Simulation of the cyclopropanecarbaldehyde and cyclopropylethanone photoisomerization processes and calculation of the quantum yields of the reactions

The cyclopropanecarbaldehyde → 2-butenal and cyclopropylethanone → 3-pentenone-2 photoisomerization processes were simulated. The calculated quantum yields of the products are in quantitative agreement with experimental data. The validity of the method proposed for the calculation of quantum yields of photochemical reactions was confirmed. It was found that if the condition of relative smallness of the optical transition probabilities as compared to the quantum beat frequency is met, the quantum yields can be quantitatively estimated with satisfactory accuracy directly from the transition probabilities without running the full calculation of the phototransformation kinetics. It was shown that the integral characteristics of photochemical reactions (quantum yields) are highly responsive to the conformational state of the molecules involved in the process.     

A modified method for calculating quantum yields of photochemical reactions

The previously proposed approach to calculation of quantum yields of photochemical reactions has been improved. The new version uses a different procedure of accounting for the asymmetry (anharmonicity) of potential wells of the molecules involved in the photochemical conversion. The form of a doubleminimum potential energy surface has been considered in a more correct manner. It has been shown that the number of model parameters is reduced by two thirds compared with the model used previously, adequately reflecting the characteristics of structural transformations of polyatomic molecules in which a relatively small part of the total number of coordinates are transformed. The quantum yields of photochemical transformations of six dienes into their cyclic isomers have been calculated. Quantitative agreement of the calculated values with the experimental data has been achieved for all the reactions. It has been shown that the model parameters have good transferability in a series of related molecules, thereby rendering the simulation of photochemical processes by the method in question predictive.     

Simulation of photochemical reactions of butadiene and calculation of the quantum yields

The photochemical reactions of butadiene-1,3 have been simulated. The calculated quantum yields of the products quantitatively agree with experimental data (deviation from the experimental data in on average less than 30%). The efficacy of the method in predicting photochemical processes of various types (isomerization, decomposition) occurring simultaneously via different pathways has been shown. It has been confirmed that the quantum beat frequency of resonating states can be used as a parameter of the method and, as such, allows obtainable quantitative estimates to be refined.     

Quasiclassical trajectory study of reactive and dissociative processes in H2+H2: comparison with quantum-mechanical calculations

Quasiclassical trajectory calculations have been carried out for H(2)(v(1)=high)+H(2)(v(2)=low) collisions within a three degrees of freedom model where five different geometries of the colliding complex were considered. Within this approach, probabilities for different competitive processes are studied: four center reaction, collision induced dissociation, reactive dissociation, and three-body complex formation. The purpose is to compare in detail with equivalent quantum-mechanical wave packet calculations [Bartolomei et al., J. Chem. Phys 122, 064305 (2005)], especially the behavior of the probabilities near reaction thresholds. Quasiclassical calculations compare quite well with the quantum-mechanical ones for collision induced dissociation as well as for the four center reaction, although quantum effects become very important near thresholds, particularly for lower v(1)'s and for the four center process. Less quantitative agreement is found for reactive dissociation and three-body complex formation. It is found that most quantum effects are due to differences between quantum and classical vibrational distributions of H(2)(v(1)=high). Zero point energy violation has been found in the classical reactive-dissociative probabilities. Extension of these findings to full-dimensional treatments is examined.     

A mathematical model of photochemical transformations: Analysis of the influence of basic characteristics of the model

Basic aspects of the choice of parameters entering a system of differential equations that simulate the sequence of chemical transformations in the case of initiation of a reaction by electromagnetic pulse excitation of reactant molecules are discussed. These parameters are the probabilities of spontaneous and stimulated dipole–dipole transitions and the frequency of quantum beats that lead to the reaction. A method for an a priori estimation of optimum values of these frequencies on the basis of fundamental characteristics of intramolecular processes has been specified. It has been noted that in theoretical prediction of the course of chemical reactions, the solution of the problem in the natural coordinate system (distance between the atoms), rather than Cartesian coordinates, can be more appropriate.     

Isotopic replacement in ionic systems: the 4He2+ + 3He-->3He 4He+ + 4He reaction

Full quantum dynamics calculations have been carried out for the ionic reaction (4)He(2) (+)+(3)He and state-to-state reactive probabilities have been obtained using both time-dependent and time-independent approaches. An accurate ab initio potential-energy surface has been employed for the present quantum dynamics and the two sets of results are shown to be in agreement with each other. The results for zero total angular momentum suggest a marked presence of atom exchange (isotopic replacement) reaction with probabilities as high as 60%. The reaction probabilities are only weakly dependent on the initial vibrational state of the reactants, while they are slightly more sensitive to the degree of rotational excitation. A brief discussion of the results for selected higher total angular momentum values is also presented, while the l-shifting approximation [S. K. Gray et al., Phys. Chem. Chem. Phys. 1, 1141 (1999)] has been used to provide estimates of the total reaction rates for the title process. Such rates are found to be large enough to possibly become experimentally accessible.     

Reduced classical trajectory equations for electronically non-adiabatic transition on photochemical pericyclic reactions

It may be difficult to use the classical trajectory equations (CTE) for the estimation of electronically non-adiabatic transition probabilities in photochemical pericyclic reactions because of many nuclear degrees of freedom. In order to avoid this difficulty, the CTE were reformulated in terms of the reaction path coordinates, and the reduced CTE were derived, in which the system was restricted to move one-dimensionally along the postulated reaction path. As an application, the non-adiabatic decay from the lowest excited state to the ground state was investigated for the conrotatory and disrotatory processes of the photochemical electrocyclic reaction of 1,3-cis-butadiene to form cyclobutene.     

An analysis of the accuracy of an initial value representation surface hopping wave function in the interaction and asymptotic regions

The behavior of an initial value representation surface hopping wave function is examined. Since this method is an initial value representation for the semiclassical solution of the time independent Schrodinger equation for nonadiabatic problems, it has computational advantages over the primitive surface hopping wave function. The primitive wave function has been shown to provide transition probabilities that accurately compare with quantum results for model problems. The analysis presented in this work shows that the multistate initial value representation surface hopping wave function should approach the primitive result in asymptotic regions and provide transition probabilities with the same level of accuracy for scattering problems as the primitive method.     

Using variable and fixed topological indices for the prediction of reaction rate constants of volatile unsaturated hydrocarbons with OH radicals

Volatile organic compounds (VOCs) play an important role in different photochemical processes in the troposphere. In order to predict their impact on ozone formation processes a detailed knowledge about their abundance in the atmosphere as well as their reaction rate constants is required. The QSPR models were developed for the prediction of reaction rate constants of volatile unsaturated hydrocarbons. The chemical structure was encoded by constitutional and topological indices. Multiple linear regression models using CODESSA software was developed with the RMS(CV) error of 0.119 log units.The chemical structure was encoded by six topological indices. Additionally, a regression model using a variable connectivity index was developed. It provided worse cross-validation results with an RMS(CV) error of 0.16 log units, but enabled a structural interpretation of the obtained model. We differentiated between three classes of carbon atoms: sp2-hybridized, non-allylic sp3-hybridized and allylic sp3-hybridized. The structural interpretation of the developed model shows that most probably the most important mechanisms are the addition to multiple bonds and the hydrogen atom abstraction at allylic sites.     

Proton transfer in a polar solvent from ring polymer reaction rate theory

We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz-Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.     

Surface temperature effect on the scattering of D2(v = 0, j = 0)-Cu(111) system

We perform four-dimensional (4D?2D) as well as six-dimensional (6D) quantum dynamics on a parametrically time- and temperature-dependent effective Hamiltonian for D(2)(v, j)-Cu(111) system, where such effective potential has been derived through a mean-field approach between molecular degrees of freedom and surface modes with Bose-Einstein probability factor for their initial state distribution. We present the convergence of the theoretically calculated sticking probabilities employing 4D?2D quantum dynamics with increasing number of surface atoms as well as layers for rigid surface and the surface at a particular temperature, where the temperature-dependent sticking probabilities appear exclusively dictated by those surface modes directed along the Z-axis. The sticking and state-to-state transition probabilities obtained from 6D quantum dynamics are shown as a function of initial kinetic energy of the diatom at different surface temperature. Theoretically calculated sticking probabilities display the similar trend with the experimentally measured one.     

ENERGETICS OF PHOTOPHYSICAL PROCESSES IN CHLOROPHYLL-LIKE MOLECULES

Abstract— The values of the absolute quantum yields of fluorescence and of intersystem crossing have been obtained for porphin and its derivatives by methods based on relative measurements involving flash photolysis. For a given compound the sum of these quantum yields is unity within experimental error which shows that the energetics of the molecules investigated is determined by competition of only two processes, viz., fluorescence and intersystem crossing, while internal conversion plays a negligible role. The values of the corresponding transition probabilities have been determined with the help of phase-fluorometric measurements. The dependence of the transition probabilities on molecular structure is discussed.     

Extension of QM/MM docking and its applications to metalloproteins

To overcome the limitation of conventional docking methods which assume fixed charge model from force field parameters, combined quantum mechanics/molecular mechanics (QM/MM) method has been applied to docking as a variable charge model and shown to exhibit improvement on the docking accuracy over fixed charge based methods. However, it has also been shown that there are a number of examples for which adoption of variable‐charge model fails to reproduce the native binding modes. In particular, for metalloproteins, previously implemented method of QM/MM docking failed most often. This class of proteins has highly polarized binding sites at which high‐coordinate‐numbered metal ions reside. We extend the QM/MM docking method so that protein atoms surrounding the binding site along with metal ions are included as quantum region, as opposed to only ligand atoms. This extension facilitates the required scaling of partial charges on metal ions leading to prediction of correct binding modes in metalloproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Detection of free nickel monocarbonyl, NiCO: rotational spectrum and structure

Unsaturated transition metal carbonyls are important in processes such as organometallic synthesis, homogeneous catalysis, and photochemical decomposition of organometallics. In particular, a metal monocarbonyl offers a zeroth-order model for interpreting the chemisorption of a CO molecule on a metal surface in catalytic activation processes. Quite large numbers of theoretical papers have appeared which predict spectroscopic and structural properties of transition metal carbonyls. The nickel monocarbonyl NiCO has been one of the metal carbonyls most extensively studied by the theoretical calculations. At least 50 theoretical studies have been published on this simplest transition metal carbonyl up to the present time. However, experimental evidence of NiCO is much more sparse than theoretical predictions, and the actual structure of NiCO has never been determined by any experimental methods. This Communication reports the first preparation of free nickel monocarbonyl and observation of its rotational transitions. The NiCO molecule was generated by the sputtering reaction of a Ni cathode in the presence of CO. The accurate bond lengths of Ni-C and C-O were experimentally determined from isotopic data and were compared with the theoretical predictions for the first time.     

TSNet: predicting transition state structures with tensor field networks and transfer learning

Transition states are among the most important molecular structures in chemistry, critical to a variety of fields such as reaction kinetics, catalyst design, and the study of protein function. However, transition states are very unstable, typically only existing on the order of femtoseconds. The transient nature of these structures makes them incredibly difficult to study, thus chemists often turn to simulation. Unfortunately, computer simulation of transition states is also challenging, as they are first-order saddle points on highly dimensional mathematical surfaces. Locating these points is resource intensive and unreliable, resulting in methods which can take very long to converge. Machine learning, a relatively novel class of algorithm, has led to radical changes in several fields of computation, including computer vision and natural language processing due to its aptitude for highly accurate function approximation. While machine learning has been widely adopted throughout computational chemistry as a lightweight alternative to costly quantum mechanical calculations, little research has been pursued which utilizes machine learning for transition state structure optimization. In this paper TSNet is presented, a new end-to-end Siamese message-passing neural network based on tensor field networks shown to be capable of predicting transition state geometries. Also presented is a small dataset of S_N2 reactions which includes transition state structures – the first of its kind built specifically for machine learning. Finally, transfer learning, a low data remedial technique, is explored to understand the viability of pretraining TSNet on widely available chemical data may provide better starting points during training, faster convergence, and lower loss values. Aspects of the new dataset and model shall be discussed in detail, along with motivations and general outlook on the future of machine learning-based transition state prediction.

Transition states are among the most important molecular structures in chemistry, critical to a variety of fields such as reaction kinetics, catalyst design, and the study of protein function.     

The photolysis of n-butyraldehyde in isooctane at 313 nm

The effects of aldehyde concentration, incident light intensity, and temperature on the quantum yields of reaction products were studied. Mechanisms for primary and secondary photochemical processes were suggested, and primary quantum yields as well as rate constant ratios were derived. Reversibility of intramolecular γ-hydrogen transfer and disproportionation of the radical pair formed in the reaction of an excited triplet and ground state molecule were shown to provide important pathways for radiationless decay of the triplet state.     

Quantum initial conditions in quasi-classical trajectory calculations

The quantum distribution of initial conditions suggested recently by Careless and Hyatt as a means of “phase-averaging” classical trajectories is shown to lead to reaction probabilities which depend on the initial distance between the reagents even when this distance is sufficiently large for the corresponding interaction energy to vanish. We used that distribution to calculate reaction probabilities for the collinear H + H₂ exchange reaction on a potential energy surface for which quasi-classical and exact quantum results had been previously obtained. The dependence of the resulting reaction probabilities on the arbitrarily chosen value of the initial atom-molecule separation was substantial. We conclude that the use of such quantum distributions for initial conditions is physically unacceptable.     

A quantum theory of chemical processes and reaction rates based on diabatic electronic functions coupled in an external field

The method discussed in this work provides a theoretical framework where simple chemical reactions resemble any other standard quantum process, i.e., a transition in quantum state mediated by the electromagnetic field. In our approach, quantum states are represented as a superposition of electronic diabatic basis functions, whose amplitudes can be modulated by the field and by the external control of nuclear configurations. Using a one-dimensional three-state model system, we show how chemical structure and dynamics can be represented in terms of these control parameters, and propose an algorithm to compute the reaction probabilities. Our analysis of effective energy barriers generalizes previous ideas on structural similarity between reactant, and product, and transition states using the geometry of conventional reaction paths. In the present context, exceptions to empirical rules such as the Hammond postulate appear as effects induced by the environment that supplies the external field acting on the quantum system.     

The ring-opening reaction of chromenes: a photochemical mode-dependent transformation

The efficiency of the photochemical ring-opening of chromenes (or benzopyrans) depends on the vibronic transition selected by the chosen excitation wavelength. In the present work, ab initio CASPT2//CASSCF calculations are used to determine the excited-state ring-opening reaction coordinate for 2H-chromene (C) and 2,2-diethyl-2H-chromene (DEC) and provide an explanation for such an unusual mode-dependent behavior. It is shown that excited-state relaxation and decay occur via a multimodal and barrierless (or nearly barrierless) reaction coordinate. In particular, the relaxation out of the Franck-Condon involves a combination of in-plane skeletal stretching and out-of-plane modes, while the second part of the reaction coordinate is dominated exclusively by a different out-of-plane mode. Population of this last mode is shown to be preparatory with respect to both C-O bond breaking and decay via an S(1)/S(0) conical intersection. The observed mode-dependent ring-opening efficiency is explained by showing that the vibrational mode corresponding to the most efficient vibronic transition has the largest projection onto the out-of-plane mode of the reaction coordinate. To support the computationally derived mechanism, we provide experimental evidence that the photochemical ring-opening reaction of 2,2-dimethyl-7,8-benzo(2H)chromene, that similarly to DEC exhibits a mode-dependent photoreaction, has a low ( approximately 1 kcal mol(-1)) activation energy barrier.