Photoionization-induced dynamics of ammonia: ab initio potential energy surfaces and time-dependent wave packet calculations for the ammonia cation

An analytical anharmonic six-dimensional three-sheeted potential energy surface for the ground and first excited states of the ammonia cation has been developed which is tailored to model the ultrafast photoinduced dynamics. Selected ab initio cuts, obtained by multireference configuration interaction calculations, have been used to determine the parameters of a diabatic representation for this Jahn-Teller and pseudo-Jahn-Teller system. The model includes higher-order coupling terms both for the Jahn-Teller and for the pseudo-Jahn-Teller matrix elements. The relaxation to the ground state is possible via dynamical pseudo-Jahn-Teller couplings involving the asymmetric bending and stretching coordinates. The photoelectron spectrum of NH3 and the internal conversion dynamics of NH3+ have been determined by wave packet propagation calculations employing the multiconfigurational time-dependent Hartree method. Three different time scales are found in the dynamics calculations for the second absorption band. The ultrafast Jahn-Teller dynamics of the two excited states occurs on a 5 fs time scale. The major part of the internal conversion to the ground state takes place within a short time scale of 20 fs. This fast internal conversion is, however, incomplete and the remaining excited state population does not decay completely even within 100 fs.     

Structure and dynamics of hydrated NH(4) (+): an ab initio QM/MM molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH(4) (+) in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree-Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH(4) (+) is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH(4) (+) in water. This phenomenon has resulted from multiple coordination, which drives the NH(4) (+) to translate and rotate quite freely within its surrounding water molecules. In addition, a "structure-breaking" behavior of the NH(4) (+) is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.     

Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation

An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 ?, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.     

The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water

The performance of density functional theory methods for the modeling of condensed aqueous systems is hard to predict and validation by ab initio molecular simulation of liquid water is absolutely necessary. In order to assess the reliability of these tests, the effect of temperature on the structure and dynamics of liquid water has been characterized with 16 simulations of 20 ps in the temperature range of 280-380 K. We find a pronounced influence of temperature on the pair correlation functions and on the diffusion constant including nonergodic behavior on the time scale of the simulation in the lower temperature range (which includes ambient temperature). These observations were taken into account in a consistent comparison of a series of density functionals (BLYP, PBE, TPSS, OLYP, HCTH120, HCTH407). All simulations were carried out using an ab initio molecular dynamics approach in which wave functions are represented using Gaussians and the density is expanded in an auxiliary basis of plane waves. Whereas the first three functionals show similar behavior, it is found that the latter three functionals yield more diffusive dynamics and less structure.     

An ab initio molecular orbital study on the gas-phase rapid reaction of the silicon cation Si with ammonia

The gas-phase rapid ion-molecule reaction Si⁺ (²P) + NH₃→ SiNH₂⁺ + H is theoretically investigated by the ab initio molecular orbital methods. Several possible pathways (A, B, C) on its potential energy surface have been examined, discussed and compared. Theoretical calculations indicate that pathway A is favourable in energy and that the reaction begins by forming a collision complex of the ion-dipole molecule Si-NH⁺₃, which forms with no barrier into the first energy well of the reaction coordinate. Migration of an H atom from an N atom to a Si atom forms the intermediate HSi-NH⁺₂, which corresponds to the second energy well and can fragment to the observed product SiNH⁺₂ by losing an H atom from the Si atom. The barriers for migration and fragmentation are 52.5 and 38.6 kcal mol⁻¹ respectively. Pathway A has a negative activation energy of −42.1 kcal mol⁻¹.     

Computing the 7Li NMR chemical shielding of hydrated Li+ using cluster calculations and time-averaged configurations from ab initio molecular dynamics simulations

Ab initio molecular dynamics (AIMD) simulations have been used to predict the time-averaged Li NMR chemical shielding for a Li(+) solution. These results are compared to NMR shielding calculations on smaller Li(+)(H(2)O)(n) clusters optimized in either the gas phase or with a polarizable continuum model (PCM) solvent. The trends introduced by the PCM solvent are described and compared to the time-averaged chemical shielding observed in the AIMD simulations where large explicit water clusters hydrating the Li(+) are employed. Different inner- and outer-coordination sphere contributions to the Li NMR shielding are evaluated and discussed. It is demonstrated an implicit PCM solvent is not sufficient to correctly model the Li shielding, and that explicit inner hydration sphere waters are required during the NMR calculations. It is also shown that for hydrated Li(+), the time averaged chemical shielding cannot be simply described by the population-weighted average of coordination environments containing different number of waters.     

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.     

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.     

An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

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.     

Molecular orbital propagation to accelerate self-consistent-field convergence in an ab initio molecular dynamics simulation

Based on the idea of molecular orbital (MO) propagation, we propose a novel effective method for predicting initial guesses for the self-consistent-field calculations in direct ab initio molecular dynamics (AIMD) simulations. This method, called LIMO, adopts the Lagrange interpolation (LI) polynomial technique and predicts initial MO coefficients at the next AIMD step by using several previous results. Taking into account the crossing and/or mixing of MOs leads to orbital invariant formulas for the LIMO method. We also propose a simple method for determining the optimal degree of the LI polynomial, which corresponds to the number of previous steps. Numerical tests confirm that this proposed method is both effective and feasible.     

The molecular structure of fluoromalononitrile as determined by gas-phase electron diffraction and ab initio calculations

The molecular structure of fluoromalononitrile was studied by means of gas-phase electron diffraction and quantum mechanical methods using HF/6-31G(d), MP2/6-311++G(2df,2pd) and DFT/B3LYP/6-31G(d), B3PW91/6-31G(d), B3LYP/6-311++G(2df,2pd) and B3PW91/6-311++G(2df,2pd). The r(g) and angle(alpha) structural parameters we obtained from the present analysis are: CC=1.487(5) A, CN=1.157(3) A, CF=1.386(5) A, CH=1.096 A (ass.), angleCCC=106.7(1.0) degrees , angleCCF=108.0(0.7) degrees , angleCCN=177.6(2.0) degrees . Uncertainties in parenthesis are 3sigma.     

Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics

Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Photochemistry of visual pigment chromophore models by ab initio molecular dynamics

Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

The dynamics and spectroscopic fingerprint of hydroxyl radical generation through water dimer ionization: ab initio molecular dynamic simulation study

Water decomposition process was investigated by ab initio molecular dynamic simulations using a model of (H(2)O)(2)(+) clusters. The proton transfer (PT) process from the cationic H-donor water to the H-acceptor water for the formation of (HO˙)·H(3)O(+) was predicted as about 90 fs on average calculated at CCSD level of theory. The valence-electron transfer (VET) process through the formation of hemibond interaction between neutral and cationic water, (H(2)O)(2)(+), was also identified in several collected trajectories. Both PT and VET processes were found to propagate along two orthogonal reaction coordinates, the former was through an intermolecular hydrogen bond and the latter required oxygen-oxygen hemibonding. Significant difference of the theoretical electronic transitions along the VET trajectories was also observed in comparison with the non-VET cases, being calculated at SAC-CI level. The strong absorption features of hemibonding (H(2)O)(2)(+) may introduce an interesting consideration for experimental design to monitor the water decomposition process.     

Wavelet transform analysis of ab initio molecular dynamics simulation: application to core-excitation dynamics of BF3

We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF(3) (B1s --> 2a(2) (')) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs.     

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.