A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives

More than a half century ago it became feasible to simulate, using classical-mechanical equations of motion, the dynamics of molecular systems on a computer. Since then classical-physical molecular simulation has become an integral part of chemical research. It is widely applied in a variety of branches of chemistry and has significantly contributed to the development of chemical knowledge. It offers understanding and interpretation of experimental results, semiquantitative predictions for measurable and nonmeasurable properties of substances, and allows the calculation of properties of molecular systems under conditions that are experimentally inaccessible. Yet, molecular simulation is built on a number of assumptions, approximations, and simplifications which limit its range of applicability and its accuracy. These concern the potential-energy function used, adequate sampling of the vast statistical-mechanical configurational space of a molecular system and the methods used to compute particular properties of chemical systems from statistical-mechanical ensembles. During the past half century various methodological ideas to improve the efficiency and accuracy of classical-physical molecular simulation have been proposed, investigated, evaluated, implemented in general simulation software or were abandoned. The latter because of fundamental flaws or, while being physically sound, computational inefficiency. Some of these methodological ideas are briefly reviewed and the most effective methods are highlighted. Limitations of classical-physical simulation are discussed and perspectives are sketched.

Origin of thiocyanate spectral shifts in water and organic solvents

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

Laser induced degradation of bacterial spores during micro-Raman spectroscopy

Micro-Raman spectroscopy combined with optical tweezers is a powerful method to analyze how the biochemical composition and molecular structures of individual biological objects change with time. In this work we investigate laser induced effects in the trapped object. Bacillus thuringiensis spores, which are robust organisms known for their resilience to light, heat, and chemicals are used for this study. We trap spores and monitor the Raman peak from CaDPA (calcium dipicolinic acid), which is a chemical protecting the spore core. We see a correlation between the amount of laser power used in the trap and the release of CaDPA from the spore. At a laser power of 5 mW, the CaDPA from spores in water suspension remain intact over the 90 min experiment, however, at higher laser powers an induced effect could be observed. SEM images of laser exposed spores (after loss of CaDPA Raman peak was confirmed) show a notable alteration of the spores' structure. Our Raman data indicates that the median dose exposure to lose the CaDPA peak was ∼60 J at 808 nm. For decontaminated/deactivated spores, i.e., treated in sodium hypochlorite or peracetic acid solutions, the sensitivity on laser power is even more pronounced and different behavior could be observed on spores treated by the two chemicals. Importantly, the observed effect is most likely photochemical since the increase of the spore temperature is in the order of 0.1 K as suggested by our numerical multiphysics model. Our results show that care must be taken when using micro-Raman spectroscopy on biological objects since photoinduced effects may substantially affect the results.

A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions

A fixed multi-site interaction charge (FMIC) model was proposed for the accurate prediction of intermolecular electrostatic interactions based on the quantum mechanical linear response of a molecule to an external electric field. In such a model, some additional off-center interaction sites were added for capturing multipole interactions for a given molecule. By multivariate least-square fitting analysis of the calculated QM/MM interactions of a given molecule with the electrostatic environment and the electrostatic potentials of the environment at the pre-defined distributed interaction sites, the FMIC of the molecule was obtained. The model system of CO in myoglobin (Mb) was utilized to demonstrate the derivation of the FMIC. The accuracy of FMIC in predicting the electrostatic interactions between CO and the Mb environment was investigated using 10 000 different Mb-CO configurations generated from the 400 ps QM/MM MD simulation. In comparison to the QM/MM calculations at the B3LYP/aug-cc-pVTZ/ff99SB level, the mean unsigned error (MUE) of the results based on the FMIC model was merely 0.10 kcal mol^-1, and the root mean square error (RMSE) was only 0.13 kcal mol^-1, which are significantly lower than the results predicted by the ESP charge model (MUE = 1.45 kcal mol^-1, and RMSE = 1.7 kcal mol^-1, respectively). The transferability of FMIC was tested by applying the obtained FMIC in the wild type Mb-CO system to the mutants of V68F and H64L Mb-CO systems. The MUEs of the obtained results for 10 000 different configurations are both smaller than 0.2 kcal mol^-1 for the V68F and H64L Mb-CO systems in comparison to the B3LYP/aug-cc-pVTZ/ff99SB calculations, and the RMSEs are also lower than 0.2 kcal mol^-1 for both mutants. The applications of FMIC were extended to model the electrostatic interactions between a hydrogen fluoride molecule and 492 waters in a truncated octahedron box; our study showed that the FMIC could give satisfactory results with a MUE of 0.12 kcal mol^-1 and a RMSE of 0.16 kcal mol^-1 in comparison to the B3LYP/aug-cc-pVDZ/TIP3P calculations for 10 000 different configurations generated using the 10 ns classical MD simulation. Therefore, the FMIC method provides an accurate and efficient tool for predicting intermolecular electrostatic interactions, which can be utilized in the future development of molecular force fields.

An electrostatic energy-based charge model for molecular dynamics simulation

The interactions of the polar chemical bonds such as C=O and N-H with an external electric field were investigated, and a linear relationship between the QM/MM interaction energies and the electric field along the chemical bond is established in the range of weak to intermediate electrical fields. The linear relationship indicates that the electrostatic interactions of a polar group with its surroundings can be described by a simple model of a dipole with constant moment under the action of an electric field. This relationship is employed to develop a general approach to generating an electrostatic energy-based charge (EEC) model for molecules containing single or multiple polar chemical bonds. Benchmark test studies of this model were carried out for (CH₃)₂-CO and N-methyl acetamide in explicit water, and the result shows that the EEC model gives more accurate electrostatic energies than those given by the widely used charge model based on fitting to the electrostatic potential (ESP) in direct comparison to the energies computed by the QM/MM method. The MD simulations of the electric field at the active site of ketosteroid isomerase based on EEC demonstrated that EEC gave a better representation of the electrostatic interaction in the hydrogen-bonding environment than the Amber14SB force field by comparison with experiment. The current study suggests that EEC should be better suited for molecular dynamics study of molecular systems with polar chemical bonds such as biomolecules than the widely used ESP or RESP (restrained ESP) charge models.

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model

In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategies to partition QM determined molecular electron densities into atomic subregions. The partitioned atomic densities are subsequently used to compute atomic dispersion coefficients from effective exchange-hole-dipole moment (XDM) calculations. In order to derive values for the repulsive van der Waals parameters from first principles, we use a simple volume relation to scale effective atomic radii. Explicit inclusion of higher order dispersion coefficients was tested for a series of alkanes, and we show that combining C6 and C8 attractive terms together with a C11 repulsive potential yields satisfying models when used in combination with our van der Waals parameters and electrostatic and bonded parameters as directly obtained from quantum calculations as well. This result highlights that explicit inclusion of higher order dispersion terms could be viable in simulation, and it suggests that currently available QM analysis methods allow for first-principles parametrization of molecular mechanics models.

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge-on-spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico-chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed-phase polarizabilities, and starting from the non-polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure-liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure-liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen-bonding and non-hydrogen-bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.

Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models

We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study

The effect of ion binding on the structural, mechanical, dynamic and electrostatic properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in a 0.5 M aqueous NaCl solution is investigated using classical atomistic molecular dynamics simulation with different force-field descriptions for ion-ion and ion-lipid interactions. Most importantly, the repulsive Lennard-Jones parameters for the latter were modified, such that approximately similar binding of cations and anions to the lipid membrane is achieved. This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Furthermore, various parameters characterizing membrane structure, elasticity, order and dynamics are analyzed. It is found that ion binding as observed in simulations involving the modified in comparison to the original force-field description leads to: (i) a smaller salt-induced change in the area per lipid, which is in closer agreement with the experiment; (ii) a decrease in the area compressibility and bilayer thickness to values comparable to a bilayer in pure water; (iii) lipid deuterium order parameters and lipid diffusion coefficients on nanosecond timescales that are very similar to the values for a membrane in pure water. In general, salt effects on the structural properties of a POPC bilayer in an aqueous sodium-chloride solution appear to be reproduced reasonably well by the new force-field description. An analysis of membrane-membrane disjoining pressure suggests that the smaller salt-induced change in area per lipid induced by the new force-field description is not due to the alteration of membrane-associated net charge, but must rather be understood as a consequence of ion-specific effects on the arrangement of lipid molecules.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R² value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R² values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

Multiscale Modeling in the Clinic: Drug Design and Development

A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multiscale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales have become increasingly important. Multiscale approaches present in silico opportunities to advance laboratory research to bedside clinical applications in pharmaceuticals research. This is achievable through the capability of modeling to reveal phenomena occurring across multiple spatial and temporal scales, which are not otherwise readily accessible to experimentation. The resultant models, when validated, are capable of making testable predictions to guide drug design and delivery. In this review we describe the goals, methods, and opportunities of multiscale modeling in drug design and development. We demonstrate the impact of multiple scales of modeling in this field. We indicate the common mathematical and computational techniques employed for multiscale modeling approaches used in pharmacometric and systems pharmacology models in drug development and present several examples illustrating the current state-of-the-art models for (1) excitable systems and applications in cardiac disease; (2) stem cell driven complex biosystems; (3) nanoparticle delivery, with applications to angiogenesis and cancer therapy; (4) host-pathogen interactions and their use in metabolic disorders, inflammation and sepsis; and (5) computer-aided design of nanomedical systems. We conclude with a focus on barriers to successful clinical translation of drug development, drug design and drug delivery multiscale models.

Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited

The asymmetric solvation of ions can be defined as the tendency of a solvent to preferentially solvate anions over cations or cations over anions, at identical ionic charge magnitudes and effective sizes. Taking water as a reference, these effects are quantified experimentally for many solvents by the relative acity (A) and basity (B) parameters of the Swain scale. The goal of the present study is to investigate the asymmetric solvation of ions using molecular dynamics simulations, and to connect the results to this empirical scale. To this purpose, the charging free energies of alkali and halide ions, and of their hypothetical oppositely charged counterparts, are calculated in a variety of solvents. In a first set of calculations, artificial solvent models are considered that present either a charge or a shape asymmetry at the molecular level. The solvation asymmetry, probed by the difference in charging free energy between the two oppositely charged ions, is found to encompass a term quadratic in the ion charge, related to the different solvation structures around the anion and cation, and a term linear in the ion charge, related to the solvation structure around the uncharged ion-sized cavity. For these simple solvent models, the two terms are systematically counteracting each other, and it is argued that only the quadratic term should be retained when comparing the results of simulations involving physical solvents to experimental data. In a second set of calculations, 16 physical solvents are considered. The theoretical estimates for the acity A are found to correlate very well with the Swain parameters, whereas the correlation for B is very poor. Based on this observation, the Swain scale is reformulated into a new scale involving an asymmetry parameter Σ, positive for acitic solvents and negative for basitic ones, and a polarity parameter Π. This revised scale has the same predictive power as the original scale, but it characterizes asymmetry in an absolute sense, the atomistic simulations playing the role of an extra-thermodynamic assumption, and is optimally compatible with the simulation results. Considering the 55 solvents in the Swain set, it is observed that a moderate basity (Σ between -0.9 and -0.3, related to electronic polarization) represents the baseline for most solvents, while a highly variable acity (Σ between 0.0 and 3.0, related to hydrogen-bond donor capacity modulated by inductive effects) represents a landmark of protic solvents.

Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase

A supra-atomic coarse-grained (CG) force field for liquid n-alkanes is presented. The model was calibrated using experimental thermodynamic data and structural as well as energetic properties for 14 n-alkanes as obtained from atomistic fine-grained (FG) simulations of the corresponding hydrocarbons using the GROMOS 45A3 biomolecular force field. A variation of the nonbonded force-field parameters obtained from mapping the FG interactions onto the CG degrees of freedom to fit the density and heat of vaporization to experimental values turned out to be mandatory for a correct reproduction of these data by the CG model, while the bonded force-field parameters for the CG model could be obtained from a Boltzmann-weighted fit with some variations with respect to the corresponding properties from the FG simulations mapped onto the CG degrees of freedom. The model presents 6 different CG bead types, for bead sizes from 2 to 4 distinguishing between terminal and nonterminal beads within an alkane chain (end or middle). It contains different nonbonded Lennard-Jones parameters for the interaction of CG alkanes with CG water. The CG alkane model was further tested by comparing predictions of the excess free energy, the self-diffusion constant, surface tension, isothermal compressibility, heat capacity, thermal expansion coefficient, and shear viscosity for n-alkanes to experimental values. The CG model offers a thermodynamically calibrated basis for the development of CG models of lipids.

Direct computation of parameters for accurate polarizable force fields

We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.

A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities

Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects.