A direct ab initio dynamics study of the water-assisted tautomerization of formamide

Direct ab initio dynamics calculations based on a canonical variational transition-state theory with several multidimensional semiclassical tunneling approximations were carried out to obtain rate constants for the water-assisted tautomerization of formamide. The accuracy of the density functionals, namely, B-LYP, B3-LYP, and BH&H-LYP, were examined. We found that the BH&H-LYP method yields the most accurate transition-state properties when comparing it to ab initio MP2 and QCISD results, whereas B-LYP and B3-LYP methods predict barrier heights too low. Reaction path information was calculated at both the MP2 and nonlocal hybrid BH&H-LYP levels using the 6–31G(d,p) basis set. At the BH&H-LYP level, we found that the zero-point energy motion lowers the barrier to tautomerization in the formamide-water complex by 3.6 kcal/mol. When tunneling is considered, the activation energy at the BH&H-LYP level at 300 K is 17.1 kcal/mol. This is 3.4 kcal/mol below the zero-point-corrected barrier and 7.0 kcal/mol below the classical barrier. Excellent agreement between BH&H-LYP and MP2 rate constants further supports the use of BH&H-LYP for rate calculations of large systems. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 861–874, 1997     

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.     

Ionization dynamics of aminopyridine dimer: a direct ab initio molecular dynamics (MD) study

The ionization dynamics of an aminopyridine dimer (AP)(2) has been investigated by means of the direct ab initio molecular dynamics (MD) method. It was found that the reaction process was composed of three steps after the vertical ionization of (AP)(2): dimer approach, proton transfer and energy relaxation. The timescales of these processes were 50-100, 10-20, and 200 fs, respectively. The timescale of the dimer approach was dependent on the initial separation between AP(+) and AP. After the ionization, AP approached gradually the ionized AP(+). The proton of AP(+) was transferred to AP at the nearest intermolecular distance, while the potential energy was quickly dropped according to the proton transfer. The energy relaxation of the dimer cation was significantly faster than that of the monomer cation. The mechanism of ionization dynamics of (AP)(2) was discussed on the basis of the theoretical results.     

Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.     

Direct ab initio dynamics study of the OH + HOCO reaction

The reaction between OH and HOCO has been examined using the coupled-cluster method to locate and optimize the critical points on the ground-state potential energy surface. The energetics are refined using the coupled-cluster method with basis set extrapolation to the complete basis set (CBS) limit. Results show that the OH + HOCO reaction produces H2O + CO2 as final products and the reaction passes through an HOC(O)OH intermediate. In addition, the OH + HOCO reaction has been studied using a direct dynamics method with a dual-level ab initio theory. Dynamics calculations show that hydrogen bonding plays an important role during the initial stages of the reaction. The thermal rate constant is estimated over the temperature range 250-800 K. The OH + HOCO reaction is found to be nearly temperature-independent at lower temperatures, and at 300 K, the thermal rate constant is predicted to be 1.03 x 10(-11) cm3 molecule(-1) s(-1). In addition, there may be an indication of a small peak in the rate constant at a temperature between 300 and 400 K.     

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.     

Ab initio molecular dynamics study on the electron capture processes of protonated methane (CH5+)

Electron capture dynamics of protonated methane (CH5(+)) have been investigated by means of a direct ab initio molecular dynamics (MD) method. First, the ground and two low-lying state structures of CH5 (+) with eclipsed Cs , staggered Cs and C2v symmetries were examined as initial geometries in the dynamics calculation. Next, the initial structures of CH5 (+) in the Franck-Condon (FC) region were generated by inclusion of zero point energy and then trajectories were run from the selected points on the assumption of vertical electron capture. Two competing reaction channels were observed: CH5 (+) + e (-)--> CH4 + H (I) and CH5 (+) + e (-) --> CH3 + H2 (II). Channel II occurred only from structures very close to the s- Cs geometry for which two protons with longer C-H distances are electronically equivalent in CH5 (+). These protons have the highest spin density as hydrogen atoms following vertical electron capture of CH5 (+) and are lost as H2. On the other hand, channel I was formed from a wide structural region of CH5 (+). The mechanism of the electron capture dynamics of CH5 is discussed on the basis of the theoretical results.     

Interaction between thymine dimer and flavin-adenine dinucleotide: a DFT and direct ab initio molecular dynamics study

The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.     

An ab initio SCF + CI study of the SH3 and SF3 radicals

The symmetric sulfuranyl radicals SH₃ and SF₃ are studied by means of ab initio SCF + CI calculations. All geometries are optimized at the UHF level using analytical gradients. SH₃ is found to be a transition state corresponding to a hydrogen exchange reaction, whereas SF₃ is stable with respect to decomposition to SF₂ + F.     

Nonadiabatic electron wavepacket dynamics of molecules in an intense optical field: an ab initio electronic state study

A theory of quantum electron wavepacket dynamics that nonadiabatically couples with classical nuclear motions in intense optical fields is studied. The formalism is intended to track the laser-driven electron wavepackets in terms of the linear combination of configuration-state functions generated with ab initio molecular orbitals. Beginning with the total quantum Hamiltonian for electrons and nuclei in the vector potential of classical electromagnetic field, we reduce the Hamiltonian into a mixed quantum-classical representation by replacing the quantum nuclear momentum operators with the classical counterparts. This framework gives equations of motion for electron wavepackets in an intense laser field through the time dependent variational principle. On the other hand, a generalization of the Newtonian equations provides a matrix form of forces acting on the nuclei for nonadiabatic dynamics. A mean-field approximation to the force matrix reduces this higher order formalism to the semiclassical Ehrenfest theory in intense optical fields. To bring these theories into a practical quantum chemical package for general molecules, we have implemented the relevant ab initio algorithms in it. Some numerical results in the level of the semiclassical Ehrenfest-type theory with explicit use of the nuclear kinematic (derivative) coupling and the velocity form for the optical interaction are presented.     

Ab initio direct dynamics study of cyclopropyl radical ring-opening

Quasiclassical direct dynamics simulations, at the CASSCF(3,3)/6-31G(d) level of theory, are used to study the stereochemistry of the electrocyclic ring-opening reaction of the cyclopropyl radical. The trajectories are initiated at the reaction's transition state (TS), with their initial conditions sampled from the TS's 174 degrees C Boltzmann distribution. Intrinsic reaction coordinate calculations predict the overall reaction to have disrotatory stereochemistry. Though this is the preferred initial reaction stereochemistry in the trajectories, 43% of the trajectories follow the conrotatory path. Four unique trajectory types are observed during 200 fs dynamics of the product allyl radical. Intramolecular vibrational energy redistribution and internal rotation are incomplete on this time scale, and a statistical distribution of the allyl isomers is not observed.     

TheRate: Program for ab initio direct dynamics calculations of thermal and vibrational-state-selected rate constants

We introduce TheRate (THEoretical RATEs), a complete application program with a graphical user interface (GUI) for calculating rate constants from first principles. It is based on canonical variational transition-state theory (CVT) augmented by multidimensional semiclassical zero and small curvature tunneling approximations. Conventional transition-state theory (TST) with one-dimensional Wigner or Eckart tunneling corrections is also available. Potential energy information needed for the rate calculations are obtained from ab initio molecular orbital and/or density functional electronic structure theory. Vibrational-state-selected rate constants may be calculated using a diabetic model. TheRate also introduces several technical advancements, namely the focusing technique and energy interpolation procedure. The focusing technique minimizes the number of Hessian calculations required by distributing more Hessian grid points in regions that are critical to the CVT and tunneling calculations and fewer Hessian grid points elsewhere. The energy interpolation procedure allows the use of a computationally less demanding electronic structure theory such as DFT to calculate the Hessians and geometries, while the energetics can be improved by performing a small number of single-point energy calculations along the MEP at a more accurate level of theory. The CH₄+H↔CH₃+H₂ reaction is used as a model to demonstrate usage of the program, and the convergence of the rate constants with respect to the number of electronic structure calculations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1039–1052, 1998     

Energy-flow dynamics in the molecular channel of propanal photodissociation, C2H5CHO --> C2H6 + CO: direct ab initio molecular dynamics study

Direct ab initio molecular dynamics calculations have been carried out for the molecular channel of the photodissociation of propanal, C2H5CHO --> C2H6 + CO, at the RMP2(full)/cc-pVDZ level of ab initio molecular orbital theory. The initial conditions were generated using the microcanonical sampling to put the excess energy randomly into all vibrational modes of the TS. Starting from the TS, a total of approximately 700 trajectories were numerically integrated for 100 fs. The obtained final energy distributions for the C2H6 and CO fragments and their relative translational motion were found to be quite similar to those obtained for the acetaldehyde reaction, CH3CHO --> CH4 + CO, in our previous study (Chem. Phys. Lett. 2006, 421, 549) despite the fact that the number of degree of freedom for C2H6 is larger than that for CH4. The coupling between the intrinsic reaction coordinate and one of the generalized normal modes orthogonal to it was predicted substantially strong around s = 1.4 amu(1/2) bohr, and it is expected that the energy flow out of C2H6 proceeds through this coupling. However, the obtained energy distributions strongly suggest that the coupling among the modes in C2H6 is quite small and the intramolecular energy redistribution does not occur efficiently in this molecule.     

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.     

Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study

Ab initio methods were used to shed light on fundamental aspects of the enzymatic mechanism of guanosine triphosphate hydrolysis in the Cdc42/Cdc42GAP complex. The calculations focused on the nucleophilic addition of the catalytic water molecule to the gamma-phosphate phosphorus atom. A large model system was required to correctly reproduce the electrostatic properties on the active site. The model turned out to reproduce most of the electrostatic field of the biological complex at the reactants. Our calculations established the H-bond pattern of the catalytic water (WAT), which turned out to interact with Q61 and T35, in the most stable conformation. This ruled out the possibility that the catalytic water transferred its proton directly to the gamma-phosphate. Furthermore, the calculations suggested that the electronic structure of WAT was very different from that in the bulk. Finally, this study showed that during the reaction, WAT transferred a proton to Gln61, consistent with the available X-ray data on a transition-state analogue/enzyme complex(19) and with the decrease of activity in the Q61E mutant.     

Direct ab initio molecular dynamics study of the two photodissociation channels of formic acid

A total of ∼1200 trajectories have been integrated for the two photodissociation channels of formic acid, HCOOH → H₂O + CO (1) and HCOOH → CO₂ + H₂ (2), which occur with 248 and 193 nm photons, using the direct ab initio molecular dynamics method at the RMP2(full)/cc-pVDZ level of theory. It was found that the percentage of the energy distributed to a relative translational mode in reaction (2) is much larger than that in reaction (1). This is mainly due to the difference in the geometry of transition state (TS); the H₂O geometry in the TS of reaction (1) was predicted to significantly deviate from the equilibrium one, whereas the CO₂ and H₂ geometries in the TS of reaction (2) were found to be more similar to their equilibrium ones. It was also found that the product diatomic molecules, CO and H₂, are both vibrationally and rotationally excited. The calculated relative population of the vibrationally excited CO for the 248 nm photodissociation was consistent with experiment.     

Theoretical study of single-electron capture in the N5+ + He and O6+ + He collisions by means of ab initio methods

Partial cross sections of single-electron capture on the n = 3 levels have been determined theoretically for the N⁵⁺ + He and O⁶⁺ + He collisions by means of a semiclassical method using ab initio potential energy curves and radial and rotational coupling matrix elements. The different behavior of these two isoelectronic systems is fairly well reproduced by our calculations.     

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.     

Structure and conformation of cyclobutylsilane: an electron diffraction and ab initio study

A gas electron diffraction study of cyclobutylsilane results in a mixture of equatorial and axial conformers, with the equatorial confomer slightly more stable (Δ G = 0.8 ± 0.4 kJ mol⁻¹). The cyclobutyl ring is distorted with the adjacent bonds longer (C₁---C₂ = 1.573 (4) Å) than the opposite bonds (C₂---C₃ = 1.557 (4) Å). The experimental values for the energy difference between the two conformers and for the geometric parameters are reproduced very well by ab initio calculations. The importance of silicon 3d orbitals in the interpretation of ring distortion is ambiguous, but on the basis of the ab initio calculations the participation of silicon 3d functions is negligible.     

Free energy profiles for monomer capture in Grubbs- and SHOP-type olefin polymerization catalysts: a constraint ab initio molecular dynamics study

Density functional theory together with Car-Parrinello ab initio molecular dynamics simulation has been used to investigate the free energy profiles (FEP) of monomer capture in Grubbs- and SHOP-type olefin polymerization catalysts. The FEPs along the reaction coordinates at 300 K were determined directly by a point wise thermodynamic integration technique. Comparison between potential energy profile (PEP) and the FEP has been made. The results show that, for both catalysts, the PEP for the monomer ethylene uptake by the metal center is a typical Morse curve without energy barrier. However, a small barrier (1.8 kcal/mol for Grubbs catalyst and 2.4 kcal/mol for SHOP catalyst) exists on the FEP. The pi complexation energy on the FES at 300 K is higher by 10-12 kcal/mol over that on the PES. The differences between FES and PES are due to entropy contribution. Slow growth simulations on the ethylene capture process show that the ethylene attacks the metal center by an asynchronous mode. This indicates that the forming of the pi-bonding between the metal and ethylene is initiated by electrophilic attack of the metal to one of the ethylene carbons.