Targeted Car-Parrinello molecular dynamics: elucidating double proton transfer in formic acid dimer

The targeted molecular dynamics method, making possible the study of rare events, has been assessed in the framework of Car-Parrinello ab initio molecular dynamics. As a test case, we have studied the staggered-eclipsed rotation of ethane. The technique has subsequently been applied to investigate the nature of double proton transfer in formic acid dimer. The latter is found to follow a concerted transfer mechanism involving an essentially planar transition state. A "funnel-like region" of the potential energy surface is identified, where floppy intermolecular modes stiffen upon approaching the transition state.     

Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system

We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.     

Hydration of Y3+ ion: a Car-Parrinello molecular dynamics study

The solvation shell structure of Y3+ and the dynamics of the hydrated ion in an aqueous solution of 0.8 M YCl3 are studied in two conditions with and without an excess proton by using first principles molecular dynamics method. We find that the first solvation shell around Y3+ contains eight water molecules forming a square antiprism as expected from x-ray absorption near edge structure in both the conditions we examined. A detailed analysis relying upon localized orbitals reveals that the complexation of water molecules with yttrium cation leads to a substantial amount of charge redistribution particularly on the oxygen atoms, giving rise to the chemical shifts of approximately -20 ppm in 17O nuclear magnetic resonance relative to the computed nuclear shieldings of the bulk water.     

Hyperfine coupling tensors of the benzosemiquinone radical anion from Car-Parrinello molecular dynamics.

Based on Car-Parrinello ab initio molecular dynamics simulations of the benzosemiquinone radical anion in both aqueous solution and the gas phase, density functional calculations provide the currently most refined EPR hyperfine coupling (HFC) tensors of semiquinone nuclei and solvent protons. For snapshots taken at regular intervals from the molecular dynamics trajectories, cluster models with different criteria for inclusion of water molecules and an additional continuum solvent model are used to analyse the HFCs. These models provide a detailed picture of the effects of dynamics and of different intermolecular interactions on the spin-density distribution and HFC tensors. Comparison with static calculations allows an assessment of the importance of dynamical effects, and of error compensation in static DFT calculations. Solvent proton HFCs depend characteristically on the position relative to the semiquinone radical anion. A point-dipolar model works well for in-plane hydrogen-bonded protons but deviates from the quantum chemical values for out-of-plane hydrogen bonding.     

Dissociation energy and vibrational predissociation dynamics of the ammonia dimer

Experiments using infrared excitation of either the intramolecular symmetric N-H stretch (ν(NH,S)) or the intramolecular antisymmetric N-H stretch (ν(NH,A)) of the ammonia dimer ((NH(3))(2)) in combination with velocity-map ion imaging provide new information on the dissociation energy of the dimer and on the energy disposal in its dissociation. Ion imaging using resonance enhanced multiphoton ionization to probe individual rovibrational states of one of the ammonia monomer fragments provides recoil speed distributions. Analyzing these distributions for different product states gives a dissociation energy of D(0) = 660 ± 20 cm(-1) for the dimer. Fitting the distributions shows that rotations are excited up to their energetic limit and determines the correlation of the fragment vibrations. The fragments NH(3)(ν(2) = 3(+)) and NH(3)(ν(2) = 2(+)) have a vibrational ground-state partner NH(3)(ν = 0), but NH(3)(ν(2) = 1(+)) appears in partnership with another fragment in ν(2) = 1. This propensity is consistent with the idea of minimizing the momentum gap between the initial and final states by depositing a substantial fraction of the available energy into internal excitation.     

Through hydrogen-bond vibrational coupling in hydrogen-bonding chains of 4-pyridones with implications for peptide amide I absorptions: density functional theory compared with transition dipole coupling

We present B3LYP/D95** calculations on the C=O and N-H couplings in H-bonded chains of 4-pyridones. 14C-substitutions are used to decouple various vibrations for purposes of illustration. The coupled C=O vibrations bear analogy to the amide I bands of proteins and peptides. The coupling of the C=O's occurs primarily via the cooperative H-bonds rather than transition dipole coupling (TDC), as demonstrated by the fact that (1) the couplings are greater than previously reported for similar studies on formamides despite the larger distance between the C=O's in the pyridone chains (TDC coupling decreases with distance) and (2) the red shifts (also greater than for formamides) can be attributed to the changes in the geometries (particularly the C=O bond lengths) of the individual 4-pyridones in the H-bonding chains induced by the H-bonds and resulting polarization of the monomers.     

Calculation of the hydrogen-bond NMR shift in the water dimer

The shielding constant of the hydrogen-bonded proton in the linear perpendicular water dimer is calculated from the SCF MO LCGO wavefunction unsing the uncoupled Hartree-Fock variation-perturbation procedure of Karplus and Kolker. The obtained result (27.61 ppm) is compared with the experimental estimate of the proton shielding in the liquid water (25.62 ppm). Comparing with the proton shielding in the water molecule, calculated previously within the same approximation (28.30 ppm), the non-empirical hydrogen-bond shift of −0.69 ppm is found.     

Car-Parrinello molecular dynamics study of anharmonic systems: a Mannich base in solution

A Car-Parrinello molecular dynamics study was performed for 4,5-dimethyl-2-(N,N-dimethylaminomethyl)phenol, a Mannich base, to investigate the vibrational properties in solution of its intramolecular hydrogen bond. The dynamic behavior of this hydrogen-bonded system was investigated using an explicit solvent model. Addition of a nonpolar solvent permitted inclusion of delicate environmental effects on the strongly anharmonic system which was studied from first principles. Molecular dynamics and a posteriori quantization of the O-H motion were applied to reproduce the vibrational features of the O-H stretching mode. Consistent application of Car-Parrinello dynamics based on the density functional theory with subsequent solution of the vibrational Schr?dinger equation for the O-H stretching motion offers an effective method for strongly anharmonic systems, and this is supported by the comparison of the results with experimental spectra. As a further element of the intramolecular hydrogen bond study, the effects of deuteration were taken into account and a successful application of the O-H stretching mode quantization technique to the liquid phase is demonstrated. This provides a valuable computational methodology for investigations incorporating nuclear quantum effects in the liquid phase and enzyme active centers and can be used to investigate numerous systems that are not readily susceptible to experimental analysis.     

Car-Parrinello molecular dynamics study of the rearrangement of the valeramide radical cation

Car-Parrinello molecular dynamics (CPMD) studies of neutral (1) and ionized (1 (+.)) valeramide are performed with the aim of providing a rationalization for the unusual temperature effect on the dissociation pattern of 1(+.) observed in mass spectrometric experiments. According to CPMD simulations of neutral valeramide 1 performed at approximately 500 K, the conformation with the fully relaxed carbon backbone predominates (96 %). Conformational changes involving folding of the carbon backbone into conformers that would allow intramolecular H transfers are predicted not to take place spontaneously at this temperature because of the barrier heights associated with these transitions (3.5 and 6.9 kcal mol(-1)), which cannot be overcome by thermal motion alone. For 1(+.), CPMD simulations performed at approximately 300 K reveal a substantial stability of a conformation in which the carbon backbone is fully relaxed; no reaction is observed even after 7 ps. However, when conformers with already folded carbon-backbones are used as initial geometries in the CPMD simulations, the gamma-hydrogen migration (McLafferty rearrangement resulting in C(3)H(6)) is already completed within 2 ps. For this important process, the free activation energy associated with both a required conformational change and the subsequent H transfer equals 4.5 kcal mol(-1), while for the formally related delta-H shift (which eventually gives rise to the elimination of C(2)H(4)/C(2)H(5.)) it amounts to 7.0 kcal mol(-1). Since the barriers associated with conformational changes are energetically more demanding than those of the corresponding hydrogen transfers, 1(+.) is essentially trapped by conformational barriers and long-lived at approximately 300 K. At elevated temperatures (500 K), the preferred reaction (within 7.3 ps) in the CPMD simulation corresponds to the McLafferty rearrangement. The estimated free activation energy associated with this process amounts to 2.5 kcal mol(-1), while the free activation energy for the delta-H transfer equals 4.4 kcal mol(-1). This relatively small free activation energy for the McLafferty rearrangement might cause dissociation of a substantial fraction of 1(+.) prior to the time-delayed mass selection, which would reduce the C3/C2 ratio in the experiments conducted with metastable ions that have a lifetime in the order of some micros at a source temperature of 500 K.     

Car-Parrinello molecular dynamics study of the blue-shifted F3CH...FCD3 system in liquid N2.

Fluoroform, as confirmed by both experimental and theoretical studies, can participate in improper H-bond formation, which is characterized by a noticeable increase in the fundamental stretching frequency nu(C-H) (so-called blue frequency shift), an irregular change of its integral intensity, and a C-H bond contraction. A Car-Parrinello molecular dynamics simulation was performed for a complex formed by fluoroform (F3CH) and deuterated methyl fluoride (FCD3) in liquid nitrogen. Vibrational analysis based on the Fourier transform of the dipole moment autocorrelation function reproduces the blue shift of the fundamental stretching frequency nu(C-H) and the decrease in the integral intensity. The dynamic contraction of the C-H bond is also predicted. The stoichiometry of the solvated, blue-shifted complexes and their residence times are examined.     

Imaging study of vibrational predissociation of the HCl-acetylene dimer: pair-correlated distributions

The state-to-state predissociation dynamics of the HCl-acetylene dimer were studied following excitation in the asymmetric C-H (asym-CH) stretch and the HCl stretch. Velocity map imaging (VMI) and resonance enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Different vibrational predissociation mechanisms were observed for the two excited vibrational levels. Following excitation in the of the asym-CH stretch fundamental, HCl fragments in upsilon = 0 and j = 4-7 were observed and no HCl in upsilon = 1 was detected. The fragments' center-of-mass (c.m.) translational energy distributions were derived from images of HCl (j = 4-7), and were converted to rotational state distributions of the acetylene co-fragment by assuming that acetylene is generated with one quantum of C-C stretch (nu(2)) excitation. The acetylene pair-correlated rotational state distributions agree with the predictions of the statistical phase space theory, restricted to acetylene fragments in 1nu(2). It is concluded that the predissociation mechanism is dominated by the initial coupling of the asym-CH vibration to a combination of C-C stretch and bending modes in the acetylene moiety. Vibrational energy redistribution (IVR) between acetylene bending and the intermolecular dimer modes leads to predissociation that preserves the C-C stretch excitation in the acetylene product while distributing the rest of the available energy statistically. The predissociation mechanism following excitation in the Q band of the dimer's HCl stretch fundamental was quite different. HCl (upsilon = 0) rotational states up to j = 8 were observed. The rovibrational state distributions in the acetylene co-fragment derived from HCl (j = 6-8) images were non-statistical with one or two quanta in acetylene bending vibrational excitation. From the observation that all the HCl(j) translational energy distributions were similar, it is proposed that there exists a constraint on conversion of linear to angular momentum during predissociation. A dimer dissociation energy of D(0) = 700 +/- 10 cm(-1) was derived.     

Simulation of vibrational spectra of polydichlorophosphazene by molecular dynamics calculations: A study of the relaxed and stretched polymer

The infrared and Raman spectra (frequencies and intensities) of polydichloro-phosphazene are calculated with the help of molecular dynamics methods; the spectral patterns are analysed in relation to the bond conformations along the backbone. The application of a longitudinal stress to the polymeric chains and the corresponding spectral variations are simulated by the use of an expanded simulation box.     

Intramolecular vibrational energy redistribution involving the torsion in CF3CH3: a molecular dynamics study

Classical trajectory calculations on intramolecular vibrational energy redistribution (IVR) involving the torsion in 1,1,1-trifluoroethane (TFE) are reported. Two potential energy functions (PEFs) are used to describe the potential energy surface. The "full" PEF gives excellent agreement with the experimental vibrational frequencies. The "simple" PEF omits nondiagonal interaction terms, but still gives very good agreement with the experimental frequencies. The "simple" PEF is intended to minimize mode-mode coupling. Neither PEF includes the HF elimination reaction. Calculations are carried out both with nominal microcanonical selection of initial coordinates and momenta, and with a modified selection method that places controlled amounts of energy in the torsion. Total (classical) vibrational energies from 0.005 to 140 kcal mol(-1) are investigated. The calculated time constants describing energy flow out of the torsional mode are <10 ps for classical vibrational energies near the classical reaction threshold energy (approximately 75 kcal mol(-1)) and greater. It is found that the rate of decay from the torsion largely depends on the amount of energy in the other vibrational modes. Analysis using power spectra shows that the torsional mode in TFE is strongly coupled to the other vibrational modes. These results strongly suggest that vibrational energy in TFE will not be sequestered in the torsion for time periods greater than a few tens of picoseconds when the molecule has enough energy to react via HF elimination.     

Effects of hydrogen-bond and cooperativity in the vibrational spectra of Luminol

Luminol, one of the most popular electrochemiluminescence systems used in forensic chemistry, proved to be a suitable system to study the importance of cooperativity in hydrogen-bond chains. The computational pairwise approach PiMM was applied to the system and a thorough band assignment was accomplished. Hydrogen-bond and hydrogen-bond cooperativity effects were assessed through a confrontation of energy, geometry and wavenumber changes from monomer and dimer on one hand and dimer and “full-cluster” trimer on the other. For the first time the PiMM method was also used to successfully predict changes in band relative intensities.     

Revisiting the structure of (LiCH3)n aggregates using Car-Parrinello molecular dynamics

The theoretical study of (LiMe)(n) aggregates using Car-Parrinello molecular dynamics was undertaken. With respect to a quantum chemical static treatment, this approach furnishes supplementary information about the structural parameters. Equilibrium structures are indeed stable to ca. 300 K, provided the methyl groups in the aggregates are considered to rotate essentially freely. The Li-C distance depends on the coordination number of Li and not so much on the degree of aggregation. Finally, above 650 K, the cubic LiCH(3) tetramer (which is energetically favored) undergoes an entropy-driven rearrangement to a planar structure.     

Car-Parrinello molecular dynamics study of the initial dinitrogen reduction step in Sellmann-type nitrogenase model complexes

We have studied reduction reactions for nitrogen fixation at Sellmann-type model complexes with Car-Parrinello simulation techniques. These dinuclear complexes are especially designed to emulate the so-called open-side FeMoco model. The main result of this work shows that in order to obtain the reduced species several side reactions have to be suppressed. These involve partial dissociation of the chelate ligands and hydrogen atom transfer to the metal center. Working at low temperature turns out to be one necessary pre-requisite in carrying out successful events. The successful events cannot be described by simple reaction coordinates. Complicated processes are involved during the initiation of the reaction. Our theoretical study emphasizes two experimental strategies which are likely to inhibit the side reactions. Clamping of the two metal fragments by a chelating phosphane ligand should prevent dissociation of the complex. Furthermore, introduction of tert-butyl substituents could improve the solubility and should thus allow usage of a wider range of (mild) acids, reductants, and reaction conditions.     

Intermolecular vibrational modes and orientational dynamics of cooperative hydrogen-bonding dimer of 7-azaindole in solution

We observed the low-frequency Raman-active intermolecular vibrational modes of 7-azaindole in CCl(4) by femtosecond Raman-induced Kerr effect spectroscopy. To understand the dynamical aspects and vibrational modes of 7-azaindole in the solution, the ultrafast dynamics of 1-benzofuran in CCl(4) was also examined as a reference and ab initio quantum chemistry calculations were performed for 7-azaindole and 1-benzofuran. The cooperative hydrogen-bonding vibrational bands of 7-azaindole dimer in CCl(4) appeared at 89 cm(-1) and 105 cm(-1) represent the overlap of stagger and wheeling modes and the intermolecular stretching mode, respectively. They are almost independent of the concentration in the solution. We further found from the low-frequency differential Kerr spectra of the solutions with neat CCl(4) that the intermolecular motion in the low frequency region below 20 cm(-1) was less active in the case of 7-azaindole/CCl(4) than in the case of 1-benzofuran/CCl(4). The slow orientational relaxation time in 7-azaindole/CCl(4) is ~3.5 times that in 1-benzofuran/CCl(4) because of the nature of the dimerization of 7-azaindole.     

Nature of vibrational coupling in helical peptides: an isotopic labeling study

Infrared (IR) and vibrational circular dichroism (VCD) spectra were measured for a series of isotopically ((13)C on two or more amide Cdouble bond]O) labeled, 25 residue, alpha-helical peptides of the sequence Ac-(AAAAK)(4)AAAAY-NH(2) that were also studied in the previous paper. Theoretical IR and VCD simulations were performed for correspondingly isotopically labeled Ac-A(24)-NHCH(3) constrained to an alpha-helical conformation by use of property tensor transfer from density functional theory (DFT) calculations on Ac-A(10)-NHCH(3). The simulations predicted and experiments confirmed that the vibrational coupling constants between i, i + 1 and i, i + 2 residues differ in sign, thus leading to a reversal of the (13)C VCD pattern and explaining the large shift in the (13)C amide I frequency as reported in the previous paper. The sign of the coupling constant remained consistent for larger label separation (with the exception of i, i + 4) and for more labels with uniform separation. Such effects confirm that the isotopically labeled group vibrations are essentially only coupled to each other and are effectively uncoupled from those of the unlabeled groups. This development confirms the utility of isotopic labels for site-specific structural studies with vibrational spectra. Observed spectral effects cannot be explained by considering only transition dipole coupling (TDC) between amide oscillators, particularly for smaller label separations, but the TDC and ab initio predicted couplings roughly converge at large separation.     

Seven-dimensional quantum dynamics study of the H+NH3-->H2+NH2 reaction

Initial state-selected time-dependent wave packet dynamics calculations have been performed for the H+NH3-->H2+NH2 reaction using a seven-dimensional model and an analytical potential energy surface based on the one developed by Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The model assumes that the two spectator NH bonds are fixed at their equilibrium values. The total reaction probabilities are calculated for the initial ground and seven excited states of NH3 with total angular momentum J=0. The converged cross sections for the reaction are also reported for these initial states. Thermal rate constants are calculated for the temperature range 200-2000 K and compared with transition state theory results and the available experimental data. The study shows that (a) the total reaction probabilities are overall very small, (b) the symmetric and asymmetric NH stretch excitations enhance the reaction significantly and almost all of the excited energy deposited was used to reduce the reaction threshold, (c) the excitation of the umbrella and bending motion have a smaller contribution to the enhancement of reactivity, (d) the main contribution to the thermal rate constants is thought to come from the ground state at low temperatures and from the stretch excited states at high temperatures, and (e) the calculated thermal rate constants are three to ten times smaller than the experimental data and transition state theory results.     

Quantum dynamics study of H+NH3-->H2+NH2 reaction

We report in this paper a quantum dynamics study for the reaction H+NH3-->NH2+H2 on the potential energy surface of Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The quantum dynamics calculation employs the semirigid vibrating rotor target model [J. Z. H. Zhang, J. Chem. Phys. 111, 3929 (1999)] and time-dependent wave packet method to propagate the wave function. Initial state-specific reaction probabilities are obtained, and an energy correction scheme is employed to account for zero point energy changes for the neglected degrees of freedom in the dynamics treatment. Tunneling effect is observed in the energy dependency of reaction probability, similar to those found in H+CH4 reaction. The influence of rovibrational excitation on reaction probability and stereodynamical effect are investigated. Reaction rate constants from the initial ground state are calculated and are compared to those from the transition state theory and experimental measurement.