Ionization of aqueous cations: photoelectron spectroscopy and ab initio calculations of protonated imidazole

Photoelectron spectroscopy and ab initio calculations employing a nonequilibrium polarizable continuum model were employed for determining the vertical ionization potential of aqueous protonated imidazole. The experimental value of 8.96 eV is in in excellent agreement with calculations, which also perform quantitatively for ionization of aqueous alkali cations as benchmark species. The present results show that protonation of imidazole increases its vertical ionization potential up in water by 0.7 eV, which is significantly larger than the resolution of the experiment or the error of the calculation. This combined experimental and computational approach may open the possibility for quantitatively analyzing the protonation state of histidine, of which imidazole is the titratable side chain group, in aqueous peptides and proteins.     

Electron binding energies of hydrated H3O+ and OH-: photoelectron spectroscopy of aqueous acid and base solutions combined with electronic structure calculations

The electronic structure of hydrated H3O+ and OH- is probed in a water jet by photoelectron spectroscopy employing 100 eV photons. The first ionization potential for OH- at 9.2 eV and the second ionization potential for H3O+ at 20 eV are resolved, corresponding to the removal of an electron from the 2ppi highest occupied molecular orbital and from the 1e orbital, respectively. These assignments are supported by present computational results based on a combination of molecular dynamics and ab initio calculations.     

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.     

The molecular energy levels of the azoles: A study by photoelectron spectroscopy and ab initio molecular orbital calculations

HeI photoelectron spectroscopy and ab initio calculations have been applied to the azoles, providing sets of energy levels that correlate well with each other in the upper valence shell region. Observed IPs are assigned to the three π- and to the five o-levels that involve (principally) valence shell p orbitals. The observed vibration structure is not particularly informative as an aid to assignment since both π-and σ-levels give some bands with vibration structure. The calculations provide in addition to eigenvalues (energy levels) a set of eigenvectors, permitting analysis of the bonding characteristics of the levels, and trends apparent within the series.     

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.     

Ab initio calculations for absorption and emission energies of alkali halide crystals doped with thallium

We calculate transition energies associated with optical properties of thallium doping in alkali halide crystals via an atomic cluster of minimal size where an sp‐valence‐shell impurity enters as a substitutional defect in the model crystal. Hartree–Fock (HF), density functional theory (DFT), and configuration interaction (CI) [CIS (CI with single excitation) and QCISD (single plus double and quadruple excitation)] calculations are performed to theoretically obtain the absorption and emission energies as vertical transitions evaluated at the ground and first excited‐state optimized geometries, respectively, where the optimization is carried out separately with the HF and DFT methods. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 785–790, 2000     

Microscopic solvation of NaBO2 in water: anion photoelectron spectroscopy and ab initio calculations

We investigated the microscopic solvation of NaBO(2) in water by conducting photoelectron spectroscopy and ab initio studies on NaBO(2)(-)(H(2)O)(n) (n = 0-4) clusters. The vertical detachment energy (VDE) of NaBO(2)(-) is estimated to be 1.00 ± 0.08 eV. The photoelectron spectra of NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) are similar to that of bare NaBO(2)(-), except that their VDEs shift to higher electron binding energies (EBE). For the spectra of NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4), a low EBE feature appears dramatically in addition to the features observed in the spectra of NaBO(2)(-)(H(2)O)(0-2). Our study shows that the water molecules mainly interact with the BO(2)(-) unit in NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) clusters to form Na-BO(2)(-)(H(2)O)(n) type structures, while in NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4) clusters, the water molecules can interact strongly with the Na atom, therefore, the Na-BO(2)(-)(H(2)O)(n) and Na(H(2)O)(n)···BO(2)(-) types of structures coexist. That can be seen as an initial step of the transition from a contact ion pair (CIP) structure to a solvent-separated ion pair (SSIP) structure for the dissolution of NaBO(2).     

Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics.

We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

Electron transfer reactions in photoelectron emission spectroscopy of aqueous solutions

Lowering of the emission yield of anions by certain cations (e.g. H⁺, Fe²⁺, Ba²⁺) is interpreted as the result of electron transfer between anions and cations. An equation is derived which predicts the exponential dependence of the yield on concentration of electron acceptor at constant emitter concentration. This equation is verified by experiment.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

A set of molecular models for alkali and halide ions in aqueous solution

This work presents new molecular models for alkali and halide ions in aqueous solution. The force fields were parameterized with respect to the reduced liquid solution density at 293.15 K and 1 bar, considering all possible ion combinations simultaneously. The experimental target data are reproduced with a high accuracy over a wide range of salinity. The ion models predict structural properties of electrolyte solutions well, such as pair correlation functions and hydration numbers. The force fields provide good predictions of the properties studied here in combination with different models for water.     

Flexible H2O2 in water: electronic structure from photoelectron spectroscopy and ab initio calculations

The effect of hydration on the electronic structure of H(2)O(2) is investigated by liquid-jet photoelectron spectroscopy measurements and ab initio calculations. Experimental valence electron binding energies of the H(2)O(2) orbitals in water are, on average, 1.9 eV red-shifted with respect to the gas-phase molecule. A smaller width of the first peak was observed in the photoelectron spectrum from the solution. Our experiment is complemented by simulated photoelectron spectra, calculated at the ab initio level of theory (with EOM-IP-CCSD and DFT methods), and using path-integral sampling of the ground-state density. The observed shift in ionization energy upon solvation is attributed to a combination of nonspecific electrostatic effects (long-range polarization) and of the specific interactions between H(2)O(2) and H(2)O molecules in the first solvation shell. Changes in peak widths are found to result from merging of the two lowest ionized states of H(2)O(2) in water due to conformational changes upon solvation. Hydration effects on H(2)O(2) are stronger than on the H(2)O molecule. In addition to valence spectra, we report oxygen 1s core-level photoelectron spectra from H(2)O(2)(aq), and observed energies and spectral intensities are discussed qualitatively.     

Conformational studies of n-propylamine by combined ab initio MO calculations and Raman spectroscopy

The results of ab initio SCF-MO calculations performed with a 3-21G(N*) basis set, for fully optimized geometries of five conformations of n-propylamine, are presented. The calculated relative order of total energies for these conformers is TT≈GG′>TG>GT>GG. At 300 K, the Boltzmann distribution of populations is 18, 37, 20, 19 and 7%, respectively.Raman spectra of n-propylamine and n-propylamine-N-d₂ in the liquid phase exhibit a number of bands whose temperature-dependent intensities clearly suggest the occurrence of different conformers in simultaneous equilibria. Deuteration of the amine group originates pairs of Raman bands at 428 and 440 cm⁻¹ and at 863 and 885 cm⁻¹. The bands at 428 and 885 cm⁻¹ are favoured by reduction of temperature. Normal coordinate calculations permit the assignment of the Raman and i.r. spectra in good agreement with experimental evidence. Among the five possible conformers of n-propylamine, it is possible to detect the presence of at least three conformations in the liquid phase, corresponding to the skeletal trans (TT and GT) and at least one of the skeletal gauche (TG, GG or GG′) forms. In the solid phase, only the bands ascribed to the TT form were observed.The ab initio results for the isolated molecule show that the all-trans conformation, TT, and the conformation GG′ have the smallest energies. On the other hand, the vibrational results for the liquid and solid phases indicate that the all-trans conformation, TT, is the more populated form. In addition, this conformer presents the highest calculated dipole moment, in good agreement with the liquid phase Raman spectroscopic results which point out that this conformation is favoured by polar solvents. Intermolecular interactions operating in the liquid n-propylamine, possibly of the hydrogen bonding type, are responsible for altering the relative order of conformational stability as predicted by the ab initio SCF-MO results for the isolated molecule.     

Insights into photodissociation dynamics of propionyl chloride from ab initio calculations and molecular dynamics simulations

The potential energy surfaces of isomerization, dissociation, and elimination reactions for CH3CH2COCl in the S0 and S1 states have been mapped with the different ab initio calculations. Mechanistic photodissociation of CH3CH2COCl at 266 nm has been characterized through the computed potential energy surfaces, the optimized surface crossing structure, intrinsic reaction coordinate, and ab initio molecular dynamics calculations. Photoexcitation at 266 nm leads to the CH3CH2COCl molecules in the S1 state. From this state, the C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the matrix and the internal conversion to the ground state prevails in the condensed phase. The HCl eliminations as a result of internal conversion to the ground state become the dominant channel upon photodissociation of CH3CH2COCl in the argon matrix at 10 K.     

Specific interactions and binding free energies between thermolysin and dipeptides: molecular simulations combined with ab initio molecular orbital and classical vibrational analysis

Thermolysin (TLN) is a metalloprotease widely used as a nonspecific protease for sequencing peptide and synthesizing many useful chemical compounds by the chemical industry. It was experimentally shown that the activity and functions of TLN are inhibited by the binding of many types of amino acid dipeptides. However, the binding mechanisms between TLN and dipeptides have not been clarified at the atomic and electronic levels. In this study, we investigated the binding mechanisms between TLN and four dipeptides. Specific interactions and binding free energies (BFEs) between TLN and the dipeptides were calculated using molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital (FMO) methods. The molecular systems were embedded in solvating water molecules during calculations. The calculated BFEs were qualitatively consistent with the trend of the experimentally observed inhibition of TLN activity by binding of the dipeptides. In addition, the specific interactions between the dipeptides and each amino acid residue of TLN or solvating water molecules were elucidated by the FMO calculations.     

The electronic structure of some heterocycles with bridgehead nitrogen: photoelectron spectra and ab initio molecular orbital calculations

He(I) and He(II) photoelectron spectra are reported for the cycl[3,3,3]azine (1), cycl[3,2,2]azine (2), indolizine (6) and imidazo[1,2-a] pyridine (7), as well as He(I) spectra for related compounds (3–5). Ab initio molecular orbital calculations have been used to assign the spectra of 1, 2, 3, 6 and 7, and to give information about the nature of the π-electron energy levels. The first IP for 1 is singularly low (5.86 eV), and this has been interpreted in terms of occupancy of the 1a₁'' orbital which is normally vacant in related compounds. In the cyclazines, the nitrogen lone pair seems to be split into two π-levels.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.