Ab Initio Classical Trajectory Research Articles

Nonadiabatic simulations of photoisomerization and dissociation in ethylene using abinitio classical trajectories.

We simulate the nonadiabatic dynamics of photo-induced isomerization and dissociation in ethylene using abinitio classical trajectories in an extended phase space of nuclear and electronic variables. This is achieved by employing the linearized semiclassical initial value representation method for nonadiabatic dynamics, where discrete electronic states are mapped to continuous classical variables using either the Meyer-Miller-Stock-Thoss representation or a more recently introduced spin mapping approach. Trajectory initial conditions are sampled by constraining electronic state variables to a single initial excited state and by drawing nuclear phase space configurations from a Wigner distribution at a finite temperature. An ensemble of classical abinitio trajectories is then generated to compute thermal population correlation functions and analyze the mechanisms of isomerization and dissociation. Our results serve as a demonstration that this parameter-free semiclassical approach is computationally efficient and accurate, identifying mechanistic pathways in agreement with previous theoretical studies and also uncovering dissociation pathways observed experimentally.

Influence of second-order saddles on reaction mechanisms

The transition state, a first-order saddle point on the potential energy surface, plays a central role in understanding the mechanism, dynamics, and rate of chemical reactions. However, we recently identified energetically accessible second-order saddles (SOS) in certain reactions and showed that the SOS plays a crucial role in the dynamics of the reactions [Pradhan et al., Phys. Chem. Chem. Phys., 2019, 21, 12837; Rashmi et al., Regul. Chaotic Dyn., 2021, 26, 119]. In the present work, we investigated the role of second-order saddle points on the dynamics of the thermal denitrogenation of 1-pyrazoline using ab initio classical trajectory simulations at the CASSCF(4,4)/6-31+G* level of theory, for total energies of 130, 140, and 150 kcal mol-1 available to the system. In this unimolecular dissociation reaction, the SOS point is 4 kcal mol-1 higher in energy than the synchronous bond-breaking transition state and opens up an additional reaction pathway. We found that the fraction of molecules following the synchronous bond-breaking pathway decreased with an increase in the total available energy in the reaction, accompanied by an increase in the fraction following the asynchronous pathway. To further understand the competition between the transition state and the SOS pathways, we investigated the mechanism of halogen-substituted 1-pyrazolines where the SOS energies are comparable to that of the transition states.

Second-order Saddle Dynamics in Isomerization Reaction

The role of second-order saddle in the isomerization dynamics was investigated by considering the $$E-Z$$ isomerization of guanidine. The potential energy profile for the reaction was mapped using the ab initio wavefunction method. The isomerization path involved a torsional motion about the imine (C-N) bond in a clockwise or an anticlockwise fashion resulting in two degenerate transition states corresponding to a barrier of 23.67 kcal/mol. An alternative energetically favorable path ( $$\sim$$ 1 kcal/mol higher than the transition states) by an in-plane motion of the imine (N-H) bond via a second-order saddle point on the potential energy surface was also obtained. The dynamics of the isomerization was investigated by ab initio classical trajectory simulations. The trajectories reveal that isomerization happens via the transition states as well as the second-order saddle. The dynamics was found to be nonstatistical with trajectories exhibiting recrossing and the higher energy second-order saddle pathway preferred over the traditional transition state pathway. Wavelet based time-frequency analysis of internal coordinates indicate regular dynamics and existence of long-lived quasi-periodic trajectories in the phase space.

Theoretical investigation of the isomerization pathways of diazenes: torsion vs. inversion.

Diazenes are an important family of organic compounds used widely in synthetic and materials chemistry. These molecules have a planar geometry and exhibit cis-trans isomerization. The simplest of all these molecules - diazene (N2H2) - has been subjected to several experimental and theoretical studies. Two mechanisms have been proposed for the cis-trans isomerization of diazene, which are an in-plane inversion and an out-of-plane torsion. The activation energies for these pathways are similar and the competition between these two mechanisms has been discussed in the literature based on electronic structure theory calculations. Three decades ago, a classical dynamics investigation of diazene isomerization was carried out using a model Hamiltonian and it was indicated that the in-plane inversion is forbidden classically because of a centrifugal barrier and the out-of-plane torsion is the only isomerization pathway. In the present work, we investigated the cis-trans isomerization dynamics of diazene using ab initio classical trajectory simulations at the CASSCF(2,2)/aug-cc-pVDZ level of electronic structure theory. The simulation results confirmed the presence of the aforementioned centrifugal barrier for the inversion and torsion was the only observed pathway. The calculations were repeated for a similar system (difluorodiazene, N2F2) and again the centrifugal barrier prevented the inversion pathway.

Ab-initio classical trajectory study the dissociation of ClN3: The pathway lead to cyclic-N3

The dissociation dynamics of ClN3 have been studied by ab-initio classical trajectory and static potential energy surface calculations. The energies and structures of molecular isomers and transition states are obtained from optimization. Three isomers and five transition states of ClN3 are identified, and it is confirmed that the cyclic-N3 can be generated directly dissociation from one of isomers and from bending linear-N3 after dissociation. The classical trajectories simulations provide the ultrafast formation dynamics of cyclic-N3 during the dissociation, and the calculation of dissociation dynamics of ClN3 provides us a new insight on the pathway of formation cyclic-N3 from molecules.

Classical dynamics simulations of interstellar glycine formation via $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2}\hbox {O}$$ CH 2 = NH + CO + H 2 O reaction

Formation of simple organic species such as glycine in the interstellar medium and transportation to earth via meteorites is considered to be a possible route for ‘Origin of Life’ on earth. Glycine formation has been proposed to occur via two different pathways involving formaldehyde ( $$\hbox {HCHO}$$ ) and methanimine ( $$\hbox {CH}_{2} = \hbox {NH}$$ ) as key intermediates. In the second pathway, which is the topic of this paper, $$\hbox {CH}_{2} = \hbox {NH}$$ reacts with $$\hbox {CO}$$ and $$\hbox {H}_{2} \hbox {O}$$ forming neutral glycine. In a recent article (Nhlabatsi et al. in Phys. Chem. Chem. Phys. 18:375, 2016), detailed electronic structure calculations were reported for the reaction between $$\hbox {CH}_{2} = \hbox {NH}$$ , $$\hbox {CO}$$ and $$(\hbox {H}_{2} \hbox {O})_n$$ , $$n = 1, 2, 3$$ , and 4, forming glycine in the interstellar media. The presence of additional water molecule(s) for this reaction reduces reaction barrier - thus exhibiting a catalytic effect. This effect was described in terms of efficient proton transfer mediated by the additional water molecule through a relay transport mechanism. In the present article, we report ab initio classical trajectory simulations for the interstellar formation of glycine for the above mentioned reaction with $$n = 1$$ and 2. The trajectories were generated on-the-fly over a density functional B3LYP/6-31++G(3df,2pd) potential energy surface. Our simulations indicate that the above proposed catalytic effect by the additional water molecule(s) may not be a classical effect. Synopsis: Glycine formation in the interstellar media via the $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2} \hbox {O}$$ reaction was investigated by classical chemical dynamics simulations. This reaction has a large barrier which reduces in presence of additional water molecules. Our simulations indicate that the proposed catalytic effect by the additional water molecules may not be a classical effect.

Weak-field few-femtosecond VUV photodissociation dynamics of water isotopologues

We present a joint experimental and theoretical study of the VUV-induced dynamics of ${\mathrm{H}}_{2}\mathrm{O}$ and its deuterated isotopologues in the first excited state ($\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{A}{\phantom{\rule{0.28em}{0ex}}}^{1}{B}_{1}$) utilizing a VUV-pump VUV-probe scheme combined with $ab$ initio classical trajectory calculations. 16-fs VUV pulses centered at 161 nm created by fifth-order harmonic generation are employed for single-shot pump-probe measurements. Combined with a precise determination of the VUV pulses' temporal profile, they provide the necessary temporal resolution to elucidate sub-10-fs dissociation dynamics in the 1+1 photon ionization time window. Ionization with a single VUV photon complements established strong-field ionization schemes by disclosing the molecular dynamics under perturbative conditions. Kinetic isotope effects derived from the pump-probe experiment are found to be in agreement with our by ab initio classical trajectory calculations, taking into account photoionization cross sections for the ground and first excited state of the water cation.

Molecular dynamics of methylamine, methanol, and methyl fluoride cations in intense 7 micron laser fields.

Fragmentation and isomerization of methylamine (CH3NH2(+)), methanol (CH3OH(+)), and methyl fluoride (CH3F(+)) cations by short, intense laser pulses have been studied by ab initio classical trajectory calculations. Born-Oppenheimer molecular dynamics (BOMD) on the ground-state potential energy surface were calculated with the CAM-B3LYP/6-31G(d,p) level of theory for the cations in a four-cycle laser pulse with a wavelengths of 7 μm and intensities of 0.88 × 10(14) and 1.7 × 10(14) W/cm(2). The most abundant reaction path was CH2X(+) + H (63-100%), with the second most favorable path being HCX(+) + H2 (0-33%), followed by isomerization to CH2XH(+) (0-8%). C-X cleavage after isomerization was observed only in methyl fluoride. Compared to random orientation, CH3X(+) with the C-X aligned with the laser polarization gained energy nearly twice as much from laser fields. The percentage of CH3(+) + X dissociation increased when the C-X bond was aligned with the laser field. Alignment also increased the branching ratio for H2 elimination in CH3NH2(+) and CH3OH(+) and for isomerization in CH3OH(+).

Molecular dynamics of methanol cation (CH3OH+) in strong fields: Comparison of 800 nm and 7 μm laser fields

Fragmentation and isomerization of methanol cation by short, intense laser pulses were studied by ab initio classical trajectory simulations using CAM-B3LYP/6-31G(d,p) calculations. Compared to random orientation, CH3OH+ with the CO bond aligned with the laser polarization gained nearly twice as much energy from the laser field, in accordance with the higher vibrational intensities in the mid-IR range for aligned CH3OH+. The energy gained by CH3OH+ from 7μm and 800nm laser pulses with intensities of 0.88×1014 and 1.7×1014W/cm2 is proportional to the intensity and the wavelength squared of the laser field.

Molecular Dynamics of Methanol Monocation (CH3OH+) in Strong Laser Fields

Experimental studies by Yamanouchi and co-workers indicate that an intense 40 fs 800 nm laser pulse can cause CH3OH(+) to isomerizes during the pulse. The potential energy surfaces of methanol neutral, monocation, and singlet and triplet dication were explored using the CBS-APNO, CBS-QB3, CAM-B3LYP, and B3LYP levels of theory. Ab initio classical trajectories were calculated in the presence of a 2.9 × 10(14) W/cm(2) 800 nm laser field for methanol monocation on the ground state potential energy surface using the CAM-B3LYP/6-31G(d,p) level of theory. With only zero point energy, CH3OH(+) gained less than 15 kcal/mol from the 40 fs laser pulse, which was not enough to overcome any of the barriers for isomerization or fragmentation. To simulate extra energy deposited during the ionization process, 75, 100, and 125 kcal/mol of vibrational energy was added to the initial structures. After 400 fs, the distribution of product was CH2OH(+) + H (79-81%), HCOH(+) + H2 (9-13%), CH2OH2(+) (1-3%), CH3(+) + OH (1-3%), and CH2(+) + H2O (<0.5%). The estimated kinetic energy releases are in accord with experimental findings. Experimental results using a probe pulse to ionize CH3OH(+) to the dication showed substantial fraction C-O dissociation in both CH3OH(+) and CH2OH2(+) after the pulse. Because very few CH2OH2(+) → CH2(+) + H2O trajectories were seen in the simulation, the calculations suggest that some of the processes observed experimentally must occur on excited state surfaces or may be due to coupled nuclear-electron dynamics during the pump pulse.

Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds

Charge sensitivity analysis in AMBER force-field resolution has been used in quest for detectors of hydrogen bonds (HBs). The process of HB formation was investigated on ab initio classical trajectories (B3LYP/6-31G*) of different nucleobase pairs. Several charge sensitivities, namely: electronegativity, hardness, Fukui function (FF), and polarization matrix, were analyzed. The global and constrained equilibria were considered. It was demonstrated that FF indices and polarization matrix elements are good detectors of HB formation.

Ab Initio Molecular Dynamics Study of the Reaction between Th+and H2O†

The gas phase reaction of Th(+) with H(2)O to produce HThO(+) + H and ThO(+) + H(2) was investigated using density functional theory and coupled cluster methods. RRKM calculations of the branching ratio favor the H atomic elimination channel in disagreement with experiment. Ab initio classical trajectory calculations were carried out to obtain a better model of the molecular dynamics. The molecular dynamics simulations yield a branching ratio of ca. 80% for the H(2) elimination channel to 20% for the H atomic elimination channel in qualitative agreement with the observed ratio of 65% to 35%.

Ab Initio Classical Trajectory Study of the Fragmentation of C3H4Dications on the Singlet and Triplet Surfaces

Ab initio molecular dynamics have been used to examine the fragmentation of allene, propyne, and cyclopropene dications on the singlet and triplet potential energy surfaces. Accurate energies and barrier heights were computed at the CBS-APNO level of theory. Classical trajectories were calculated at the B3LYP/6-31G(d,p) level of theory. To simulate vertical double ionizations of allene, propyne, and cyclopropene by short, intense laser pulses, the trajectories were started from the corresponding neutral geometries and were given ca. 240 kcal/mol excess kinetic energy; 200 trajectories were integrated for each case. Approximately one-third of the trajectories underwent extensive rearrangement before dissociation. Proton dissociation is the dominant pathway for all six cases, accounting for 50-75% of the trajectories. H(2)/H(2)(+) is produced in ca. 20% of the trajectories on the singlet propyne and cyclopropene dication surface. The calculated ratio of CH(+)/CH(2)(+)/CH(3)(+) compares favorably to that obtained in laser-induced Coulomb explosion of allene. The yield of CH(2)(+) is ca. 12% on the singlet and triplet allene dication surfaces compared to 6% or less in the other cases, whereas CH(+) is favored on the singlet propyne dication surface (12% vs 0-8% on the other surfaces). CH(3)(+) is formed primarily by direct dissociation on the triplet propyne dication surface (5% vs <1% on the other surfaces). The small amount of H(3)(+) seen experimentally for allene indicates that rearrangement can occur before dissociation. The dynamics simulations confirm that extensive isomerization occurs, even though the initial kinetic energy was too high to yield H(3)(+).

Ab initio study of the Cl+H2S atmospheric reaction: is there a breakdown of the transition state theory?

The atmospheric reaction of H2S with Cl was investigated using high level ab initio calculations and Canonical Variational Transition State Theory (CVTST). The adduct formation step is the dynamical bottleneck, and the rate constant was calculated to be 1.2 × 10−9 cm3 molecule−1 s−1, which is around ten times greater than the upper experimental value. Additional ab initio classical trajectory calculations show that the adduct formed in the initial collision can easily dissociate, recrossing the variational transition state. The stabilization of this species depends on the vibrational excitation of H2S molecule, which requires an almost collinear SH-Cl collision. These dynamical effects provide an explanation for the substantial error in the rate constant obtained using CVTST.

A Single Transition State Serves Two Mechanisms. The Branching Ratio for CH2O•- + CH3Cl on Improved Potential Energy Surfaces

The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods. A bond additivity correction has been constructed to improve the Hartree-Fock potential energy surface (BAC-UHF). A satisfactory balance between good energetics and affordable AIMD calculations can be achieved with BH&HLYP/6-31G(d) and BAC-UHF/6-31G(d) calculations. Approximately 200 ab initio classical trajectories were calculated for each level of theory with initial conditions sampled from a thermal distribution at 298 K at the transition state. Three types of trajectories were distinguished: trajectories that go directly to ET product, trajectories that go to Sub(C) product, and trajectories that initially go into the Sub(C) valley and then dissociate to ET products. The BH&HLYP/6-31G(d) calculations overestimate the number of nonreactive and direct ET trajectories because the transition state is too early. For the BH&HLYP and BAC-UHF methods, about one-third of the trajectories that initially go into the Sub(C) valley dissociate to ET products, compared to just over half with UHF/6-31G(d) in the earlier study. This difference can be attributed to a better value for the calculated energy release from the initial transition state and to an improved Sub(C) --> ET barrier height with the BH&HLYP and BAC-UHF methods.

Classical trajectory calculations of intramolecular vibrational energy redistribution. II. Phenol-water complex.

Ab initio classical trajectory calculations have been applied to the intramolecular vibrational energy redistribution process of an O-H stretching vibration for phenol cation, [phenol]+, and its hydrogen-bonded water complex, [phenol-water]+. In phenol cation, a single narrow peak in the power spectrum, obtained by Fourier transformation of the autocorrelation function of its total momentum, indicates that the initial energy given to the O-H stretching oscillator of the phenol moiety is conserved and no energy flow occurs. On the other hand, for phenol-water cation, the calculated broadened power spectrum implies that the initial energy is not conserved and the energy flow causes an energy redistribution among various vibrational modes.

Exploring potential energy surfaces for chemical reactions: an overview of some practical methods.

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.

Recurrence plot analysis of nonlinear vibrational dynamics in H 3+ molecule

An ab initio classical trajectories obtained from the simulation of vibrational mode dynamics of H 3 + molecule were analyzed by Fourier transform and recurrence plot analysis. As has been found, at a particular value of energy supplied to vibrational modes (slightly above the zero point energy) the character of vibrational motion changes from regular to chaotic.

Potential Energy Surfaces and Dynamical Behavior of Two Rigidly Linked Bichromophoric Molecules Studied by CASSCF Computations and Ab Initio Classical Trajectory Simulations

Potential energy surface analysis and classical trajectory simulations have been used to study intramolecular electronic energy transfer (IEET) in two aliphatic diketones that each contains two rigidly linked carbonyl chromophores. This article provides evidence that two geometric coordinates (the carbonyl bond lengths) and two singlet diabatic states (characterized by specific excitation of either one carbonyl chromophore or the other) are needed to understand the mechanism of IEET in these systems. Although computations show that a nonadiabatic transition step is involved in the process, IEET is mainly an adiabatic mechanism of intramolecular vibrational redistribution (IVR) on the lowest excited state into the vibrations of the chromophore that is not initially excited. Dynamics calculations show that this redistribution is slower in the molecule characterized by the more extended σ-bond bridge. It is demonstrated that the σ-bond bridge not only enhances interchromophoric electronic coupling via through-bond interactions compared to through-space interactions, it also controls the IEET process by promoting IVR from one side of the molecule into the other.

Glyoxal photodissociation. II. An ab initio direct classical trajectory study of C2H2O2→CO+H2CO

Photodissociation of glyoxal via the H2CO+CO channel has been investigated by ab initio classical trajectory calculations using Becke’s three-parameter hybrid functional method with split valence and polarized basis set [B3LYP/6-311G(d,p)]. To model the experimental conditions, trajectories were started from a microcanonical ensemble at the transition state with 8.5 kcal/mol excess energy distributed among the vibrational modes and the transition vector. The CO product was produced with a broad rotational distribution but with almost no vibration excitation. When combined with the results from the H2+2CO channel, the calculated vibrational and rotational distributions of CO are in excellent agreement with the experimental observations. The rotational distribution of H2CO was very broad ranging up to J=85. The H2CO product has significant vibrational excitation in the out-of-plane bending, CH2 rocking, CH2 scissoring, and CO stretching modes. For both the H2+2CO and the CO+H2CO channels, the majority of available energy was partitioned into translations.