Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

Influence of the water molecules (n?=?1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

Influence of the addition of water molecules (n = 1–6) on the interaction energy between Li⁺, Na⁺, K⁺ cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation–π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation–π interaction indicates that there is a correlation between the electron density (ρ(r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule.     

IRMPD spectroscopy of metal-ion/tryptophan complexes

Infrared multiple-photon dissociation (IRMPD) spectroscopy is employed to obtain detailed binding information on singly charged silver and alkali metal-ion/tryptophan complexes in the gas phase. For these complexes the presence of the salt bridge (i.e. zwitterionic) tautomer can be virtually excluded, except for perhaps a few percent in the case of Li+. Two low-energy structures having the charge solvation form are shown to be likely, where the metal cation is either in a tridentate N/O/Ring conformation or in a bidentate O/Ring conformation. These two structures can be conveniently discriminated and their relative quantities can be approximated by IR spectroscopy, based principally on diagnostic modes near approximately 1150 (N/O/Ring) and 1400 (O/Ring) cm(-1). Interestingly, the smaller cation complexes (i.e. Ag+ and Li+) display exclusively the N/O/Ring conformation, whereas the O/Ring conformer becomes progressively more abundant with increasing alkali metal size, eventually representing the majority of the ion population for Rb+ and Cs+. These spectroscopic findings are in excellent agreement with thermochemical density functional theory (DFT) calculations, giving support to the utility of high-level quantum-chemical calculations for such systems. Moreover, in contrast to other mass spectrometry-based techniques, IRMPD spectroscopy allows clear differentiation and semi-quantitative approximation of these metal-ligand binding motifs, thereby underlining its importance in thermochemical model benchmarking.     

Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes

Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative.     

The reversal by sulfate of the denaturant activity of guanidinium

Guanidinium (Gdm+) chloride is a powerful protein denaturant, whereas the sulfate dianion (SO42-) is a strong stabilizer of folded protein states; Gdm2SO4 is effectively neutral in its effects on protein stability. While the "neutralizing" effects of protein-stabilizing solutes on the activity of denaturants can be broadly interpreted in terms of additive effects of the solutes, recent experimental and simulation studies support a role for hetero-ion interactions in the effect of sulfate on Gdm+ denaturation [Mason, P. E.; et al. J. Phys. Chem. B 2005, 109, 24185-24196]. Here we describe an experimental strategy for testing this mechanism that involves spectroscopic analysis of the separate effects of alkali metal sulfates (Na2SO4, Rb2SO4), GdmCl, and Gdm2SO4 on the folded populations of several peptides chosen to dissect specific noncovalent contributions to the conformational stability of proteins [alanine-based helical peptides stabilized by hydrogen bonds, tryptophan zipper (trpzip) peptides stabilized largely by cross-strand indole-indole interactions]. While the trpzip peptides are highly sensitive to GdmCl denaturation, they are unaffected by NaCl, Na2SO4, or Gdm2SO4, indicating that the reversal of the denaturant activity of Gdm+ by sulfate in this case is not due to competing stabilizing (sulfate) and destabilizing (Gdm+) interactions. Gdm2SO4 was found to retain considerable denaturant activity against alanine-based alpha-helical peptides. The differences in the effects of Gdm2SO4 on the two peptide types can be understood in terms of the different mechanisms of Gdm+ denaturation of trpzip peptides and helical peptides, respectively, and the specific nature of Gdm+ and SO42- ionic "clustering" that differentially affects the ability of Gdm+ to make the molecular interactions with the peptides that underlie its denaturant activity.     

Study on the Cation-π Interactions between Ammonium Ion and Aromatic π Systems

The nature and strength of the cation-π interactions between NH4^＋ and toluene, p-cresol, or Me-indole were studied in terms of the topological properties of molecular charge density and binding energy decomposition. The results display that the diversity in the distribution pattern of bond and cage critical points reflects the profound influence of the number and nature of substituent on the electron density of the aromatic rings. On the other hand, the energy decomposition shows that dispersion and repulsive exchange forces play an important role in the organic cation （NH4^＋）-π interaction, although the electrostatic and induction forces dominate the interaction. In addition, it is intriguing that there is an excellent correlation between the electrostatic energy and ellipticity at the bond critical point of the aromatic π systems, which would be helpful to further understand the electrostatic interaction in the cation-π complexes.     

Site specific interaction between ZnO nanoparticles and tryptophan: a first principles quantum mechanical study

First principles density functional theory calculations are performed on tryptophan-ZnO nanoparticles complex in order to study site specific interactions between tryptophan and ZnO. The calculated results find the salt bridge structure involving the -COOH group and ZnO cluster to be energetically more favorable than other interacting sites, such as indole and amine groups in tryptophan. The interaction between tryptophan and ZnO appears to be mediated by both ionic and hydrogen bonds. The calculated molecular orbital energy levels and charge distributions suggest non-radiative energy transfer from an excited state of tryptophan to states associated with ZnO, which may lead to a reduction in the emission intensity assigned to the π-π* transition of the indole functional group of tryptophan.     

Binding motifs of silver in prion octarepeat model peptides: a joint ion mobility, IR and UV spectroscopies, and theoretical approach

Transition metal-ion complexation is essential to the function and structural stability of many proteins. We studied silver complexation with the octarepeat motif ProHisGlyGlyGlyTrpGlyGln of the prion protein, which shows competitive sites for metal chelation including amide, indole and imidazole groups. This octapeptide is known as a favourable transition metal binding site in prion protein. We used ion mobility spectrometry (IMS), infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations (DFT) to identify the binding motifs of a silver cation on HisGlyGlyGlyTrp peptide as well as on peptide subsequences. Ultra-violet photodissociation (UVPD) and collision induced dissociation mass spectrometry together with the time-dependent density functional method was then exploited to study the influence of binding sites on optical properties and on the ground and excited states reactivity of the peptide. We show that the metal cation is bound to the π-system of the indole group and a nitrogen atom of the imidazole group and that charge transfers from the indole group to the silver cation occur in excited electronic states.     

DFT Study of Alkali Metal Atom Adsorption on Defect-Free MgO(001) Surface

The adsorption of isolated alkali metal atoms (Li, Na, K, Rb, and Cs) on defect-free sur-face of MgO(001) has been systemically investigated with density functional theory using a pseudopotential plane-wave approach. The adsorption energy calculated is about -0.72 eV for the lithium on top of the surface O site and about one third of this value for the other alkali metals. The relatively strong interaction of Li with the surface O can be explained by a more covalent bonding involved, evidenced by results of both the projected density of states and the charge density difference. The bonding mechanism is discussed in detail for all alkali metals.     

Alkali metals in ethylenediamine: a computational study of the optical absorption spectra and NMR parameters of [M(en)3(δ+)·M(δ-)] ion pairs

The optical absorption spectra of alkali metals in ethylenediamine have provided evidence for a third oxidation state, -1, of all of the alkali metals heavier than lithium. Experimentally determined NMR parameters have supported this interpretation, further indicating that whereas Na(-) is a genuine metal anion, the interaction of the alkali anion with the medium becomes progressively stronger for the larger metals. Herein, first-principles computations based upon density functional theory are carried out on various species which may be present in solutions composed of alkali metals and ethylenediamine. The energies of a number of hypothetical reactions computed with a continuum solvation model indicate that neither free metal anions, M(-), nor solvated electrons are the most stable species. Instead, [Li(en)(3)](2) and [M(en)(3)(δ+)·M(δ-)] (M = Na, K, Rb, Cs) are predicted to have enhanced stability. The M(en)(3) complexes can be viewed as superalkalis or expanded alkalis, ones in which the valence electron density is pulled out to a greater extent than in the alkali metals alone. The computed optical absorption spectra and NMR parameters of the [Li(en)(3)](2) superalkali dimer and the [M(en)(3)(δ+)·M(δ-)] superalkali-alkali mixed dimers are in good agreement with the aforementioned experimental results, providing further evidence that these may be the dominant species in solution. The latter can also be thought of as an ion pair formed from an alkali metal anion (M(-)) and solvated cation (M(en)(3)(+)).     

On the copper(II) ion coordination by prion protein HGGGW pentapeptide model

The interaction of the octapeptide domain of the prion protein with the transition-metal-ion Cu2+ was studied at the DFT level by using the HGGGW pentapeptide as a model to mimic the PHGGGWGQ octarepeat sequence. Ten complexes, in which the metal ion exhibits different coordinations, were considered. Our results indicate that the lowest-energy structure is characterized by a tetracoordinated metal center and that this tendency of the ion to assume the square planar geometry is strong enough to prevent the addition of a further water molecule in its coordination sphere. The role of tryptophan was found to cause a lowering of the system energy due to the stabilizing effect of the electrostatic interaction between the Trp aromatic indole and histidine imidazole rings.     

Theoretical study of alpha/beta-alanine and their protonated/alkali metal cationized complexes

Density functional theory has been employed to model the structure and the relative stabilities of alpha/beta-alanine conformers and their protonated and alkali metal cationized complexes. In general, we find that the behavior of the beta-alanine (beta-Ala) system is quite similar to that of alpha-alanine (alpha-Ala). However, the presence of the methylene group (-CH2-) at the beta position in beta-Ala leads to a few key differences. First, the intramolecular hydrogen bonding patterns are different between free alpha- and beta-Ala. Second, the stability of zwitterionic species (in either the free ligand or alkali metal cationized complexes) is often enhanced in beta-Ala. Third, the preferred mode of alkali metal cation (M+) binding may also differ in alpha- and beta-Ala. Natural energy decomposition analysis has been applied here to gain further insight into the effects of the ligand, cation size, and mode of binding on the nature of interaction in these M+-Ala complexes.     

Affinity capillary electrophoresis and density functional theory employed for the characterization of hexaarylbenzene-based receptor complexation with alkali metal ions

In this study, affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations were combined to investigate non-covalent binding interactions between the hexaarylbenzene-based receptor (R) and alkali metal ions, Rb(+) and Cs(+) , in methanol. The apparent binding (stability) constants (K(b) ) of the complexes of receptor R with alkali metal ions in the methanolic medium were determined by ACE from the dependence of effective electrophoretic mobility of the receptor R on the concentration of Rb(+) and Cs(+) ions in the BGE using a non-linear regression analysis. The receptor R formed relatively strong complexes both with rubidium (log K(b) =4.04±0.21) and cesium ions (log K(b) =3.72±0.22). The structural characteristics of the above alkali metal ion complexes with the receptor R were described by ab initio density functional theory calculations. These calculations have shown that the studied cations bind to the receptor R because they synergistically interact with the polar ethereal fence and with the central benzene ring via cation-π interaction.     

Why alkali metals preferably bind on structural defects of carbon nanotubes: a theoretical study by first principles

By using ab initio calculations we investigated the interaction of alkali metal atoms and alkali metal cations with perfect and defective carbon nanotubes. Our results show that the alkali metals prefer to interact with the pentagons and heptagons that appear on the defective site of the carbon nanotube rather than with the hexagons. The alkali metals remain always positively charged not depending on their charge state (neutral, cation) or the different carbon ring that they interact with. The molecular orbital energy level splitting from a defect creation on the carbon nanotube along with the localization of charge-electron density on the defect, results in binding the alkali metals more efficient. More interestingly, metallic sodium appears to bind very weak on the nanotube compared to the rest of alkali metals. The Na anomaly is attributed to the fact that unlike the K case, sodium's inner p shell falls energetically lower than carbon nanotube's p molecular orbitals. As a result, the Na p shell is practically excluded from any binding energy contribution. In the alkali metal cation case the electronegativity trend is followed.     

Selective endo and exo binding of alkali metals to corannulene

The ion size matters: The structures of corannulene monoanions crystallized with Cs(+) and Rb(+) ions in the presence of [18]crown-6 reveal the intrinsic binding preferences of alkali metals and allow evaluation of the bowl deformation caused by negative charge distribution and metal binding. The large cesium cation coordinates exclusively to the concave face of C(20) H(10) (-) , whereas the smaller rubidium cation exhibits convex binding.     

Recognition of alkali metal halide contact ion pairs by uranyl-salophen receptors bearing aromatic sidearms. The role of cation-pi interactions

Hard anions have long been known to bind strongly to the uranium of uranyl-salophen complexes. Upon functionalization of the salophen framework with one or two benzyloxy substituents, efficient ditopic receptors for alkali metal ions are obtained. The solid-state structures of complexes formed by the two-armed receptor 1 with CsF and with the chlorides of K+, Rb+, and Cs+ reported here reveal the existence of dimeric supramolecular assemblies in which two receptor units assemble into capsules fully enclosing (MX)2 ion quartets. In addition to the strong coordinative binding of the anion to the uranyl center and to electrostatic cation-anion interactions, stabilizing interactions arise from coordination of each cation to six oxygens, three from each receptor, and most importantly, to two aromatic sidearms belonging to different receptors. There are marked differences in organization at the supramolecular level in the CsCl complex of the one-armed receptor 3, in that four uranyl-salophen units instead of two are assembled in a capsule-like arrangement housing a (CsCl)2 ion quartet. However, both receptors achieve the common goal of having each metal cation in close contact with carbon atoms of two aromatic rings. 1H NMR data provide strong evidence that cation-pi(arene) interactions with the sidearms participate in binding also in solution.     

Investigation of homo- and heterodimer alkali metal cation complexes of resorc[4]arenes by electrospray ionization mass spectrometry

Resorc[4]arenes are compounds with interesting properties, mainly because of their ability to form host-guest complexes with the guest located inside the cavity. The size of the guest limits the complexation, as shown by a competition experiment with tetraalkylammonium ions of different size. By electroscopy ionization tandem mass spectrometric experiments on resorc[4]arene heterodimers bearing an alkali metal ion as guest, it was found that there must be two different binding mechanisms for alkali metal ions with high surface charge density (Li(+) and Na(+)) on the one hand compared with those with a lower surface charge density on the other hand (K(+), Rb(+), Cs(+)).     

Understanding the reactivity and basicity of zeolites: a periodic DFT study of the disproportionation of N(2)O(4) on alkali-cation-exchanged zeolite Y

The disproportionation of N(2)O(4) into NO(3)(-) and NO(+) on Y zeolites has been studied through periodic DFT calculations to unravel 1) the role of metal cations and the framework oxygen atoms and 2) the relationship between the NO(+) stretching frequency and the basicity of zeolites. We have considered three situations: adsorption on site II cations with and without a cation at site III and adsorption on a site III cation. We observed that cations at sites II and III cooperate to stabilize N(2)O(4) and that the presence of a cation at site III is necessary to allow the disproportionation reaction. The strength of the stabilization is due to the number of stabilizing interactions increasing with the size of the cation and to the Lewis acidity of the alkali cations, which increases as the size of the cations decreases. In the product, NO(3)(-) interacts mainly with the cations and NO(+) with the basic oxygen atoms of the tetrahedral aluminium through its nitrogen atom. As the cation size increases, the NO(3)(-)...cation interaction increases. As a result, the negative charge of the framework is less well screened by the larger cations and the interaction between NO(+) and the basic oxygen atoms becomes stronger. NO(+) appears to be a good probe of zeolite basicity, in agreement with experimental observations.     

Cation [M = H+, Li+, Na+, K+, Ca2+, Mg2+, NH4+, and NMe4+] interactions with the aromatic motifs of naturally occurring amino acids: a theoretical study

Ab initio (HF, MP2, and CCSD(T)) and DFT (B3LYP) calculations were done in modeling the cation (H(+), Li(+), Na(+), K(+), Ca(2+), Mg(2+), NH(4)(+), and NMe(4)(+)) interaction with aromatic side chain motifs of four amino acids (viz., phenylalanine, tyrosine, tryptophan and histidine). As the metal ion approaches the pi-framework of the model systems, they form strongly bound cation-pi complexes, where the metal ion is symmetrically disposed with respect to all ring atoms. In contrast, proton prefers to bind covalently to one of the ring carbons. The NH(4)(+) and NMe(4)(+) ions have shown N-H...pi interaction and C-H...pi interaction with the aromatic motifs. The interaction energies of N-H...pi and C-H...pi complexes are higher than hydrogen bonding interactions; thus, the orientation of aromatic side chains in protein is effected in the presence of ammonium ions. However, the regioselectivity of metal ion complexation is controlled by the affinity of the site of attack. In the imidazole unit of histidine the ring nitrogen has much higher metal ion (as well as proton) affinity as compared to the pi-face, facilitating the in-plane complexation of the metal ions. The interaction energies increase in the order of 1-M < 2-M < 3-M < 4-M < 5-M for all the metal ion considered. Similarly, the complexation energies with the model systems decrease in the following order: Mg(2+) > Ca(2+) > Li(+) > Na(+) > K(+) congruent with NH(4)(+) > NMe(4)(+). The variation of the bond lengths and the extent of charge transfer upon complexation correlate well with the computed interaction energies.