Interaction of metal ions with biomolecular ligands: how accurate are calculated free energies associated with metal ion complexation?

To address fundamental questions in bioinorganic chemistry, such as metal ion selectivity, accurate computational protocols for both the gas-phase association of metal-ligand complexes and solvation/desolvation energies of the species involved are needed. In this work, we attempt to critically evaluate the performance of the ab initio and DFT electronic structure methods available and recent solvation models in calculations of the energetics associated with metal ion complexation. On the example of five model complexes ([M(II)(CH(3)S)(H(2)O)](+), [M(II)(H(2)O)(2)(H(2)S)(NH(3))](2+), [M(II)(CH(3)S)(NH(3))(H(2)O)(CH(3)COO)], [M(II)(H(2)O)(3)(SH)(CH(3)COO)(Im)], [M(II)(H(2)S)(H(2)O)(CH(3)COO)(PhOH)(Im)](+) in typical coordination geometries) and four metal ions (Fe(2+), Cu(2+), Zn(2+), and Cd(2+); representing open- and closed-shell and the first- and second-row transition metal elements), we provide reference values for the gas-phase complexation energies, as presumably obtained using the CCSD(T)/aug-cc-pVTZ method, and compare them with cheaper methods, such as DFT and RI-MP2, that can be used for large-scale calculations. We also discuss two possible definitions of interaction energies underlying the theoretically predicted metal-ion selectivity and the effect of geometry optimization on these values. Finally, popular solvation models, such as COSMO-RS and SMD, are used to demonstrate whether quantum chemical calculations can provide the overall free enthalpy (ΔG) changes in the range of the expected experimental values for the model complexes or match the experimental stability constants in the case of three complexes for which the experimental data exist. The data presented highlight several intricacies in the theoretical predictions of the experimental stability constants: the covalent character of some metal-ligand bonds (e.g., Cu(II)-thiolate) causing larger errors in the gas-phase complexation energies, inaccuracies in the treatment of solvation of the charged species, and difficulties in the definition of the reference state for Jahn-Teller unstable systems (e.g., [Cu(H(2)O)(6)](2+)). Although the agreement between the experimental (as derived from the stability constants) and calculated values is often within 5 kcal·mol(-1), in more complicated cases, it may exceed 15 kcal·mol(-1). Therefore, extreme caution must be exercised in assessing the subtle issues of metal ion selectivity quantitatively.     

IrII(ethene): metal or carbon radical?

One-electron oxidation of [(Me(n)tpa)Ir(I)(ethene)]+ complexes (Me(3)tpa = N,N,N-tri(6-methyl-2-pyridylmethyl)amine; Me(2)tpa = N-(2-pyridylmethyl)-N,N,-di[(6-methyl-2-pyridyl)methyl]-amine) results in relatively stable, five-coordinate Ir(II)-olefin species [(Me(n)tpa)Ir(II)(ethene)](2+) (1(2+): n = 3; 2(2+): n = 2). These contain a "vacant site" at iridium and a "non-innocent" ethene fragment, allowing radical type addition reactions at both the metal and the ethene ligand. The balance between metal- and ligand-centered radical behavior is influenced by the donor capacity of the solvent. In weakly coordinating solvents, 1(2+) and 2(2+) behave as moderately reactive metallo-radicals. Radical coupling of 1(2+) with NO in acetone occurs at the metal, resulting in dissociation of ethene and formation of the stable nitrosyl complex [(Me(3)tpa)Ir(NO)](2+) (6(2+)). In the coordinating solvent MeCN, 1(2+) generates more reactive radicals; [(Me(3)tpa)Ir(MeCN)(ethene)](2+) (9(2+)) by MeCN coordination, and [(Me(3)tpa)Ir(II)(MeCN)](2+) (10(2+)) by substitution of MeCN for ethene. Complex 10(2+) is a metallo-radical, like 1(2+) but more reactive. DFT calculations indicate that 9(2+) is intermediate between the slipped-olefin Ir(II)(CH(2)=CH(2)) and ethyl radical Ir(III)-CH(2)-CH(2). resonance structures, of which the latter prevails. The ethyl radical character of 9(2+) allows radical type addition reactions at the ethene ligand. Complex 2(2+) behaves similarly in MeCN. In the absence of further reagents, 1(2+) and 2(2+) convert to the ethylene bridged species [(Me(n)tpa)(MeCN)Ir(III)(mu(2)-C(2)H(4))Ir(III)(MeCN)(Me(3)tpa)](4+) (n = 3: 3(4+); n = 2: 4(4+)) in MeCN. In the presence of TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxo), formation of 3(4+) from 1(2+) in MeCN is completely suppressed and only [(Me(3)tpa)Ir(III)(TEMPO(-))(MeCN)](2+) (7(2+)) is formed. This is thought to proceed via radical coupling of TEMPO at the metal center of 10(2+). In the presence of water, hydrolysis of the coordinated acetonitrile fragment of 7(2+) results in the acetamido complex [(Me(3)tpa)Ir(III)(NHC(O)CH(3)))(TEMPOH)](2+) (8(2+)).     

Does the HO2 radical react with ketones?

The possible reactions of HO₂ with five ketones were studied using a flow tube reactor equipped with a laser magnetic resonance detector. We did not observe reactive loss of HO₂ in any of the five reactions. We place upper limits of <8 × 10⁻¹⁶, <7 × 10⁻¹⁶, <5 × 10⁻¹⁶, <4 × 10⁻¹⁶, and <9 × 10⁻¹⁶ (in units of cm³; molecule⁻¹ S⁻¹) at 298 K for the reactions of HO₂ with CH₃COCH₃, CH₃COC₂H₅, CH₃COC₃H₇, C₂H₅COC₂H₅, and CH₃COC₄H₉, respectively, to give products other than an adduct. We conclude that their reactions with HO₂ are unlikely to be important loss processes for ketones in the atmosphere. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 573–580, 2000     

Where to bind in buckybowls? The dilemma of a metal ion

An exhaustive computational study at the M05-2X/cc-pVDZ level which explores the binding possibilities of cations (Li(+), Na(+), K(+) and Cu(+)) to the concave and convex sides of the hub and rim rings of prototypical buckybowls, sumanene (C(21)H(12)) and corannulene (C(20)H(10)), has been carried out. Five distinct minima on the potential energy surface of sumanene and four on the potential energy surface of corannulene were identified. The complex where the metal ion binds to the convex side of the 6-membered rim ring is adjudged as the most stable complex for both the bowls considered. The cation-π interaction energies of buckybowls are compared with model systems such as benzene, cyclopentadiene, indene and coronene. Energy decomposition analysis has also been performed to delineate the contribution from various components contributing to the cation-π binding strength.     

Triggers for β-sheet formation at the hydrophobic-hydrophilic interface: high concentration, in-plane orientational order, and metal ion complexation

Amyloid formation plays a causative role in neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. Soluble peptides form β-sheets that subsequently rearrange into fibrils and deposit as amyloid plaques. Many parameters trigger and influence the onset of the β-sheet formation. Early stages are recently discussed to be cell-toxic. Aiming at understanding various triggers such as interactions with hydrophobic-hydrophilic interfaces and metal ion complexation and their interplay, we investigated a set of model peptides at the air-water interface. We are using a general approach to a variety of diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes that are connected to amyloid formation. Surface sensitive techniques combined with film balance measurements have been used to assess the conformation of the peptides and their orientation at the air-water interface (IR reflection-absorption spectroscopy). Additionally, the structures of the peptide layers were characterized by grazing incidence X-ray diffraction and X-ray reflectivity. The peptides adsorb to the air-water interface and immediately adopt an α-helical conformation. This helical intermediate transforms into β-sheets upon further triggering. The factors that result in β-sheet formation are dependent on the peptide sequence. In general, the interface has the strongest effect on peptide conformation compared to high concentrations or metal ions. Metal ions are able to prevent aggregation in bulk but not at the interface. At the interface, metal ion complexation has only minor effects on the peptide secondary structure, influencing the in-plane structure that is formed in two dimensions. At the air-water interface, increased concentrations or a parallel arrangement of the α-helical intermediates are the most effective triggers. This study reveals the role of various triggers for β-sheet formation and their complex interplay. Our main finding is that the hydrophobic-hydrophilic interface largely governs the conformation of peptides. Therefore, the present study implies that special care is needed when interpreting data that may be affected by different amounts or types of interfaces during experimentation.     

Are gas-phase reactions of five-coordinate divalent metal ion complexes affected by coordination geometry?

Five-coordinate metal complex ions of the type [ML](2+) [where M = Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II) and L= 1,9-bis(2-pyridyl)-2,5,8-triazanonane (DIEN-(pyr)(2)) and 1,9-bis(2-imidazolyl)-2,5,8-triazanonane (DIEN-(imi)(2)] have been reacted with acetonitrile in the gas phase using a modified quadrupole ion trap mass spectrometer. The kinetics and thermodynamics of these reactions show that the reactivity of these complexes is affected by metal electronic structure and falls into three groups: Mn(II) and Ni(II) complexes are the most reactive, Fe(II) and Co(II) complexes exhibit intermediate reactivity, and Cu(II) and Zn(II) complexes are the least reactive. To help explain the experimental trends in reactivity, theoretical calculations have been used. Due to the relatively large size of the metal complexes involved, we have utilized a two-layered ONIOM method to perform geometry optimizations and single point energy calculations for the [ML](2+) and [ML + CH(3)CN](2+) systems. The calculations show that the reactant five-coordinate complexes ([ML](2+)) exhibit structures that are slightly distorted trigonal bipyramidal geometries, while the six-coordinate complexes ([ML + CH(3)CN](2+)) have geometries that are close to octahedral. The Delta G values obtained from the ONIOM calculations roughly agree with the experimental data, but the calculations fail to completely explain the trends for the different metal complexes. The failure to consider all possible isomers as well as adequately represent pi-d interactions for the metal complexes is the likely cause of this discrepancy. Using the angular overlap model (AOM) to obtain molecular orbital stabilization energies (MOSE) also fails to reproduce the experimental trends when only sigma interactions are considered but succeeds in explaining the trends when pi interactions are taken into account. These results indicate that the pi-donor character of the CH(3)CN plays a subtle, yet important, role in controlling the reactivity of these five-coordinate complexes. Also, the AOM calculations are consistent with the experimental data when the [ML](2+) complexes have high-spin trigonal bipyramidal configurations. Generally, these results suggest that ion-molecule reactions can be very sensitive to metal complex coordination geometry and thus may have some promise for providing gas-phase coordination structure.     

Does the gradient-regulated connection improve the description of correlated metal bond properties?

Gradient-regulated connection (GRAC) is a generalized gradient approximation exchange density functional designed by combining the revPBE and PW91 exchange functionals to impose their behaviors in the slowly- and fast-varying density regions, respectively. Such a construction allows one single density functional to accurately estimate both covalent and weak interactions occurring in main-group-based molecular systems. For the first time, the assessment of the performance of the GRAC exchange functional is extended to the modeling of various metal bond energy and structure properties. This assessment shows that when GRAC is coupled with the Perdew, Burke, Ernzerhof (PBE) correlation, the resulting exchange-correlation density functional is an excellent alternative to global hybrids to model bond dissociation energy, atomic electronic excitation energy, and bond length structure properties of single-reference metal bonds. It also shows that coupling with the Tognetti, Cortona, Adamo (TCA) correlation constitutes a robust approach to tackle energy bond properties of organometallic complexes with multi-reference character.     

IrII(ethene): metal or carbon radical? Part II: oxygenation via iridium or direct oxygenation at ethene?

Treatment of [(Me3tpa)IrII(ethene)]2+ (Me(3)tpa =N,N,N-tri(6-methyl-2-pyridylmethyl)amine)(1(2+)) with dioxygen in weakly coordinating solvents results in formation of [(Me3tpa)IrIII(ethene)(superoxo)]2+ (4a2+). In the presence of DMPO (DMPO = 5,5-dimethyl-2-pyrrolidine-1-oxide) DMPO is substituted for ethene, and subsequently oxidized to DMPOX by the superoxo fragment to give [(Me3tpa)IrIII(DMPOX)]2+ (7(2+); DMPOX = 5,5-dimethyl-2-pyrrolidone-1-oxide). In acetonitrile, in the absence of DMPO, oxygenation of 1(2+) to [(Me3tpa)IrIII(formylmethyl)(MeCN)]2+ (2(2+)) is observed. In the presence of DMPO the formation of 2(2+) and 7(2+) is competing. Oxygenation of 1(2+) to 2(2+) may proceed via 4a(2+), involving an insertion mechanism at the metal. However, a mechanism based on olefin ligand non-innocence seems a reasonable alternative. This involves formation of acetonitrile adduct [(Me3tpa)Ir(ethene)(MeCN)]2+ (3(2+)), which has a significant metalla-ethyl radical (IrIII-CH2CH2*) character, allowing attack of 3O2 directly at the ethene ligand. Both pathways are discussed on the basis of experimental observations and DFT geometry optimizations.     

The metal cation chelating capacity of astaxanthin. Does this have any influence on antiradical activity?

In this Density Functional Theory study, it became apparent that astaxanthin (ASTA) may form metal ion complexes with metal cations such as Ca?2, Cu?2, Pb?2, Zn?2, Cd?2 and Hg?2. The presence of metal cations induces changes in the maximum absorption bands which are red shifted in all cases. Therefore, in the case of compounds where metal ions are interacting with ASTA, they are redder in color. Moreover, the antiradical capacity of some ASTA-metal cationic complexes was studied by assessing their vertical ionization energy and vertical electron affinity, reaching the conclusion that metal complexes are slightly better electron donors and better electron acceptors than ASTA.     

Can radical cations of the constituents of nucleic acids be formed in the gas phase using ternary transition metal complexes?

Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of ternary transition metal complexes of [M(L(3))(N)](2+) (where M = copper(II) or platinum(II); L(3) = diethylenetriamine (dien) or 2,2':6',2'-terpyridine (tpy); N = the nucleobases: adenine, guanine, thymine and cytosine; the nucleosides: 2'deoxyadenosine, 2'deoxyguanosine, 2'deoxythymine, 2'deoxycytidine; the nucleotides: 2'deoxyadenosine 5'-monophosphate, 2'deoxyguanosine 5'-monophosphate, 2'deoxythymine 5'-monophosphate, 2'deoxycytidine 5'-monophosphate) was examined as a means of forming radical cations of the constituents of nucleic acids in the gas phase. In general, sufficient quantities of the ternary complexes [M(L(3))(N)](2+) could be formed for MS/MS studies by subjecting methanolic solutions of mixtures of a metal salt [M(L(3))X(2)] (where M = Cu(II) or Pt(II); L(3) = dien or tpy; X = Cl or NO(3)) and N to ESI. The only exceptions were thymine and its derivatives, which failed to form sufficient abundances of [M(L(3))(N)](2+) ions when: (a) M = Pt(II) and L(3) = dien or tpy; (b) M = Cu(II) and L(3) = dien. In some instances higher oligomeric complexes were formed; e.g., [Pt(tpy)(dG)(n)](2+) (n = 1-13). Each of the ternary complexes [M(L(3))(N)](2+) was mass-selected and then subjected to collision-induced dissociation (CID) in a quadrupole ion trap. The types of fragmentation reactions observed for these complexes depend on the nature of all three components (metal, auxiliary ligand and nucleic acid constituent) and can be classified into: (i) a redox reaction which results in the formation of the radical cation of the nucleic acid constituent, N(+.); (ii) loss of the nucleic acid constituent in its protonated form; and (iii) fragmentation of the nucleic acid constituent. Only the copper complexes yielded radical cations of the nucleic acid constituent, with [Cu(tpy)(N)](2+) being the preferred complex due to suppression, in this case, of the loss of the nucleobase in its protonated form. The yields of the radical cations of the nucleobases from the copper complexes follow the order of their ionization potentials (IPs): G (lowest IP) > A > C > T (highest IP). Sufficient yields of the radical cations of each of the nucleobases allowed their CID reactions (in MS(3) experiments) to be compared to their even-electron counterparts.     

Does an ethene/benzenium ion complex exist? A discrepancy between B3LYP and MP2 predictions

To investigate the possible existence of a complex between the benzenium ion and ethene, computations employing B3LYP and MP2 were carried out. The two methodologies gave conflicting answers; B3LYP confirmed the existence, but according to MP2, the structure found by B3LYP transforms into an ethylbenzenium ion. Computations utilizing the CCSD and QCISD methods showed the B3LYP result to be correct; 21 kJ/mol is needed to separate the two moieties.     

Does the reagent gas influence collisional activation when performing in situ chemical ionization with an ion trap mass spectrometer?

Users of ion trap mass spectrometers frequently develop methods that associate chemical ionization with tandem mass spectrometry detection. With apparatus using internal ionization, the chemical reagent is present in the trap during the collision induced dissociation (CID) step and one may wonder if the reagent influences the fragmentation ratios in MS/MS. We report a comparison of the fragmentation ratios of protonated molecules when using the most common reagents (methane, ammonia, methanol, acetonitrile, isobutane) for performing in situ chemical ionization. Four molecules were chosen in the medical field to serve as models: alprazolam, diazepam, flunitrazepam and acetaminophen. In the non-resonant CID mode, the influence of the reagent mass is clearly seen in spite of its low partial pressure in the ion trap; the reagent acts as a "heavy target": the degree of fragmentation increases with the molecular weight of the reagent. In the resonant CID mode, there is no evident correlation between the fragmentation ratio of MH(+) ions and the nature of the CI reagent; a slight shift of the secular frequency of the precursor ion, which tends to reduce the CID efficiency, could compensate for the "heavy target" effect underscored in the non-resonant mode.     

Selective and unusual fluoride ion complexation by a steroidal receptor using OH...F- and CH...F- interactions: a new motif for anion coordination?

[structure: see text] A novel cholaphane has been synthesized from a naturally occurring bile acid in just two steps. It has an ability to bind two fluoride ions selectively utilizing the glycolate motif in chloroform. This "inside-out" cyclodextrin analogue encapsulates fluoride through O-H...F(-) and C-H...F(-) interaction.     

Rigid versus flexible: how important is ligand "preorganization" for metal ion recognition by lower rim-functionalized calix[4]arenes?

For an assessment of the outcomes from use of an appropriately "preorganized" calixarene-based ionophore versus its conformationally mobile prototype, solvent extraction propensities of flexible calix[4]arene di-[N-(X-sulfonyl)carboxamides] for alkali, alkaline earth metal cations, Pb2+, Ag+ and Hg2+ are compared with those for seven new rigid analogs fixed in the cone, partial cone and 1,3-alternate conformations. For each of the metal ions, the preferred calix[4]arene conformation was determined from the NMR spectra for the metal salt of the flexible ligand. Except for Ag+, flexible calix[4]arene di-[N-(X-sulfonyl)carboxamides] were found to provide greater metal ion extraction efficiency and better selectivity than the corresponding "preorganized" ionophores.     

Does Li4Ti5O12 need carbon in lithium ion batteries? Carbon-free electrode with exceptionally high electrode capacity

A carbon-free Li(4)Ti(5)O(12) electrode has shown excellent electrochemical performance without any effort to enhance the electrical conductivity. Partial reduction of Ti(4+) and a metallic Li(7)Ti(5)O(12) phase are suggested to be possible origins of the exceptional behavior.     

Tl(I)‐the strongest structure‐breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study

Structural and dynamical properties of the Tl(I) ion in dilute aqueous solution have been investigated by ab initio quantum mechanics in combination with molecular mechanics. The first shell plus a part of the second shell were treated by quantum mechanics at Hartree-Fock level, the rest of the system was described by an ab initio constructed potential. The radial distribution functions indicate two different bond lengths (2.79 and 3.16 A) in the first hydration shell, in good agreement with large-angle X-ray scattering and extended X-ray absorption fine structure spectroscopy results. The average first shell coordination number was found as 5.9, and several other structural parameters such as coordination number distributions, angular distribution functions, and tilt- and theta-angle distributions were evaluated. The ion-ligand vibration spectrum and reorientational times were obtained via velocity auto correlation functions. The Tl-O stretching force constant is very weak with 5.0 N m(-1). During the simulation, numerous water exchange processes took place between first and second hydration shell and between second shell and bulk. The mean ligand residence times for the first and second shell were determined as 1.3 and 1.5 ps, respectively, indicating Tl(I) to be a typical "structure-breaker". The calculated hydration energy of -84 +/- 16 kcal mol(-1) agrees well with the experimental value of -81 kcal mol(-1). All data obtained for structure and dynamics of hydrated Tl(I) characterize this ion as a very special case among all monovalent metal ions, being the most potent "structure-breaker", but at the same time forming a distinct second hydration shell and thus having a far-reaching influence on the solvent structure.     

How fast do metal organic polyhedra form in solution? Kinetics of [Cu2(5-OH-bdc)2L2]12 formation in methanol

The present study utilizes rapid mixing techniques together with fast optical spectroscopy to probe the assembly of [Cu2(5-OH-bdc)2L2]12 formation in methanol. The data reveal five distinct kinetic steps involved in the formation of the Cu-nanoball in methanol with lifetimes of <15 ms, 26 ms, 310 ms, 4 s, and 45 s. From these results two possible mechanistic pathways are proposed based upon fragment isomerization followed by condensation. Both mechanisms involve fast building unit assembly (<15 ms) followed by either concerted or sequential fragment isomerization (activation controlled) coupled with condensation.