Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine

Interaction of Cysteine with Li+ and LiF in the Presence of (H2O) n (n = 0-6) Clusters

The interaction between cysteine with Li⁺ and LiF in the microcosmic water environment was investigated to elucidate how ions interact with amino acids and the cation-anion correlation effect involved. The structures of Cys·Li⁺(H₂O) _n and Cys·LiF(H₂O) _n (n = 0-6) were characterized using ab initio calculations. Our studies show that the water preferentially interacts with Li⁺/LiF. In Cys·Li⁺(H₂O)_0-6, Li⁺ interacts with amino nitrogen, carbonyl oxygen, and hydrophobic sulfur of Cys to form a tridentate mode, whereas in Cys·LiF(H₂O) _n , Li⁺ and F^- work in cooperation and interact with carbonyl oxygen and hydroxyl hydrogen of Cys to form a bidentate type. The neutral and zwitterionic forms are essentially isoenergetic when the water number reaches three in the presence of Li⁺, whereas this occurs at four water molecules in the presence of LiF. Further research revealed that the interaction between Li⁺/LiF and Cys was mainly electrostatic, followed by dispersion, and the weakest interaction occurs at the transition from the neutral form to zwitterionic form. Natural population analysis charge analyses show that for Cys·Li⁺(H₂O) _n , the positive charge is mostly concentrated on Li⁺ except for the system containing three water molecules. For Cys·LiF(H₂O) _n , the positive charge is centered on the LiF unit in the range n = 0-6, and at n = 5, electron transfer from Cys to water occurs. Our study shows that the contribution of anions in zwitterionic state stabilization should be addressed more generally along with cations.

Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations

In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) with backbone (amide C═O) and C-terminal carboxylate (COO^-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PP_II) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH₃⁺ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn²⁺) can specifically coordinate to the COO^- group in bidentate and pseudo-bridging forms simultaneously. For Zn²⁺, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.

Electronic transport in a graphene single layer: application in amino acid sensing

We modeled a type of field-effect transistor device based on graphene for the recognition of amino acids with a potential application in the building of a protein sequencer. The theoretical model used was a combination of density functional theory (DFT) with the non-equilibrium Green's function (NEGF) in order to describe the coherent transport in molecular devices. First, we studied the physisorption of each amino acid on a graphene sheet and we reported the adsorption energy, the adsorption distances, the equilibrium configuration and the charge transfer of ten amino acids that can be considered as representative of all of the amino acids: histidine (His), alanine (Ala), aspartic acid (Asp), tyrosine (Tyr), arginine (Arg), glutamic acid (Glu), glycine (Gly), phenylalanine (Phe), proline (Pro) and lysine (Lys). As a result, significant differences were found in the density of states (DOS) after adsorption and there was a change in the semi-metallic character of the graphene due to the lysine and arginine interactions. Furthermore, we noticed changes in the electrical characteristics of the devices, as the amino acids adsorbed onto the surface of the graphene. The curves of current vs. bias voltage (I-Vb) display a distinct response for each amino acid, i.e. the I-Vb curves produce a characteristic footprint for each amino acid. We identified a possible rectification mechanism related to the voltage profile asymmetry, where the amino acids can control the transport characteristics in the device, i.e. Lys and Phe amino acids physisorbed on graphene act as a molecular diode, where electrons can easily flow in one direction and decrease in the other. This may be promising for the prospect of biosensors: graphene could be used as an amino acid detector.

Competitive sequestration of Ni(II) and Eu(III) on montmorillonite: role of molar Ni:Eu ratios and coexisting oxalate

The competitive binding trends of Ni(II) and Eu(III) on montmorillonite in the absence/presence of Na-oxalate are explored by using batch sorption/desorption technique, speciation modeling, and X-ray diffraction (XRD) analysis. With a series of molar Ni:Eu ratios (i.e., 1:1, 5:1, 10:1, 1:5, and 1:10), the coexisting Ni(II) did not affect the sequestration behaviors and immobilization mechanisms of Eu(III). In contrast, the presence of Eu(III) obviously suppressed the sorption percentages of Ni(II) in the acidic pH range. Even though no obvious influence of Eu(III) on the macroscopic binding trends of Ni(II) was observed under alkaline conditions, the fraction of Ni(II) adsorbed by the inner-sphere complexation mechanism decreased and that of Ni(II) precipitation increased with rising molar Ni:Eu ratio. The coexisting Na-oxalate did not influence Eu(III) sorption, while inhibited the sorption of Ni(II). The XRD analysis indicated the potential formation of two Eu-oxalate precipitate phases (i.e., Eu₂(C₂O₄)₃·xH₂O(s)-1 and Eu₂(C₂O₄)₃·xH₂O(s)-2) at different pH values (4.0 and 6.5) and Na-oxalate concentrations (ranging from 0.5 to 5.0 mM). Interestingly, the Eu₂(C₂O₄)₃·xH₂O(s)-2 phase would be transformed into the Eu₂(C₂O₄)₃·xH₂O(s)-1 solid with the increase of Na-oxalate concentration. The research findings could provide essential data for evaluating the fate of coexistent Eu(III) and Ni(II) in the complicated aquatic environment.

Mobility of hydrated alkali metal ions in metallosupramolecular ionic crystals

The ion-conducting behaviour of alkali metal ions in ionic solids (M₆[1]·nH₂O) resembles that in aqueous solutions; the solid-state conductivities increase in the order of M = Li⁺ < Na⁺ < K⁺.

The design and creation of ionic crystals that show high mobility of ionic species in the solid state has long been a research topic of considerable attention not only due to the practical applications of these materials but also due to the correlation of such ionic species with ion-transport biological systems. In this work, we report the mobility of alkali metal ions (M = Li⁺, Na⁺, K⁺) in the ionic crystals M₆[Rh₄Zn₄O (l-cysteinate)₁₂]·nH₂O (M₆[1]·nH₂O). In M₆[1]·nH₂O, alkali metal ions are distributed in a disordered manner, together with a number of water molecules, within a rigid hydrogen-bonded framework of anionic clusters of [1]^6–. The alternating current conductivities of M₆[1]·nH₂O in the solid state increase in the order of Li₆[1]·nH₂O < Na₆[1]·nH₂O < K₆[1]·nH₂O, which is opposite to the order of the naked ionic radii. The conductivities reach the superionic level of σ = 1.3 × 10^–2 S cm^–1 at 300 K for a single crystal of K₆[1]·nH₂O. These results reflect the high mobility of hydrated alkali metal ions in the crystal lattice of M₆[1]·nH₂O, which is supported by solid-state NMR spectroscopy, together with ion diffusion experiments in the solid state. The high mobility leads to quick exchange of K⁺ ions in K₆[1]·nH₂O with Li⁺ and Na⁺ ions with retention of single crystallinity.

Water Microsolvation Can Switch the Binding Mode of Ni(II) with Small Peptides

Ni(II) ions can be caged by surrounding peptide ligands in two basic binding patterns: the "iminol" (IM) binding pattern, where chelation occurs by deprotonated amide nitrogens, or the charge-solvated (CS) binding pattern, where chelation occurs by amide carbonyl oxygens. Gas-phase observation may clarify the factors affecting this choice in solution and in peptide and protein matrices. Infrared spectroscopic determination of gas-phase structures shows here how microsolvation by just one water molecule switches the balance of this choice from IM to CS for the Ni²⁺Gly₃ complex, in contrast with the always-CS structure of the Ni²⁺Gly₄ complex. Quantum-chemical calculations indicate that CS complexation is even more favored in the aqueous limit. Considering gas-phase conditions as comparable to low-pH solutions can reconcile this prediction with the common observation of IM-type binding in solutions at higher pH. This is likely the first gas-phase observation of solvation-induced IM-to-CS transition in oligopeptide complexes with doubly charged transition-metal ions.

Theoretical and experimental studies on the structure–property relationship of chiral N,N′-dioxide–metal catalysts probed by the carbonyl–ene reaction of isatin

Variation of the linkage or chiral backbone of an N,N′-dioxide ligand adjusts the blocking effect of ortho-iPr on the reaction site, affecting the enantiodifferentiation of two competing pathways.

Understanding the cation specific effects on the aqueous solubility of amino acids: from mono to polyvalent cations

Based on solubility and molecular dynamics studies, a consistent and refined molecular description of the effect of the cation on the solubility of amino acids based on specific interactions of the cations with the negatively charged moieties of the biomolecules is proposed.

Physicochemical investigations of the metal complexes ofl-valine with doubly charged ions of nickel, copper and zinc: a combined experimental and computational approach

Molecular electrostatic potentials inl-Val and its metal complexes.

Salting-in with a salting-out agent: explaining the cation specific effects on the aqueous solubility of amino acids

Although the understanding of ion specific effects on the aqueous solubilities of biomolecules is crucial for the development of many areas of biochemistry and life sciences, a consensual and well-supported molecular picture of the phenomena has not yet been established. Mostly, the influence of cations and the nature of the molecular interactions responsible for the reversal of the Hofmeister trend in aqueous solutions of amino acids and proteins are still defectively understood. Aiming at contributing to the understanding of the molecular-level mechanisms governing the cation specific effects on the aqueous solubilities of biocompounds, experimental solubility measurements and classical molecular dynamics simulations were performed for aqueous solutions of three amino acids (alanine, valine, and isoleucine), in the presence of a series of inorganic salts. The evidence gathered suggests that the mechanism by which salting-in inducing cations operate in aqueous solutions of amino acids is different from that of anions, and allows for a novel and consistent molecular description of the effect of the cation on the solubility based on specific interactions of the cations with the negatively charged moieties of the biomolecules.

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.

Experimental and theoretical investigation of the proton-bound dimer of lysine

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.

Bridging interactions and selective nanoparticle aggregation mediated by monovalent cations

Selective aggregation and precipitation of like-charged nanoparticles (NPs) covered with carboxylate ligands can be induced by different monovalent cations. The ordering of critical concentrations required for NP precipitation is Cs(+) ≫ K(+) > Li(+) > Na(+) > Rb(+) and does not correlate with the size of hydrated cations M(+), nor can it be predicted by the Hofmeister series. On the other hand, different anions have no effect on the precipitation trends. These observations are rationalized by a theoretical model combining the elements of the DLVO theory with molecular-level calculations. The key component of the model is the cation-specific binding of various metal cations to the carboxylate ligands.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of L-histidine and zwitterionic L-histidine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-histidine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water on structures of His·M(H2O)m, m=0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K+ systems) suggest metallic complexes of the neutral L-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of L-histidine in the presence of the metal cations Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to L-histidine is exhibited by the Cu2+ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from -130 to -1,300 kJ/mol), and upon hydration are appreciably lowered.