Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

Accurately predicting receptor–ligand binding free energies is one of the holy grails of computational chemistry with many applications in chemistry and biology. Many successes have been reported, but issues relating to sampling and force field accuracy remain significant issues affecting our ability to reliably calculate binding free energies. In order to explore these issues in more detail we have examined a series of small host–guest complexes from the SAMPL6 blind challenge, namely octa-acids (OAs)–guest complexes and Curcurbit[8]uril (CB8)–guest complexes. Specifically, potential of mean force studies using umbrella sampling combined with the weighted histogram method were carried out on both systems with both known and unknown binding affinities. We find that using standard force fields and straightforward simulation protocols we are able to obtain satisfactory results, but that simply scaling our results allows us to significantly improve our predictive ability for the unknown test sets: the overall RMSD of the binding free energy versus experiment is reduced from 5.59 to 2.36 kcal/mol; for the CB8 test system, the RMSD goes from 8.04 to 3.51 kcal/mol, while for the OAs test system, the RSMD goes from 2.89 to 0.95 kcal/mol. The scaling approach was inspired by studies on structurally related known benchmark sets: by simply scaling, the RMSD was reduced from 6.23 to 1.19 kcal/mol and from 2.96 to 0.62 kcal/mol for the CB8 benchmark system and the OA benchmark system, respectively. We find this scaling procedure to correct absolute binding affinities to be highly effective especially when working across a “congeneric” series with similar charge states. It is less successful when applied to mixed ligands with varied charges and chemical characteristics, but improvement is still realized in the present case. This approach suggests that there are large systematic errors in absolute binding free energy calculations that can be straightforwardly accounted for using a scaling procedure. Random errors are still an issue, but near chemical accuracy can be obtained using the present strategy in select cases.     

Physicochemical characterization and molecular modeling study of host–guest systems of aripiprazole and functionalized cyclodextrins

Journal of Thermal Analysis and Calorimetry - Aripiprazole (ARP), an innovative atypical antipsychotic drug, exhibits very low aqueous solubility, affecting its dissolution and absorption and high...     

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

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.     

Free-energy calculations of the host–guest association in grafted supramolecular assemblies

Herein, we investigate the impact of grafting macrocyclic hosts with hydrophobic cavities onto a gold surface on the association with a guest molecule of particular importance to applications for molecular machines. We establish that the increase of the grafted alkyl chain length and number of anchor points strengthens the binding of the guest with the β-cyclodextrin host. This is the opposite effect with the p-sulfonatocalix[4]arene host for which the grafting considerably reduces the strength of the host–guest association. The structural and thermodynamic characterizations, carried out with free energy simulations, are combined to rationalize the differences in the association process in both heterogeneous and homogeneous conditions.     

A non-recycle flow still for the experimental determination of vapor–liquid equilibria in reactive systems

Experiments for the determination of vapor–liquid equilibrium (VLE) data with a Non-Recycle Flow Still (NFS) are described. Due to short residence times, the NFS is especially suited for systems with thermally unstable components and for reactive mixtures. VLE data of the latter are necessary for modeling reactive distillation processes. With the NFS isobaric data both at atmospheric and at reduced pressure can be gained. The potential of this technique is demonstrated and validated with the well-known, non-reactive systems methanol–ethanol and ethanol–water. The other (mainly reactive) binary mixtures investigated stem from two esterification systems (methyl formate and ethyl acetate production) and one etherification system (tert-amyl methyl ether production). The NRTL equation is used for modeling of the VLE data. The data acquired with the NFS are compared with literature data (whenever possible) or with results of group contribution methods.     

Testing the effect of the cavity size and the number of molecular substitutions in host–guest complexes formed by 2-hydroxypropyl-cyclodextrins and n-octyl-β-d-glucopyranoside

The thermodynamic characterization of host–guest complex formation processes based on modified cyclodextrins (CDs) presents several difficulties that are absent when using native CDs. They are mainly due to the relatively wide distribution of the degree of molecular substitution and also to the indeterminacy in the location of the modified groups. A more common trouble would arise from the coexistence of coupled processes, such as CD-surfactant complexation and surfactant demicellization. In the present work a reasonable approach based on the analysis of isothermal titration calorimetric measurements is employed to assess the effect of the number of molecular substitutions as well as of the CD cavity size in supra-molecular complexes formed by 2-hydroxypropyl-CDs and n-octyl-β-d-glucopyranoside. The employed method considers both first- (1:1) and second-order (1:2 and 2:1) stoichiometries. The results were significantly different from those previously observed for native CDs. The substituted groups increase entropically the stability of 1:1 species based on α-CD, while compete with the surfactant for the CD cavity in the case of 1:1 and 1:2 species based on β- and γ-CD, respectively. Also, the modified β-CD seems to enhance the formation of non-inclusion second-order complexes.     

Spun films of perylene diimide derivative for the detection of organic vapors with host–guest principle

The optical characterization and chemical vapor sensing properties of 1,7-dibromo-N,N′-(bicyclohexyl)-3,4:9,10-perylene diimide thin film against to organic vapors were discussed in this study by using spin coating, UV–Vis spectroscopy, atomic force microscopy, surface plasmon resonance (SPR) and Quartz Crystal Microbalance (QCM) techniques. The perylene diimide thin films were fabricated with a refractive index values from 1.55 to 1.60 and thicknesses in the range between 15.80 and 26.32 nm using different spin speeds from 1000 to 5000 rpm. In this study, perylene diimide thin film sensor was exposed to dichloromethane, chloroform, carbon tetrachloride, tetrahydrofuran and ethyl acetate vapors by using both SPR and QCM techniques. Also, the swelling behaviors of the perylene diimide thin films prepared at different spin speeds were investigated with respect to dichloromethane vapor at the room temperature by using SPR data. Diffusion coefficients were found to be 11.34?×?10^?17 (1000 rpm), 2.56?×?10^?17 (3000 rpm) and 0.38?×?10^?17 cm² s^?1 (5000 rpm) for dichloromethane vapor by using the Fick’s law of diffusion. It might be proposed that perylene diimide thin film optical chemical sensor element has a good sensitivity and selectivity for the dichloromethane vapor at room temperature.     

Comparing of the host–guest interaction in the Hofmann-1,10-diaminodecane and Hofmann-1,12-diaminododecane-type clathrates

M(1,12-diaminododecane)Ni(CN)4.G (M = Co, Ni or Cd; G = chlorobenzene; 1,2-; 1,3- or 1,4- dichlorobenzene) clathrates were prepared in powder form for the first time and their infrared spectra were reported and then compared with M(1,10-diaminodecane)Ni(CN)₄.1,5G (M = Co, Ni or Cd; G = chlorobenzene; 1,2-; 1,3- or 1,4-dichlorobenzene) clathrates. The spectral results suggest that the characteristic ν(CN) and δ(NiCN) frequencies are found to be similar to those known for the Hofmann type compounds, in that prepared compounds are similar in structure to this type compounds and their structures consist of polymeric layers [M–Ni(CN)₄]_∞ with the 1,12-diaminododecane molecule bound to the metal atom (M). Also, the results suggest that the ligand molecule with 10 to 12 of chain length have no effect on vibrational bands of the guest molecules in the similar Hofmann-diam-type clathrates. The normal mode frequencies and corresponding vibrational assignments of chlorobenzene and 1,2-; 1,3- or 1,4-dichlorobenzene in the ground state were calculated by DFT/B3LYP level of theory using the 6-311G(d, p) basis set in Gauss-view. In addition, these theoretical results were compared to the experimental results for the vibrational modes of host molecules.     

Cyclodextrin-based polymeric materials for the specific recovery of polyphenolic compounds through supramolecular host–guest interactions

While the specific recovery of valuable chemicals from waste streams represents an environmentally-friendly and potentially economically-relevant alternative to synthetic chemical productions, it remains a largely unmet challenge. This is partially explained by the complexity of designing sorption materials able to target one specific compound and able to function in complex matrices. In this work, a series of cyclodextrin-based polymers (CDPs) were designed to selectively extract phenolic compounds from a complex organic matrix that is olive oil mill wastewater (OMW). In order to endow these polymers with selective adsorption properties, several monomers and cross-linkers were screened and selected. The adsorption properties of the CDPs produced were first tested with selected phenolic compounds commonly found in OMW, namely syringic acid, p-coumaric acid, tyrosol and caffeic acid. The selected CDPs were subsequently tested for their ability to adsorb phenolic compounds directly from OMW, which is known to possess a high and complex organic content. It was demonstrated through high-performance liquid chromatography-mass spectroscopy analyses that efficient removal of phenolic compounds from OMW could be achieved but also that two compounds, namely tyrosol and hydroxytyrosol, could be selectively extracted from OMW.     

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host–guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye–Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.     

The quantitative determination of the S0—T1 absorption in pyrene with the use of intracavity absorption spectroscopy

The spin-forbidden S₀—T₁ transition of pyrene was quantitatively investigated by applying intracavity absorption spectroscopy. The measurements were carried out in benzolic solutions. The molar decadic extinction coefficient of the 0—0 transition was determined to 6.0 × 10⁻⁴ dm³mol⁻¹ cm⁻¹. The integral absorptivity was calculated to 2.94 × 10⁻² dm³ mol⁻¹ cm⁻¹ and yielded an intrinsic phosphorescence lifetime of 55.4 s. The intracavity absorptions were measured in a cavity-dumped Rhodamine 6G dye laser. Absorbances were recorded in the range between 8 × 10⁻⁴ and 5 × 10⁻⁶.     

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

Molecular containers such as cucurbit[7]uril (CB7) and the octa-acid (OA) host are ideal simplified model test systems for optimizing and analyzing methods for computing free energies of binding intended for use with biologically relevant protein–ligand complexes. To this end, we have performed initially blind free energy calculations to determine the free energies of binding for ligands of both the CB7 and OA hosts. A subset of the selected guest molecules were those included in the SAMPL4 prediction challenge. Using expanded ensemble simulations in the dimension of coupling host–guest intermolecular interactions, we are able to show that our estimates in most cases can be demonstrated to fully converge and that the errors in our estimates are due almost entirely to the assigned force field parameters and the choice of environmental conditions used to model experiment. We confirm the convergence through the use of alternative simulation methodologies and thermodynamic pathways, analyzing sampled conformations, and directly observing changes of the free energy with respect to simulation time. Our results demonstrate the benefits of enhanced sampling of multiple local free energy minima made possible by the use of expanded ensemble molecular dynamics and may indicate the presence of significant problems with current transferable force fields for organic molecules when used for calculating binding affinities, especially in non-protein chemistries.     

A shotgun approach for the identification of platinum–protein complexes

A shotgun approach including peptide-based OFFGEL-isoelectric focusing (IEF) fractionation has been developed with the aim of improving the identification of platinum-binding proteins in biological samples. The method is based on a filter-aided sample preparation (FASP) tryptic digestion under denaturing and reducing conditions of cisplatin–, oxaliplatin–, and carboplatin–protein complexes, followed by OFFGEL-IEF separation of the peptides. Any risk of platinum loss is minimized throughout the procedure due to the removal of the reagents used after each stage of the FASP method and the absence of thiol-based reagents in the focusing buffer employed in the IEF separation. The platinum–peptide complexes stability after the FASP digestion and the IEF separation was confirmed by size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS). The suitability of peptide-based OFFGEL-IEF fractionation for reducing the sample complexity for further nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analysis has been demonstrated, allowing the detection of platinum-containing peptides, with significantly lower abundance and ionization efficiency than unmodified peptides. nLC-MS/MS analysis of selected OFFGEL-IEF fractions from tryptic digests with different complexity degrees: standard human serum albumin (HSA), a mixture of five proteins (albumin, transferrin, carbonic anhydrase, myoglobin, and cytochrome-c) and human blood serum allowed the identification of several platinum–peptides from cisplatin–HSA. Cisplatin-binding sites in HSA were elucidated from the MS/MS spectra and assessed considering the protein three-dimensional structure. Most of the potential superficial binding sites available on HSA were identified for all the samples, including a biologically relevant cisplatin-cross-link of two protein domains, demonstrating the capabilities of the methodology.

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Graphical Abstract Graphical abstract shows the several steps involved in the identification of platinum-protein complexes: FASP digestion of proteins, peptide fractionation by OFFGEL-IEF and identification of Pt-complexes by nLC-ESIMS/MS

     

Spectroscopic characterization of laser induced breakdown in aluminium–lithium alloy samples for quantitative determination of traces

We present here the results of the application of laser induced breakdown spectroscopy (LIBS) to a sample of a solid aluminum–lithium alloy, in which the latter component is at a very low concentration and whose proportion should be determined. The samples were placed in a vacuum chamber filled with a controlled xenon atmosphere, and the emission lines of this element were used to determine the electronic density and temperature of the laser generated plasma. Then, by means of a specially designed algorithm, it is possible to quantify the lithium content in the sample. The laser produced aluminum–lithium alloy plasma was generated by a pulsed Nd⁺³:YAG laser (50 mJ) the pulse repetition frequency used was varied according to requirement from 1 to 20 Hz. Satisfactory results were obtained for the analytical determination of lithium contents in aluminum–lithium alloys. The lithium concentration was determined in values as low as 300–400 ppm.     

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

We calculate the absolute binding free energies of tetra-methylated octa-acids host–guest systems as a part of the SAMPL6 blind challenge (receipt ID vq30p). We employed two different free energy simulation methods, i.e., the umbrella sampling (US) and double decoupling method (DDM). The US method was used with the weighted histogram analysis method (WHAM) (US-WHAM scheme). In the DDM scheme, Hamiltonian replica-exchange method (HREM) was combined with the Bennett acceptance ratio (BAR) (HREM-BAR scheme). We obtained initial binding poses via molecular docking using GalaxyDock-HG program, which is developed for the SAMPL challenge. The root mean square deviation (RMSD) and the mean absolute deviations (MAD) using US-WHAM scheme were 1.33 and 1.02 kcal/mol, respectively. The MAD was the top among all submissions, however the correlation with respect to experiment was unexceptional. While the RMSD and MAD via HREM-BAR scheme were greater than US-WHAM scheme, (i.e., 2.09 and 1.76 kcal/mol), their correlations were slightly better than US-WHAM. The correlation between the two methods was high. Further discussion on the DDM method can be found in a companion paper by Han et al. (receipt ID 3z83m) in the same issue.