Effect Of Microsolvation Research Articles

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 effects on the electron binding energies of halide anions

Ab initio electron propagator calculations in the partial third order (P3) and P3+ approximations were performed to obtain vertical electron detachment energies (VEDEs) of fluoride and chloride clusters with one through three molecules of water. Larger clusters of F− and Cl− with six water molecules were also treated with and without the polarisable continuum model (PCM). For the smaller clusters, good agreement between calculated VEDEs and peak positions in photoelectron spectra is achieved. Large shifts in VEDEs are observed for both hexameric fluoride–water and chloride–water complexes when the PCM is applied. Significant changes in coordination geometries about the chloride anion also occur in this model. In all fluoride complexes, Dyson orbitals for the lowest VEDEs are delocalised over oxygen atoms. On the contrary, for the case of chloride–water clusters, the Dyson orbitals corresponding to the lowest VEDEs are localised on the anion.

Effects of Microhydration on the Electronic Properties ofortho-Aminobenzoic Acid

High-level density functional electronic structure calculations have been performed to analyze the effect of microsolvation with water on the electronic properties of ortho-aminobenzoic acid (o-Abz). The hydrogen-bonded interaction of the o-Abz molecule with one to three water molecules, o-Abz···(H2O)n (n = 1–3), has been considered in two different situations, once the solvent water molecules are placed close to the carboxyl (−COOH) group of o-Abz producing the o-Abz···[H2O]nCOOH complexes and when the water molecules are placed close to the amino (−NH2) group producing the o-Abz···[H2O]nNH2 clusters. Variation of the vibrational spectra and energetics upon hydrogen-bond formation are analyzed and compared with available experimental data. The effect of cooperativity is also analyzed. Overall, the hydrogen-bonded o-Abz···[H2O]nCOOH clusters are found to be more stable than the o-Abz···[H2O]nNH2 clusters.

Effect of microsolvation on hydrogen trapping potential of metal ions

A thorough analysis is carried out to understand how the microsolvation affects the hydrogen adsorbing capacity of metal ions in the presence as well as absence of the counter ions. Calculations are done at different levels of theory by using different functionals and basis sets and also by using the BSSE correction. The Be2+ ion doped systems exhibit stronger interaction with the hydrogen molecule than the other metal doped systems. The extent of interaction is less affected by the method of computation. The reaction free energy values imply that adsorption on alkaline earth metal doped systems is spontaneous at room temperature. Interaction energies are favorable for hydrogen adsorption on the systems containing alkaline earth metal ions and the gravimetric density of adsorbed hydrogen molecule is more in those containing the alkali metal ions.

Effects of Microsolvation on the Stability of Zwitterionic Valine

We present calculations for valine (Val) - (n = 0-5) to examine the effects of microsolvating water on the relative stability of the zwitterionic vs. canonical forms of Val. We calculate the structures, energies and Gibbs free energies of the conformers at B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p) and MP2/aug-cc-pvdz level of theory. We find that five water molecules are needed to stabilize the zwitterionic form of Val. By calculating the barriers of the canonical zwitterionic pathways of Val - conformers, we suggest that both forms of Val - may be observed in low temperature gas phase.

Microsolvation effects on the stability of polyalanine in extended and polyproline II conformation

AbstractMicrosolvation of a polyalanine chain in a fully extended structure (FES) and polyproline II conformation (PP‐II) is studied using density functional theory. Infinitely long systems are investigated to form infinite networks of hydrogen bonds (hbs) along the microsolvation shells. In this manner hbs cooperative effect is evaluated. The stability of microsolvated PP‐II respect to microsolvated FES is investigated by changing the number of adsorbed water molecules per residue (nw) from 2 to 11. It is found that PP‐II stability strongly depends on the nw value. For example, PP‐II is more stable respect to FES by ∼14 kcal/mol for nw = 9, however its stability drops to ∼4 kcal/mol for nw = 10. It is shown that such behavior is connected to cooperative effects at the hydration shell, where water‐water hbs strengthen up to 46%. Besides backbone‐water hbs weaken, most notably in FES where its strength is diminished by 36%. Such interplay between water‐water and backbone‐water hydrogen bonding leads to a marginal stability of PP‐II respect to FES for nw ≥ 10. © 2012 Wiley Periodicals, Inc.

Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies

Molecular dynamics (MD) simulations were carried out to study the conformational characteristics of Glycine Dipeptide (GD) in the presence of explicit water molecules for over 10ns with a MD time step of 2fs. The density functional theory (DFT) methods with 6-311G** basis set have been employed to study the effects of microsolvation on the conformations of GD with 5–10 water molecules. The interaction energy with BSSE corrections and the strength of the intermolecular hydrogen bond interactions have been analyzed. The Bader's Atoms in Molecules (AIM) theory has been employed to investigate H-bonding patterns in water interacting complexes. The natural bond orbital (NBO) analysis has been carried out to analyze the charge transfer between proton acceptor to the antibonding orbital of the XH bond in the hydrated complexes. NMR calculations have been carried out at B3LYP/6-311G (2d, 2p) level of theory to analyse the changes in structure and hydrogen bonding environment that occur upon solvation.

Structure of singly hydrated, protonated phospho-tyrosine

Tandem mass spectrometry is a powerful analytical technique for distinguishing phosphorylated from non-phosphorylated peptides, and also to locate the phosphorylated site. It is however desirable to further extend the tandem MS capacities via the development of structure specific activation techniques. This work is part of an ongoing project which aims at characterizing the environment of the phosphate group using tunable IRMPD. The effect of microsolvation of protonated phospho-tyrosine on the phosphate environment has been investigated using a combination of tandem MS experiments and quantum chemical calculations. Infrared spectra have been recorded in the 900–1900 cm −1 and 2500–3750 cm −1 regions using a free electron laser and a tabletop laser, respectively. Water is found to form a hydrogen bonded bridge between the otherwise nearly isolated phosphate and ammonium groups. Theoretical and experimental results also provide consistent evidences for two weaker hydrogen bonds between the two other NH bonds with the π-aromatic ring and the carboxylic CO. The MP2 calculated IR absorption spectrum of the lowest energy structure allows for a clear band assignment. As compared to intramolecular direct interaction between the phosphate and the ammonium, the two hydrogen bonds associated with the water bridge between these groups are found to have a larger impact on their IR structure-specific probes. This is reflected by the red-shift of the P O stretch, and also the blue shift of the umbrella mode of the ammonium. Special attention is paid to the 2500–3750 cm −1 spectral range. While the phosphate OH stretching modes are not affected by the addition of water, the red shifts of the three ammonium NH stretches are found to be significant and quite different for their three types of non-covalent interactions.

Microsolvation Effect on the Twist of β-sheets

Under certain circumstances β-sheets prefer to be twisted instead of flat. To get insight into the reasons of such preference, bare and microsolvated parallel and antiparallel two-strand polyalanine β-sheets are investigated using density functional theory. Full geometry optimizations show that microsolvation increases interstrand twisting and promotes a flat to twist transition. It is found that the latter behavior is connected to compressive strain resulting from microsolvation. Residues in flat β-sheets adjust the sense of its local intrastrand twist, which leads to the appearance of interstrand twist, to release strain and to favor water-water hydrogen bonding. The predicted microsolvation effect is corroborated analyzing the geometry of residues forming β-sheet motifs in protein crystals.

Microsolvation of Uracil and Its Conjugate Bases: A DFT Study of the Role of Solvation on Acidity

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N(1) and N(3) conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one-three), rings (three-five waters), or cages (five-six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol(-1) in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.

Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1–3) complexes

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H(2)O)(n) (n = 1-3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H(2)O)(n) (n = 1-3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1-3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H(2)O)(3) complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.

Effect of Solvation on the Vertical Ionization Energy of Thymine: From Microhydration to Bulk

The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.

CO2 Capturing Mechanism in Aqueous Ammonia: NH3-Driven Decomposition−Recombination Pathway

Capturing CO2 by aqueous ammonia has recently received much attention due to its advantages over other state-of-the-art CO2-capture technology. Thus, understanding this CO2-capturing mechanism, which has been causing controversy, is crucial for further development toward advanced CO2 capture. The CO2 conversion mechanism in aqueous ammonia is investigated using ab initio calculations and kinetic simulations. We show full details of all reaction pathways for the NH3-driven conversion mechanism of CO2 with the pronounced effect of microsolvation. Ammonia performs multiple roles as reactant, catalyst, base, and product controller. Both carbamic and carbonic acids are formed by the ammonia-driven trimolecular mechanism. Ammonia in microsolvation makes the formation of carbamic acid kinetically preferred over carbonic acid. As the concentration of CO2 increases, the dominant product becomes carbonic acid. The conversion from carbamic acid into carbonic acid occurs through the decomposition−recombination pathwa...

DFT modeling on the suitable crown ether architecture for complexation with Cs+ and Sr2+ metal ions

Crown ether architectures were explored for the inclusion of Cs(+) and Sr(2+) ions within nano-cavity of macrocyclic crown ethers using density functional theory (DFT) modeling. The modeling was undertaken to gain insight into the mechanism of the complexation of Cs(+) and Sr(2+) ion with this ligand experimentally. The selectivity of Cs(+) and Sr(2+) ions for a particular size of crown ether has been explained based on the fitting and binding interaction of the guest ions in the narrow cavity of crown ethers. Although, Di-Benzo-18-Crown-6 (DB18C6) and Di-Benzo-21-Crown-7 (DB21C7) provide suitable host architecture for Sr(2+) and Cs(+) ions respectively as the ion size match with the cavity of the host, but consideration of binding interaction along with the cavity matching both DB18C6 and DB21C7 prefers Sr(2+) ion. The calculated values of binding enthalpy of Cs metal ion with the crown ethers were found to be in good agreement with the experimental results. The gas phase binding enthalpy for Sr(2+) ion with crown ether was higher than Cs metal ion. The ion exchange reaction between Sr and Cs always favors the selection of Sr metal ion both in the gas and in micro-solvated systems. The gas phase selectivity remains unchanged in micro-solvated phase. We have demonstrated the effect of micro-solvation on the binding interaction between the metal ions (Cs(+) and Sr(2+)) and the macrocyclic crown ethers by considering micro-solvated metal ions up to eight water molecules directly attached to the metal ion and also by considering two water molecules attached to metal-ion-crown ether complexes. A metal ion exchange reaction involving the replacement of strontium ion in metal ion-crown ether complexes with cesium ion contained within a metal ion-water cluster serves as the basis for modeling binding preferences in solution. The calculated O-H stretching frequency of H(2)O molecule in micro-solvated metal ion-crown complexes is more red-shifted in comparison to hydrated metal ions. The calculated IR spectra can be compared with an experimental spectrum to determine the presence of micro-solvated metal ion-crown ether complexes in extractant phase.

Inhibition of acid‐induced decomposition of diphenyltriazenes by complexation with cyclodextrins

AbstractAcid‐promoted NN bond cleavage in 1,3‐diphenyltriazenes (X‐Ph‐N=N‐NH‐Ph‐X; X = H, 4‐OCH3), leading to formation of diazonium ions and anilines, is strongly inhibited in aqueous solutions in the presence of cyclodextrins (CDs). The inhibition is ascribed to the formation of inclusion complexes that render the guest diphenyltriazene significantly less basic as a result of the less polar nature of the CD cavity (a microsolvent effect). Association equilibrium constants for 1:1 host–guest complexes increase in the order α‐CD <β‐CD ∼ permethyl‐β‐CD < hydroxypropyl‐β‐CD, with values for X = 4‐OCH3 being larger than those for X = H. In the case of α‐CD, formation of 2:1 host–guest complexes is also involved. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 567–574, 2010

Structure and Stability of γ-Aminobutyric acid-(H2O)n(n = 0-5) Clusters: Zwitterionic vs. Canonical forms

Calculations are presented for the γ-aminobutyric acid-(H 2 O) n (n = 0-5) clusters in both canonical and zwitterionic forms. We examine the effects of microsolvation on the structures and transformation between the canonical and zwitterionic forms. The canonical forms are predicted to be more stable for n = 0-4. With five microsolvating water molecules, the two forms of γ-aminobutyric acid become quasidegenerate, with the energies of zwitterionic forms slightly (by 1 - 3 kcal/mol) higher. The lowest energy zwitterionic conformer of γ-aminobutyric acid-(H 2 O) 5 cluster is calculated to isomerize to canonical form through a barrier-less proton transfer process and is thus predicted to be kinetically unstable. Therefore, we predict that the canonical conformers of y-aminobutyric acid should be observed predominantly in the gas phase at low temperature in presence of up to five water molecules.

Conformational effect on the preferential binding of alkali metal cation with crown ether: A molecular level investigation

We report density functional theory (DFT) based study to predict various conformation of free 12-crown-4 ether and its complexes with alkali metal cations. The optimized geometries, binding energies, and binding enthalpies of crown ether–cation complexes have been determined with a correlated hybrid density functional, namely Becke’s three-parameter functional, B3LYP using split valence basis function, 6-311++G(d, p). Geometry optimizations for all the conformers of free 12-crown-4 ether and its metal cation complexes are carried out with several initial guess structures based on semi-empirical PM3 optimized results. The optimized structure for free 12-crown-4 ether and its metal cation complexes obtained from the present DFT calculation confirmed the experimentally reported structures. The calculated values of the gas phase binding energy for lithium ion is always found to be higher than that of the sodium ion for all the conformers of macrocyclic 12-crown-4 ethers reported in the present study. Expected preferential binding of Li+ ion over Na+ ion in case of a particular conformer of 12-crown-4 ligand is reversed due to micro-solvation effects reflecting its significant influence towards metal ion selectivity. The density functional theoretical calculated values of binding enthalpy are in fair agreement with the available reported experimental values.

Homolytic versus Heterolytic Dissociation of Alkalimetal Halides: The Effect of Microsolvation

Herein we report density functional calculations of homolytic and heterolytic dissociation energies of the diatomic alkalimetal halides MX (M=Li, Na, K, Rb, and Cs and X=F, Cl, Br, I, and At) and their corresponding microsolvated structures MX(H(2)O)(n) (n=1 to 4). Our results show that the homolytic dissociation energy of the MX(H(2)O)(n) species increases with the number of water molecules involved in the microsolvated salts. On the other hand, the heterolytic dissociation energy follows exactly the opposite trend. As a result, while for the isolated diatomic alkalimetal halides, homolytic dissociation is always favored over heterolytic dissociation, the latter is preferred for CsF and CsCl already for n=2, and for n=4 it is the preferential mode of dissociation for more than half of the species studied.

Preferential interaction of charged alkali metal ions (guest) within a narrow cavity of cyclic crown ethers (neutral host): A quantum chemical investigation

The binding interaction of alkali metal ions (charged guest) within the narrow cavity of crown ethers (neutral host) of different cavity size has been studied using quantum chemical density functional theory. Different conformational structures, binding energies and various thermodynamic parameters of free crown ethers and their metal ion complexes have been determined with the B3LYP functional using a large split valence 6-311++G(d,p) basis set. Geometry optimization was performed using guess structures obtained from semi-empirical PM3 optimized structures without imposing any symmetry restriction. The calculated values of binding enthalpy increase with increase in cavity size, i.e., with increase in donor O atoms and are found to be in good agreement with gas phase experimental results. We have demonstrated the effect of micro-solvation on the binding interaction between the alkali metal ions (Li + and Na +) and the macrocyclic crown ethers by considering micro-solvated metal ions up to six water molecules directly attached to the metal ion. A metal ion exchange reaction involving the replacement of lithium ion in metal ion–crown ether complexes with sodium ion contained within a metal ion–water cluster serves as the basis for modeling binding preferences in solution. An attempt has been made to study the effect of micro-solvation on the binding interaction of metal ions with crown ethers by considering two water molecules attached to metal ion–crown ether complexes. The calculated O H stretching frequency of H 2O molecule in micro-solvated metal ion–crown complexes is less blue-shifted in comparison to hydrated metal ions. The calculated IR spectra can be compared with an experimental spectrum to determine the presence of micro-solvated metal ion–crown ether complexes in extractant phase.

Microsolvation and Protonation Effects on Geometric and Electronic Structures of Tryptophan and Tryptophan-Containing Dipeptides

Photodissociation spectroscopy of solvated clusters of protonated tryptophan (TrpH(+)) and dipeptides containing tryptophan (Val-TrpH(+), Ala-TrpH(+), and Gly-TrpH(+)) has been carried out at low temperature to investigate the protonation and solvation effects on the electronic spectrum. For the protonated dipeptides, the S(1)-S(0) transition exhibits a substantial red shift due to the stronger interaction between the NH(3)(+) group and the indole pi ring. The S(1)-S(0) spectra of TrpH(+)(CH(3)OH)(n) clusters exhibit a drastic change with the number of methanol molecules. This behavior is interpreted in terms of the decrease in the interaction between the pi pi* and the repulsive pi sigma* states. Ala-TrpH(+) and Gly-TrpH(+) exhibit an extensive spectral change with addition of two methanol molecules. This change is ascribed to a conformational change, which is induced by the insertion of solvent molecule in between the NH(3)(+) group and the indole pi ring.