A joint QM/MD study on α-, β- and γ-cyclodextrins in selective complexation with cathinone

In this article, density functional theory (DFT) calculations and 30 ns molecular dynamic (MD) simulations were performed to investigate the ability of α-, β- and γ-cyclodextrins (CDs) to form selective complexes with cathinone. DFT calculations in the gas phase, water, chloroform and methanol reveal that the solvents, reduce the stability of the complexes. Optimized structures confirm that α-CD cannot encapsulate cathinone, completely, while other CDs showed an opposite behavior. DFT calculations indicate that cathinone has the most stable complex with γ-CD in comparison to the α- and β-CDs. Natural bond orbital and quantum theory of atoms in molecules analyses reveal that the electrostatic interactions between cathinone and CDs are the driving force of the complex formation. MD simulations confirm that different solvents play an important role in the stability of the cathinone complexes and the obtained MD results are in good agreement with the DFT calculations.     

Oxoanion binding by guanidiniocarbonylpyrrole cations in water: a combined DFT and MD investigation

Structures and properties of nonbonding interactions involving guanidinium-functionalized hosts and carboxylate substrates were investigated by a combination of ab initio and molecular dynamics approaches. The systems under study are on one hand intended to be a model of the arginine-anion bond, so often observed in proteins and nucleic acids, and on the other to provide an opportunity to investigate the influence of molecular structure on the formation of supramolecular complexes in detail. Use of DFT calculations, including extended basis sets and implicit water treatment, allowed us to determine minimum-energy structures and binding enthalpies that compared well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions through three hydrogen bonds, one of which is bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting of a rotation of about 180 degrees around the guanidiniocarbonylpyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed in the presence of explicit water molecules by use of the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM-PBSA) and linear interaction energy (LIE) approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes cannot be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible for several low-energy metastable structures.     

A computational study of regioselectivity in a cyclodextrin-mediated Diels-Alder reaction: revelation of site selectivity and the importance of shallow binding and multiple binding modes

The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.     

γ-环糊精和波尼松龙的相互作用分子动力学模拟和自由能计算

运用分子动力学（Molecular dynamics,MD）和MM—PBSA（molecular mechanics／Poisson Boltzmann surfaeearea）相结合的方法预测了γ-环糊精（γ-cyclodextrin,γ-CD）和波尼松龙的包结模式．在MD模拟过程中,波尼松龙分别采用A环和D环两种取向从γ-CD大口端进入其空腔．在MD轨迹采样基础上,采用高效MM—PBSA方法计算了两种取向的包结自由能．结果表明,计算包结自由能值和实验包结自由能值非常吻合．进一步分析各个能量项,发现范德华相互作用能为包结的主要驱动力．通过比较两种取向的包结自由能大小,预测D环取向为优势包结模式．     

Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse‐grained molecular dynamics simulations with a weighted histogram analysis method

We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with the weighted histogram analysis method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse‐grained (CG) force field (MARTINI) is less prone to significant error induced by inadequate‐sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3–4 residue peptide segments while leaving the remaining peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and reliably estimate the binding free energy between an arbitrary peptide and an MHC class II molecule. © 2017 Wiley Periodicals, Inc.     

Atom accurate structure determination of alprazolam/cyclodextrin inclusion complexes by ROESY and computational approaches

A lot of interest has been seen in computational methods that provide reliable atom accurate structures of different molecular systems. In this article, we describe the complexation of alprazolam (ALP) with three cyclodextrins, i.e., α-, β- and γ-CD. ROESY spectra showed that no complex was formed between ALP and α-CD however, ring A of ALP formed ICs with β- and γ-CD. Therefore, structures of ALP/β-CD and ALP/γ-CD were obtained by a combination of NMR (2D-ROESY) and computational methods by a quantitative ROESY approach. Here we determined the structures of CD ICs by a method recently used in our laboratory and then the structures were obtained independently by DFT (B3LYP functional and def2-TZVP basis set). The structures obtained by both methods were compared with each other. Results demonstrated that our method provides reasonable structures comparable to DFT, and can be used to obtain highly atom accurate structures of CD inclusion complexes. Quantitative ROESY analysis of MM and MD structures consume less time and are cheap as compared to DFT, which is highly CPU demanding and time taking. Negative values of binding energy showed that the process of inclusion was spontaneous and complexes formed were stable. The large negative value of binding energy for ALP/β-CD as compared to ALP/γ-CD showed a higher binding affinity of ALP towards β-CD. FMO studies also revealed the higher HOMO-LOUMO gap for inclusion complexes as compared to pure ALP. Intermolecular H-bonds formed in both the complexes are also one of the forces responsible for inclusion complex formation.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

芳杂环类多重氢键分子钳人工受体对中性分子的识别性能研究

根据多点氢键识别原理,设计合成了新的分子钳受体1～6。研究了其对巴比妥 、尿素、二苯甲酮、戊二酰亚胺等中性分子的识别性能。用差紫外光谱法测定了结 合常数和自由能变化（ΔG）。结果表明,所有分子钳受体与所考察的客体分子均 形成1：1型超分子配合物,识别作用的推动力主要为多重氢键的协同作用。讨论了 主客体间尺寸/形状、几何互补等因素对形成超分子配合物的影响。并利用~1H NMR、计算机模拟作辅助手段对实验结果和现象进行了解释。     

A Molecular Modeling for the Complexation of Cyclobis(paraquat-p-phenylene) with Substituted Benzenes and Biphenyls

The molecular recognition of cyclobis(paraquat-p-phenylene), 14+, has drawn great attention recently, due to its important applications in the design and synthesis of electrochemically and chemically switchable rotaxanes, photoactive rotaxanes, and other molecular devices1. Usually, this type of molecular recognition was investigated with the methods including X-ray, NMR, UV, and IR. However, since these methods usually have difficulties in providing a detailed understanding of the energeti…     

Complexation of Eu(III), Am(III) and Cm(III) with Dicarboxylates: Thermodynamics and Structural Aspects of the Binary and Ternary Complexes

The complexation of Eu(III), Am(III) and Cm(III) with dicarboxylate anions with O, N or S donor groups was measured in I=6.60 mol⋅kg⁻¹ (NaClO₄) at temperatures of 0–60 °C by potentiometry and solvent extraction. The complexation thermodynamics of these complexes show that their stability is due to highly favorable complexation entropies because the complexation enthalpies are endothermic. Luminescence studies with Eu(III) and Cm(III) were used to measure the hydration numbers of the complexes. NMR spectra of ¹H and ¹³C were used to determine the binding modes of La(III) with the ligands. The formation of 1:1:1 ternary complexes of M(EDTA)⁻ with the dicarboxylate ligands was studied to determine changes in coordination of the metal cation with formation of the ternary species. The complexation of ternary complexes changes from bidentate to monodentate as the chain length between the binding sites of the dicarboxylates increases from 1 (malonate) to 4 (adipate). DFT computations were used to confirm the structural aspects of the interaction of these complexes.     

Complexation between tert-butyl ketones and beta-cyclodextrin. Structural study by NMR and MD simulations

A structural study (NMR and MD) of the complexation between tert-butyl ketones and beta-cyclodextrin has been performed. A priority order for the alkyl and phenyl groups composing the ketones has been determined based on association constants: Ph- > C(6)H(11)- = t-Bu- > Bu-, Pr-, Me-. Geometries for the complexes are proposed based on NOE values and on the MD simulations. Bimodal complexation occurs in all the compounds studied.     

Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1

The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

Density functional theory study of uranium(VI) aquo chloro complexes in aqueous solution

Mixed uranyl aquo chloro complexes of the type [UO2(H2O)xCly]2-y (y = 1, 2, 3, 4; x + y = 4, 5) have been optimized at the BLYP, BP86, and B3LYP levels of density functional theory in vacuo and in a polarizable continuum modeling bulk water (PCM) and have been studied at the BLYP level with Car-Parrinello molecular dynamics (MD) simulations in the gas phase and in explicit aqueous solution. Free binding energies were evaluated from static PCM data and from pointwise thermodynamic integration involving constrained MD simulations in water. The computations reveal significant solvent effects on geometric and energetic parameters. Based on the comparison of PCM-optimized or MD-averaged uranyl-ligand bond distances with EXAFS-derived values, the transition between five- and four-coordination about uranyl is indicated to occur at a Cl content of y = 2 or 3.     

Fluoride-selective binding in a new deep cavity calix[4]pyrrole: experiment and theory

A new "super-extended cavity" tetraacetylcalix[4]pyrrole derivative was synthesized and characterized, and X-ray crystal structures of complexes bound to fluoride and acetonitrile were obtained. The binding behavior of this receptor was investigated by NMR titration, and the complex was found to exclusively bind fluoride ions in DMSO-d(6). This unusual binding behavior was investigated by Monte Carlo free energy perturbation simulations and Poisson calculations, and the ion specificity was seen to result from the favorable electrostatic interactions that the fluoride gains by sitting lower in the phenolic cavity of the receptor. The effect of water present in the DMSO on the calculated free energies of binding was also investigated. Owing to the use of a saturated ion solution, the effect of contaminating water is small in this case; however, it has the potential to be very significant at lower ion concentrations. Finally, the adaptive umbrella WHAM protocol was investigated and optimized for use in binding free energy calculations, and its efficiency was compared to that of the free energy perturbation calculations; adaptive umbrella WHAM was found to be approximately two times more efficient. In addition, structural evidence demonstrates that the protocol explores a wider conformational range than free energy perturbation and should therefore be the method of choice. This paper represents the first complete application of this methodology to "alchemical" changes.     

Free Energy Level Correction by Monte Carlo Resampling with Weighted Histogram Analysis Method

Free energy calculations may provide vital information for studying various chemical and biological processes. Quantum mechanical methods are required to accurately describe interaction energies, but their computations are often too demanding for conformational sampling. As a remedy, level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed. Here, we present a variation of a Monte Carlo (MC) resampling approach in relation to the weighted histogram analysis method (WHAM). We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling, and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme. It can also provide a guide for checking the uncertainty of the level-corrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement. We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water, and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.     

Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.     

Experimental (NMR) and Theoretical (MD Simulations) Studies on the Conformational Preference of Three Cycloalkanols when Included in β-Cyclodextrin

The inclusion complexes between three cycloalkanols (cyclopentanol, cyclohexanol and cycloheptanol) and β-cyclodextrin (β-CD) have been studied by NMR experiments, and by molecular dynamics (MD) simulations. Complexes present medium to small association constants. All experimental data show the equatorial conformer as the most stable after complexation because no changes were detected in the coupling constants of the H1 protons. Intermolecular ROE experiments suggest that while cyclopentanol is deeply included into the β-CD cavity, cyclohexanol and cycloheptanol occupy mainly the wider entrance. The MD simulations agree with the experimental data (equatorial conformers are always the most stable), and average geometries coincide with those deduced from the ROE experiments.     

Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and pi stacking

Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol (-1) difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and pi-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H...X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.