The investigation of nonadiabatic effects for the N + ND → N2 + D reaction

Nonadiabatic quantum dynamical calculations have been carried out on the two coupled potential energy surfaces (1²A′ and 2²A′) (Mota et al., J Theor Comput Chem 2009, 8, 849) for the title reaction. Initial state‐resolved reaction probabilities and cross sections for ground and excited states for collision energies of 0.005–1.0 eV are determined, respectively. Nonadiabatic transition is enhanced about four times by isotopic substitution of N + NH by N + ND reaction. It turns out that the nonadiabatic effects exert no significant contribution in the N + ND → N₂ + D reaction. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Excited-state nonadiabatic dynamics simulations on the heptazine and adenine in a water environment: A mini review

Studying the excited-state decay process is crucial for materials research because what happens to the excited states determines how effective the materials are for many applications, such as photoluminescence and photocatalysis. The high computational cost, however, limits the use of high-accuracy theoretical approaches for analyzing research systems containing a significant number of atoms. Time-dependent density functional theory is a practical approach to investigate the photorelaxation processes in these systems, as demonstrated in the studies of the excited-state decays of heptazine-water clusters and adenine in water described in this review. Here, we highlight the importance of conical intersections in the excited-state decay processes of these systems using the aforementioned examples. In the heptazine-water and adenine-water systems, these intersections are associated with the photocatalytic water splitting reaction, caused by a barrierless reaction called water to adenine electron-driven proton transfer. We expect the result would be helpful for researching the excited-state decays of graphitic carbon nitride materials and DNA nucleotides.     

Probing highly efficient photoisomerization of a bridged azobenzene by a combination of CASPT2//CASSCF calculation with semiclassical dynamics simulation

Mechanism of phototriggered isomerization of azobenzene and its derivatives is of broad interest. In this paper, the S(0) and S(1) potential energy surfaces of the ethylene-bridged azobenzene (1) that was recently reported to have highly efficient photoisomerization were determined by ab initio electronic structure calculations at different levels and further investigated by a semiclassical dynamics simulation. Unlike azobenzene, the cis isomer of 1 was found to be more stable than the trans isomer, consistent with the experimental observation. The thermal isomerization between cis and trans isomers proceeds via an inversion mechanism with a high barrier. Interestingly, only one minimum-energy conical intersection was determined between the S(0) and S(1) states (CI) for both cis → trans and trans → cis photoisomerization processes and confirmed to act as the S(1) → S(0) decay funnel. The S(1) state lifetime is ～30 fs for the trans isomer, while that for the cis isomer is much longer, due to a redistribution of the initial excitation energies. The S(1) relaxation dynamics investigated here provides a good account for the higher efficiency observed experimentally for the trans → cis photoisomerization than the reverse process. Once the system decays to the S(0) state via CI, formation of the trans product occurs as the downhill motion on the S(0) surface, while formation of the cis isomer needs to overcome small barriers on the pathways of the azo-moiety isomerization and rotation of the phenyl ring. These features support the larger experimental quantum yield for the cis → trans photoisomerization than the trans → cis process.     

The keto→enol photoisomerization of N‐salicilydenemethylfurylamine: Nonadiabatic ab initio dynamics simulation

The photoinduced isomerization of cis‐keto and trans‐keto isomers in N‐salicilydenemethylfurylamine has been studied using the surface‐hopping approach at the CASSCF level of theory. After the cis‐keto or trans‐keto isomer is excited to S₁ state, the molecule initially moves to a excited‐state local minimum. The torsional motion around relative bonds in the chain drives the molecule to approach a keto‐form conical intersection and then nonadiabatic transition occurs. According to our full‐dimensional dynamics simulations, the trans‐keto and enol photoproducts are responsible for the photochromic effect of cis‐keto isomer excited to S₁ state, while no enol isomer was obtained in the photoisomerization of trans keto on excitation. The cis keto to enol and cis keto to trans keto isomerizations are reversible photochemical reactions. It is confirmed that this aromatic Schiff base is a potential molecular switch. Furthermore, the torsion of C N bond occurs in the radiationless decay of trans‐keto isomer, while it is completely suppressed by an intramolecular hydrogen bonding interaction in the dynamics of cis‐keto form. Moreover, the excited‐state lifetime of cis keto is longer than that of trans‐keto form due to the O···H N hydrogen bond.     

Detailed mechanism for photoinduced cytosine dimerization: a semiclassical dynamics simulation

Semiclassical dynamics simulation is used to study dimerization of two stacked cytosine molecules following excitation by ultrashort laser pulses (25 fs fwhm, Gaussian, 4.1 eV photon energy). The initial excited state was found to form an ultrashort exciton state, which eventually leads to the formation of an excimer state by charge transfer. When the interbase distance, defined as an average value of C(5)-C(5)' and C(6)-C(6)', becomes less than 3 ?, charge recombination occurs due to strong intermolecular interaction, eventually leading to an avoided crossing within 20-30 fs. Geometries at the avoided crossing, with average intermolecular distance of about 2.1 ?, are in accord with CASSCF/CASPT2 calculations. Results indicate that the C(2)-N(1)-C(6)-C(5) and C(2)'-N(1)'-C(6)'-C(5)' dihedral angles' bending vibrations play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to a nonadiabatic transition to the electronic ground state.     

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited‐State Relaxation

Electronic structure calculations and nonadiabatic dynamics simulations (more than 2000 trajectories) are used to explore the Z–E photoisomerization mechanism and excited‐state decay dynamics of two arylazopyrazole photoswitches. Two chiral S₁/S₀ conical intersections with associated enantiomeric S₁ relaxation paths that are barrierless and efficient (timescale of ca. 50 fs) were found. For the parent arylazopyrazole (Z8) both paths contribute evenly to the S₁ excited‐state decay, whereas for the dimethyl derivative (Z11) each of the two chiral cis minima decays almost exclusively through one specific enantiomeric S₁ relaxation path. To our knowledge, the Z11 arylazopyrazole is thus the first example for nearly stereospecific unidirectional excited‐state relaxation.     

The decay mechanism of photoexcited guanine - a nonadiabatic dynamics study

Ab initio surface hopping dynamics calculations were performed for the biologically relevant tautomer of guanine in gas phase excited into the first ππ? state. The results show that the complete population of UV-excited molecules returns to the ground state following an exponential decay within ～220 fs. This value is in good agreement with the experimentally obtained decay times of 148 and 360 fs. No fraction of the population remains trapped in the excited states. The internal conversion occurs in the ππ? state at two related types of conical intersections strongly puckered at the C2 atom. Only a small population of about 5% following an alternative pathway via a nπ? state was found in the dynamics.     

Femtosecond fluorescence dynamics of rotation-restricted azobenzenophanes: new evidence on the mechanism of trans --> cis photoisomerization of azobenzene

The ultrafast relaxation dynamics of two rotation-restricted (azobenzeno-2S-phane and azobenzeno-4S-phane) and one rotation-free (4,4'-dimethylazobenzene) azobenzene derivatives were investigated using femtosecond fluorescence up-conversion on both S(1)(n,pi) and S(2)(pi,pi) excitations. On S(2) excitation, pulse-limited kinetics with a decay coefficient of approximately 100 fs corresponding to ultrafast S(2) --> S(1) relaxation is found to be common for all molecules under investigation regardless of the molecular structure. This indicates that a direct rotational relaxation on the S(2) surface is unfavorable. On S(1) excitation, we observed biphasic fluorescence decay with a femtosecond component attributed to the decay of the Franck-Condon state prepared by excitation and a picosecond component attributed to the deactivation of the relaxed molecule on the S(1) surface. This picosecond component is slowed by at least a factor of 2 for the rotation-restricted 2S-bridged molecule compared to that of the rotation-free molecule; for the even stronger rotation-restricted azobenzeno-4S-phane, the decrease is by a factor of 10. These differences in deactivation suggest that the relaxed states and probably the trajectories for rotation-free and rotation-restricted molecules are different on the S(1) surface, which should be important for the quantum yield of photoisomerization.     

Nonadiabatic relaxation dynamics of water anion cluster and its isotope effects by ring‐polymer molecular dynamics simulation

We have applied a recently developed hybrid quantum ring‐polymer molecular dynamics method to the nonadiabatic p → s relaxation dynamics in water anion clusters to understand the isotope effects observed in previous experiments. The average relaxation times for (H₂O)₅₀^? and (D₂O)₅₀^? were calculated at 120 and 207 fs, respectively, and are comparable to the experimental results. Therefore, we conclude that nuclear quantum effects play an essential role in understanding the observed isotope effects for water anion cluster nonadiabatic dynamics. The nonadiabatic relaxation mechanisms are also discussed in detail. © 2014 Wiley Periodicals, Inc.     

Ab initio molecular dynamics simulation of a water-hydrogen fluoride equimolar mixture.

Hydrogen fluoride and water can be mixed in any proportion. The resulting solutions have unique acidic properties. In particular, hydrogen fluoride undergoes a weak-to-strong acidity transition with increasing concentration of HF To supplement the knowledge already obtained on dilute or moderately concentrated solutions and gas-phase aggregates, an equimolar mixture is studied here by Car-Parrinello molecular dynamics. The natures of the ions and of the complexes formed in the equimolar liquid were determined. Specifically, H3O+, H5O2+, FH-OH2, and HF2- were spontaneously obtained while only hydronium and fluoride ions pre-exist in the equimolar crystal. The behaviour of the proton in the equimolar liquid was compared with mixtures of other proportions simulated previously in an attempt to relate proton dynamics to acidity. In the same way, the behaviour of HF2- was also examined. In this case, proton localization and transfer appeared to be driven by the fluctuating environment of the solvated ion.     

Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

Photodissociation of 1,2-dioxetane: An excited state nonadiabatic dynamics study

Dioxetanes are a class of high energy molecules that show unique ability to dissociate thermally onto excited state products. Quite recently, it attracts much attention due to their role in what is known as “dark secondary metabolite”. The present work, presents a comprehensive investigation of the photochemical and photophysical properties of 1,2-dioxetane. Several post HF-methods were utilized. The behavior of the excited states of 1,2-dioxetane, was explored by simulating the ultra-violet photoabsorption spectrum and nonadiabatic dynamics of 1,2-dioxetane. Simulation of the photoabsorption spectrum was performed within the nuclear ensemble approximation, sampling a Wigner distribution with 500 points; whereas, the surface hopping approach was utilized to simulate the dynamics. Dynamic simulations have been started in two different spectral windows centered at 7.5 and 9.0 eV, corresponding to populations of states S₆ and S₇, respectively. The time domain for such simulations is 100 fs. The dynamics in the spectral window centered about 7.5 eV show 24% probability to originate from excited state 6 (n_O-σ*_CO) suggesting the dissociation of the C–O bonds. Whereas, dynamics in the spectral windows centered about 9.0 eV, show 67% probability to originate from state 7 (n_O-σ*_OO) predicting an O–O dissociation.     

Inertial effects on the intramolecular vibrational energy redistribution and nonadiabatic photoisomerization of a 2,3-substituted 1,3-butadiene: a quasi-classical CASSCF dynamics study

Quasi-classical CASSCF trajectory calculations have been carried out on s-cis-1,3-butadiene and substituted 2,3-dideuterio-1,3-butadiene (DDB) to assess the inertial effect on the ultrafast nonadiabatic deactivation of their first singlet excited states. Calculations indicate that even this modest increase in the mass of the 2,3-substituents noticeably affects the photodynamics of cis --> trans isomerization, by reducing the efficiency of the vibrational energy leakage between the initial relaxation and subsequent nonadiabatic decay modes. In qualitative agreement with experimental findings on related 1,3-dienes, the slowing down of the intramolecular vibrational energy redistribution (IVR) upon substitution results in extended excited-state lifetimes and reorients the photoregioselectivity toward cis rotamers and cyclic products.     

Homolysis of N-alkoxyamines: a computational study.

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (Tc), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.     

First-principles simulation of the photoreaction of a capped azobenzene: the rotational pathway is feasible.

We present first-principles molecular dynamics simulations of azobenzene and a sterically hindered derivative in the first excited state. The restricted open-shell Kohn-Sham (ROKS) approach is employed to describe the motion in the lowest excited state. The rotational pathway is observed in the molecular dynamics simulations for both azobenzene and its azacrown ether capped derivative.     

Computational study on the working mechanism of a stilbene light-driven molecular rotary motor: sloped minimal energy path and unidirectional nonadiabatic photoisomerization

The working mechanism of a geometrically overcrowded, chiral stilbene light-driven molecular rotary motor [(2R,2R)-2,2',7,7'-tetramethyl-1,1'-bis(indanylidene), 3] has been investigated by a potential energy surface (PES) study. The reaction paths of the two photoinitiated cis-trans (or E/Z) isomerization processes, namely, (P,P)-stable-cis→(M,M)-unstable-trans-3 and (P,P)-stable-trans→(M,M)-unstable-cis-3, have been explored at the CASPT2//CASSCF level of theory. The minimal energy reaction paths (MEPs) of these two processes are nearly parallel on the PESs, separated by a ridge of high inversion barrier. The MEPs have a remarkably steep slope, which drives C═C bond rotation unidirectionally. The asymmetric bias on the excited-state MEPs is caused by the substituents on the "fjord" region as well as by the phenyl moieties. The overall photoisomerization reaction can be described as a three-state (1B→2A→1A) multimode mechanism: The molecule excited to the 1B state first crosses one of the sloped 1B/2A seams, and then follows two cooperative torsional reaction modes to cross preferentially one of the two 2A/1A conical intersections to reach the isomerized ground-state product.     

The excited-state chemistry of phycocyanobilin: a semiempirical study.

Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A- into a B- and C-form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pK(B)* of approximately 9.5 units. The acidity is only slightly enhanced with a drop in pK(A)* of only approximately 1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B- and C-forms.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

Influence of electron doping on the hydrogenation of fullerene C60 : a theoretical investigation

The influence of electron attachment on the stability of the mono- and dihydrogenated buckminsterfullerene C(60) was studied using density functional theory and semiempirical molecular orbital techniques. We have also assessed the reliability of computationally accessible methods that are important for investigating the reactivity of graphenic species and surfaces in general. The B3LYP and M06L functionals with the 6-311+G(d,p) basis set and MNDO/c are found to be the best methods for describing the electron affinities of C(60) and C(60)H(2) . It is shown that simple frontier molecular orbital analyses at both the AM1 and B3LYP/6-31G(d) levels are useful for predicting the most favourable position of protonation of C(60)H(-) , that is, formation of the kinetically controlled product 1,9-dihydro[60]fullerene, which is also the thermodynamically controlled product, in agreement with experimental and previous theoretical studies. We have shown that reduction of exo- and endo-C(60)H makes them more stable in contrast to the reduction of the exo,exo-1,9-C(60)H(2) , reduced forms of which decompose more readily, in agreement with experimental electrochemical studies. However, most other dihydro[60]fullerenes are stabilized by reduction and the regioselectivity of addition is predicted to decrease as the less stable isomers are stabilized more by the addition of electrons than the two most stable ones (1,9 and 1,7).