz and the interval of temperatures (10°C-42°C). Samples were provided by utilizing an extended donor pool. The results reveal that the temperature dependence of the characteristic relaxation times is described by the Arrhenius law. Furthermore, it conforms to a Meyer-Neldel compensation, whereby the pre-factor of the relaxation times is dependent on the activation energy. This entropy/enthalpy compensation is traced to the interaction between bulk water dynamic clusters and other milk constituents. A statistical correlation between the Somatic Cell Count, a traditional measure of milk quality, and the relaxation times is provided as well, opening new vistas for the industrial classification of milk.

Understanding the structure and hydrogen bonding network of (H2O)32 and (H2O)33: an improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of atoms in molecules (QTAIM) analysis

Large water clusters are of particular interest because of their connection to liquid water and the intricate hydrogen bonding networks they possess.

On the cooperativity of association and reference energy scales in thermodynamic perturbation theory

Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bonding energy scale as well as a reference energy scale which accounts for dispersion and orientationally averaged multi-pole attractions. These energy scales are always treated independently. In recent years, extensive first principles quantum mechanics calculations on small water clusters have shown that both hydrogen bond and reference energy scales depend on the number of incident hydrogen bonds of the water molecule. In this work, we propose a new methodology to couple the reference energy scale to the degree of hydrogen bonding in the fluid. We demonstrate the utility of the new approach by showing that it gives improved predictions of water-hydrocarbon mutual solubilities.

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions

Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

The mechanism of the dielectric relaxation in water

The water spectra from Raman and Dielectric spectroscopies are combined to present a cohesive description of water dynamics up to the THz region.

The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

What is the primary mover of water dynamics?

We present evidence that the microscopic origin of both the excess wing and the main relaxation process of pure water is the same.

Efficient and accurate fragmentation methods

Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.

Distribution of topologically distinct isomers of water clusters and dipole moments of constituent water molecules at finite atmospheric temperatures

Hydrogen-bonding (HB) patterns correspond to topologically distinct isomers of a water cluster and can be expressed by digraphs. We make use of the HB pattern to divide the configuration space of a water cluster ((H2O)n, n = 3-8) at a finite temperature. Each configuration of a water cluster generated in Monte Carlo (MC) simulation is classified into an HB pattern. The number of observed HB patterns increases exponentially with the cluster size, whereas the population of the most abundant HB pattern decreases. The populations of the HB patterns are transformed into the relative Helmholtz energies. At a finite temperature, it can be observed that isomers other than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced, depending on the molecular circumstance. The change is rationalized by the difference in the local HB type of the water molecule in the HB network.

Shape control of electrodeposited copper films and nanostructures through additive effects

The use of electrolyte additives to affect nanocrystallite shape and film morphology in electrodeposited copper films is presented. Linear sweep and cyclic voltammetry, atomic force microscopy (AFM), scanning electron microscopy (SEM), and X-ray diffraction (XRD) methods are employed to investigate the effects of alcohol additives and the organic additive malachite green (MG), on copper electrodeposited onto polycrystalline gold electrodes. The use of additives affects the deposition process by increasing cathodic peak potentials and decreasing corresponding peak currents. Copper films deposited from electrolyte solutions with additives show additive-specific nanostructure and crystallite morphology. Film analysis reveals a greater than five times reduction in both film roughness and grain size in the presence of even small concentrations of the additive MG. Use of MG results in the preferential electrodeposition of oriented, square pyramidal crystallites, while alcohol additives result in tetrahedral crystallite textures. These shape-controlled additive effects are supported by additive adsorption energy calculations, which indicate preferential interactions, and differential growth kinetics on different facets of the film's growing nanostructures during electrodeposition. This approach offers a new and cost-effective route to achieve shape-controlled surface nanostructure.

Accurate first principles model potentials for intermolecular interactions

The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

Quadrupolar NMR Spin Relaxation Calculated Using Ab Initio Molecular Dynamics: Group 1 and Group 17 Ions in Aqueous Solution

Electric field gradient (EFG) fluctuations for the monoatomic ions (7)Li(+), (23)Na(+), (35)Cl(-), (81)Br(-), and (127)I(-) in aqueous solution are studied using Car-Parrinello ab initio molecular dynamics (aiMD) simulations based on density functional theory. EFG calculations are typically performed with 1024 ion-solvent configurations from the aiMD simulation, using the Zeroth Order Regular Approximation (ZORA) relativistic Hamiltonian. Autocorrelation functions for the spherical EFG tensor elements are computed, transformed into the corresponding spectral densities (under the extreme narrowing condition), and subsequently converted into NMR quadrupolar relaxation rates for the ions. The relaxation rates are compared with experimental data. The order of magnitude is correctly predicted by the simulations. The computational protocol is tested in detail for (81)Br(-).

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.