Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution

Molecular dynamics simulations have been carried out for ethanolamine as a pure liquid and in aqueous solution at 298 and 333 K. The ethanolamine force field has been parametrized to reproduce intramolecular energies from quantum mechanical calculations and experimentally determined properties of the liquid. The results are presented for conformer distributions, density, enthalpy of vaporization, self-diffusion constant, dielectric constant, and radial distribution functions. The results strongly suggest that the main (O-C-C-N) dihedral tends to stay in its gauche conformers in solution and that the ethanolamine molecules populate conformers with a significant degree of intramolecular hydrogen bonding. This result is also supported by results from a continuum solvation model. Simulation of a 10 mol % aqueous ethanolamine system suggests that ethanolamine is preferentially solvated to by water molecules. The results suggest that ethanolamine dimer formation in aqueous solution is very limited. Simulations were also carried out for CO2 in an aqueous ethanolamine system. The results suggest that CO2 has a comparable level of attraction to ethanolamine and water. The degree of interaction between CO2 and the amine and alcohol functionalities in ethanolamine also appear to be of comparable strength.     

Relaxation study of strong hydrogen bond lifetime in gas phase

Laser temperature jump and shock tube techniques have been used to measure the monomer-dimer relaxation time in the gas phase. With the former method, the lifetime of the cyclic dimer of acetic acid is found to increase from 3 μs at 315 K to 16 μs at 285 K. The activation energy has been determined to be 11.4 ± 0.8 kcal mol^?1. A step-wise mechanism of dissociation is discussed.     

Measuring acetic acid dimer modes by ultrafast time-domain Raman spectroscopy

Acetic acid is capable of forming strong multiple hydrogen bonds and therefore different dimeric H-bonded structures in neat liquid phase and in solutions. The low frequency Raman spectra of acetic acid (neat, in aqueous solution and as a function of temperature) were obtained by ultrafast time and polarization resolved optical Kerr effect (OKE) measurements. Isotropic OKE measurements clearly reveal a specific totally symmetric mode related to the dimeric structure H-bond stretching mode. The effects of isotope substitution, water dilution and temperature on this mode were investigated. These results together with anisotropic OKE measurements and density functional theory calculations for a number of possible dimers provide strong evidence for the cyclic dimer structure being the main structure in liquid phase persisting down to acetic acid concentrations of 10 M. Some information about the dimer structure and concentration dependence was inferred.     

In silico calculation of acidity constants of carbonic acid conformers

In order to explore the aqueous acid chemistry of carbonic acid, we employ a constrained ab initio molecular dynamics (AIMD) technique to study acid dissociations of its three conformers including CC (cis-cis), CT (cis-trans), and TT (trans-trans). The simulations of reagent states reveal similar hydration characteristics for them: the hydroxyls donate H-bonds to solvating waters but no obvious H-bonding exists between hydroxyl oxygen atoms and waters. It is found that the CC conformer dissociates spontaneously to bicarbonate within picoseconds whereas the other two can stay for relatively long simulation times. This suggests that CC has the strongest acidity among the three conformers and it is not stable in water. The simulations indicate that the symmetrical hydroxyls of TT conformer have a pKa value of 3.11 and the two asymmetrical hydroxyls of CT show different pKa values: 2.60 and 3.75, respectively. Overall, these results confirm the recent experimental measurement: about 4.0 for deuterated carbonic acid. By analyzing the dissociation processes, it is revealed that the differences of the acid constants stem from the initial steps of hydroxyls stretches. This simulation study provides a quantitative and microscopic basis for better understanding the reactivity of aqueous carbonate species.     

Coordination environment of aqueous uranyl(VI) ion

Water dissociation from [UO2(OH2)5]2+ is studied with Car-Parrinello molecular dynamics simulations (using the BLYP density functional) in the gas phase and in aqueous solution. Free energies, DeltaA, are estimated from pointwise thermodynamic integration using one U-O(H2) distance as a reaction coordinate. While an isomeric, four-coordinate complex, [UO2(OH2)4]2+.H2O, is more stable than the five-coordinate reactant in the gas phase (DeltaA = -2.2 kcal/mol), the former is strongly disfavored in water (DeltaA = +8.7 kcal/mol).     

Vibrational dynamics of carboxylic acid dimers in gas and dilute solution

Ultrafast mid-IR transient absorption spectroscopy has been used to study the vibrational dynamics of hydrogen-bonded cyclic dimers of trifluoroacetic acid and formic acid in both the gas and solution phases (0.05 M in CCl(4)). Ultrafast excitation of the broad O-H cyclic dimer band leads, in the gas phase, to large-scale structural changes of the dimer creating a species with a distinct free O-H stretching band on 20 ps and 200 ps timescales. These timescales are assigned to ring-opening and dissociation of the dimer, respectively. In the solution phase, no such structural rearrangement occurs and our results are consistent with previous studies. The gas phase dynamics are insensitive to both the specific excitation energy (over a span of 550 cm(-1)) and the chemical identity of the dimer.     

Equilibrium thermodynamic studies in water: reactions of dihydrogen with rhodium(III) porphyrins relevant to Rh-Rh, Rh-H, and Rh-OH bond energetics

Aqueous solutions of rhodium(III) tetra p-sulfonatophenyl porphyrin ((TSPP)Rh(III)) complexes react with dihydrogen to produce equilibrium distributions between six rhodium species including rhodium hydride, rhodium(I), and rhodium(II) dimer complexes. Equilibrium thermodynamic studies (298 K) for this system establish the quantitative relationships that define the distribution of species in aqueous solution as a function of the dihydrogen and hydrogen ion concentrations through direct measurement of five equilibrium constants along with dissociation energies of D(2)O and dihydrogen in water. The hydride complex ([(TSPP)Rh-D(D(2)O)](-4)) is a weak acid (K(a)(298 K) = (8.0 +/- 0.5) x 10(-8)). Equilibrium constants and free energy changes for a series of reactions that could not be directly determined including homolysis reactions of the Rh(II)-Rh(II) dimer with water (D(2)O) and dihydrogen (D(2)) are derived from the directly measured equilibria. The rhodium hydride (Rh-D)(aq) and rhodium hydroxide (Rh-OD)(aq) bond dissociation free energies for [(TSPP)Rh-D(D(2)O)](-4) and [(TSPP)Rh-OD(D(2)O)](-4) in water are nearly equal (Rh-D = 60 +/- 3 kcal mol(-1), Rh-OD = 62 +/- 3 kcal mol(-1)). Free energy changes in aqueous media are reported for reactions that substitute hydroxide (OD(-)) (-11.9 +/- 0.1 kcal mol(-1)), hydride (D(-)) (-54.9 kcal mol(-1)), and (TSPP)Rh(I): (-7.3 +/- 0.1 kcal mol(-1)) for a water in [(TSPP)Rh(III)(D(2)O)(2)](-3) and for the rhodium hydride [(TSPP)Rh-D(D(2)O)](-4) to dissociate to produce a proton (9.7 +/- 0.1 kcal mol(-1)), a hydrogen atom (approximately 60 +/- 3 kcal mol(-1)), and a hydride (D(-)) (54.9 kcal mol(-1)) in water.     

Molecular dynamics simulations of helix-forming, amine-functionalized m-poly(phenyleneethynylene)s

We present here the results of all-atom and united-atom molecular dynamics (MD) simulations that were used to examine the folding behavior of an amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomer in aqueous environment. The parallelized GROMACS MD simulation code and OPLS force field were used for multiple MD simulations of m-PPE oligomers containing 24 phenyl rings in extended, coiled and helix conformations separately in water to determine the minimum energy conformation of the oligomer in aqueous solvent and what interactions are most important in determining this structure. Simulation results showed that the helix is the preferred minimum energy conformation of a single oligomer in water and that Lennard-Jones interactions are the dominant forces for the stabilization of the helix. In addition, these solvophobic interactions are strong enough to maintain the helix conformation at temperatures up to 523 K.     

Conformational free energy surface of the linear DPDPE peptide: cost of pre-organization for disulfide bond formation

We have calculated the free energy differences between four conformers of the linear form of the opioid pentapeptide DPDPE in aqueous solution. The conformers are Cyc, representing the structure adopted by the linear peptide prior to disulfide bond formation, β _C and β _E , two slightly different β-turns previously identified in unconstrained molecular dynamics simulations, and Ext, an extended structure. Our simulations indicate that β _E is the most stable of the studied conformers of linear DPDPE in aqueous solution, with β _C , Cyc and Ext having free energies higher by 2.3, 6.3, and 28.2 kcal/mol, respectively. The free energy differences of 4.0 kcal/mol between β _C and Cyc, and 6.3 kcal/mol between β _E and Cyc, reflect the cost of pre-organizing the linear peptide into a conformation conducive for disulfide bond formation. Such a conformational change is a pre-requisite for the chemical reaction of S–S bond formation to proceed. The relatively low population of the cyclic-like structure agrees qualitatively with observed lower potency and different receptor specificity of the linear form relative to the cyclic peptide, and with previous unconstrained simulation results. Free energy component analysis indicates that the moderate stability difference of 4.0–6.3 kcal/mol between the β-turns and the cyclic-like structure results from cancellation of two large opposing effects. In accord with intuition, the relaxed β-turns have conformational strain 43–45 kcal/mol lower than the Cyc structure. However, the cyclic-like conformer interacts with water about 39 kcal/mol strongly than the open β-turns. Our simulations are the first application of the recently developed multidimensional conformational free energy thermodynamic integration (CFTI) protocol to a solvated system, with fast convergence of the free energy obtained by fixing all flexible dihedrals. Additionally, the availability of the CFTI multidimensional free energy gradient leads to a new decomposition scheme, giving the contribution of each fixed dihedral to the overall free energy change and providing additional insight into the microscopic mechanisms of the studied processes. Received: 20 April 1998 / Accepted: 9 September 1998 / Published online: 7 December 1998     

Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal

Different biomolecular force fields (OPLS‐AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the C_a atoms of lysozymes are about 0.1 to 0.2 nm from OPLS‐AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B‐factors, whereas OPLS‐AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten‐fold slower than in bulk phase. The directional and average water diffusivities from OPLS‐AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS‐AA and AMBER03 predict larger hydrophilic solvent‐accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS‐AA for lysozyme and the Kirkwood‐Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid

We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.     

Kinetics and mechanism of the oxidation of dibenzothiophene in hydrocarbon solution Oxidation by aqueous hydrogen peroxide-acetic acid mixtures

The oxidation of white oil solutions of dibenzothiophene (DBT) by aqueous hydrogen peroxide-acetic acid solutions was studied kinetically at 50–100°. Under these conditions, the rate of DBT oxidation was found to be first order in acetic acid, second order in hydrogen peroxide, and inversely proportional to the water concentration. The activation energy between 50–100° in 64·5% acetic acid was 14 kcal/mole. We have also found that the monoxide is oxidized about 1·4 times faster than DBT. A mechanism consistent with the kinetic data has been postulated. The rate-determining step appears to be attack of a peracetic acid-hydrogen peroxide dimer on the sulfur atom of DBT.     

New insight on the origin of the unusual acidity of Meldrum's acid from ab initio and combined QM/MM simulation study.

Ab initio molecular orbital and combined QM/MM Monte Carlo simulations have been carried out to investigate the origin of the unusually high acidity of Meldrum's acid. Traditionally, the high acidity of Meldrum's acid relative to that of methyl malonate has been attributed to an additive effect due to the presence of two E esters in the dilactone system. However, the present study reveals that there is significant nonadditive effect that also makes major contributions. This results from preferential stabilization of the enolate anion over that of Meldrum's acid due to anomeric stereoelectronic interactions. To investigate solvent effects on the acidity in aqueous solution, the relative acidities of Z and E conformers of methyl acetate have been determined in combined ab initio QM/MM simulations. There is significant solvent effect on the conformational equilibria for both the neutral ester and its enolate anion in water, leading to stabilization of the E stereoisomer. However, the computed solvent effect of 4.4 kcal/mol in favor of the E isomer of methyl acetate is largely offset by the favorable solvation of 3.4 kcal/mol for the E conformer of the enolate anion. This leads to an enhanced acidity of 3.4 kcal/mol for the (E)-methyl acetate in water over the Z conformer. In Meldrum's acid, it is the preferential stabilization of the enolate anion due to anomeric effects coupled with the intrinsically higher acidity of the E conformation of ester that is responsible for its high acidity.     

A vibrational sum frequency spectroscopy study of the liquid-gas interface of acetic acid-water mixtures: 1. Surface speciation

Aqueous acetic acid solutions have been studied by vibrational sum frequency spectroscopy (VSFS) in order to acquire molecular information about the liquid-gas interface. The concentration range 0-100% acetic acid has been studied in the CH/OH and the C-O/C=O regions, and in order to clarify peak assignments, experiments with deuterated acetic acid and water have also been performed. Throughout the whole concentration range, the acetic acid is proven to be protonated. It is explicitly shown that the structure of a water surface becomes disrupted even at small additions of acetic acid. Furthermore, the spectral evolution upon increasing the concentration of acetic acid is explained in terms of the different complexes of acetic acid molecules, such as the hydrated monomer, linear dimer, and cyclic dimer. In the C=O region, the hydrated monomer is concluded to give rise to the sum frequency (SF) signal, and in the CH region, the cyclic dimer contributes to the signal as well. The combination of results from the CH/OH and the C-O/C=O regions allows a thorough characterization of the behavior of the acetic acid molecules at the interface to be obtained.     

The effect of hydrogen bonding on oligoleucine structure in water: A molecular dynamics simulation study

Molecular dynamics simulations were conducted in order to improve our understanding of the forces that determine polyleucine chains conformations and govern polyleucine self-assembly in aqueous solutions. Simulations of 10 repeat unit oligoleucine in aqueous solution were performed using the optimized potential for liquid simulations (OPLS) - all atom force field using the canonical ensemble for a minimum of 1.3 ns. These simulations provided information on conformations, chain collapse and intermolecular aggregation. Simulations indicate that single isotactic oligoleucine chains in dilute solution assume tightly packed, regular hairpin conformations while atactic oligoleucine assumes a much less regular and less compact structure. The regular, compact collapsed isotactic chain exhibited a greater degree of intramolecular hydrogen bonding and an increased level of hydrophobic t-butyl functional group aggregation compared to the atactic chain. This occurs at the expense of reduced leucine-water hydrogen bonding.     

Molecular Dynamics Insights into Electron-Catalyzed Dissociation Repair of Cyclobutane Pyrimidine Dimer

Excess electrons are not only an important source of radiation damage, but also participate in the repair process of radiation damage such as cyclobutane pyrimidine dimer (CPD). Using ab initio molecular dynamics (AIMD) simulations, we reproduce the single excess electron stepwise catalytic CPD dissociation process in detail with an emphasis on the energy levels and molecular structure details associated with excess electrons. On the basis of the AIMD simulations on the CPD aqueous solution with two vertically added excess electrons, we exclude the early-proposed [2+2]-like concerted synchronous dissociation mechanism, and analyze the difference between the symmetry of the actual reaction and the symmetry of the frontier molecular orbitals which deeply impact the mechanism. Importantly, we propose a new model of the stepwise electron-catalyzed dissociation mechanism that conforms to the reality. This work not only provides dynamics insights into the excess electron catalyzed dissociation mechanism, but also reveals different roles of two excess electrons in two bond-cleavage steps (promoting versus inhibiting).     

Ab initio GB study of prebiotic synthesis of purine precursors from aqueous hydrogen cyanide: dimerization reaction of HCN in aqueous solution

Ab initio MO GB theory which includes the continuum model of solvent effect using generalized Born formula has been applied to the dimerization reaction of HCN in aqueous solution which is the starting step in prebiotic synthesis of purine precursors from aqueous hydrogen cyanide. Three steps considered were: (i) the reaction of HCN and H₂O to produce the CN⁻ anion, (ii) the reaction of CN⁻ with HCN to give the NC–CH=N⁻ anion, and (iii) the addition of a proton to the anion to give iminoacetonitrile. The formation of CN⁻ ion from HCN in aqueous solution requires 15.1 kcal/mol (the experimental value estimated from the dissociation constant of HCN in water is 14.8 kcal/mol). The reaction of CN⁻ with HCN requires the activation energy of 32.2 kcal/mol (MP2/6-31++G^**//HF/6-31++G^**) to give the dimer. This barrier height is reduced to 26.1 kcal/mol when HCN is associated with H₃O⁺. In the presence of NH₃ in aqueous solution, CN⁻ is produced easily by the reaction of HCN and NH₃ with a low activation energy of 4.3 kcal/mol. It was shown that the formation of CN⁻ becomes easier in ammoniacal solution, and the dimerization occurs efficiently in aqueous solutions which contain NH₃.     

A theoretical study of the photodetachment and intramolecular hydrogen-bonding energies of hydrogen maleate anions

Three low-lying conformers of the hydrogen maleate anions (HMAs) regarding cis-HMA(HB) having the O-...HO intramolecular hydrogen bond (HB), cis-HMA(nHB) without the HB, and trans-HMA are studied by density functional theory (B3LYP) combined with natural bond orbital (NBO) and atoms-in-molecules (AIM) analyses. The photoelectron spectra of cis- and trans-HMA conformers recorded by Woo et al. (J. Phys. Chem. A 2005, 109, 10633) are reassigned on the basis of the present electron propagator theory calculations, indicating the significant energy differences between the Dyson orbitals and canonical molecular orbitals due to the electron-correlation and orbital relaxation effects considered in the electron propagator theory. The NBO associated with the natural resonance theory analyses and AIM electron topological study show that the strong O-...HO in cis-HMA(HB) has the remarkable characteristics of three-center four-electron hyperbond, and the bonding strength of ca. 30 kcal/mol is recommended with the reference calculations of the HO-...HOH complex. The further calculations for the microhydrated cis-HMA(HB) clusters indicate that the O-...HO bonding strength decreases in water solution.     

Experimental dipole moments for nonisolatable acetic acid structures in a nonpolar medium. A combined spectroscopic, dielectric, and DFT study for self-association in solution

Acetic acid can exist in many possible structural forms depending on its surrounding medium. A recently developed inverse problem methodology (J. Phys. Chem. B 2007, 111, 13064-13074) was utilized in order to elucidate acetic acid structures in a dilute nonpolar medium. In this regard, simultaneous and stopped-flow measurements of the bulk solution densities, refractive indices, relative permittivities, and IR spectra of acetic acid in toluene were performed at several different concentrations in a semibatch closed-loop experimental setup at 298.15 K and 0.1013 MPa. This combined IR spectroscopic and dielectric, density, and refractive index analysis was employed in order to distinguish acetic acid structures and to further determine the dipole moments of the monomer, cyclic dimer, and "lumped-sum" open dimers. The infrared spectra were first analyzed to provide qualitative understanding as well as quantitative estimates for each acetic acid species. Subsequently, the dipole moments of these species were calculated using a direct approach which was primarily based on response surface models. The present method allows the determination of individual dipole moments not only for the monomer but also for the cyclic dimer and the open dimer. The results obtained from this study experimentally show that the cyclic dimer with centrosymmetric structure has a dipole moment approximately 0 D. The results also suggest that the linear dimers are present as mixtures of linear dimers structures. The existence of the linear dimers mixture was also indicated by the experimental infrared analysis of the OH-stretching region (particularly for measurements in n-hexane as solvent) and comparison of these spectra with DFT predictions. Finally, the present methodology which incorporates simultaneous physicochemical and spectroscopic analysis is undoubtedly useful for physicochemical characterization for other nonisolatable solute species and self-associated structures in solution.