A DFT study of determination of the reactive sites of the acetylcholine and its agonists: In the gas phase and dielectric medium

The reactive behavior of acetylcholine and its agonist molecules have been investigated using B3LYP hybrid density functional method at the 6‐311++G** basis set level, in the gas phase and aqueous phase. The calculations have been performed to obtain optimized geometries, relative reactivities, net atomic charges, HOMO, and LUMO energies. The solvent effect has been analyzed by using the continuum model (IPCM) and, the obtained results have shown that the all molecules have been stabilized more by solvent dielectric constant. For Ach and its analogues, it has been very well known that esteratic site and quaternary ammonium group which have reflected the difference in biological activity have been the two of the most important active site for interactions between molecule and its receptor. The structures of these analogues have provided an essential foundation for subsequent structure‐activity analysis of ligand binding at acetylcholine receptors, neuronal uptake inhibitors and transporters. Molecular modeling predictions will be important initial steps toward the development of novel pharmaceuticals in the fight acetylcholine‐related neurological disorders. This work is therefore expected to facilitate the design and development of new biologically active Ach analogues to treat Ach‐related neurological disorders and, specially is used to qualitative understanding of the reactivity and related properties and, so on can be used to a preselection of new ligands which at the moment is taken essentially from empirical knowledge. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Acetylcholine in water: Ab-initio potential and Monte Carlo simulation

Ab initio SCF-LCAO-MO computations using a minimal basis set have been carried out on the acetylcholine ion in different conformations. The rotational barrier around the C9-C8-O1-C2 dihedral angle (τ₁) has been also calculated: the curve presents a broad minimum. SCF calculations have been carried out on the system Ach-water at 468 different separations and/or orientations; the interaction energies were then fitted to a pair potential function used in Monte Carlo (MC) simulations of Ach water solution. The rdfs indicate a global first hydration shell with about 38 waters. Details about the hydration shell are presented. The overall MC results indicate that for the Ach ion in water solution at room temperature relative free rotation is possible around τ₁, and that Ach is well represented as a large positively charged hydrated globe with a small mobile tail free of strong interactions with the surrounding water molecules.     

从头计算研究乙酰胆碱构象和分子静电势

在Hartree－Fock和二级Moller－Plesset微扰理论MP2水平，用6－31G对乙酰胆碱进行了从头计算研究，发现了旁式和反式两种稳定构象．经零点振动能校正后，在Hartree－Fock级别旁式较反式稳定0．24kJ·mol~(-1)；而在MP2级别，反式较旁式稳定2．07kJ·mol~(-1).谐振动频率在HF／6－31G水平计算.还给出了两种构象的MP2分子静电势图.     

Detection of Anticholinesterase Agents in Drinking Water by use of Tandem Packed Bed Reactors with Human Red Blood Cell Acetylcholinesterase and Choline Oxidase in a Switching Flow System

Abstract

A flow system for the sensitive monitoring of acetylcholinesterase (ACHE) inhibitors is reported. The mobile phase contained acetylcholine (ACH) and choline (CH) as substrates. Red blood cell membrane ACHE was adsorbed on glass fibres. A tandem packed bed bioreactor system with reactors containing ACHE and choline oxidase (CHO), respectively, converted acetylcholine and choline selectively to hydrogen peroxide which was continuously detected by an electrochemical detector. The presence of ACHE inhibitors caused decreases in ACHE activity and hydrogen peroxide production, the decrease of the response being proportional with the concentration, reaction time and inhibiting strength of the solutes. Switching of the reactors enabled the detection of substances which inhibit CHO (e.g. the oxime HLö 7, which is used for the regeneration of ACHE), stopped-flow injection of inhibitors and their long time reaction with ACHE. Flow kinetic studies of both CHO and ACHE were performed to determine optimum conditions for the measurement. The limits of detection for paraoxon and physostigmine in drinking water were found to be 1 nM, and for malathion and parathion-methyl, 2 μM and 8 μ, respectively.     

Transfer Thermodynamics of Protein in Denaturing and Stabilizing Media

Free energies of transfer (ΔG_t) of RibonucleaseA (RNaseA) from water to aqueous solutions of urea (4 M, 6 M and 8 M), a protein denaturing solvent as well as ΔG_t of RibonucleaseA, β‐Lactoglobulin, α‐Chymotripsin and ChymotrypsinogenA from water to aqueous glycerol (10%, 20%, 30% and 40%), a protein stabilizing solvent has been dissected into cavity term [ΔG_t(cav)] and interaction term [ΔG_t(int)]. The interaction free energy includes all types of interactions like hard‐soft, hydrogen bonding, electrostatic, etc. The cavity forming free energies have been calculated using the standard version of scaled particle theory (SPT) with well‐reported SPT parameters. It has been found that transfer free energies of cavity terms ΔG_t(cav) for native protein from water to urea‐water and water to aqueous glycerol follow almost opposite trends. This primarily indicates there may be some correlation between cavity creation energies and protein denaturing and stabilizing ability of a solvent. The results are in agreement with those obtained from preferential binding coefficient studies in these media.     

Sarin and Soman: Structure and Properties

The most stable conformers of sarin (isopropyl methylphosphonoflouridate) and soman (pinacolyl methylphosphonofluoridate) are determined in high-level-correlated calculations with extended Gaussian basis sets. The two molecules are found to have three low-energy conformers each. For both molecules two of the lowest energy conformers have almost the same energies with a very small barrier separating the corresponding minima. The third conformer of sarin is found to lie about 1 kcal/mol above the lowest energy form. For soman the corresponding value is equal to about 4 kcal/mol. The significance of these data for the mechanism of the toxic action of sarin and soman is discussed. According to our investigations sarin and soman are highly similar electronically and differences in their features arise mostly from the size and spatial arrangement of the alkoxy substituent at phosphorus. Also the influence of solvents on the conformations and solvation energies of sarin and soman is investigated.     

Towards a force field based on density fitting

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.     

Transport of acetylcholine in a membrane

A laminate model of the cleft-plus-postsynaptic membrane structure of the neuromuscular junction was studied. In order to prepare a model of the postsynaptic membrane, the properties of acetylcholine (Ach) receptor-rich vesicles purified from Torpedo fish were measured. Immobilization of vesicles was demonstrated by various methods, in particular, by investigating collagen and carrageenan matrices as models of the fluidfilled fibrous matrix of the cleft. It was found that a laminated system employing a liquid membrane-containing vesicle suspension, together with a swollen collagen membrane, is an appropriate model for examining important transport/reception aspects of the cleft-plus-postsynaptic membrane structure. Combined transport with immobilization of Ach in the liquid membrane system was elucidated and effective diffusivities in the vesicle suspension layer were calculated. Effective diffusivities of the composite system simulating the cleft and the postsynaptic membrane were evaluated as well. These data illustrate the importance of penetrant immobilization in retarding the diffusion process during neurotransmission.     

Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine

Acylation of acetylcholine (ACh) catalyzed by acetylcholinesterase (AChE) has been studied using high-level theoretical calculations on a model system that mimics the reaction center of the enzyme, and compared with uncatalyzed acylation reaction. The geometries of all the intermediates and transition states, activation energies, and solvent effects have been calculated. The calculations predict simultaneous formation of two short-strong hydrogen bonds (SSHB) in the rate-determining transition state structures [the first SSHB involves the hydrogen atom of Ser-200 (H(s)) and another involves the hydrogen atom of His-440 (H(h))]. In the intermediate states, the H-bond corresponding to H(h) involves SSHB, whereas the one corresponding to H(s) does not.     

High-level ab initio computations of structures and interaction energies of naphthalene dimers: origin of attraction and its directionality

The intermolecular interaction energies of naphthalene dimers have been calculated by using an aromatic intermolecular interaction model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order M?ller-Plesset perturbation interaction energy near saturation and the CCSD(T) correction term obtained using a medium-size basis set. The estimated interaction energies of the set of geometries explored in this work show that two structures emerge as being the lowest energy, and may effectively be considered as isoenergetic on the basis of the errors inherent in out extrapolation procedure. These structures are the slipped-parallel (Ci) structure (-5.73 kcal/mol) and the cross (D2d) structure (-5.28 kcal/mol). The T-shaped (C2v) and sandwich (D2h) dimers are substantially less stable (-4.34 and -3.78 kcal/mol, respectively). The dispersion interaction is found to be the major source of attraction in the naphthalene dimer. The electrostatic interaction is substantially smaller than the dispersion interaction. The large dispersion interaction is the cause of the large binding energies of the cross and slipped-parallel dimers.     

A theoretical investigation of the interactions between water molecules and ionic liquids

Quantum chemical calculations have been used to investigate the interaction between water molecules and ionic liquids based on the imidazolium cation with the anions [Cl(-)], [Br(-)], [BF(4)(-)], and [PF(6)(-)]. The predicted geometries and interaction energies implied that the water molecules interact with the Cl(-), Br(-), and BF(4)(-0 anions to form X(-)...W (X = Cl or Br, W = H(2)O), 2X-...2W, BF(4)(-)...W, and W...BF(4)(-)...W complexes. The hydrophobic PF(6)(-) anion could not form a stable complex with the water molecules at the density functional theory (DFT) level. Further studies indicate that the cation could also form a strong interaction with the water molecules. The 1-ethyl-3-methylimidazolium cation (Emim(+)) has been used as a model cation to investigate the interaction between a water molecule and a cation. In addition, the interaction between the ion pairs and the water was studied by using 1-ethyl-3-methylimidazolium chloride (Emim x Cl) as a model ionic liquid. The strengths of the interactions in these categories follow the trend anion-W > cation-W > ion pair-W.     

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.     

Dipole–reaction field interaction model for the solvent reorganization energy and its application to the benzoquinone–benzoquinone anion radical system

 Based on the spherical cavity approximation and the Onsager model, a dipole–reaction field interaction model has been proposed to elucidate the solvent reorganization energy of electron transfer (ET). This treatment only needs the cavity radius and the solute dipole moment in the evaluation of the solvent reorganization energy, and fits spherelike systems well. As an application, the ET reaction between p-benzoquinone and its anion radical has been investigated. The inner reorganization energy has been calculated at the level of MP2/6–31+G, and the solvent reorganization energies of different conformations have been evaluated by using the self-consistent reaction field approach at the HF/6–31+G level. Discussions have been made on the cavity radii and the values are found to be reasonable when compared with the experimental ones of some analogous intramolecular ET reactions. The ET matrix element has been determined on the basis of the two-state model. The fact that the value of the ET matrix element is about 10 times larger than RT indicates that this ET reaction can be treated as an adiabatic one. By invoking the classical Marcus ET model, a value of 4.9 × 10⁷M⁻¹s⁻¹ was obtained for the second-order rate constant, and it agrees quite well with the experimental one. Received: 19 October 2001 / Accepted: 17 January 2002 / Published online: 3 May 2002     

Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water

Cation-pi interactions have been proposed to be important contributors to protein structure and function. In particular, these interactions have been suggested to provide significant stability at the solvent-exposed surface of a protein. We have investigated the magnitude of cation-pi interactions between phenylalanine (Phe) and lysine (Lys), ornithine (Orn), and diaminobutanoic acid (Dab) in the context of an alpha-helix and have found that only the Phe...Orn interaction provides significant stability to the helix, stabilizing it by -0.4 kcal/mol. This interaction energy is in the same range as a salt bridge in an alpha-helix, and equivalent to the recently reported Trp...Arg interaction in an alpha-helix, despite the fact that Trp...guanidinium interactions have been proposed to be stronger than Phe...ammonium interactions. These results indicate that even the simplest cation-pi interaction can provide significant stability to protein structure and demonstrate the subtle factors that can influence the observed interaction energies in designed systems.     

A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor

GABA(C) (rho) receptors are members of the Cys-loop superfamily of neurotransmitter receptors, which includes nicotinic acetylcholine (nACh), 5-HT(3), and glycine receptors. As in other members of this family, the agonist binding site of GABA(C) receptors is rich in aromatic amino acids, but while other receptors bind agonist through a cation-pi interaction to a tryptophan, the GABA(C) binding site has tyrosine at the aligning positions. Incorporating a series of tyrosine derivatives at position 198 using unnatural amino acid mutagenesis reveals a clear correlation between the cation-pi binding ability of the side chain and EC(50) for receptor activation, thus demonstrating a cation-pi interaction between a tyrosine side chain and a neurotransmitter. Comparisons among four homologous receptors show variations in cation-pi binding energies that reflect the nature of the cationic center of the agonist.     

DFT-B3LYP and SMD study on the interactions between aza-, diaza-, and triaza-12-crown-4 (A n -12-crown-4, n = 1, 2, 3) with Na+ in the gas phase and acetonitrile solution

B3LYP/6-311G level of theory is used to study the interactions between aza-, diaza-, and triaza- 12-crown-4 ligands as host molecules and Na⁺ ion as a guest species. Minimum energy structures, complexes binding energies, basis set superposition errors, and various thermodynamic parameters of free ligands, ion, and complexes have been calculated based on the proposed level of theory. A simple thermodynamic cycle with and without different acetonitrile cluster sizes inside the cavity of Na⁺, has been used to calculate the stability constants of aza-12-crown-4 complex. All solvation free energy estimations have been done with using SMD model. Results show that with introducing more acetonitrile molecules in the cavity of guest species, the absolute deviation is reduced. In addition, a good linear correlation between experimental complex formation constants and binding energies of complexes has been obtained. Calculated results, which are in agreement with the experimental data, predict that the interaction energy of triaza- is more than diaza-12-crown-4, which in turn is greater than aza-12-crown-4 with Na⁺ ion.     

Assay of Acetylcholinesterase Activity and Electrochemical Determination of Fenthion in Oil-in-water Emulsion

Organophosphates (OPs) have been widely used as pesticides,insecticides or even chemical warfare agents.Acetylcholinesterase (ACHE) inhibition has been employed to develop verious assay methods for detection of pesticides with the advantages of low cost,simple procedure and quick assay time.The study of acetylcholinesterase (ACHE) activity and OPs inhibition in the solution containing organic solvent is extremely important owing to poor solubility of Ops in water and a higher solubility in organic solvents.     

In silico prediction of drug solubility: 1. Free energy of hydration

As a first step in the computational prediction of drug solubility the free energy of hydration, DeltaG*(vw) in TIP4P water has been computed for a data set of 48 drug molecules using the free energy of perturbation method and the optimized potential for liquid simulations all-atom force field. The simulations were performed in two steps, where first the Coulomb and then the Lennard-Jones interactions between the solute and the water molecules were scaled down from full to zero strength to provide physical understanding and simpler predictive models. The results have been interpreted using a theory assuming DeltaG*(vw) = A(MS)gamma + E(LJ) + E(C)/2 where A(MS) is the molecular surface area, gamma is the water-vapor surface tension, and E(LJ) and E(C) are the solute-water Lennard-Jones and Coulomb interaction energies, respectively. It was found that by a proper definition of the molecular surface area our results as well as several results from the literature were found to be in quantitative agreement using the macroscopic surface tension of TIP4P water. This is in contrast to the surface tension for water around a spherical cavity that previously has been shown to be dependent on the size of the cavity up to a radius of approximately 1 nm. The step of scaling down the electrostatic interaction can be represented by linear response theory.     

A computational model of the nicotinic acetylcholine binding site

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro--erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).