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[Display omitted] Dielectric effects and the coupled electrostatics between the nanoconfined and the internal/external aqueous media contribute to the observed deviations of chemistry within the nanoconfined environment when compared with unconfined systems. A systematic understanding has remained elusive, especially with respect to background salt concentration and boundary condition effects like the nanopore surface chemistry and the reference state used to calculate free energies. We utilize molecular dynamics simulations along with thermodynamic integration to determine the free energy difference associated with acid-base chemistry in 2 nm and 4 nm slit pores open to a bulk-like reservoir. pK a increases are predicted when confining acetic acid, formic acid, and bicarbonate in the slits at infinite dilution conditions. We find that confinement weakens the acids, and the modulation of outer pore surface dipole magnitudes can tune the pK a shift values, suggesting that purely "intrinsic" electrostatic effect on confinement may not exist. At sufficiently high salt concentrations, the dielectric/electrostatic effects on pK a values diminish due to charge screening effects. These discoveries enable future modifications of nanopore chemistries to achieve desirable properties for industrial applications. [ABSTRACT FROM AUTHOR]

Noble gas solubility in silicate melts has provided important insights into how these gases are incorporated into the Earth's interior and how they can be used as tracers of geochemical processes. However, previous studies have shown conflicting results regarding the noble gas solubility in silicate melts at high pressures. Some suggest that a drastic drop in solubility occurs above 5 GPa, while others indicate that maximum solubility is reached at this pressure but the solubility keeps unchanged when the pressure further increases. To clarify this discrepancy and gain a better understanding of the underlying mechanisms, we conducted a solubility investigation using the thermodynamic integration (TI) method and molecular dynamics (MD) simulations based on a machine-learning based force-field called deep potential (DP), which was trained by density functional theory (DFT) calculations. The effects of temperature, pressure and melt composition were investigated up to ∼30 GPa, 2500 K for the melt of model basalt, olivine and enstatite. Our results showed that the solubility of all noble gases (He, Ne and Ar) increased with temperature, while they increased with pressure until maximum solubility was reached at around 5 GPa. Beyond this pressure, solubility gradually decreased as pressure continued to increase. The structural and dynamic analysis of silicate melts revealed an abnormal increase in the self-diffusivity of oxygen atoms in silicate melts from ambient pressure to ∼5–8 GPa, which can be attributed to the formation of Si/Al-O 5-6 in the melts upon compression. Interestingly, the upper limit pressure (5–8 GPa) for this abnormal increase in oxygen diffusivity was also the pressure at which noble gas solubilities reached their maximum. Our findings suggest that the maximum noble gas solubility at around 5 GPa may be a universal phenomenon in silicate melts. However, the specific values and changing trends of solubility depend on the specific melt compositions and noble gases. The complexity of noble gas solubility in silicate melts at high temperatures and pressures suggests that there is significant potential for improving the high-pressure noble gas partition coefficients between minerals, silicate melts, and even the Earth's core. Such improvements would extend our understanding of the behavior of noble gases in the Earth's interior and their role in tracing geodynamic processes. [ABSTRACT FROM AUTHOR]

Solubility in water, free energy of solvation (ΔG s o l v ) and free energy of hydration (ΔG h y d ) were determined for 86 organic liquids using Molecular Dynamics simulations in order to find out the relation among these properties. Both, correlation between ΔG h y d and solubility and correlation between ΔG s o l v and solubility are not clearly defined. However, by defining Δ s =ΔG s o l v − Δ G h y d , it is found a numerical relation between Δ s and solubility. This result was verified for pentane, ethanol and, hexanol of three different force fields (TraPPE-UA, CHARMM and, GROMOS). Also, it was studied the relation of these properties by increasing hydrophobicity in a functional group through the number of carbon atoms of the hydrocarbon chain. In this last case, the mentioned relation was also found. [ABSTRACT FROM AUTHOR]

Recently, we have investigated the cucurbit[7]uril (CB7) recognition of the α- and β-anomers of neutral, protonated, and acetylated forms of glucosamine in water. In the present work, we employed molecular dynamics (MD) and thermodynamic integration methods (TI) to investigate the recognition of these molecules by cucurbit[6]uril (CB6) and cucurbit[8]uril (CB8). MD revealed the formation of stable 1:1 inclusion complexes by all studied molecules with cucurbit[n]urils (CBn), and 2:1 complex by the α-anomer of the acetylated form of glucosamine with the large homologue CB8. CB6 forms roughly twice as many hydrogen bonds with the guest molecules as CB8. MM-PBSA results indicated that the electrostatic contribution to the binding free energy of each guest:CB complex was larger for CB6 than for CB8, and that CB6 and CB8 have lower affinity toward the different forms of glucosamine compared to CB7. Furthermore, TI was used to estimate the relative affinities of CB6 and CB8 toward the α- and β-anomers for each form of the studied glucosamine and compare with CB7.

Cardiac troponin C (cTnC) is the critical Ca2+‐sensing component of the troponin complex. Binding of Ca2+ to cTnC triggers a cascade of conformational changes within the myofilament that culminate in force production. Hypertrophic cardiomyopathy (HCM)‐associated TNNC1 variants generally induce a greater degree and duration of Ca2+ binding, which may underly the hypertrophic phenotype. Regulation of contraction has long been thought to occur exclusively through Ca2+ binding to site II of cTnC. However, work by several groups including ours suggest that Mg2+, which is several orders of magnitude more abundant in the cell than Ca2+, may compete for binding to the same cTnC regulatory site. We previously used isothermal titration calorimetry (ITC) to demonstrate that physiological concentrations of Mg2+ may decrease site II Ca2+‐binding in both N‐terminal and full‐length cTnC. Here, we explore the binding of Ca2+ and Mg2+ to cTnC harbouring a series of TNNC1 variants thought to be causal in HCM. ITC and thermodynamic integration (TI) simulations show that A8V, L29Q and A31S elevate the affinity for both Ca2+ and Mg2+. Further, L48Q, Q50R and C84Y that are adjacent to the EF hand binding motif of site II have a more significant effect on affinity and the thermodynamics of the binding interaction. To the best of our knowledge, this work is the first to explore the role of Mg2+ in modifying the Ca2+ affinity of cTnC mutations linked to HCM. Our results indicate a physiologically significant role for cellular Mg2+ both at baseline and when elevated on modifying the Ca2+ binding properties of cTnC and the subsequent conformational changes which precede cardiac contraction. [ABSTRACT FROM AUTHOR]

Point defects are crucial in determining the quality of germanium crystals. A quantitative understanding of the thermodynamic formation properties of the point defects is necessary for the subsequent control of the defect formation during crystal growth. Here, molecular dynamics simulations were employed to investigate the formation energies, total formation free energies and formation entropies of the point defects in a germanium crystal. As far as we know, this is the first time that the total formation free energies of point defects in a germanium crystal have been reported in the literature. We found that the formation energies increased slightly with temperature. The formation free energies decreased significantly with an increase in temperature due to the increase in entropy. The estimated total formation free energies at the melting temperature are ~1.3 eV for self-interstitial and ~0.75 eV for vacancy, corresponding to a formation entropy of ~15 kB for both types of point defects. [ABSTRACT FROM AUTHOR]

Protein-ligand binding is among the most fundamental phenomena underlying all molecular biology, and a greater ability to more accurately and robustly predict the binding free energy of a small molecule ligand for its cognate protein is expected to have vast consequences for improving the efficiency of pharmaceutical drug discovery. We briefly reviewed a number of scientific and technical advances that have enabled alchemical free energy calculations to recently emerge as a preferred approach, and critically considered proper validation and effective use of these techniques. In particular, we characterized a selection bias effect which may be important in prospective free energy calculations, and introduced a strategy to improve the accuracy of the free energy predictions.

The paper presents analysis of precision of a phonon-based free energy calculation technique (Temperature Dependent Effective Potential method) in comparison with the thermodynamic integration method within classical molecular dynamics. It is shown that the use of the second order force constants is insufficient for accurate calculations of free energies at elevated temperatures due to noticeable anharmonic contributions to lattice vibrations. On the other hand, reliable calculations of the crystal phase equilibrium lines requires free energy accuracy better than 1–3 meV per atom. Based upon the obtained results the Temperature Dependent Effective Potential technique is applied to the detailed study of the solid-state Zr phase diagram from ab initio molecular dynamics that may be achieved if force constants up to the fourth order are used. The calculated zirconium phase diagram is in good agreement with experiment. The α − β − ω triple point was determined at P ≈ 6. 74 GPa, T ≈ 837 K. [Display omitted] [ABSTRACT FROM AUTHOR]

The anomalies properties of water have been interpreted theoretically using several all-atom and coarse-grained water models. Here we use a robust and traditional free energy approach to develop the solid-liquid coexistence curve for water using coarse-grained monatomic mW and machine-learned bond order potential (ML-BOP) water models. We employ the pseudo-supercritical thermodynamic path in combining multiple histogram reweighting (MHR) and Gibbs-Duhem integration. The ML-BOP model has a broad density-temperature hysteresis loop and shows lower maximum and minimum densities as compared to the mW model. The computed excess Helmholtz free energy and the Gibbs free energy at the approximate melting temperature are higher for the ML-BOP model in comparison with the mW model. The pressure dependence fusion curve for both water models aligns with the literature. This analysis indicates that the free energy method accurately captures the solid-liquid transformation and the thermodynamic melting point of water. [Display omitted] [ABSTRACT FROM AUTHOR]

Experimental binding free energies of 27 adamantyl amines against the influenza M2(22-46) WT tetramer, in its closed form at pH 8, were measured by ITC in DPC micelles. The measured K d 's range is ~44 while the antiviral potencies (IC 50) range is ~750 with a good correlation between binding free energies computed with K d and IC 50 values (r = 0.76). We explored with MD simulations (ff19sb, CHARMM36m) the binding profile of complexes with strong, moderate and weak binders embedded in DMPC, DPPC, POPC or a viral mimetic membrane and using different experimental starting structures of M2. To predict accurately differences in binding free energy in response to subtle changes in the structure of the ligands, we performed 18 alchemical perturbative single topology FEP/MD NPT simulations (OPLS2005) using the BAR estimator (Desmond software) and 20 dual topology calculations TI/MD NVT simulations (ff19sb) using the MBAR estimator (Amber software) for adamantyl amines in complex with M2(22-46) WT in DMPC, DPPC, POPC. We observed that both methods with all lipids show a very good correlation between the experimental and calculated relative binding free energies (r = 0.77–0.87, mue = 0.36–0.92 kcal mol-1) with the highest performance achieved with TI/MBAR and lowest performance with FEP/BAR in DMPC bilayers. When antiviral potencies are used instead of the K d values for computing the experimental binding free energies we obtained also good performance with both FEP/BAR (r = 0.83, mue = 0.75 kcal mol-1) and TI/MBAR (r = 0.69, mue = 0.77 kcal mol-1). [Display omitted] • We measured K d values for 27 adamantyl amines to influenza A M2TM WT measured with ITC in DPC micelles pH 8, differing by a factor of ~44. • The compounds antiviral potencies (IC 50 s) range was ~750 and there is a good correlation (r = 0.76) between Δ G b s computed with K d s and IC 50 s. • We investigated with MD simulations and ff19sb, CHARMM36m force fields the binding profile of the adamantyl amines. • In MD simulations were tested DMPC, DPPC, POPC or viral mimetic membranes and different experimental starting structures. • FEP/BAR and TI/MBAR binding free energy calculations based on K d values in the tested lipid systems show r = 0.77–0.87, mue = 0.36–0.92 kcal mol−1. • The highest performance was achieved with TI/MBAR and lowest performance with FEP/BAR for M2TM WT complexes in DMPC bilayers. • FEP/BAR or TI/MBAR showed good performance based on IC 50 values, r = 0.69, mue = 0.77 kcal mol−1 or r = 0.83, mue = 0.75 kcal mol−1. [ABSTRACT FROM AUTHOR]

The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all intramolecular interactions preserved. This paper reports a new procedure that makes it possible to these calculations in LAMMPS. The procedure is tested against built-in GROMACS capabilities. The model compounds chosen to test our methodology are ethanol and biphenyl. The LAMMPS and GROMACS results obtained are in good agreement with each other. This work should help perform solvation free energy calculations in LAMMPS and/or other molecular dynamics software having no built-in functions to implement the decoupling approach. [ABSTRACT FROM AUTHOR]

Molecular dynamics calculations of a mixed micelle composed of sodium dodecyl sulfate (SDS) and octaethylene glycol monododecyl ether (C12E8) were performed for six compositions (SDS/C12E8 = 100/0, 80/20, 60/40, 40/60, 20/80, and 0/100) to investigate the composition dependence of the mixed micelle structure and solubilization of cyclohexane, benzene, and phenol molecules by the micelle. The radial density distribution of the hydrophilic polyoxyethylene (POE) group of C12E8 as a function of distance from the micelle center is very sharp for micelles with high SDS content because the POE group captures a Na+ ion in solution and wraps around it to form a compact crown‐ether‐like complex. The hydrophobic dodecyl groups of SDS and C12E8 were separately distributed in the mixed micelle core. ΔG(r) evaluated for each solute showed that despite the structural changes of the micelle the binding strength of the solute molecules to the micelle did not change significantly. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Knowledge of the abundance and distribution of light elements in the core is fundamental to the understanding of the Earth and other planetary systems. Recent studies (Li et al., 2018; Mashino et al., 2019) suggest the particular importance of carbon for explaining core properties, yet knowledge of carbon partitioning between the outer and inner core is unknown. By using the quasiharmonic approximation, ab initio molecular dynamics, and thermodynamic integration techniques, we have computed the chemical potential of carbon in liquid Fe and solid hcp‐Fe at core conditions. We find that substitutional carbon is more stable than interstitial carbon and other carbon defect cluster structures in solid Fe. Lattice strain and overcoordination effects lead to a high chemical potential of C in solid Fe compared to the liquid, and consequently carbon partitions almost completely into the liquid. We find that carbon can account for most of the density jump at the inner‐core boundary. This provides an alternative mechanism to the necessity of an oxygen‐rich outer core and may have significant implications for the composition and structure of the deep Earth. Key Points: The chemical potential of C in solid and liquid Fe was calculated using ab initio methodsC almost completely partitions into liquid iron in the Fe‐C binary system at Earth's core conditionsThe presence of C in the outer core may account for most of the density jump at the ICB [ABSTRACT FROM AUTHOR]

Highlights • A cavity-based method to calculate relative solubilities of large solutes in pairs of solvents is presented. • The cavity-based method is benchmarked against direct molecular simulations employing coarse-grained fluid models. • Relative solubilities of pyrene in heptane and toluene are calculated at high pressures and temperatures. Abstract In this paper, we benchmark a cavity-based simulation method for calculating the relative solubility of large molecules in explicit solvents. The essence of the procedure is the accounting of the Gibbs energy change associated with an alchemical thermodynamic cycle where, in sequence, a cavity is created in a solvent, a solute is inserted in the cavity and the cavity is annihilated. The Gibbs energy change is equated to the excess chemical potential allowing the comparison of solubilities in different solvents. The results obtained using the cavity-based method are compared to direct large-scale molecular dynamics simulations performed using coarse-grained models for calculating the partition coefficient of pyrene between heptane and toluene. We demonstrate the applicability of this cavity-based technique under high pressure/temperature conditions. [ABSTRACT FROM AUTHOR]

We present a molecular dynamics simulation study of alkali metal cation transport through the double‐helical and the head‐to‐head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists of a sequence of transport reactions, absolute free energies of solvation and cycles of alchemical transmutations of the ions. In this manner, we can reliably estimate free energies and their statistical errors via a least‐squares method without imposing external forces on the system. Within the double helical channel, we find a free energy surface typical for hopping transport between isoenergetic sites of ion localization, separated by comparatively large activation barriers. For fast transport through the head‐to‐head conformation, the thermodynamic network scheme starts to break down. © 2018 Wiley Periodicals, Inc. Ion migration in the gramicidin protein channel is simulated using a thermodynamic integration network, which consists of transport reactions, absolute free energies of solvation and alchemical transmutations of ions. For a double helical channel, we find a free energy surface typical for hopping transport between isoenergetic sites of ion localization, whereas the scheme starts to break down for fast transport through a head‐to‐head conformation. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The solid-liquid interfacial free energy, γ , was computed for the Cu-Zr system. • γ was found to increase with decreasing temperature. • Two methods for computing γ were found to be in agreement. Abstract The solid-liquid portion of the equilibrium phase diagram at the Cu rich side of a Finnis-Sinclair description of Cu-Zr was determined by a combination of molecular dynamics and semi-grand canonical Monte Carlo simulations and the model system was found to be in very good agreement with experiment. Molecular dynamics simulations and the capillary fluctuation method were used to compute the solid-liquid interfacial free energy, γ , and its anisotropy as a function of undercooling. Unlike the case of pure metals and in contrast to most previous atomistic studies in alloy systems, γ was found to increase with decreasing temperature and the increase is quite pronounced. To verify the unusual results, the excess energy and number of Zr atoms were computed for the [1 0 0] interface and from the excess thermodynamic quantities γ was obtained through a thermodynamic integration. The results of the two approaches for computing γ are in agreement to within the statistical uncertainties. The implications of the temperature behavior of γ is discussed in terms of crystal nucleation from the melt and glass formation. [ABSTRACT FROM AUTHOR]

Mutation in the ethionamide (ETH) activating enzyme, EthA, is the main factor determining resistance to this drug, used to treat TB patients infected with MDR and XDR Mycobacterium tuberculosis isolates. Many mutations in EthA of ETH resistant (ETH-R) isolates have been described but their roles in resistance remain uncharacterized, partly because structural studies on the enzyme are lacking. Thus, we took a two-tier approach to evaluate two mutations (Y50C and T453I) found in ETH-R clinical isolates. First, we used a combination of comparative modeling, molecular docking, and molecular dynamics to build an EthA model in complex with ETH that has hallmark features of structurally characterized homologs. Second, we used free energy computational calculations for the reliable prediction of relative free energies between the wild type and mutant enzymes. The ΔΔG values for Y50C and T453I mutant enzymes in complex with FADH2-NADP-ETH were 3.34 (+/−0.55) and 8.11 (+/−0.51) kcal/mol, respectively, compared to the wild type complex. The positive ΔΔG values indicate that the wild type complex is more stable than the mutants, with the T453I complex being the least stable. These are the first results shedding light on the molecular basis of ETH resistance, namely reduced complex stability of mutant EthA.

Since polyphenols are highly bioactive, their separation and purification are active research topics. In the optimization of such processes, the trend of solubility at different conditions is of major interest, although obtaining experimental solubility data for polyphenols is lengthy and costly. A simple and previously explored thermodynamic integration (TI) procedure was applied to estimate the Gibbs hydration free energies at different temperatures for benzoic acid, (+)-catechin and toluene. These hydration energies were compared with experimental solubilities. An extensive test with 10 replications comprising a total of 200 molecular dynamics (MD) TI simulations was conducted. Linear trends were observed for the estimated Gibbs hydration free energy at different temperatures. Electrostatic contributions showed a strong effect for the studied polyphenols due to hydrogen bonds. Lennard-Jones (LJ) contributions to hydration free energies were small, being more significant for toluene due to cavity formation. The estimated Gibbs free energy of hydration presented an exponential trend for benzoic acid and (+)-catechin when compared to experimental solubility data. These trends were fitted to an empirical expression. To understand the physical meaning of the empirical fitting parameters, the effect of temperature in the sublimation enthalpy and in the entropy of the solid solute should be estimated. [ABSTRACT FROM AUTHOR]

The phase equilibria knowledge of fatty acid and water mixtures play a crucial role in the design and operation of processes such as bio-diesel synthesis, sea water desalination and novel solvent design. Experimental data on the mutual solubility of fatty acid and water are scattered and limited. Atomistic molecular simulation approach can be a viable substitute for these predictions. In this work, a molecular simulation method is proposed that does not require molecular transfer between dense phases as in the Gibbs ensemble method and is based on determining phase equilibria by computing and equating the fugacity of water in the two phases. Assuming that the fugacity of water-rich phase is identical to that of pure water, an expression for the solubility of fatty acid in water is derived. In the current formalism, fugacity is determined by computing the residual chemical potential of water and fatty acids via thermodynamic integration. Mutual solubility between water and three different fatty acids are calculated over a range of temperatures and shown to yield good agreement with experimental data. Microscopic structural properties elucidating the role of the hydrogen bonding interactions between water and fatty acid and the aggregation of water molecules which gives rise to the observed macroscopic properties are also studied. [ABSTRACT FROM AUTHOR]

Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate carboxylase–oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5‐step carboxylase reaction, the substrate Ribulose‐1,5‐bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2. Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation. However, details of the roles and protonation states of active‐site residues, and sources of protons and water, remain highly speculative. Large‐scale computations on active‐site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi‐empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO2 complex and associated active‐site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO2; both hydration and CC bond scission require early protonation of CO2 in the RuBP.CO2 complex; CC bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3‐gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis–Menten‐like complex corresponding to the empirical Km (=Kc) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We report the calculation of the potential of mean force (PMF) of different types of associations by various techniques: two no biased methods (thermodynamic integration and finite difference thermodynamic integration), a constraint biased technique (adaptive biasing force) and an umbrella biased method (umbrella sampling).We apply these methodologies to the association between two methane molecules in water, to the formation of an ion pair in water and to the formation of an insertion complex between a macrocycle and a cation. The different PMFs are compared to each other on the basis of the depth of the free energy minimum and on the location of different specific points. [ABSTRACT FROM AUTHOR]

Knowledge of free energies of crystalline solid phases is pivotal in determination of phase equilibria; however, their computations using molecular simulations are quite challenging. In this paper, we apply the Einstein molecule method to compute the excess free energies of crystalline molecular solids comprising of molecules described by flexible models. This work can be viewed as an extension of the method described in Aragones et al. [J Chem Phys. 2013;139:a034104]. In this article, we present our calculations of the free energies of ice-Ih described by q-TIP4P/F model and Orcinol Form I described by the OPLS-AA forcefield. The free energies computed for ice-Ih are in agreement with previous reported results, and those of Orcinol are shown to be thermodynamically consistent. We demonstrate that the efficiency of our calculations compares favourably with existing methods. The method described here can be easily implemented in popular publicly available molecular dynamics packages without any modification to their existing source codes. [ABSTRACT FROM AUTHOR]

The paper reviews several modern methods for calculation of Helmholtz free energy, associated with atomic vibrations: quasiharmonic approximation, self-consistent lattice dynamics method, calculation based on velocity autocorrelation function, temperature-dependent effective potential and thermodynamic integration. The results of free energy calculation by these methods are compared with each other in a wide temperature range, and their applicability is discussed. As a tool we use classical molecular dynamics modeling on the example of bcc molybdenum and fcc aluminum. The relation is observed between how the vibrational spectrum changes with temperature due to the anharmonicity of the potential and how free energy is reproduced. All methods are consistent with each other within 10 meV/at. at relatively low temperatures. At high temperatures, the discrepancy reaches tens of meV/at., although the relative error is less than 5%. [ABSTRACT FROM AUTHOR]

The free energy is central to statistical mechanics and thermodynamics, and its accurate calculation via. computational modelling is important for a large number of applications, especially when its experimental value is hard to obtain. Several established and general methods for calculating the Helmholtz free energy across different length scales, including continuum, atomistic and quantum mechanical, are compared and analyzed. A computational approach is then proposed to calculate the temperature dependences of internal energy and absolute Helmholtz free energy for solid and liquid phases with the coupling of thermodynamic integration (TI) and harmonic approximation calculations from both classical molecular dynamics (MD) and density functional theory (DFT). We use the Lennard-Jones system as an example ( i.e. argon) for the demonstration of the approach. It is observed that the free energy transits smoothly from being describable by the harmonic approximation to including anharmonic effects at a transition temperature around 0.56 T m ; below this temperature, the quantum behavior of atoms is important. At higher temperatures ( T  > 0.56 T m ), the TI and harmonic approximation results for the Helmholtz free energy functions become increasingly divergent with the increase of temperature. This work demonstrates that a multiscale approach employing TI, MD, and DFT can provide accurate calculations of the temperature dependence of absolute Helmholtz free energy for both solid and liquid phases. [ABSTRACT FROM AUTHOR]

The octanol–water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values. [ABSTRACT FROM AUTHOR]

Targeting drugs to the inflamed intestinal tissue(s) represents a major advancement in the treatment of inflammatory bowel disease (IBD). In this work we present a powerful in-silico modeling approach to guide the molecular design of novel prodrugs targeting the enzyme PLA, which is overexpressed in the inflamed tissues of IBD patients. The prodrug consists of the drug moiety bound to the sn-2 position of phospholipid (PL) through a carbonic linker, aiming to allow PLA to release the free drug. The linker length dictates the affinity of the PL-drug conjugate to PLA, and the optimal linker will enable maximal PLA-mediated activation. Thermodynamic integration and Weighted Histogram Analysis Method (WHAM)/Umbrella Sampling method were used to compute the changes in PLA transition state binding free energy of the prodrug molecule (∆∆G) associated with decreasing/increasing linker length. The simulations revealed that 6-carbons linker is the optimal one, whereas shorter or longer linkers resulted in decreased PLA-mediated activation. These in-silico results were shown to be in excellent correlation with experimental in-vitro data. Overall, this modern computational approach enables optimization of the molecular design of novel prodrugs, which may allow targeting the free drug specifically to the diseased intestinal tissue of IBD patients. [ABSTRACT FROM AUTHOR]

Recently, we have investigated the cucurbit[7]uril (CB7) recognition of the α- and β-anomers of neutral, protonated, and acetylated forms of glucosamine in water. In the present work, we employed molecular dynamics (MD) and thermodynamic integration methods (TI) to investigate the recognition of these molecules by cucurbit[6]uril (CB6) and cucurbit[8]uril (CB8). MD revealed the formation of stable 1:1 inclusion complexes by all studied molecules with cucurbit[ n ]urils (CB n), and 2:1 complex by the α-anomer of the acetylated form of glucosamine with the large homologue CB8. CB6 forms roughly twice as many hydrogen bonds with the guest molecules as CB8. MM-PBSA results indicated that the electrostatic contribution to the binding free energy of each guest:CB complex was larger for CB6 than for CB8, and that CB6 and CB8 have lower affinity toward the different forms of glucosamine compared to CB7. Furthermore, TI was used to estimate the relative affinities of CB6 and CB8 toward the α- and β-anomers for each form of the studied glucosamine and compare with CB7. [ABSTRACT FROM AUTHOR]

This work explores the use of continuous thermodynamic integration in field-theoretic simulations of a symmetric diblock copolymer melt. Free energies of the lamellar and disorder phases are evaluated by thermodynamic integration from a reference state (an Einstein crystal, λ = 0) to a diblock copolymer (λ = 1). This is followed by integration over the interaction parameter, χ b, to locate the order-disorder transition (ODT). Then the equilibrium lamellar spacing and free energy cost of stretching and compressing lamellae are examined. The ODT, lamellar spacing, and compression modulus are consistent with previous calculations, though found faster and more precisely. The above quantities do not depend on simulation box size, suggesting that finite-size effects are small and simulating two lamellar periods is sufficient to accurately evaluate bulk behavior. Furthermore, the statistical uncertainty in the ODT increases quickly with system size, suggesting that small systems may lead to more precise results. [ABSTRACT FROM AUTHOR]

GSK3β kinase is a noteworthy target for discovery of the drugs that will be used to treat several diseases. In the effort to identify a new inhibitor lead compound, we utilized thermodynamic integration ( TI)-molecular dynamics ( MD) simulation and kinase assay to investigate the bindings between GSK3β kinase and five compounds that were analogous to a known inhibitor with an available crystal structure. TI- MD simulations of the first two compounds (analogs 1 and 2) were used for calibration. The computed binding affinities of analogs 1 and 2 agreed well with the experimental results. The rest three compounds (analogs 3- 5) were newly obtained from a database search, and their affinity data were newly measured in our labs. TI- MD simulations predicted the binding modes and the computed ΔΔ G values have a reasonably good correlation with the experimental affinity data. These newly identified inhibitors appear to be new leads according to our survey of GSK3β inhibitors listed in recent review articles. The predicted binding modes of these compounds should aid in designing new derivatives of these compounds in the future. [ABSTRACT FROM AUTHOR]

Knowledge of trace element partition coefficients is crucial for our understanding of global element cycles. While a great number of experimental studies on mineral-melt partitioning have been performed in the past, the influence of melt structure on partitioning has mostly been considered empirically. This is mainly due to the lack of reliable structure models for typical melts at the relevant pressure and temperature conditions. Molecular dynamics simulations on the other hand may open a new window into this problem as they provide a unique approach to both structural and thermodynamic properties of minerals and melts. In this contribution, we employ first-principles and classical molecular dynamics simulations to (1) explore further a new approach to predict trace element partitioning between several silicate melts and (2) simultaneously investigate the structural controls of the observed partitioning. Specifically, we use a thermodynamic integration scheme to investigate the partitioning behavior of various trace elements (Y, La, As) in a granitic and gabbroic as well as two Ti-bearing melts and compare our data to experimental findings. Our results indicate that, similar to the lattice strain model, partitioning in melts as well seems to depend on an ideal coordination environment for each trace element and on how well this environment can be accommodated in a specific melt. [ABSTRACT FROM AUTHOR]

The dopamine and serotonin transporter proteins (DAT, SERT) play a vital role in behavior and mental illness. Although their substrate transport has been studied extensively, the molecular basis of their selectivity is not completely understood yet. In this study, we exploit molecular dynamics simulations combined with mutagenesis studies to shed light on the driving factors for DAT-over-SERT selectivity of a set of cathinones. Results indicate that these compounds can adopt two binding modes of which one is more favorable. In addition, free energy calculations indicated the substrate binding site (S1) as the primary recognition site for these ligands. By simulating DAT with SERT-like mutations, we hypothesize unsubstituted cathinones to bind more favorably to DAT, due to a Val152 offering more space, as compared to the bulkier Ile172 in SERT. This was supported by uptake inhibition measurements, which showed an increase in activity in SERT-I172V. [ABSTRACT FROM AUTHOR]

An approach to determining the nucleation barrier and interfacial free energy (surface tension) based on molecular dynamics simulations of structural transformations, in particular, the formation of new phase nuclei, is reported. The approach is based on the thermodynamic integration method, wherein key elements are trajectories characterizing the potential energy change, which are obtained from independent numerical experiments. An important feature of the approach is its applicability to both equilibrium and nonequilibrium systems, as well as the possibility of determining the above thermodynamic characteristics for small new-phase nuclei, with a significant curvature of the surface. For example, we present the temperature dependencies of the surface tension of water droplet nuclei for water vapor nucleation and of the nucleation barrier to crystal nucleation in two model glassy systems, which are computed within the framework of the proposed approach. The calculated values of the surface tension coefficient of water droplet nuclei are compared with the available experimental data. [ABSTRACT FROM AUTHOR]

As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol for OAH with TI and 1.9 kcal mol for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds. [ABSTRACT FROM AUTHOR]

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett's acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. [ABSTRACT FROM AUTHOR]

• The manuscript explores the dependence of transport properties of amino acids like cystine and valline. • It provides thermodynamic properties like Free energy of solvation for those two amino acids in water. • We explore how these seemingly different properties like transport and thermodynamic are related in those amino acids. The study of thermodynamic and transport properties of amino acids gives access to knowledge about interactions between distinct molecules necessary to understand a variety of biological processes. In this work, we have performed molecular dynamics simulations of valine and cysteine peptides with lengths of (n) = 1, 2, 4, 8 & 16 monomers in an aqueous environment to estimate the solvation free energy and diffusion coefficients. We modeled our system using OPLS-AA parameter sets and TIP3P water at 310 K temperature. Solvation free energy of both the peptides have been reported using two thermodynamic integration (TI) based methods: TI and TI-CUBIC. The solvation free energy of both the peptides increases with the chain length. The estimated values using both methods are in good agreement with a statistical error of < 3%. The solvent accessible surface area (SASA) of solutes and hydrogen bonds between solute and solvent have also been presented to get more insights on solvation processes. The increase in solvation energy of both peptides with chain length is further corroborated by increase in the number of hydrogen bond (between peptide and water) and SASA with the chain length. In addition, the self diffusion coefficient of both solute and solvent along with their binary diffusion coefficient have been estimated for both the peptides. Furthermore, the effect of chain length on solvation free energy as well as diffusion coefficients have been studied. [ABSTRACT FROM AUTHOR]

Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2/ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one-step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients $$D_{cw}$$ of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in $$\log D_{cw}$$ of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental $$D_{cw}$$ data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations. [ABSTRACT FROM AUTHOR]