Detailed investigation of the binding abilities of the heterodomain of a multiHis cyclopeptide toward Cu(II) ions.

Cyclopeptides hold significant relevance in various fields of science and medicine, due to their unique structural properties and diverse biological activities. Cyclic peptides, characterized by intrinsically higher conformational order, exhibit remarkable stability and resistance to proteolytic degradation, making them attractive candidates for developing targeted drug delivery systems. The aim of this work is to elucidate the unique coordination properties of the multi-His cyclic peptide with c(HDHKHPHHKHHP) sequence (HDCP - heterodomain cyclopeptide). This peptide, indeed, is able to form homo- and hetero-dinuclear complexes in a wide pH range, being thus a good chelator for Cu(II) ions. Herein, we present the results of a combined study, involving potentiometric, spectroscopic (UV-Vis, CD, and EPR), and computational investigations, on its coordination properties. To better understand the interaction pattern with Cu(II) metal ions, two other peptides, each one bearing only one of the two binding domains of HDCP are also considered in this study: c(HDHKHPGGKGGP) = CP1, c(GKGGKPHHKHHP) = CP2, which share sequence fragments of HDCP and allow separate investigations of its coordination domains.

Through-space scalar spin-spin coupling: from rigid intramolecular cases to short-lived van der Waals complexes.

We will discuss, with the help of few selected examples, how the concept of through-space scalar spin-spin coupling between non covalently bonded nuclei has evolved in recent years. We will first present systems where 'no covalent bond' actually means that the two atoms are separated by a large number of bonds; then we will see cases where it is referred to true van der Waals dimers, but with the two atoms somehow constrained in their positions; we will finish with the most recent examples of liquids and even gaseous mixtures with full translational degrees of freedom in a regime of intermolecular/interatomic fast exchange.

Influence of Anion Species on Liquid-Liquid Phase Separation in [EMIm+][X-]/Benzene Mixtures.

When a molar excess of benzene is mixed with an ionic liquid (IL), liquid-liquid phase separation may appear with a pure liquid phase almost composed of only benzene molecules separated from a liquid clathrate phase with benzene molecules dissolved in the IL. Our previous study (J. Phys. Chem. B, 124, 7929, 2020) on long-chain IL/benzene systems has concluded that benzene molecules, as planar nonpolar ones, majorly dissolve in the IL nonpolar domains consisting of cationic alkyl side chains. Nevertheless, the above mechanism is inadequate for explaining the experimental observations that benzene can also dissolve in IL systems with very short alkyl side chains. In this study, by molecular dynamics simulation of the [EMIm+][X-]/benzene mixtures with X- being Cl-, NO3-, PF6-, or Tf2N-, we still observe liquid-liquid phase separation of the pure benzene phase from a liquid clathrate (mixed IL/benzene) phase where benzene molecules are almost equally distributed near imidazolium rings through π-stacking or near alkyl side chains. The anion species strongly influences the solubility of benzene and the ratio of the two liquid phases via the alteration of anionic charge density, which tunes the strength of the electrostatic interaction among ions and thus the probability of benzene molecules interacting with both imidazolium rings and alkyl side chains: a larger anionic charge density corresponds to a lower solubility of benzene.

Pathway for Water Transport through Breathable Nanocomposite Membranes of PEBAX with Ionic Liquid [C12C1im]Cl.

Water transport through membranes is an attractive topic among the research dedicated to dehydration processes, microenvironment regulation, or more simply, recovery of freshwater. Herein, an atomistic computer simulation is proposed to provide new insights about a water vapor transport mechanism through PEBAX membranes filled with ionic liquid (IL) [C12C1im]Cl. Starting from experimental evidence that indicates an effective increase in water permeation as the IL is added to the polymer matrix (e.g., up to 85·10-3 (g·m)/(m2·day) at 318.15 K for PEBAX@2533 membranes loaded with 70% of IL), molecular dynamics simulations are proposed to explore the key role of IL in water transport inside membranes. The polar region composed of anions and cationic head groups of the IL is demonstrated to serve as the pathway for water transport through the membrane. Water molecules always stay near the pathway, which becomes wider and thus has a larger water-accessible area with increasing IL concentration. Hence, the diffusion coefficients of water molecules and ions increase as the IL concentration increases. The simulation provides useful indications about a microscopic mechanism that regulates the transport of water vapor through a kind of PEBAX/IL membrane, resulting in full agreement with the experimental evidence.

Phase coexistence in [C22/C1MIm]+[NO3]- ionic-liquid mixtures and first-order phase transitions from homogeneous liquid to smectic B by varying the cation ratio.

We perform molecular dynamics simulations to investigate the transition processes of [C22/C1MIm]+[NO3]- binary mixtures by varying the cation ratio of C22 to C1 at a fixed temperature of 400 K. The cation ratio is tuned by ranging C22 percentage from 0% to 100% with a fixed number of 4096 total simulated ion pairs. Our simulated-annealing results indicate that, at 400 K, pure C1 is a homogeneous liquid whilst pure C22 is an ionic liquid crystal (ILC) of smectic-B (SmB) type. With increasing C22 percentage, the system goes through a first-order phase transition from homogeneous liquid to nano-fragment liquid in the range from 15% to 17.5%, during which some of the individual cationic alkyl side chains locally aggregate to form small bundles "floating" in the polar "solvent" composed of anions and cationic head groups. Although the side chains in each bundle are parallelly aligned, the bundles distribute randomly without a global orientation. As the C22 percentage further increases, another first-order phase transition occurs to bring the system into the SmB ILC phase. Particularly, when the C22 percentage is in the range from 45% to 50%, the SmB phase coexists with the liquid phase containing both individual and bundled alkyl side chains.

Computational NMR spectroscopy of 205 Tl.

We have investigated the NMR chemical shift of 205 Tl in several thallium compounds, ranging from small covalent Tl(I) and Tl(III) molecules to supramolecular complexes with large organic ligands and some thallium halides. NMR calculations were run at the ZORA relativistic level, with and without spin-orbit coupling using few selected GGA and hybrid functionals, namely BP86, PBE, B3LYP, and PBE0. We also tested solvent effects both at the optimization level and at the NMR calculation step. At the ZORA-SO-PBE0 (COSMO) level of theory we find a very good performance of the computational protocol that allows to discard or retain possible structures/conformations based on the agreement between the calculated chemical shift and the experimental value.

Phase behaviour of mixtures of charged soft disks and spheres.

We have investigated the phase behaviour of mixtures of soft disks (Gay-Berne oblate ellipsoids, GB) and soft spheres (Lennard-Jones, LJ) with opposite charge as a model of ionic liquid crystals and colloidal suspensions. We have used constant volume Molecular Dynamics simulations and fixed the stoichiometry of the mixture in order to have electroneutrality; three systems have been selected GB : LJ = 1 : 2, GB : LJ = 1 : 1 and GB : LJ = 2 : 1. For each system we have selected three values of the scaled point charge q* of the GB particles, namely 0.5, 1.0 and 2.0 (and a corresponding negative scaled charge of the LJ particles that depends on the stoichiometric ratio). We have found a very rich mesomorphism with the formation, as a function of the scaled temperature, of the isotropic phase, the discotic nematic phase, the hexagonal columnar phase and crystal phases. While the structure of the high temperature phases was similar in all systems, the hexagonal columnar phases exhibited a highly variable morphology depending on the scaled charge and stoichiometry. On the one hand, GB : LJ = 1 : 2 systems form lamellar structures, akin to smectic phases, with an alternation of layers of disks (exhibiting an hexagonal columnar phase) and layers of LJ particles (in the isotropic phase). On the other hand, for the 2 : 1 stoichiometry we observe the formation of a frustrated hexagonal columnar phase with an alternating tilt direction of the molecular axis. We rationalize these findings based on the structure of the neutral ion pair dominating the behaviour at low temperature and high charge.

Activation of Vegetable Oils by Reaction with Maleic Anhydride as a Renewable Source in Chemical Processes: New Experimental and Computational NMR Evidence.

Vegetable oils are bio-based and sustainable starting materials that can be used to develop chemicals for industrial processes. In this study, the functionalization of three vegetable oils (grape, hemp, and linseed) with maleic anhydride was carried out either by conventional heating or microwave activation to obtain products that, after further reactions, can enhance the water dispersion of oils for industrial applications. To identify the most abundant derivatives formed, trans-3-octene, methyl oleate, and ethyl linoleate were reacted as reference systems. A detailed NMR study, supported by computational evidence, allowed for the identification of the species formed in the reaction of trans-3-octene with maleic anhydride. The signals in the 1H NMR spectra of the alkenyl succinic anhydride (ASA) moieties bound to the organic chains were clearly identified. The reactions achieved by conventional heating were carried out for 5 h at 200 °C, resulting in similar or lower amounts of ASA units/g of oil with respect to the reactions performed by microwave activation, which, however, induced a higher viscosity of the samples.

Correction: The structuring effect of the alkyl domains on the polar network of ionic liquid mixtures: a molecular dynamics study.

Correction for 'The structuring effect of the alkyl domains on the polar network of ionic liquid mixtures: a molecular dynamics study' by Valerio Mazzilli et al., Phys. Chem. Chem. Phys., 2022, 24, 18783-18792, https://doi.org/10.1039/D2CP02786K.

The structuring effect of the alkyl domains on the polar network of ionic liquid mixtures: a molecular dynamics study.

By using molecular dynamics simulations, we investigate the structural and dynamic properties of mixtures of 1,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide, [C1C1im][Tf2N] and 1-dodecyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide, [C12C1im][Tf2N] (also C1 and C12 in short). Such mixtures feature an imidazolium bistriflimide salt with a very short alkyl chain, not giving rise to any nano-segregation as a pure component, with another one with a longer alkyl chain that exhibits a substantial nano-segregation as a pure liquid. As the mole fraction of the long-chain component C12 is increased, the so-called pre-peak of the structure factor S(q), occurring in the region 1-3 nm-1, shows a shift to higher values of the wavevector q, mirroring a decrease of the corresponding correlation length. Moreover, the intensity of the pre-peak strongly increases with the C12 concentration. These results are in very good agreement with experimental X-ray scattering data in the literature. On the other hand, the diffusion of the ions is found to exhibit a simple behaviour consistent with the increased viscosity of the mixture, and these results are also in good agreement with NMR experimental data from the literature. The simulation results are rationalized as caused by a structuring effect, similar to the hydrophobic effect, of the alkyl domains of the C12 component dissolved in the "solvent" represented by the C1 cation, the Tf2N- anion and the C12 cation head. In short, the exclusion of the alkyl chains from the polar network, a process mostly governed by electrostatic interactions, favours the formation of hydrophobic domains, which in turn exert a structuring effect on the ions of the polar domains, favouring a stronger ionic interaction. This is finally reflected in a shorter correlation length and a higher intensity of the pre-peak of the structure factor S(q) as the C12 mole fraction is increased. At variance with the microscopic structure, the diffusion of all three types of ions is not strongly influenced by the nano-segregation and is essentially dependent on the viscosity of the mixture.

The effect of hydration on the stability of ionic liquid crystals: MD simulations of [C14C1im]Cl and [C14C1im]Cl·H2O.

The thermal range of the stability of Ionic Liquid Crystal (ILC) phases of imidazolium ILCs, and the type of the mesophase itself are affected by several molecular structural features, the two prominent ones being the alkyl chain length and the counter-anion. Hydration is also very important: monohydrate samples of 1-alkyl-3-methylimidazolium halides have a higher clearing point and a wider thermal range of the stability of the ionic smectic phase, compared with the analogous anhydrous sample. To understand the reasons, at a microscopic level, for such increased stability due to hydration, we run classical Molecular Dynamics (MD) simulations of a typical ionic liquid crystal, 1-tetradecyl-3-methylimidazolium chloride, and of its monohydrate form. We tested a full-charge non-polarizable force field and a scaled-charge version having the total charge of the ions scaled by a factor of 0.80. Comparison of the structural and dynamic properties with available experimental data reveals that the scaling of the charge by a factor of 0.80 results in a good agreement between simulated and experimental data and it sheds light on the microscopic mechanism responsible for the increased stability of the monohydrated phase. A hydrogen-bond network between water and the chloride anion is established in the ionic layer which increases the stability of the ionic layer; this in turn increases the nano-segregation between the ionic and hydrophobic layers which eventually produce an increased order of the alkylic layer as well.

Xenon Diffusion in Ionic Liquids with Blurred Nanodomain Separation.

The dynamics of xenon gas, loaded in a series of 1-alkyl-3-methylimidazolium based ionic liquids, probes the formation of increasingly blurred polar/apolar nanodomains as a function of the anion type and the cation chain length. Exploiting 129 Xe NMR spectroscopy techniques, like Pulse Gradient Spin Echo (PGSE) and inversion recovery (IR), the diffusion motion and relaxation times are determined for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [Cn C1 im][TFSI]. A correlation between the ILs nano-structure and both xenon diffusivity and relaxation times, as well as chemical shifts, is outlined. Interestingly, comparison with previous results of the same properties in the homologous imidazolium chlorides and hexafluorophospate shows an opposite trend with the alkyl chain length. Classical molecular dynamics (MD) simulations are used to calculate the xenon and cation and anion diffusion coefficients in the same systems, including imidazolium cations with longer chains (n=4, 6, 8 … 20). An almost quantitative agreement with the experiments validates the MD simulations and, at the same time, provides the necessary structural and dynamic microscopic insights on the nano-segregation and diffusion of xenon in bistriflimide, chloride and hexafluorphosphate salts allowing to observe and rationalize the shaping effect of the cation in the nanostructure.

Liquid-Liquid Phase Separation of Viologen Bistriflimide/Benzene Mixtures: Role of the Dual Ionic and Organic Nature of Ionic Liquids.

Liquid-liquid phase separation occurs at room temperature when mixing an excess of benzene with solid viologen bistriflimide salts with various alkyl side-chain lengths. A liquid phase composed of (almost) pure benzene is above the other sponge-like liquid phase with salt absorbed in benzene. Nuclear magnetic resonance experiments indicate that the mole ratio of benzene/salt in the sponge-like phase remains unchanged upon varying the amounts of (nonexcessive) salt or benzene. Moreover, the benzene/viologen salt mole ratio in the sponge-like phase increases linearly with respect to the side-chain length of the cation. Similarly, when an excess of viologen salt is added in benzene, a sponge-like liquid phase composed of salt absorbed by benzene is observed in equilibrium with some solid viologen salt neither dissolved nor absorbed by the solvent. The mole ratio of the sponge-like liquid phase again increases linearly with side-chain length, while it remains independent of the relative amount of benzene and viologen salt as long as the latter is in excess. Finally, when appropriate amounts of benzene and viologen salt are mixed, a single sponge-like liquid phase is observed at an intermediate composition between the lower and upper limits. Molecular dynamics simulations reveal that because of their dual ionic and organic nature, when absorbed in benzene, the studied salts form nanoscale segregated liquid structures, akin ionic liquids, with a continuous polar network composed of anions and cationic charged groups, along with nonpolar domains composed of alkyl cationic side chains. Benzene molecules are preferentially absorbed inside the nonpolar region, which effectively expands the nonpolar region to be sponge-like and consequently liquidizes the viologen salt. The linearity of the benzene/salt ratio in the upper and lower phase boundaries comes from the fact that the effective volume of the nonpolar region for accommodating benzene molecules grows linearly with cationic alkyl side-chain length. The occurrence of the above phenomena is attributed to the nonpolar feature of benzene molecules, and there is no evidence of π-π or ion-π interaction between the ions and benzene molecules. Moreover, the diffusion of benzene in the sponge-like phase is found to be close to that in n-alkanes, supporting the idea of nanoscale segregation of polar and nonpolar regions in the sponge-like phase. The revealed mechanism is anticipated to be general for understanding liquid-liquid phase separation observed in mixtures of organic salts (ionic liquids) having relatively long alkyl chains with small organic molecules.

Xenon Dynamics in Ionic Liquids: A Combined NMR and MD Simulation Study.

The translational dynamics of xenon gas dissolved in room-temperature ionic liquids (RTILs) is revealed by 129Xe NMR and molecular dynamics (MD) simulations. The dynamic behavior of xenon gas loaded in 1-alkyl-3-methylimidazolium chloride, [CnC1im]Cl (n = 6, 8, 10), and hexafluorophosphate, [CnC1im][PF6] (n = 4, 6, 8, 10) has been determined by measuring the 129Xe diffusion coefficients and NMR relaxation times. The analysis of the experimental NMR data demonstrates that, in these representative classes of ionic liquids, xenon motion is influenced by the length of the cation alkyl chain and anion type. 129Xe spin-lattice relaxation times are well described with a monoexponential function, indicating that xenon gas in ILs effectively experiences a single average environment. These experimental results can be rationalized based on the analysis of classical MD trajectories. The mechanism described here can be particularly useful in understanding the separation and adsorption properties of RTILs.

Computational NMR Spectroscopy of Ionic Liquids: [C4C1im]Cl/Water Mixtures.

In this work, I have analyzed the structure of binary mixtures of 1-butyl-3-methylimidazolium chloride ionic liquid, [C4C1im]Cl, and water, using computational NMR spectroscopy. The structure of the complex fluid phase, where the ionic and hydrophobic nature of ionic liquids is further complicated by the addition of water, is first generated by classical Molecular Dynamics (MD) and then validated by calculating the NMR properties with DFT at the ONIOM(B3LYP/cc-pVTZ//B3LYP/3-21G) on clusters extracted during the MD trajectories. Three ionic liquid/water mixtures have been considered with the [C4C1im]Cl mole fraction of 1.00, 0.50, and 0.01, that is the pure ionic liquid [C4C1im]Cl, the equimolar [C4C1im]Cl/water mixture, and a diluted solution of [C4C1im]Cl in water. A good agreement is obtained with published experimental data that, at the same time, validates the structural features obtained from the MD and the force field used, and provides an example of the power of NMR spectroscopy applied to complex fluid phases.

One-bond 1 J(15 N─19 F) spin-spin coupling constants of cationic fluorinating reagents: Insights from DFT calculations.

We have investigated, by means of density functional theory protocols, the one-bond 1 J(15 N─19 F) spin-spin coupling constants in a series of fluorinating reagents, containing the N─F bond, recently studied experimentally. The results of the calculations show a very good linear relationship with the experimental values, even though only the M06-2X(PCM)/pcJ-2//B3LYP/6-311G(d,p) level affords a very low mean absolute error. The calculations allow to analyze the various molecular orbitals contributions to the J coupling and to rationalize the observed positive sign, corresponding to a negative sign of the reduced spin-pin coupling constant K(N─F). Moreover, of the four Ramsey contributions, only the diamagnetic spin orbit is negligible, whereas the paramagnetic spin orbit and spin dipole terms decrease the magnitude of the Fermi contact (FC) term by an amount that goes from a minimum of 35% up to more than 60% of the FC term itself. Several effects have been investigated, namely, the contribution of the long-range solvent reaction field, relativistic corrections, and conformational and vibrational effects.

Influence of the ion size on the stability of the smectic phase of ionic liquid crystals.

The thermotropic phase behavior of ionic liquids and ionic liquid crystals based on novel N-alkyl-3-methylpyridinium halides, trihalides and dichloroiodates was experimentally studied by polarized optical spectroscopy (POM) and differential scanning calorimetry (DSC) as well as by molecular dynamics (MD) simulation. In the experiments, the existence and thermal range of stability of the smectic phase of these ionic liquid crystals are found to strongly depend on the volume ratio between the cation and anion, that is their relative size. Only compounds with a relatively large volume ratio of the cation to anion, i.e., those with longer cationic alkyl chains and monoatomic halide anions, have a stable smectic A phase. Both melting points and clearing points increase with such a ratio. The MD simulation results qualitatively agree very well with the experimental data and provide molecular details which can explain the experimentally observed phenomena: the stronger van der Waals interactions from the longer alkyl chains and the stronger electrostatic interactions from the smaller anions with a higher charge density increase the stability of both the crystal phase and the smectic phase; this also prevents the ionic layers from easily mixing with the hydrophobic regions, a mechanism that ultimately leads to a nanosegregated isotropic liquid phase.

A coarse-grained model of ionic liquid crystals: the effect of stoichiometry on the stability of the ionic nematic phase.

We have investigated, by means of molecular dynamics simulations, the phase behaviour of mixtures of charged ellipsoidal Gay-Berne (GB) particles and spherical Lennard-Jones (LJ) particles, as a coarse-grained model of ionic liquid crystals (ILCs). The anisotropic GB particles represent cations usually found in ILCs, for example, pyridinium or bipyridinium salts, while the spherical LJ particles are taken as a model of anions like common halides, hexafluorophosphate and tetrafluoroborate. Here we have focused our attention on the effect of the stoichiometry of the system (that is, the GB : LJ ratio n : m in the salt formula [GB]n[LJ]m) on the stability and thermal range of the ionic liquid crystal phases formed, with special attention to the ionic nematic phase. To isolate the stoichiometry effect, a comparison of four different systems with GB : LJ ratios of 1 : 3, 1 : 2, 1 : 1 and 2 : 1 is made by keeping the packing fraction and the charge of the minor component fixed. Our results suggest a way to improve the stability of the ionic nematic phase by enhancing the anisotropic van der Waals interaction compared to the Coulomb interaction, and by increasing the proportion of anisotropic particles in the mixture.

A combined LX-NMR and molecular dynamics investigation of the bulk and local structure of ionic liquid crystals.

The unique power of NMR spectroscopy in anisotropic media (LX-NMR) as a tool to obtain local and bulk structural information, combined with the effectiveness of molecular dynamics simulations at the atomistic level, shows very attractive potentialities for the study of interesting, even though still poorly understood, materials such as Ionic Liquid Crystals (ILCs). In this work, we focused our attention, in particular, on the orientational ordering of two mesophases: 1-dodecyl-3-methylimidazolium chloride, [C12C1im]Cl, and 1-dodecyl-3-methylimidazolium tetrafluoroborate, [C12C1im][BF4]. Both ILCs were studied by a 2H NMR direct investigation of the molecules forming the phases, suitably deuterated, and by 1H NMR spectroscopy, using the small rigid probe-solutes 1,4-dichlorobenzene (DCB), dissolved in [C12C1im][BF4] and [C12C1im]Cl, and 1,4-dibromobenzene (DBB) dissolved in [C12C1im][BF4], to probe the local, internal structure and organization of the mesophases. The experimental results were then compared with the predictions, by atomistic MD simulations, of the structure of the smectic phase of the two salts, at two selected temperatures, containing a single DCB molecule as a probe. The MD simulations show that the DCB solute is distributed only within the hydrophobic layers of the ILC. Orientational order parameters of the imidazolium cations and of the DCB molecule were obtained and compared with the experiments, showing a general good agreement and allowing a deeper understanding of the microscopic structure of the systems.

The 125Te Chemical Shift of Diphenyl Ditelluride: Chasing Conformers over a Flat Energy Surface.

The interest in diphenyl ditelluride (Ph2Te2) is related to its strict analogy to diphenyl diselenide (Ph2Se2), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph2Se2 and Ph2Te2 exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon⁻chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph2Te2 is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the 125Te chemical shift.