Calculation of the free energy of solvation for neutral analogs of amino acid side chains

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations. The calculations show that while the force field reproduces the experimental solvation free energies of nonpolar analogs with reasonable accuracy the solvation free energies of polar analogs in water are systematically overestimated (too positive). The dependence of the calculated free energies on the atomic partial charges was also studied.     

Solvation free energy of amino acids and side-chain analogues

The solvation free energies of amino acids and their side-chain analogues in water and cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are described by the OPLS-AA force field for the amino acids and the TIP4P model for water, and the free energies are determined by using the Bennett acceptance method. Results for the side-chain analogues in cyclohexane and in water are used to evaluate the performance of the force field for the van der Waals and the electrostatic interactions, respectively. Comparison of the calculated hydration free energies for the amino acid analogues and the full amino acids allows assessment of the additivity of the side chain contributions on the number of hydrating water molecules. The hydration free energies of neutral amino acids can be reasonably approximated by adding the contributions of their side chains to that of the hydration of glycine. However, significant nonadditivity in the free energy is found for the zwitterionic form of amino acids with polar side chains. In serine and threonine, intramolecular hydrogen bonds are formed between the polar side chains and backbone groups, leading to weaker solvation than for glycine. In contrast, such nonadditivity is not observed in tyrosine, in which the hydroxyl group is farther separated from, and therefore cannot form an intramolecular hydrogen bond with, the backbone. For histidine we find that a water molecule can form a bridge when the intramolecular hydrogen bond between the polar group and the backbone is broken.     

Are solvation free energies of homogeneous helical peptides additive?

We investigated the additivity of the solvation free energy of amino acids in homogeneous helices of different length in water and in chloroform. Solvation free energies were computed by multiconfiguration thermodynamic integration involving extended molecular dynamics simulations and by applying the generalized-born surface area solvation model to static helix geometries. The investigation focused on homogeneous peptides composed of uncharged amino acids, where the backbone atoms are kept fixed in an ideal helical conformation. We found nonlinearity especially for short peptides, which does not allow a simple treatment of the interaction of amino acids with their surroundings. For homogeneous peptides longer than five residues, the results from both methods are in quite good agreement and solvation energies are to a good extent additive.     

Effect of Higher Fatty Acids and Their Mixtures on Interfacial and Physicomechanical Properties of Vulcanized Rubbers

The interfacial characteristics of stearic and oleic acids and their mixtures were studied. The surface free energies of isoprene and butadiene-styrene rubbers and vulcanizates thereof, obtained using fatty acids and their synergistic mixture as vulcanization activators, were evaluated from the contact angles.     

The effect of the structure of cinnamic acid derivatives on their interaction with highly dispersed silica in aqueous medium

Adsorption of cinnamic, caffeic, and ferulic acids on the surface of highly dispersed silica from aqueous solutions is studied. The dependence of the structure of adsorption complexes on the molecular structure of adsorbates is determined. Values of free energies of solvation and adsorption of acids are calculated with allowance for solvation effects.     

Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants

Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.     

Monolayer properties of fatty acids : II. Surface vapor pressure and the free energy of compression

The properties of monolayers spread at the air-water interface were measured for saturated, unsaturated, and hydroxy fatty acids, differing in the type and degree of unsaturation, geometric isomerism, and position of unsaturated and hydroxy groups. Surface vapor pressures, reflecting the equilibrium between “gaseous” and “liquid” monolayer states were determined, as were the free energies of compression, ΔF_c, from essentially infinite dilution (100,000 Ų/molecule) to the area per molecule, A_e at the equilibrium spreading pressure, π_e. Surface vapor pressures and free energies of compression for saturated and unsaturated fatty acids with a double bond, or bonds, change in a manner expected because of chain-chain interactions. Hydroxy and acetylenic acids produce relatively high surface vapor pressures, despite their tendency for strong chain-chain interaction. It is concluded that chain-water interactions are very significant for the acetylenic and hydroxy acids and less so for the saturated and ethylenic acids.     

芳香甲（乙）酯）铵盐的酰胺化与酰亚胺化

用热分析方法得出,由芳香酸甲酯或乙酯与4,4’-二氨基二苯甲烷制备的铵盐的酰胺化,酰亚胺化反应,较芳香酸的铵盐更易进行,反应温度和表观活化能均比四酸铵盐时低。由铵盐生成的聚酰亚胺具有很好的热氧化稳定性。     

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.     

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

Molecular dynamics simulations in explicit solvent were applied to predict the hydration free energies for 23 small organic molecules in blind SAMPL2 test. We found good agreement with experimental results, with an RMS error of 2.82 kcal/mol over the whole set and 1.86 kcal/mol over all the molecules except several hydroxyl-rich compounds where we find evidence for a systematic error in the force field. We tested two different solvent models, TIP3P and TIP4P-Ew, and obtained very similar hydration free energies for these two models; the RMS difference was 0.64 kcal/mol. We found that preferred conformation of the carboxylic acids in water differs from that in vacuum. Surprisingly, this conformational change is not adequately sampled on simulation timescales, so we apply an umbrella sampling technique to include free energies associated with the conformational change. Overall, the results of this test reveal that the force field parameters for some groups of molecules (such as hydroxyl-rich compounds) still need to be improved, but for most compounds, accuracy was consistent with that seen in our previous tests.     

Tricarbonyltechnetium(I) and tricarbonylrhenium(I) complexed with N-methyl-2-pyridinecarboxyamide as potential radiopharmaceuticals: a computational study

The electronic and thermodynamic properties of the ‘2 + 1’ tricarbonyltechnetium(I) and -rhenium(I) mixed ligand complexes with N-methylpyridine-2-carboxyamide (MPCA) as a bidentate ligand and chloride, water, or tert-butyl-3-isocyanopropanoate (BCP), were investigated within the framework of Density Functional Theory. The atomic charges of all complexes, polarization of the CO groups, as well as the effect of transfer of π-electron density between the ligands through the metal were calculated and compared. The free energies of the reaction of formation of the isocyanide complexes in aqueous solution were calculated based on calculated total free energies in aqueous solution of the products and the substrates. The dissociation energies of the complexes were also determined in order to rationalize the experimentally observed higher resistance of the rhenium compared to the technetium complexes in the challenge experiments with the standard sulfur-containing amino acids.     

CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field

High-level ab initio calculations have been carried out to study weak CH/pi interactions and as a check of the CHARMM force field for aromatic amino acids. Comparisons with published data indicate that the MP2/cc-pVTZ level of theory is suitable for calculations of CH/pi interaction, including the T-shape benzene dimer. This level of theory was, therefore, applied to investigate CH/pi interactions between ethene or cis-2-butene and benzene in a variety of orientations. In addition, complexes between ethene and a series of model compounds (toluene, methylindole and p-cresol) representing the aromatic amino acids were studied motivated by the presence of CH/pi interactions in biological systems. Ab initio binding energies were compared to the binding energies obtained with the CHARMM22 force field. In the majority of orientations, CHARMM22 reproduces the preferred binding modes, with excellent agreement for the benzene dimer. Small discrepancies found in the calculations involving methylindole along with a survey of published thermodynamic data for the aromatic amino acids prompted additional optimization of the tryptophan force field. Partial atomic charges, Lennard-Jones parameters, and force constants were improved to obtain better intra- and intermolecular properties, with significant improvements obtained in the reproduction of experimental heats of sublimation for indole and free energies of aqueous solvation for methylindole.     

Thermodynamics of Transfer of Amino Acids from Water to Aqueous Sodium Sulfate

Abstract

The solubilities of amino acids at 288.15, 298.15 and 308.15K in water and aqueous sodium sulfate have been determined as a function of electrolyte concentration (0.5, 1.0, 1.5 mol/kg of water). It has been observed that sodium sulfate renders amino acids less scluble. The free energies of transfer of amino acids from water to aqueous sodium sulfate have been calculated from the solubility data. The enthalpies and entropies of transfer have also been estimated. The solubility and the thermodynamics of transfer data manifest that sodium sulfate generates favourable interaction between nonpolar groups of amino acids. If applied to proteins, it seems to stabilize the protein native globular structure by enhancing the intramolecular nonpolar-nonpolar group interactions.     

Ternary complexes of some rare earth metal ions with 1,2-diaminocyclohexanetetraacetic acid and hydroxy acids

1:1:1, Rare earth ions-CDTA-hydroxy acids ternary systems have been studied pH-metrically. The formation constants (log K_MLL′) and free energies of formation (ΔF°) of the resulting octa-coordinated metal ion mixed-ligand complexes have been calculated. The order of stability in terms of metal ions has been reported as: La < Pr < Nd < Gd < Dy and in terms of hydroxy acids as: TAR < MAL.     

Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods

Complete Basis Set and Gaussian-n methods were combined with CPCM continuum solvation methods to calculate pK(a) values for six carboxylic acids. An experimental value of -264.61 kcal/mol for the free energy of solvation of H(+), DeltaG(s)(H(+)), was combined with a value for G(gas)(H(+)) of -6.28 kcal/mol to calculate pK(a) values with Cycle 1. The Complete Basis Set gas-phase methods used to calculate gas-phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed-phase free energies are slightly less accurate than the gas-phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. The use of Cycle 1 and the Complete Basis Set models combined with the CPCM solvation methods yielded pK(a) values accurate to less than half a pK(a) unit.     

Local measures of intermolecular free energies in solution

Proton spin-lattice relaxation rate changes induced by freely diffusing oxygen in aqueous and mixed solvents are reported for representative amino acids and glucose. The local oxygen concentration at each spectrally resolved proton was deduced from the paramagnetic contribution to the relaxation rate. The measured relaxation increment is compared to that of the force-free diffusion relaxation model, and the differences are related to a free energy for the oxygen association with different portions of the solute molecules. The free energy differences are small, on the order of -800 to -2000 J/mol, but are uniformly negative for all proton positions measured on the amino acids in water and reflect the energetic benefit of weak association of hydrophobic cosolutes. For glucose, CH proton positions report negative free energies for oxygen association, the magnitude of which depends on the solvent; however, the hydroxyl positions report positive free energy differences relative to the force-free diffusion model, which is consistent with partial occupancy in the OH region by a solvent hydrogen bond.     

Theoretical examination of the thermodynamic factors in the selective extraction of Am3+ from Eu3+ by dithiophosphinic acids

A detailed thermodynamic examination of the selective extraction of Am(3+) from Eu(3+) by two dithiophosphinic acids was performed using DFT. By examination of two extractants with two metal ions, the most uncertain terms of these calculations were eliminated, resulting in free energies (ΔΔΔG(ext)) that are directly related to the selectivity data. The calculated relative selectivities agree well with experimental data, indicating that the extraction factor is primarily due to the binding free energy of the ligands to the metals and is not dependent on side reactions or complicated solvent effects.     

水/乙醇混合溶剂中氨基酸离解的取代基效应

用LKB-2277BioActivityMonitor测定了298.15K时甘氨酸,丙氨酸和丝氨酸在水/乙醇混合溶剂中的离解焓,计算了相应的离解熵。根据三个氨基酸分别与某一参考酸之间的质子交换反应,重点讨论了溶剂结构变化对取代基效应焓,熵变化的影响。实验结果表明在水/乙醇混合溶剂的最大结构化区域,取代基效应最为显著。认为在混合溶剂的富水区大块的似冰山结构的水分子簇的寿命大大延长。     

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

Zinc binding in HDAC inhibitors: a DFT study

Histone deacetylases (HDACs) are attractive targets for the treatment of cancers and a variety of other diseases. Most currently studied HDAC inhibitors contain hydroxamic acids, which are potentially problematic in the development of practical drugs. DFT calculations of the binding modes and free energies of binding for a variety of other functionalities in a model active site of HDAC are described. The protonation state of hydroxamic acids in the active site and the origin of the high affinity are discussed. These results emphasize the importance of a carefully chosen pKa for zinc binding and provide guidance for the design of novel, non-hydroxamic acid HDAC inhibitors.