Conformational Flexibility In Solution Research Articles

Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods.

Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.

Unveiling Möbius/Hückel Topology and Aromaticity in A Core‐Expanded [10]Annulene at Different Oxidation States

AbstractThe exploration of annulene's conformation, electronic properties and aromaticity has generated enduring interest over the years, yet it continues to present formidable challenges for annulenes with more than ten carbon atoms. In this study, we present the synthesis of a stable [10]cyclo‐para‐phenylmethine derivative (1), which bears a resemblance to [10]annulene. 1 can be readily oxidized into its respective cations, wherein electrons are effectively delocalized along the backbone, resulting in different conformations and aromaticity. Both 1 and its tetracation (14+ ⋅ 4SbF6−) exhibit a nearly planar conformation with a rectangular shape, akin to the E,Z,E,Z,Z‐[10]annulene. In contrast, the radical cation (1⋅+ ⋅ SbCl6−) possesses a doubly twisted Hückel topology. Furthermore, the dication (12+ ⋅ 2SbCl6−) displays conformational flexibility in solution and crystalizes with the simultaneous presence of Möbius‐twisted (1a2+ ⋅ 2SbCl6−) and Hückel‐planar (1b2+ ⋅ 2SbCl6−) isomers in its unit cell. Detailed experimental measurements and theoretical calculations reveal that: (1) 1 demonstrates localized aromaticity with an alternating benzenoid/quinoid structure; (2) 1a2+ ⋅ 2SbCl6− and 1b2+ ⋅ 2SbCl6− with 48π electrons are weakly Möbius aromatic and Hückel antiaromatic, respectively; (3) 14+ ⋅ 4SbF6− exhibits Hückel aromaticity (46π) and open‐shell diradical character.

Unveiling Möbius/Hückel Topology and Aromaticity in A Core-Expanded [10]Annulene at Different Oxidation States.

The exploration of annulene's conformation, electronic properties and aromaticity has generated enduring interest over the years, yet it continues to present formidable challenges for annulenes with more than ten carbon atoms. In this study, we present the synthesis of a stable [10]cyclo-para-phenylmethine derivative (1), which bears a resemblance to [10]annulene. 1 can be readily oxidized into its respective cations, wherein electrons are effectively delocalized along the backbone, resulting in different conformations and aromaticity. Both 1 and its tetracation (14+ ⋅ 4SbF6 - ) exhibit a nearly planar conformation with a rectangular shape, akin to the E,Z,E,Z,Z-[10]annulene. In contrast, the radical cation (1⋅+ ⋅ SbCl6 - ) possesses a doubly twisted Hückel topology. Furthermore, the dication (12+ ⋅ 2SbCl6 - ) displays conformational flexibility in solution and crystalizes with the simultaneous presence of Möbius-twisted (1a2+ ⋅ 2SbCl6 - ) and Hückel-planar (1b2+ ⋅ 2SbCl6 - ) isomers in its unit cell. Detailed experimental measurements and theoretical calculations reveal that: (1) 1 demonstrates localized aromaticity with an alternating benzenoid/quinoid structure; (2) 1a2+ ⋅ 2SbCl6 - and 1b2+ ⋅ 2SbCl6 - with 48π electrons are weakly Möbius aromatic and Hückel antiaromatic, respectively; (3) 14+ ⋅ 4SbF6 - exhibits Hückel aromaticity (46π) and open-shell diradical character.

C7 Epimerization of Benzylidene-Protected β-d-Idopyranosides Brings Structural Insights into Idose Conformational Flexibility.

Idose is unique among other aldohexoses because of its high conformational flexibility in solution. We herein show that benzylidene acetal-protected 3-O-acyl-β-d-idopyranosides undergo Lewis acid-catalyzed C7 epimerization with concomitant 4C1 to 1C4 ring inversion. The reaction conditions and structural parameters for this transformation to occur have been thoroughly investigated through an extensive glycosylation study combined with NMR analyses, X-ray diffraction, and quantum molecular modeling. In addition to reporting a direct, β-stereoselective idosylation approach, our work brings fundamental structural insights into the conformational flexibility of idose.

Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase.

Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.

Small-angle neutron scattering analysis of bottlebrush backbone and side chain flexibility

Bottlebrush polymers have densely tethered side chains grafted to a linear polymer backbone, resulting in stretching of both the side chains and backbone. Prior studies have reported that the side chains are only weakly stretched while the backbone is highly elongated. Here, scaling laws for the bottlebrush backbone and side chains are determined through small-angle neutron scattering analysis of a systematic series of poly(lactic acid) bottlebrush polymers synthesized via a “grafting-through” ring-opening polymerization. Scattering profiles are modeled with the empirical Guinier–Porod, rigid cylinder, and flexible cylinder models. Side chains are found to be only weakly stretched, with an end-to-end distance proportional to N0.55, while the overall bottlebrush increases in size proportional to N0.77. These results demonstrate that the bottlebrush backbone is not fully extended and that both side chains and backbone have significant conformational flexibility in solution. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016

A glycoconjugate of Haemophilus influenzae Type b capsular polysaccharide with tetanus toxoid protein: hydrodynamic properties mainly influenced by the carbohydrate.

Three important physical properties which may affect the performance of glycoconjugate vaccines against serious disease are molar mass (molecular weight), heterogeneity (polydispersity), and conformational flexibility in solution. The dilute solution behaviour of native and activated capsular polyribosylribitol (PRP) polysaccharides extracted from Haemophilus influenzae type b (Hib), and the corresponding glycoconjugate made by conjugating this with the tetanus toxoid (TT) protein have been characterized and compared using a combination of sedimentation equilibrium and sedimentation velocity in the analytical ultracentrifuge with viscometry. The weight average molar mass of the activated material was considerably reduced (Mw ~ 0.24 × 106 g.mol−1) compared to the native (Mw ~ 1.2 × 106 g.mol−1). Conjugation with the TT protein yielded large polydisperse structures (of Mw ~ 7.4 × 106 g.mol−1), but which retained the high degree of flexibility of the native and activated polysaccharide, with frictional ratio, intrinsic viscosity, sedimentation conformation zoning behaviour and persistence length all commensurate with highly flexible coil behaviour and unlike the previously characterised tetanus toxoid protein (slightly extended and hydrodynamically compact structure with an aspect ratio of ~3). This non-protein like behaviour clearly indicates that it is the carbohydrate component which mainly influences the physical behaviour of the glycoconjugate in solution.

Molecular dynamics simulation and conformational analysis of some catalytically active peptides.

The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations in explicit water of two catalytically active peptides (peptide 1: Fmoc-Phe1-Phe2-His-CONH2; peptide 2: Fmoc-Phe1-Phe2-Arg-CONH2) were performed at temperatures of 300, 400, and 500K. Conformational analysis of these peptides using Ramachandran plots identified the secondary structures of the amino acid residues involved (Phe1, Phe2, His, Arg) and confirmed their conformational flexibility in solution. Furthermore, Ramachandran maps revealed the intrinsic preference of the constituent residues of these compounds for a helical conformation. Long-range interaction distances and radius of gyration (R g) values obtained during 20 ns MD simulations confirmed their tendency to form folded conformations. Results showed a decrease in side-chain (Phe1, Phe2, His ring, and Arg) contacts as the temperature was raised from 300 to 400K and then to 500K. Finally, the radial distribution functions (RDF) of the water molecules around the nitrogen atoms in the catalytically active His and Arg residues of peptide 1 and peptide 2 revealed that the strongest water-peptide interaction occurred with the arginine nitrogen atoms in peptide 2. Our results highlight differences in the secondary structures of the two peptides that can be explained by the different arrangement of water molecules around the nitrogen atoms of Arg in peptide 2 as compared to the arrangement of water molecules around the nitrogen atoms of His in peptide 1. The results of this work thus provide detailed insight into peptide conformations which can be exploited in the future design of peptide analogs.

Structural Studies of Yeast Δ1-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State

The proline catabolic enzyme Δ1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the NAD+-dependent oxidation of γ-glutamate semialdehyde to l-glutamate. In Saccharomyces cerevisiae, ALDH4A1 is encoded by the PUT2 gene and known as Put2p. Here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of Put2p, and the determination of the oligomeric state and quaternary structure from small-angle X-ray scattering and sedimentation velocity. Using Δ1-pyrroline-5-carboxylate as the substrate, catalytic parameters kcat and Km were determined to be 1.5 s–1 and 104 μM, respectively, with a catalytic efficiency of 14000 M–1 s–1. Although Put2p exhibits the expected aldehyde dehydrogenase superfamily fold, a large portion of the active site is disordered in the crystal structure. Electron density for the 23-residue aldehyde substrate-binding loop is absent, implying substantial conformational flexibility in solution. We furthermore report a new crystal form of human ALDH4A1 (42% identical to Put2p) that also shows disorder in this loop. The crystal structures provide evidence of multiple active site conformations in the substrate-free form of the enzyme, which is consistent with a conformational selection mechanism of substrate binding. We also show that Put2p forms a trimer-of-dimers hexamer in solution. This result is unexpected because human ALDH4A1 is dimeric, whereas some bacterial ALDH4A1s are hexameric. Thus, global sequence identity and domain of life are poor predictors of the oligomeric states of ALDH4A1. Mutation of a single Trp residue that forms knob-in-hole interactions across the dimer–dimer interface abrogates hexamer formation, suggesting that this residue is the center of a protein–protein association hot spot.

Characterization of a novel copper-haem c dissimilatory nitrite reductase from Ralstonia pickettii

NiRs (nitrite reductases) convert nitrite into NO in the denitrification process. RpNiR (Ralstonia pickettii NiR), a new type of dissimilatory Cu-containing NiR with a C-terminal haem c domain from R. pickettii, has been cloned, overexpressed in Escherichia coli and purified to homogeneity. The enzyme has a subunit molecular mass of 50515 Da, consistent with sequence data showing homology to the well-studied two-domain Cu NiRs, but with an attached C-terminal haem c domain. Gel filtration and combined SEC (size-exclusion chromatography)-SAXS (small angle X-ray scattering) analysis shows the protein to be trimeric. The metal content of RpNiR is consistent with each monomer having a single haem c group and the two Cu sites being metallated by Cu(2+) ions. The absorption spectrum of the oxidized as-isolated recombinant enzyme is dominated by the haem c. X-band EPR spectra have clear features arising from both type 1 Cu and type 2 Cu centres in addition to those of low-spin ferric haem. The requirements for activity and low apparent K(m) for nitrite are similar to other CuNiRs (Cu-centre NiRs). However, EPR and direct binding measurements of nitrite show that oxidized RpNiR binds nitrite very weakly, suggesting that substrate binds to the reduced type 2 Cu site during turnover. Analysis of SEC-SAXS data suggests that the haem c domains in RpNiR form extensions into the solvent, conferring a high degree of conformational flexibility in solution. SAXS data yield R(g) (gyration radius) and D(max) (maximum particle diameter) values of 43.4 Å (1 Å=0.1 nm) and 154 Å compared with 28 Å and 80 Å found for the two-domain CuNiR of Alcaligenes xylosoxidans.

Can the conformational flexibility of cis-decalins be modulated through intramolecular O–H⋯O hydrogen bonding? Profiling the molecular and supramolecular attributes of designer cis-fused polycyclitols

In order to unravel the modalities of hydrogen bonding in conformationally flexible polycyclitols vis- à- vis their conformationally locked siblings, three diastereomeric perhydro-2,3,4a,6,7,8a-naphthalenehexols, all embodying a 4a,8a-dihydroxy- cis-decalin framework, have been synthesized via sequential stereo-controlled oxyfunctionalization of 1,4,5,8-tetrahydronaphthalene. Variable temperature NMR studies on the cis-fused polycyclitols thus obtained suggest that their inherent conformational flexibility in solution is restrained at ambient temperature owing either to the formation of a stable H-bonded molecular solvate or to the presence of strong intramolecular O–H⋯O H-bonding. Single crystal X-ray diffraction studies on the three hexols reveal an interesting commonality in their gross molecular packing and a ubiquitous presence of the R 2 2(10) dimer motif—a supramolecular synthon rarely encountered in the crystal structures of conformationally locked and axially-rich hexols.

Hydrogen bonding and solution state structure of salicylaldehyde-4-phenylthiosemicarbazone: A combined experimental and theoretical study

Hydrogen bonding in salicylaldehyde-4-phenylthiosemicarbazone ( 1) has been studied by using experimental (NMR, Raman and UV spectroscopies) and quantum chemical (DFT) methods. It has been demonstrated that 1 adopted the hydroxy-thione tautomeric form in solution as found also in the solid state and previously indicated by secondary deuterium isotope effects. Apart from the intra-molecular hydrogen bonds new interactions between 1 and solvent molecules were formed as well. Changes in NMR chemical shifts and calculations have pointed towards a formation of inter-molecular three-centered hydrogen bonds in each of the studied complexes involving OH and NH groups of 1 and associated solvent molecules. Stabilization energies of intra-molecular hydrogen bonds were found to decrease with the increase of the solvent polarity. Two-dimensional NOESY spectra indicated conformational changes in solution with respect to the structure observed in the solid state. These were accounted for by a relatively low barrier of the rotation of the N N single bond thus enabling a molecule to posses a higher conformational flexibility in solution with portions of skewed conformations. The results presented here can help in a better understanding of the role hydrogen bonds can play in bioactivity of related thiosemicarbazone derivatives and their metal complexes.

One-Dimensional Energy/Electron Transfer through a Helical Channel

We have synthesized A-D-A-type linear chain chromophores based on oligo(phenylene vinylene) as an electron donor (D) and several electron/energy acceptors (A), which are linked by an alkyl spacer with various lengths and are processed for a helical encapsulation with amylose. Photoinduced electron/energy transfers (eT/ET) of the chromophores are investigated in the presence and absence of the helical encapsulation with respect to D-A distance. Fluorescence intensity of the free chromophores is unusually small, not due to the advancement of eT/ET but most likely to self-quenching by aggregation and/or conformational flexibility in solution. By contrast, the helically encapsulated chromophores exhibit highly efficient eT/ET over a long D-A distance and a well-defined distance effect depending on the acceptor strength.

Determination of the stereochemistry of anhydroerythromycin A, the principal degradation product of the antibiotic erythromycin A

Anhydroerythromycin A arises from the acid-catalysed degradation of erythromycin A both in vitro and in vivo. It has negligible antibacterial activity, but inhibits drug oxidation in the liver, and is responsible for unwanted drug-drug interactions. Its structure has 18 chiral centres common with erythromycin A, but C-9 (the spiro carbon) is also chiral in anhydroerythromycin and its stereochemistry has not previously been reported; both 9R- and 9S-anhydroerythromycin A are plausible structures. An understanding of the chirality at C-9 was expected to throw light on the mechanism of acid-catalysed degradation of erythromycin A, a subject that has been debated in the literature over several decades. We now report a determination of the three-dimensional structure of anhydroerythromycin A, including the stereochemistry at C-9, by NMR and molecular modelling. In parallel, the relative stereochemistry of anhydroerythromycin A 2'-acetate was determined by X-ray crystallography. Both compounds were shown to have 9R stereochemistry, and anhydroerythromycin A exhibited considerable conformational flexibility in solution.

The N-terminal α-Helix of Pancreatic Phospholipase A 2 Determines Productive-mode Orientation of the Enzyme at the Membrane Surface

Phospholipase A(2) (PLA(2)) hydrolyzes glycerophospholipids to free fatty acid and lyso-phospholipid, which serve as precursors for the biosynthesis of eicosanoids and other lipid-derived mediators of inflammation and allergy. PLA(2) activity strongly increases upon binding to the surface of aggregated phospholipid. The N-terminal approximately ten residue alpha-helix of certain PLA(2) isoforms plays important roles in the interfacial activation of the enzyme by providing residues for membrane binding of PLA(2) and by contributing to the formation of the substrate-binding pocket. However, the relative contributions of the N-terminal alpha-helix and the rest of the protein in membrane binding of PLA(2) and its productive-mode orientation at the membrane surface are not well understood. Here we use a variety of biophysical approaches to determine the role of the N-terminal helix in membrane binding strength, orientation, and activity of human pancreatic PLA(2). While the full-length PLA(2) binds to membranes with a defined orientation, an engineered PLA(2) fragment DeltaN10 that lacks the N-terminal ten residues binds to membranes with weaker affinity and at random orientation, and exhibits approximately 100-fold lower enzymatic activity compared to the full-length PLA(2), indicating the key role of the N terminus in PLA(2) function. The results of polarized infrared spectroscopic experiments permit determination of the orientation of membrane-bound PLA(2) and identification of its interfacial binding surface. Moreover, the full-length PLA(2) demonstrates increased conformational flexibility in solution and is stabilized upon membrane binding, while the DeltaN10 fragment is more rigid than the full-length PLA(2) both in free and membrane-bound states. Our results suggest that the N-terminal alpha-helix supports the activation of PLA(2) by (a) enhancing the membrane binding strength, (b) facilitating a productive-mode orientation of PLA(2) at the membrane surface, and (c) conferring conformational integrity and plasticity to the enzyme.

Conformational study of a guaiacyl beta-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution.

Intramolecular H-bonding interactions were investigated in solution for the threo and erythro diastereomeric forms of a guaiacyl beta-O-4 lignin model compound by using the NMR data obtained from hydroxyl protons. Temperature coefficients of the chemical shifts (ddelta/dT) and coupling constants (3J(HCOH)) were measured in aprotic and protic solutions: DMSO-d6, acetone-d6 and acetone-d6-water. The NMR parameters do not support the existence of strong and persistent intramolecular H-bonds that could participate in the stabilization of the guaiacyl beta-O-4 structure in solution, but instead indicate that intermolecular H-bonds to solvent predominate. 1D NOE experiments nevertheless revealed the presence of a direct chemical exchange between the hydroxyl protons, suggesting the possible existence of weak and transient intramolecular H-bonding interactions. The conformational flexibility of the threo structure was also investigated in acetone solution from the measurement of long-range 1H, 1H and 1H, 13C coupling constants and from NOESY experiments. The NMR data are not consistent with any single conformation, indicating that different conformers co-exist in solution. The experimental results support the conformational flexibility predicted by molecular dynamics simulations performed in a previous study. Finally, both experimental and theoretical approaches indicate that weak intramolecular H-bonds can exist transiently in solution, breaking and reforming as the beta-O-4 molecule undergoes conformational interconversion, but cannot be invoked as possible means of conferring rigidity to the beta-O-4 structure.

Synthesis of 4-Thiothymine Based Photolabels as New Tools for Nucleic Acids Structural Studies in Solution: Formation of Long-Range Photo-Cross-Links within a Hammerhead Ribozyme Domain

The nucleosidic photolabels 2– 5, able to form long-range photo-cross-links, have been used to further investigate the tertiary folding of a hammerhead ribozyme domain. These photolabels derive from 2′-deoxyuridine which is substituted at its C-5 position with a photoactivable 4-thiothymine unit linked by a chain of various length and rigidity. Derivatives 2– 5 were inserted at strategic positions of a deoxysubstrate analogue ( dS) of a hammerhead ribozyme ( Rz). Covalent cross-links were generated by 366 nm irradiation of the Rz– dS complexes assembled under cleavage conditions. The Rz residues involved in these cross-links were mapped to give new sets of proximity data extending those previously obtained by intrinsic photolabelling with 2′-deoxy-4-thiouridine 1. Thus, compared to the zero-length cross-linker 1, photolabels 2– 5 exhibit a higher exploration capacity which depends critically upon the length and flexibility of the linker and their site of incorporation. Interestingly, in contrast to 1, these photolabels were able to cross-link residues involved in the double G:A mismatch as well as residues of the adjacent base pairs. These findings suggest that the mismatch domain exhibits an unexpected conformational flexibility in solution.

Escherichia coli SecA shape and dimensions

SecA shape and conformational flexibility in solution were studied by small angle X-ray scattering. Dimeric SecA is a very elongated molecule, 15 nm long and 8 nm wide. SecA is therefore four times as long as the membrane is wide. The two globular protomers are distinctly separated and share limited surface of intermolecular contacts. ATP, ADP or adenylyl-imidodiphosphate (AMP-PNP) binding does not alter the SecA radius of gyration. A SecA mutant that catalyzes multiple rounds of ATP hydrolysis does not undergo conformational changes detectable by small angle X-ray scattering (SAXS). We conclude that SecA conformational alterations observed biochemically during nucleotide interaction are only small-scale and localized. The ramifications of these findings on SecA/SecYEG interaction are discussed.

Solution conformation dynamics of a tetrasaccharide related to the Lewis x antigen deduced by 1H NMR NOESY, ROESY, and T-ROESY measurements

The conformational and dynamical features of a Le x tetrasaccharide analogue GaINAc(α 1–3)Gal(β 1–4)[Fuc(α 1–3)]Glc(βOMe) 1 have been studied through 1H NMR relaxation measurements. The results indicate that the different glycosidic linkages of 1 present distinct conformational flexibility in solution. In addition, the use of T-ROESY experiments in conformational analysis of oligosaccharides is explored emphasizing its scope and limitations. The conformational and dynamical features of a tetrasaccharide. GalNac(α1–3)Gal(β1–4)[Fuc(α1–3)]Glc(βOME) 1 are analysed via 1H NMR relaxation measurements.

Alkaline earth and uranyl cation complexes of a calix[4]arene-tetraamide: MD and FEP simulations in aqueous and acetonitrile solutions and X-ray structure of its Sr(Picrate)2 complex

We report the X-ray structure of the L·Sr(Picrate)2(L =tert-butyl-calix [4] arene-tetrakis(diethylamide) and MD simulations on the L·M2+ complexes in vacuo, in water and in acetonitrile solutions (M2+= Mg 2+, Ca2+, Sr2+, Ba2+), with a comparison of ‘converging’ Lc and ‘diverging’ LD conformers, In the simulated and solid-state structures of the L·Sr2+ complex, the cation is completely encapsulated within the polar pseudo-cavity of L, without coordination to its counterion in the crystal, or to solvent molecules in solution. Computations show that the L·M2+ complexes are of converging type in water and in acetonitrile. This contrasts with the L·M+ alkali cation complexes, which display conformational flexibility in solution. Subtle structural changes from Mg2+ to Ba2+ are compared in the gas phase and in solution. In the L·UO22+ hypothetical complex, simulated for comparison, the UO22 + cation is calculated to be less bound by L than the alkaline earth cations. The solvent content of the cone is shown to depend on the size of the complexed cation and modulated by the top–bottom mechanical coupling in the calixarene. Based on free energy perturbation calculations, we calculate a binding sequence of alkaline earth cations (Ca2+ > Sr2+ > Ba2+ > Mg2+) in agreement with experiment.