Study on properties of liquid ammonia via molecular dynamics simulation based on ABEEMσπ polarisable force field

Abstract

The molecular dynamics simulation has been performed to investigate the charge distribution, structural and dynamical properties of liquid ammonia at 273 K using a polarisable force field of the atom-bond electronegativity equalisation method (ABEEMσπ). One ammonia molecule in this model has eight charge sites, one N atomic site, three H atomic sites, three N–H bond sites and one lone-pair electron site. ABEEMσπ model can present the quantitative site charges of molecular ammonias in liquid and their changing in response to their surroundings. The radial distribution functions and dynamical properties are in fair agreement with the available experimental data. The first peak of g_NN(r) appears at N–N distance of ~3.50 ± 0.05 Å where most hydrogen bonds are formed. The average coordination number of the first shell is 13.0 ± 0.1 among which a central ammonia molecule intimately connects 3 ~ 4 ammonia molecules by hydrogen bonds. The power spectrum shows the vibrations of hydrogen bonds. For a reference, a simple estimation of the average hydrogen bonding energy in liquid ammonia is 6.5 ± 0.1 kcal/mol larger than 3.8 ± 0.3 kcal/mol in dimer ammonia. Our simulation results provide more detailed information about liquid ammonia.     

Combined theoretical studies on solvation and hydrogen bond interactions in glycine tripeptide

The theoretical conformational analysis of glycine tripeptide (GT) has been carried out by molecular dynamics (MD) method in order to find minimum energy conformations. The MD studies on GT with water have been carried out for over 10 ns with a time step of 2 fs using fixed charge force field (AMBER ff03). By adding the solvation effect using water as a solvent, the GT conformers identified in this study exhibit α-helical conformation. Compared with the earlier reports, this MD study is able to identify the energetically favourable GT conformations. The obtained geometry of the five most stable GT conformations was optimised using the density functional theory method at B3LYP/6-311G** level of theory. Subsequently, the effects of solvation on the conformational characteristics of five most stable GT conformers with four water molecules (the number of water molecules in the first solvation shell of GT obtained from MD study) were investigated using the same method and the same level of theory. The effect of microsolvation on the fifth GT conformer has been studied with a cluster of 11 water molecules as the first hydration shell which generates folded structure. The interaction energies of all the complexes are calculated by correcting the basis set superposition error. The strong hydrogen bond mainly contributes to the interaction energies. The atoms in molecules theory and natural bond orbital analysis were used to study the origin of H-bonds. A good correlation between the structural parameters and the properties of charge density is found. NMR calculations show that the C = O carbons of the amine groups of the first and middle glycine fragments have maximum chemical shifts.     

Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks

A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg (H ₂ O) _n )]²⁺, (n?=?3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg²⁺ causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg²⁺ to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35–2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.

Molecular dynamics and quantum chemical studies of solvent effects on cyclo glycylglycine and glycylalanine dipeptides

Hydrogen bond (H-bond) interactions between the two cyclo dipeptides, cyclo(glycyl-glycine) (CGG) and cyclo(glycyl-alanine) (CGA), and water have been studied using molecular dynamics (MD) and quantum chemical methods. The MD studies have been carried out on CGG and CGA in water using fixed charge force field (AMBER ff03) for over 10 ns with a MD time step of 2 fs. The results of this study show that the solvation pattern influences the conformations of the cyclo dipeptides. Following molecular simulations, post Hartree–Fock and density functional theory methods have been used to explore the molecular properties of the cyclo dipeptides in gaseous and aqueous phase environments. The self-consistent reaction field theory has been used to optimise the cyclopeptides in diethyl ether (? = 4.3) and water (? = 78.5), and the solvent effects have been analysed. A cluster of eight water molecules leads to the formation of first solvation shell of CGG and CGA and the strong H-bonding mainly contributes to the interaction energies. The H-bond interactions have been analysed by the calculation of electron density ρ(r) and its Laplacian ▽²ρ(r) at bond critical points using atoms in molecules theory. The natural bond orbital analysis was carried out to reveal the nature of H-bond interactions. In the solvated complexes, the keto carbons registered the maximum NMR chemical shifts.     

Kinetics of rearrangement of solvation sheath of an excited molecule of the fluorescent probe 4"-dimethylaminochalcone

Processes accompanying the quenching of the fluorescent probe 4"-dimethylaminochalcone by hydroxyl groups of the proton-donor solvent 1-butanol have been studied. The kinetics of the deactivation of the excited state of 4"-dimethylaminochalcone has been monitored from the transition absorption spectra at a time resolution of 50 fs and fluorescence decay at a time resolution of 30 ps. The data obtained allow thinking that the next picture occurs in 1-butanol. At first stage, the 4"-dimethylaminochalcone molecule in its ground state forms a hydrogen bond with an alcohol molecule. At the second stage, the absorption of light quantum and corresponding rise of the dipole moment of 4"-dimethylaminochalcone take place, the initially existing hydrogen bond is retained. The third stage consists in the rearrangement of the 4"-dimethylaminochalcone solvation shell formed by alcohol dipole molecules due to an increase of the dipole of moment 4"-dimethylaminochalcone; this rearrangement takes an energy of about 24 kJ/mol, the arrangement time constant is close to 40 ps; the initial hydrogen bond is retained. The fourth stage involves processes that lead to fluorescence quenching; their time constant is about 200 ps. Taking into account that the quenching is a much slower process than the relaxation of the solvation shell, it was supposed that the quenching is not a direct consequence of the solvation shell relaxation or the existence of the hydrogen bond formed prior to excitation. Then the fluorescence quenching of 4"-dimethylaminochalcone can be accomplished through some other processes that are observed in other fluorescent molecules: (a) rearrangement of the initial hydrogen bond from a conformation that cannot quench the fluorescence of 4"-dimethylaminochalcone to a more "effective" conformation, (b) charge transfer between the excited of molecule 4"-dimethylaminochalcone and alcohol, or (c) solvent-induced twist of the 4"-dimethylaminochalcone amino group (its withdrawal from the molecule plane) by the action of the solvent.     

Activation of G-protein-coupled receptors is thermodynamically linked to lipid solvation

Preferential lipid solvation of the G-protein-coupled A_2A adenosine receptor (A_2AR) is evaluated from 35 μs of all-atom molecular dynamics simulation. A coarse-grained transition matrix algorithm is developed to overcome slow equilibration of the first solvation shell, obtaining estimates of the free energy of solvation by different lipids for the receptor in different activation states. Results indicate preference for solvation by unsaturated chains, which favors the active receptor. A model for lipid-dependent G-protein-coupled receptor activity is proposed in which the chemical potential of lipids in the bulk membrane modulates receptor activity. The entropies associated with moving saturated and unsaturated lipids from bulk to A_2AR’s first solvation shell are evaluated. Overall, the acyl chains are more disordered (i.e., obtain a favorable entropic contribution) when partitioning to the receptor surface, and this effect is augmented for the saturated chains, which are relatively more ordered in bulk.     

Microsolvation and hydration enthalpies of CaC2O4(H2O) n (n = 0-16) and C2O4 2-(H2O) n (n = 0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree–Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as ?480.78, –302.78 and –312.73 kcal mol^?1, resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol^?1.

The solvation of bromide anion in acetonitrile: a structural study based on the combination of theoretical calculations and X-ray absorption spectroscopy

This work studies the solvation of bromide in acetonitrile by combining quantum mechanics, computer simulations and X-ray absorption near edge structure (XANES) spectroscopy. Three different sets of interaction potentials were tested, one of them derived from literature and the other two are simple modifications of the previous one to include specificities of the bromide–acetonitrile interactions. Results for microsolvation of bromide were obtained by quantum mechanical optimization and classical minimization of small clusters [Br(ACN) _n ]^?  (n = 9, 20). Analysis of molecular dynamics (MD) simulations has provided structural, dynamic and energetic aspects of the solvation phenomenon. The theoretical computation of Br K-edge XANES spectrum in solution using the structural information obtained from the different simulations has allowed the comparison among the three different potentials, as well as the examination of the main structural and dynamic factors determining the shape of the experimental spectrum.     

On the solvation of the mercury(I) ion. A structural, vibration spectroscopic and quantum chemical study

The structure of the solvated mercury(I) ion in solvents such as water, methanol, dimethylsulfoxide, N,N^′-dimethylpropyleneurea, acetonitrile and pyridine solution has been studied by means of EXAFS and/or large angle X-ray scattering (LAXS). Raman spectroscopy has been used for the determination of the Hg-Hg stretching frequencies. The Hg-Hg bond length increases with increasing solvating ability of the solvent, while the stretching frequency appears to be almost invariant. The results of quantum chemical calculations indicate a significant influence on the Hg-Hg bond from solvation. The structure of solid anhydrous mercury(I) trifluoromethanesulfonate, Hg₂(CF₃SO₃)₂ (1), has been determined by powder diffraction methods. The structure comprises of discrete molecules, where each mercury binds to an oxygen atom in the anion, forming an almost linear O-Hg-Hg-O entity; the Hg-Hg-O angle is 173° and the Hg-Hg and Hg-O bond lengths are 2.486(6) and 2.099(22) Å, respectively.     

The first solvation shell of magnesium ion in a model protein environment with formate,water, and X-NH3, H2S,imidazole, formaldehyde,and chloride as ligands: An ab initio study

The first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH₃, H₂S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate–Mg(II) ion is greater than 10 kcal mol^?1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH₃ formaldehyde, H₂O, and H₂S. © 1995 Wiley-Liss, Inc.     

The relation between the structure of the first solvation shell and the IR spectra of aqueous solutions

The spectroscopic signatures of solvated anions and cations, in the O-H stretch region of water, are studied using the POLIR potential. Shifts in the spectra are shown to correlate very well with the distribution of a particular hydrogen bond angle for the waters in the first solvation shell. The results indicate that the spectral shifts might be predicted from MD simulations in a computationally convenient fashion, avoiding an explicit calculation of the spectra, as first suggested by Sharp et al. (J Chem Phys 114(4):1791–1796, 2001).     

The influences of water solvent on the structures and stabilities of Na+–AD conformers

The influences of water solvent on the structures and stabilities of the complex ion conformers formed by the coordination of alanine dipeptide (AD) and Na⁺ have been investigated using supramolecular and polarizable continuum solvation models at the level of B3LYP/6-311++G**, respectively; 12 monohydrated and 12 dihydrated structures of Na⁺–AD complex ion were obtained after full geometrical optimization. The results showed that H₂O molecules easily bind with Na⁺ of Na⁺–AD complex ion, forming an ion-lone pair interaction with the Na–O bond length of 2.1–2.3 Å. Besides, H₂O molecules also can form hydrogen bonds O_W–H_W···O(1), O_W–H_W···O(2), N(1)–H(1)···O_W or N(2)–H(2)···O_W with O or N groups of the Na⁺–AD backbone. The most stable gaseous bidentate conformer C7AB of Na⁺–AD is still the most stable one in the solvent of water. However, the structure of the most unstable gaseous conformer α′B of Na⁺–AD collapses under the attack of H₂O molecules and changes into C7AB conformation. Computations with IEFPCM solvation model of self-consistent reaction field theory give that aqueous C5A is more stable than C7_eqB and that the stabilization energies of water solvent on monodentate conformers of Na⁺–AD complex ion (about 272–294 kJ/mol) are more than those on bidentate ones (about 243 kJ/mol).     

Site-selective binding of Zn(II) to metallo-β-lactamase L1 from Stenotrophomonas maltophilia

Extended X-ray absorption fine structure studies of the metallo-β-lactamase L1 from Stenotrophomonas maltophilia containing 1 and 2 equiv of Zn(II) and containing 2 equiv of Zn(II) plus hydrolyzed nitrocefin are presented. The data indicate that the first, catalytically dominant metal ion is bound by L1 at the consensus Zn₁ site. The data further suggest that binding of the first metal helps preorganize the ligands for binding of the second metal ion. The di-Zn enzyme displays a well-defined metal–metal interaction at 3.42 Å. Reaction with the β-lactam antibiotic nitrocefin results in a product-bound species, in which the ring-opened lactam rotates in the active site to present the S1 sulfur atom of nitrocefin to one of the metal ions for coordination. The product bridges the two metal ions, with a concomitant lengthening of the Zn–Zn interaction to 3.62 Å.     

Composition,Characteristic and Activity of Rare Earth Element-Bound Polysaccharide from Tea

The compositions and structural characteristics of rare earth elements-bound polysaccharides from tea (REE-TPS) were studied with the methods of Inductively Coupled Plasma Mass Spectrometry (ICP-MS), Gas Chromatography (GC) and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. The results show that polysaccharide from tea (TPS) was a sort of glycoprotein and coordinated with Rare Earth Elements (REE) closely. The sugar fraction was composed of Rha, Ara, Xyl, Fuc, Glc, and Gal. There existed almost all natural amino acids with Glx, Asx, and Hyp as the major parts in the protein fraction. The REEs in REE-TPS were mainly composed of La, Ce, and Nd, especially, more than 75% of them was La. The coordination atom of the first coordination shell of La in REE-TPS was oxygen, the coordination number of which was 6, and the average distance between the atoms was 2.52 Å. The second shell was formed from sulfur atoms, the coordination number and the average distance were 3 and 2.91 Å, respectively. The bio-experiments show that REE-TPS could decrease the content of blood glucose in mice significantly.     

New developments in first-principles excited-state dynamics simulations: unveiling the solvent specificity of excited anionic cluster relaxation and electron solvation

Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I^? (Solv)_n]^*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I^? (Solv)_n]^* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I^? (Solv)_n]^* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I^? (Solv)_n]^* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.     

Kinetics of the rearrangement of the solvation shell of an excited fluorescent probe 4″-dimethylaminochalcone

A study was made of the processes associated with the quenching of 4″-dimethylaminochalcone (DMAC) fluorescence by proton-donor solvent (1-butanol). The kinetics of deactivation of the DMAC excited state was assessed by transient absorption spectra with a time resolution about 50 fs and by fluorescence decay with ～30-ps resolution. The following sequence of events could thus be envisaged: (i) the DMAC molecule in the ground state (prior to excitation) makes a hydrogen bond with an alcohol molecule; (ii) absorption of a light quantum causes a corresponding increase of the DMAC dipole moment; the H-bond is retained; (iii) the solvation shell formed by alcohol dipoles is reorganized in response to the raise of the DMAC dipole moment, with an energy expenditure about 24 kJ/mol and a time constant about 40 ps; the initial H-bond is still retained; (iv) processes leading to fluorescence quenching occur with an effective time constant of nearly 200 ps. Since quenching is far slower than solvate rearrangement, one can suppose that it is not a direct consequence of shell relaxation or prior H-bonding. Thus, DMAC fluorescence quenching may involve different processes observed with other aromatic molecules: H-bond rearrangement from a nonquenching to a more ‘efficient’ conformation, charge transfer between the excited molecule and alcohol, or solvent-induced out-of-plane twist of the DMAC amino group.     

Structural characterization of the mononuclear iron site in Pseudomonas cepacia phthalate DB01 dioxygenase using X-ray absorption spectroscopy

Phthalate dioxygenase (PDO) from Pseudomonas cepacia contains a Rieske-like [2Fe-2S] cluster and a mononuclear non-heme Fe(II) site. The mononuclear iron can be replaced by a variety of divalent metal ions, although only Fe(II) permits catalytic activity. We used X-ray absorption spectroscopy to characterize the structural properties of the mononuclear iron site and to follow the structural changes in this site as a function both of Rieske site oxidation state and of phthalate binding. Data for the mononuclear site have been measured directly for PDO substituted with Co or Zn in the mononuclear site, and by difference for the native 3-Fe protein. The mononuclear site was modeled well by low Z-ligation (oxygen or nitrogen) and showed no evidence for high-Z ligands (e.g., sulfur). The relatively short average first shell bond lengths and the absence of significant outer shell scattering suggest that the mononuclear site has several oxygen ligands. With Zn in the mononuclear site, the average bond length (2.00?Å) suggests a 5-coordinate site under all conditions. In contrast, the Co- or Fe-containing mononuclear site appeared to be 6-coordinate and changed to 5-coordinate when substrate was bound, since the first shell bond length changed from 2.08 to 2.02?Å (Co) or 2.10 to 2.06?Å (Fe). The implications of these findings for the PDO mechanism are discussed.