Interaction of Co+ and Co2+ with glycine. A theoretical study

Cobalt cations are open shell systems with several possible electronic states arising from the different occupations of the 3d and 4s orbitals. The influence of these occupations on the relative stability of the coordination modes of the metal cation to glycine has been studied by means of theoretical methods. The structure and vibrational frequencies have been determined using the B3LYP method. Single-point calculations have also been carried out at the CCSD(T) level. The most stable structure of Co(+)-glycine is bidentate, with the Co(+) cation interacting with the amino group and the carbonyl oxygen of neutral glycine, and the ground electronic state being (3)A. For Co(2+)-glycine, the lowest energy structure corresponds to the interaction of the metal cation with the carboxylate group of the zwitterionic glycine, the ground electronic state being (4)A'.     

Coordination properties of the oxime analogue of glycine to Cu(II)

The coordination of Cu2+ by glyoxilic acid oxime (gao)--the oxime analogue of glycine amino acid--and its deprotonated (gao- and gao2-) species has been studied with different density functional methods. Single-point calculations have also been carried out at the single- and double- (triple) excitation coupled-cluster (CCSD(T)) level of theory. The isomers studied involve coordination of Cu2+ to electron-rich sites (O,N) of neutral, anionic, and dianionic gao species in different conformations. In contrast to Cu2+-glycine, for which the ground-state structure is bidentate with the CO2(-) terminus of zwitterionic glycine, for Cu2+-gao the most stable isomer shows monodentate binding of Cu2+ with the carbonylic oxygen of the neutral form. The most stable complexes of Cu2+ interacting with deprotonated gao species (gao- and gao2-) also take place through the carboxylic oxygens but in a bidentate manner. The results with different functionals show that, for these open shell (Cu2+-L) systems, the relative stability of complexes with different coordination environments (and so, different spin distribution) can be quite sensitive to the amount of "Hartree-Fock" exchange included in the functional. Among all the functionals tested in this work, the BHandHLYP is the one that better compares to CCSD(T) results.     

Gas phase intramolecular proton transfer in cationized glycine and chlorine substituted derivatives (M-Gly, M = Na+, Mg2+, Cu+, Ni+, and Cu2+): existence of Zwitterionic structures?

The intramolecular proton transfer in cationized glycine and chlorine substituted derivatives with M = Na+, Mg2+, Ni+, Cu+, and Cu2+ has been studied with the three parameter B3LYP density functional method. The coordination of metal cations to the oxygens of the carboxylic group of glycine stabilizes the zwitterionic structure. For all monocations the intramolecular proton transfer occurs readily with small energy barriers (1-2 kcalmol(-1)). For the dication Mg2+ and Cu2+ systems, the zwitterionic structure becomes very stable. However, whereas for Mg2+, the proton transfer process takes place spontaneously, for Cu2+ the reaction occurs with an important energy barrier. The substitution of the hydrogens of the amino group by chlorine atoms decreases the basicity of nitrogen, which destabilizes the zwitterionic structure. For monosubstituted glycine complexed with Na+, the zwitterionic structure still exists as a minimum, but for disubstituted glycine no minimum appears for this structure. In contrast, for Mg2+ complexed to mono- and disubstituted glycine, the zwitterionic structure remains the only minimum, since the enhanced electrostatic interaction with the dication overcomes the destabilizing effect of the chlorine atoms.     

DFT Mechanistic Study on Diene Metathesis Catalyzed by Ru‐Based Grubbs–Hoveyda‐Type Carbenes: The Key Role of π‐Electron Density Delocalization in the Hoveyda Ligand

The catalytic activity and catalyst recovery of two heterogenized ruthenium‐based precatalysts ( H and NO₂(4) ) in diene ring‐closing metathesis have been studied by means of density functional calculations at the B3LYP level of theory. For comparison and rationalization of the key factors that lead to higher activities and higher catalyst recoveries, four other Grubbs–Hoveyda complexes have also been investigated. The full catalytic cycle (catalyst formation, propagation, and precatalyst regeneration) has been considered. DFT calculations suggest that either for the homogeneous and heterogenized systems the activity of the catalysts mainly depends on the ability of the precursor to generate the propagating carbene. This ability does not correlate with the traditionally identified key factor, the Ru???O interaction strength. In contrast, precatalysts with lower alkoxy‐dissociation energy barriers and lower stabilities compared with the propagating carbene also present larger C1? C2 bond length (i.e., lower π character of the C? C bond that exists between the metal–carbene (Ru?C) and the phenyl ring of the Hoveyda ligand). Catalyst recovery, regardless of whether a release–return mechanism occurs or not, is also mainly determined by the π delocalization. Therefore, future Grubbs–Hoveyda‐type catalyst development should be based on fine‐tuning the π‐electron density of the phenyl moiety, with the subsequent effect on the metalloaromaticity of the ruthenafurane ring, rather than considering the modification of the Ru???O interaction.     

PtII Coordination to N1 of 9‐Methylguanine: Why it Facilitates Binding of Additional Metal Ions to the Purine Ring

The preparation and X‐ray crystal structure analysis of {trans‐[Pt(MeNH₂)₂(9‐MeG‐N1)₂]} ? {3 K₂[Pt(CN)₄]} ? 6 H₂O ( 3 a ) (with 9‐MeG being the anion of 9‐methylguanine, 9‐MeGH) are reported. The title compound was obtained by treating [Pt(dien)(9‐MeGH‐N7)]²⁺ ( 1 ; dien=diethylenetriamine) with trans‐[Pt(MeNH₂)₂(H₂O)₂]²⁺ at pH 9.6, 60 °C, and subsequent removal of the [(dien)Pt^II] entities by treatment with an excess amount of KCN, which converts the latter to [Pt(CN)₄]^2?. Cocrystallization of K₂[Pt(CN)₄] with trans‐[Pt(MeNH₂)₂(9‐MeG‐N1)₂] is a consequence of the increase in basicity of the guanine ligand following its deprotonation and Pt coordination at N1. This increase in basicity is reflected in the pK_a values of trans‐[Pt(MeNH₂)₂(9‐MeGH‐N1)₂]²⁺ (4.4±0.1 and 3.3±0.4). The crystal structure of 3 a reveals rare (N7,O6 chelate) and unconventional (N2,C2,N3) binding patterns of K⁺ to the guaninato ligands. DFT calculations confirm that K⁺ binding to the sugar edge of guanine for a N1‐platinated guanine anion is a realistic option, thus ruling against a simple packing effect in the solid‐state structure of 3 a . The linkage isomer of 3 a , trans‐[Pt(MeNH₂)₂(9‐MeG‐N7)₂] ( 6 a ) has likewise been isolated, and its acid–base properties determined. Compound 6 a is more basic than 3 a by more than 4 log units. Binding of metal entities to the N7 positions of 9‐MeG in 3 a has been studied in detail for [(NH₃)₃Pt^II], trans‐[(NH₃)₂Pt^II], and [(en)Pd^II] (en=ethylenediamine) by using ¹H NMR spectroscopy. Without exception, binding of the second metal takes place at N7, but formation of a molecular guanine square with trans‐[(Me₂NH₂)Pt^II] cross‐linking N1 positions and trans‐[(NH₃)₂Pt^II] cross‐linking N7 positions could not be confirmed unambiguously, despite the fact that calculations are fully consistent with its existence.     

Structures and stabilities of Fe2+/3+ complexes relevant to Alzheimer's disease: an ab initio study

Iron is one of the most abundant metals found in senile plaques of post mortem patients with Alzheimer's disease. However, the interaction mode between iron ions and β-amyloid peptide as well as their precise affinity is unknown. In this study we apply ab initio computational methodology to calculate binding energies of Fe(2+/3+) with the His13-His14 sequence of Aβ, as well as other important ligands such as His6 and Tyr10. Calculations were carried out at the "MP2/6-311+G(2df,2p)"//B3LYP/6-31+G(d) level of theory and solvent effects included by the IEFPCM procedure. Several reaction paths for the binding of imidazole, phenol, and the His13-His14 fragment (modeled by N-(2-(1H-imidazol-4-yl)ethyl)-3-(1H-imidazol-4-yl)propanamide) were sequentially explored. The results show that the most stable complexes containing His13-His14 and phenolate of Tyr10 are the pentacoordinated [Fe(2+)(O-HisHis)(PhO(-))(H(2)O)](+) and [Fe(3+)(N-HisHis)(PhO(-))(H(2)O)](+) compounds and that simultaneous coordination of tyrosine and His13-His14 to Fe(2+/3+) is thermodynamically favorable in water at physiological pH. Computed Raman spectra confirm the conclusion obtained by Miura et al. ( Biochemistry 2000 , 39 , 7024 ) that tyrosine is coordinated to Fe(3+) but do not exclude coordination of imidazoles. Finally, calculations of standard reduction potentials indicate that phenol coordination reduces the redox activity of the iron/Aβ complexes.     

On the mechanism of the N-glycosydic bond hydrolysis of 2��-deoxyguanosine: insights from first principles calculations

The effect of the activation of the nucleobase (leaving group) or the activation of the water molecule (nucleophile) by a general acid or a general base on the hydrolysis of the N-glycosydic bond of 2??-deoxyguanosine has been analyzed by means of density functional methods. First, we have considered two limiting cases: (1) the activation of the guanine by protonation at N7 and (2) the nucleophile attack by a hydroxyl ion, to separately evaluate the two kinds of activation. Next, we have studied the simultaneous activation of the leaving group and the nucleophile by introducing models of amino acid residues such as a formic acid (HCOOH) and imidazolium (C₃N₂H₅ ⁺), methylammonium (CH₃NH₃ ⁺) and formate (HCOO^?) ions in the system. It is shown that protonation of the nucleobase greatly catalyzes the hydrolysis of the N-glycosydic bond, the reaction occurring through a stepwise (D_N*A_N) mechanism with a discrete oxocarbenium ion intermediate. However, when a H₂O nucleophile molecule is activated by a formate anion, the reaction mechanism is a concerted A_ND_N but with different degrees of dissociative character of the transition structure depending on the acid that is activating the nucleobase.     

Mechanistic insights into dopaminergic and serotonergic neurotransmission – concerted interactions with helices 5 and 6 drive the functional outcome

Brain functions rely on neurotransmitters that mediate communication between billions of neurons. Disruption of this communication can result in a plethora of psychiatric and neurological disorders. In this work, we combine molecular dynamics simulations, live-cell biosensor and electrophysiological assays to investigate the action of the neurotransmitter dopamine at the dopaminergic D₂ receptor (D₂R). The study of dopamine and closely related chemical probes reveals how neurotransmitter binding translates into the activation of distinct subsets of D₂R effectors (i.e.: G_i2, G_oB, G_z and β-arrestin 2). Ligand interactions with key residues in TM5 (S5.42) and TM6 (H6.55) in the D₂R binding pocket yield a dopamine-like coupling signature, whereas exclusive TM5 interaction is typically linked to preferential G protein coupling (in particular G_oB) over β-arrestin. Further experiments for serotonin receptors indicate that the reported molecular mechanism is shared by other monoaminergic neurotransmitter receptors. Ultimately, our study highlights how sequence variation in position 6.55 is used by nature to fine-tune β-arrestin recruitment and in turn receptor signaling and internalization of neurotransmitter receptors.

Neurotransmitter contacts within the receptor binding site differentially contribute to the overall functional response: transmembrane helix (TM) 5 contacts promote G protein coupling whereas concerted TM5–TM6 contacts enhance β-arrestin recruitment.     

An enumeration procedure for the assembly line balancing problem based on branching by non-decreasing idle time

In this article, we present a new exact algorithm for solving the simple assembly line balancing problem given a determined cycle time (SALBP-1). The algorithm is a station-oriented bidirectional branch-and-bound procedure based on a new enumeration strategy that explores the feasible solutions tree in a non-decreasing idle time order. The procedure uses several well-known lower bounds, dominance rules and a new logical test based on the assimilation of the feasibility problem for a given cycle time and number of stations (SALBP-F) to a maximum-flow problem.