Solvation Sphere Research Articles

RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere.

We unravel the internal and collective modes of a widely studied 58-nucleotide rRNA fragment in solvent using atomically detailed molecular dynamics simulations. The variation of lifetimes for water hydrogen bonds with nucleotide groups indicates heterogeneity of water dynamics on the RNA surface. The time scales of interactions of the discrete water molecules with RNA nucleotides extend from several hundred picoseconds to a few nanoseconds. We determine all of the association sites and the spatial distribution of residence times for Mg2+, K+, and water molecules in those sites. We provide insights into the population of Mg2+ and K+ ions and water molecules in the outer sphere and how their fluctuations are intricately linked with the kinetics of the 58-mer. We find that many of the long-lived Mg2+ sites identified from the simulations agree with the locations of ions in the X-ray structure. We determine the excess ion atmosphere around the rRNA and compare it with experimental data. We investigate the collective behavior of RNA, ions, and water, by performing a joint principle component analysis for the Cartesian coordinates of the RNA phosphorus atoms and for the occupation counts of the association sites. Our results indicate that the 58-mer system is a complex polymer, composed of RNA that is encased by a fluctuating network of associated counterions, co-ions, and water.

Solvation structure for Fe(II), Co(II) and Ni(II) complexes in [P2225][NTf2] ionic liquids investigated by Raman spectroscopy and DFT calculation

The solvation structures of divalent iron, cobalt and nickel complexes in the ionic liquid, triethyl‑n‑pentylphosphonium bis(trifluoromethyl sulfonyl) amide ([P2225][NTf2]) were investigated by Raman spectroscopy. Based on a conventional analysis, the solvation numbers of Fe(II), Co(II), and Ni(II) in [P2225][NTf2] were determined to be 3.18, 3.21, and 3.14 at 298 K and 3.24, 3.32, and 3.37 at 373 K, respectively.From the temperature dependence of the Raman bands the isomerism of [NTf2]− from trans- to cis-coordinated isomer in the bulk and the first solvation sphere of the central M2+ (M = Fe, Co, and Ni) cation in [P2225][NTf2], thermodynamic properties such as ΔisoG, ΔisoH, and ΔisoS for the isomerism were evaluated. It was revealed that cis-[NTf2]− isomers were stabilized by enthalpic contribution, because ΔisoH(M) became remarkably negative in the first solvation sphere of the M2+ cation. Moreover, ΔisoH(M) contributed to the remarkable decrease in ΔisoG(M), and this result clearly indicates that cis-[NTf2]− conformers bound to M2+ cations are the preferred coordination state of [M(II)(cis-NTf2)3]− in [P2225][NTf2].The optimized geometries and the binding energies of [Fe(II)(cis-NTf2)3]−, [Co(II)(cis-NTf2)3]−, and [Ni(II)(cis-NTf2)3]− clusters were calculated by ADF simulations. The bonding energy, ΔEb, was calculated as ΔEb = Etot(cluster) − Etot(M2+) − nEtot([NTf2]−), and ΔEb ([Fe(II)(cis-NTf2)3]−), ΔEb([Co(II)(cis-NTf2)3]−), and ΔEb([Ni(II)(cis-NTf2)3]−) were calculated to be −2132.1 ± 6.4, −2254.6 ± 6.1, and −2283.4 ± 7.2 kJ mol−1, respectively. Furthermore, the bond distances of these clusters were consistent with the thermodynamic properties.

Specific optical rotation for the identification of the locus of solubilization of chiral molecules in achiral micelles

We present the first detailed experimental study of discrete wavelength resolved specific optical rotations (SORs) of chiral molecules embedded in achiral micelles. Eight different chiral compounds embedded in SDS and TX100 micelles have been used to analyze their SORs in comparison to those obtained for the same chiral molecules in achiral solvents. An important observation made is that the SORs of hydrophobic chiral molecules, α-pinene and 2-carene, in hydrophobic achiral solvents (dodecane, heptane and CCl4) are greater than those of same chiral molecules embedded in hydrophobic core of SDS micelles. This difference is envisioned to be due to the differences in microenvironments provided by achiral SDS micelle and organic solvents. The ratio of SOR for a chiral molecule in CCl4 solvent and achiral micelles is found to reflect the locus of solubilization of chiral molecule in achiral micelle. The locus of solubilization of chiral molecules in TX100 micelles has been independently verified using 1H NMR studies. The emerging general observations are: (a) when chiral molecule is located deep inside the hydrophobic core of the micelle, SOR in micelle is smaller than that in CCl4. (b) When chiral molecule is located at the interface of hydrophobic and hydrophilic regions of the micelle, SOR in micelle is slightly greater than, or equal to, that in CCl4. While quantum chemical (QC) calculations to explain these observations in micelles need significantly larger computational time line, the prospect for such calculations has been verified by undertaking QC predictions of SOR for a representative chiral molecule, fenchone, in water (with 4 Å solvation sphere), and comparing the predicted results with the corresponding experimental observations in water. The predictions and observations are found to be in good agreement. The present results are expected to provide impetus for understanding the microenvironment that influences most of the spectroscopic observations.

Corrections to “Porphyrins Sheathed in Quadrupolar Solvation Spheres of Hexafluorobenzene: Solvation-Induced Fluorescence Enhancement and Conformational Confinement”

RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrections to “Porphyrins Sheathed in Quadrupolar Solvation Spheres of Hexafluorobenzene: Solvation-Induced Fluorescence Enhancement and Conformational Confinement”Mitsuhiko Morisue*Mitsuhiko MorisueMore by Mitsuhiko Morisuehttp://orcid.org/0000-0002-7783-2492, Ikuya UenoIkuya UenoMore by Ikuya Ueno, Masaki ShimizuMasaki ShimizuMore by Masaki Shimizu, Takashi YumuraTakashi YumuraMore by Takashi Yumura, and Noriaki IkedaNoriaki IkedaMore by Noriaki IkedaCite this: J. Phys. Chem. C 2018, 122, 17, 9730Publication Date (Web):April 25, 2018Publication History Published online25 April 2018Published inissue 3 May 2018https://doi.org/10.1021/acs.jpcc.8b03608Copyright © 2018 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views262Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (178 KB) Get e-Alerts Get e-Alerts

Sequential Induction of Chirality in Helical Polymers: From the Stereocenter to the Achiral Solvent.

Several steps of chiral induction have been detected in poly(phenylacetylene)s among their different hierarchical levels of chirality by vibrational circular dichroism, namely, (i) from the stereogenic centers to the innermost polyacetylene helical covalent backbone (helixint), (ii) from this to the external helix (helixext) formed by the side phenyl pendants that form a complementary helix or counter-helix, and (iii) from this pendant helix to the helical solvation sphere (helixsolv.), the last one being observed along this work. The pendant to polyene backbone chiral induction determines the helical structure adopted by the polymer and therefore the solvation helix. This helical structure is promoted by two mechanisms: steric effects and hydrogen bonding. An important finding concerns the demonstration by VCD of how an achiral solvent becomes chirally organized owing to the template effect of the covalent polymer helices, an effect that is silent to other structural techniques such as ECD or AFM and that hence significantly broadens the scope of these previous analyses.

Local structures of titanium-ion complexes in redox flow battery electrolytes as revealed by X-ray scattering with difference analysis

We report an investigation into the local structure of Ti4+ ions in sulfuric acid solutions as electrolytes for Ti-based redox flow batteries using X-ray total scattering with difference analysis. In the X-ray scattering experiments, we analyzed two concentrated aqueous solutions, one containing 1.5M TiOSO4 and 2.0M H2SO4 (termed the Ti-SO4 system) and the other containing 3.5M H2SO4 (termed the H2SO4 system), which have the same SO42− concentration, and then subtracted the observed X-ray interference function (i(Q)) for the H2SO4 system from that of the Ti-SO4 system to obtain the difference interference function (Δi(Q)). Using Fourier transformation of Δi(Q), we successfully obtained the difference distribution function (Δg(r)), which provides information on the local structure in the first solvation sphere of the Ti ions. The obtained Δg(r) function was interpreted using two possible structural models, i.e., mononuclear and multinuclear Ti-ion complexes. Consequently, we concluded that Ti ions are six-coordinated by O atoms (SO4− and/or H2O) to form octahedral complexes and that mononuclear and multinuclear complexes coexist in the Ti-SO4 system.

Stick boundary condition at large hard sphere arising from effective attraction in binary hard-sphere mixtures.

We have studied the diffusion of a large hard-sphere solute immersed in binary hard-sphere mixtures. We reveal how the boundary condition at the solute surface is affected by the solvent density around the solute. Solving equations for a binary compressible mixture by perturbation expansions, we obtain the boundary condition depending on the size ratio of binary solvent spheres. When the size ratio is 1:2, the boundary condition lies close to the slip boundary condition. By contrast, when the size ratio becomes large, the boundary condition approaches the stick boundary condition with the addition of larger solvent spheres. We find that the transition to the stick boundary condition is caused by the increase in the solvent density around the solute due to an entropic effect.

Solid-Liquid Interface Structure of Muscovite Mica in SrCl2 and BaCl2 Solutions.

The structure of the solid–liquid interface formed by muscovite mica in contact with two divalent ionic solutions (SrCl2 and BaCl2) is determined using in situ surface X-ray diffraction using both specular and non-specular crystal truncation rods. The 0.5 monolayer of monovalent potassium present at the surface after cleavage is replaced by approximately 0.25 monolayer of divalent ions, closely corresponding to ideal charge compensation within the Stern layer in both cases. The adsorption site of the divalent ions is determined to be in the surface ditrigonal cavities with minor out-of-plane relaxations that are consistent with their ionic radii. The divalent ions are adsorbed in a partly hydrated state (partial solvation sphere). The liquid ordering induced by the presence of the highly ordered crystalline mica is limited to the first 8–10 Å from the topmost crystalline surface layer. These results partly agree with previous studies in terms of interface composition, but there are significant differences regarding the structural details of these interfaces.

Influence of Counterions on the Hydration Structure of Lanthanide Ions in Dilute Aqueous Solutions.

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to investigate diluted (0.1 M) aqueous solutions of two lanthanide ions (Ln3+), namely, La3+ and Dy3+, with triflate, nitrate, and bis(trifluoromethylsulfonyl)imide (Tf2N-) as counterions. The different complexing ability of the three anions has been highlighted by the analysis of the MD simulations: Tf2N- does not form inner-sphere complexes, while a small amount of triflate coordinates both the La3+ and Dy3+ cations in their first solvation shell. On the other hand, the nitrate ion is almost absent in the La3+ first coordination sphere, while forming contact ion pairs with Dy3+. Both lanthanide ions are found to preferentially interact with the water molecules, and the total number of oxygen atoms coordinating the Ln3+ cations in their first solvation sphere is the same in all of the solutions, regardless of whether they belong to water molecules or to the counterion. The presence of counterions in the cation first or second shell changes neither the first shell distance nor the symmetry of the hydration complex formed in solution. The MD results have been confirmed by comparison with the Ln K-edge XAS experimental data, and the quantitative analysis of the extended X-ray absorption fine structure (EXAFS) spectra of the three salt solutions has provided a definite proof of the accuracy of the force field employed in the simulations and of the MD structural result. The anion-water and water-water hydrogen bond lifetimes have been analyzed highlighting the slow down effect of the triflate, nitrate, and Tf2N- anions on the hydrogen bond dynamics in the Ln3+ first solvation shell, with the effect being stronger in the Dy3+ solutions, due to the higher charge density of the Dy3+ ion as compared to La3+.

Aqueous Solvation of SmI3: A Born-Oppenheimer Molecular Dynamics Density Functional Theory Cluster Approach.

We report the results of Born-Oppenheimer molecular dynamics (BOMD) simulations on the aqueous solvation of the SmI3 molecule and of the bare Sm3+ cation at room temperature using the cluster microsolvation approach including 37 and 29 water molecules, respectively. The electronic structure calculations were done using the M062X hybrid exchange-correlation functional in conjunction with the 6-31G** basis sets for oxygen and hydrogen. For the iodine and samarium atoms, the Stuttgart-Köln relativistic effective-core potentials were utilized with their associated valence basis sets. When SmI3 is embedded in the microsolvation environment, we find that substitution of the iodine ions by water molecules around Sm(III) cannot be achieved due to an insufficient number of explicit water molecules to fully solvate the four separate metal and halogen ions. Therefore, we studied the solvation dynamics of the bare Sm3+ cation with a 29-water molecule model cluster. Through the Sm-O radial distribution function and the evolution of the Sm-O distances, the present study yields a very tightly bound first rigid Sm(III) solvation shell from 2.3 to 2.9 Å whose integration leads to a coordination number of 9 water molecules and a second softer solvation sphere from 3.9 to 5 Å with 12 water molecules. No water exchange processes were found. The theoretical EXAFS spectrum is in excellent agreement with the experimental spectrum for Sm(III) in liquid water. The strong differences between the solvation patterns of Sm(III) vs Sm(II) are discussed in detail.

Weakly interacting solvation spheres surrounding a calixarene-protected tetrairidium carbonyl cluster: contrasting effects on reactivity of alkane solvent and silica support.

The tetrairidium carbonyl cluster Ir4L3(CO)9 (L = tert-butyl-calix[4]arene(OPr)3(OCH2PPh2) (Ph = phenyl; Pr = propyl)) on a partially dehydroxylated silica support undergoes hydrogen activation at a rate and with a mechanism different from those pertaining to the cluster in alkane solution. These results are unobvious in view of the sterically bulky ligands protecting the cluster and the nearly identical CO band frequencies in the infrared spectra characterizing the supported and dissolved Ir4L3(CO)9, both before reaction and during reaction involving decarbonylation in the presence of either helium or H2 (and H2 reacted with the clusters to form hydrides with the same Ir-H band frequencies for clusters in alkane solvent and supported on silica). The initial rates of CO loss from the supported clusters in the presence of helium were the same as those in the presence of H2. The comparison demonstrates that the rate-determining step for hydride formation on the silica-supported cluster is CO dissociation. In contrast, the comparable dissociation of CO from the cluster in n-decane solution requires a higher temperature, 343 K, and is at least an order of magnitude slower than when the clusters were supported on silica. CO dissociation is not the rate-determining step for hydrogen activation on the cluster in n-decane, as the rate is influenced by reactant H2 as well.

Introducing the Bipolar Solvent Media Using the Aqueous Mixtures of Amino Acid Anion-Based Ionic Liquids.

To carry out a chemical reaction between the reactants with largely different polarities, it becomes important to have a reaction medium that possesses both the polar and nonpolar solvation environments. In an attempt to explore the reaction media with such unique polarity properties, the present study provides a thorough understanding of the bipolar solvent media using the aqueous mixtures of amino acid anion-based ionic liquids. The highly polar behavior of the binary mixtures used in the study has been ascribed to the pure ionic liquid state. However, the less polar solvation shells have been attributed to the presence of a neutral form of the anions. Addition of water in the amino acid anion-based ionic liquids causes the protonation of a certain fraction of the anions of the ionic liquids, resulting into the formation of a less polar nonionic protonated form along with the highly polar natural anionic form. This results into the formation of two solvation spheres with different polarities, which can be seen very clearly from the presence of two absorption bands (lower wavelength absorption band and higher wavelength absorption band) in the UV-vis absorption spectrum of Reichardt's ET(30) dye and two emission bands (lower wavelength emission band and higher wavelength emission band) in the fluorescence emission spectrum of C481 dye. The values of the ETN polarity parameter corresponding to the two solvation shells having different polarities have been calculated from the deconvoluted absorption spectra of the Reichardt's ET(30) and were analyzed in three amino acid anion-based ionic liquids. Generation of the neutral form of anions in the aqueous mixtures formed via a protonation transfer reaction has been confirmed by the 1H NMR spectroscopy and UV-vis absorption spectrum of 18DHAQ dye. The study also establishes that the Reichardt's ET(30) dye can be used as a valid polarity probe to study the solvatochromic behavior of the binary mixtures of amino acid-based ionic liquids.

Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive.

Porphyrins Sheathed in Quadrupolar Solvation Spheres of Hexafluorobenzene: Solvation-Induced Fluorescence Enhancement and Conformational Confinement

Hexafluorobenzene (C6F6) strongly solvated the porphyrin ring via a quadrupolar interaction. The solvation sphere of C6F6 hindered the thermal fluctuations near the porphyrin ring and evoked remarkable photoelectronic properties of the porphyrins such as fluorescence enhancement and spectral sharpening due to confined torsional planarity.

The Structure of Ethylbenzene, Styrene and Phenylacetylene Determined by Total Neutron Scattering.

Organic solvents such as phenylacetylene, styrene and ethylbenzene are widely used in industrial processes, especially in the production of rubber or thermoplastics. Despite their important applications detailed knowledge about their structure is limited. In this paper the structures of these three aromatic solvents were investigated using neutron diffraction. The results show that many of their structural characteristics are similar, although the structure of phenylacetylene is more ordered and has a smaller solvation sphere than either ethylbenzene or styrene. Two regions within the first coordination sphere, in which the surrounding molecules show different preferable orientations with respect to the central molecule, were found for each liquid. Additionally, the localisation of the aliphatic chains reveals that they tend to favour closer interactions with each other than to the aromatic rings of the adjacent molecules.

Aqueous micro-solvation of Li+ ions: Thermodynamics and energetic studies of Li+-(H2O)n (n = 1–6) structures

The structures and thermodynamic parameters of hydrated lithium ion clusters incorporating a single lithium ion and up to six water molecules have been determined with density functional (DFT) and Hartree-Fock (HF) at the RB3LYP/631G(d,p) levels of theory. The possible formed structures are found to be 23 Li+(H2O)n complex for n=1–6. The primary solvation shell in the gas phase is confirmed to be tetrahydrated in aqueous environment. Very important role of intermolecular hydrogen bond in determining the stability of solvation process of different ions is confirmed by theoretical studies. The calculated gas phase coordination number in the first solvation sphere of a hydrated lithium metal ion is found to be four and the same is also confirmed by the experimental findings. The equilibrium lithium–oxygen distance of 1.970Å at the present B3LYP level of study is in excellent agreement with the X-ray diffraction result of 1.980Å and neutron scattering study with a result of 1.90Å for a tetrahydrated lithium cluster. NBO was analyzed and discussed.

Aqueous Solvation of SmI2: A Born-Oppenheimer Molecular Dynamics Density Functional Theory Cluster Approach.

We report the results of Born-Oppenheimer molecular dynamics (BOMD) simulations on the aqueous solvation of the SmI2 molecule at room temperature using the cluster microsolvation approach including 32 water molecules. The electronic structure calculations were done using the M062X hybrid exchange-correlation functional in conjunction with the 6-31G** basis sets for oxygen and hydrogen. For the iodine and samarium atoms the Stuttgart-Köln relativistic effective-core potentials were utilized with their associated valence basis sets. Starting from the optimized geometry of SmI2 embeded in the microsolvation environment, we find a swift substitution of the iodine ions by eight tightly bound water molecules around Sm(II). Through the Sm-O radial distribution function and the evolution of the Sm-O distances, the present study predicts a first rigid Sm(II) solvation shell from 2.6 to 3.4 Å, whose integration leads to a coordination number of 8.4 water molecules, and a second softer solvation sphere from 3.5 to ca. 6 Å. The Sm(II)-O radial distribution function is in excellent agreement with that reported for Sr2+ from EXAFS studies, a fact that can be explained because Sr2+ and Sm2+ have almost identical ionic radii (ca. 1.26 Å) and coordination numbers: 8 for Sr2+ and 8.4 for Sm2+. The theoretical EXAFS spectrum was obtained from the BOMD trajectory and is discussed in the light of the experimental spectra for Sm(III). Once microsolvation is achieved, no water exchange events were found to occur around Sm2+, in agreement with the experimental data for Eu2+ (which has a nearly identical charge-to-ionic radius relation as Sm2+), where the mean residence time of a water molecule in [Eu(H2O)8]2+ is known to be ca. 230 ps.

Thermodynamic Insight into the Solvation and Complexation Behavior of U(VI) in Ionic Liquid: Binding of CMPO with U(VI) Studied by Optical Spectroscopy and Calorimetry.

The complexation of U(VI) with octylphenyl-N,N-diisobutylcarbamoylmethylphosphine oxide (CMPO, denoted as L) in ionic liquid (IL) C4mimNTf2 was investigated by UV-vis absorption spectrophotometry and isothermal titration calorimetry. Spectro-photometric titration suggests that three successive complexes, UO2Lj2+ (j = 1-3), formed both in "dry" (water content < 250 ppm) and "wet" (water content ≈ 12 500 ppm) ionic liquid. However, the thermodynamic parameters are distinctly different in the two ILs. In dry IL, the complexation strength between CMPO and U(VI) is much stronger, with stability constants of the respective complexes more than 1 order of magnitude higher than that in wet IL. Energetically, the complexation of U(VI) with CMPO in dry IL is mainly driven by negative enthalpies. In contrast, the complexation in wet IL is overwhelmingly driven by highly positive entropies as a result of the release of a large amount of water molecules from the solvation sphere of U(VI). Moreover, comparisons between the fitted absorption spectra of complexes in wet IL and that of extractive samples from solvent extraction have identified the speciation involved in the extraction of U(VI) by CMPO in ionic liquid. The results from this study not only offer a thermodynamic insight into the complexation behavior of U(VI) with CMPO in IL but also provide valuable information for understanding the extraction behavior in the corresponding solvent extraction system.

Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0.01 ppm for 1H chemical shifts and 0.07 ppm for 13C chemical shifts. In addition, the performance of MIM-NMR has been assessed on two large peptides: the helical portion of ubiquitin ( 1UBQ ) containing 12 residues where the X-ray structure is known, and E6-binding protein of papilloma virus ( 1RIJ ) containing 23 residues where the structure has been derived from solution-phase NMR analysis. The solvation environment is incorporated in these MIM-NMR calculations, either through an explicit, implicit, or a combination of both solvation models. Using an explicit treatment of the solvent molecules within the first solvation sphere (3 Å) and an implicit solvation model for the rest of the interactions, the 1H and 13C chemical shifts of ubiquitin show excellent agreement with experiment (mean absolute deviation of 0.31 ppm for 1H and 1.72 ppm for 13C), while the larger E6-binding protein yields a mean absolute deviation of 0.34 ppm for 1H chemical shifts. The proposed MIM-NMR method is computationally cost-effective and provides a substantial speedup relative to conventional full calculations, the largest density functional NMR calculation included in this work involving more than 600 atoms and over 10,000 basis functions. The MIM-NMR solvation protocols developed in this work may pave the way for very accurate de novo prediction of NMR chemical shifts of a range of large biomolecules in the future.

Cu(H2O) n ]2+ (n = 1–6) complexes in solution phase: a DFT hierarchical study

For the theoretical modeling of energy profiles of Cu2+ reactions with biological ligands, it is indispensable to know the structure of its solvation sphere. Not withstanding the experimental and theoretical studies on this topic, nature of Cu–water complexes is still subject of intense debate. In order to gain insight into the structural features and relative stabilities of the [Cu(H2O) n ]2+ (n = 1–6) species, several of their coordination modes considering water molecules in the first and second hydration shell of Cu2+, have been considered. Electronic structure calculations were performed with the G09 quantum chemistry suite of programs. Geometries are optimized by means of DFT functionals (allocate in different rungs of the Jacob’s ladder) and the ab initio MP2 perturbation theory applying the def-SVP valence split basis set; formation of complexes is studied in gas phase and solution by application of CPCM and SMD protocols. Stabilization energies for each stoichiometry are calculated at the MP2/aug-cc-pVTZ level of theory. [Cu(H2O)2]2+, [Cu(H2O)3]2+ and [Cu(H2O)4]2+ complexes show lineal, planar trigonal and square planar structures, respectively; gas phase and CPCM results indicate that [Cu(H2O)5]2+ is isoenergetic with [Cu(H2O)4]2+(H2O), but SMD solvent effects favor formation of intramolecular hydrogen bonds. For sixfold complexes, [Cu(H2O)4]2+(H2O)2 is consistently found to be the most stable compared with [Cu(H2O)6]2+ and [Cu(H2O)5]2+(H2O). For n = 5 and 6, hydrogen bond formation in the second hydration shell competes with coordination in axial positions; results indicate that this intramolecular hydrogen bond stabilizes the complex more than axial coordination of water. In gas phase as well as solution, BHLYP outcomes are always consistent with MP2 results, evidencing the importance of exact exchange in the functional. SMD solvent effects show that water ligands are more loosely bond to the central ion that might explain a variety of complexes coexisting in solution, contrasting with gas phase where releasing a water molecule entails a higher energetic cost. Results indicate a clear tendency to improve the geometry, the symmetry and the relative stabilization energy of the Cu–water complex, toward the MP2 value, when either advancing on the Jacob’s ladder or the percentage of exact exchange in the functional increases.