Quantum model simulations

Keywords Chiral control, Current transfer, Dephasing, Molecules, Junctions, Polarized laser pulses, Quantum model simulations... 

Barth I, Manz J (2006) Periodic electron circulation induced by circularly polarized laser pulses quantum model simulations for Mg porphyrin. Angew Chem Int Ed 45 2962... 

Bala, P., Grochowsky, R, Lesyng, B., McCammon, J.A. Quantum-classical molecular dynamics. Models and applications. In Quantum mechanical simulation methods for studying biological systems, D. Bicout and M. Field, eds. Springer, Berlin (1996) 119-156. 

P. Bala, P. Grochowski, B. Lesyng, and J. A. McCammon Quantum-classical molecular dynamics. Models and applications. In Quantum Mechanical Simulation Methods for Studying Biological Systems (M. Fields, ed.). Les Houches, France (1995)... 

A more practical approach for larger systems is molecular dynamics. In this method, the properties of bonds are determined through a combination of quantum-mechanical simulation and physical experiments, and stored in a database called a (semi-empirical) force field. Then a classical (non-quantum) simulation is done where bonds are modeled as spring-like interactions. Molecular... 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

In some situations we have performed finite temperature molecular dynamics simulations [50, 51] using the aforementioned model systems. On a simplistic level, molecular dynamics can be viewed as the simulation of the finite temperature motion of a system at the atomic level. This contrasts with the conventional static quantum mechanical simulations which map out the potential energy surface at the zero temperature limit. Although static calculations are extremely important in quantifying the potential energy surface of a reaction, its application can be tedious. We have used ah initio molecular dynamics simulations at elevated temperatures (between 300 K and 800 K) to more efficiently explore the potential energy surface. 

Quantum-chemical cluster models, 34 131-202 computer programs, 34 134 methods, 34 135-138 for chemisorption, 34 135 the local approach, 34 132 molecular orbital methods, 34 135 for surface structures, 34 135 valence bond method, 34 135 Quantum chemistry, heat of chemisorption determination, 37 151-154 Quantum conversion, in chloroplasts, 14 1 Quantum mechanical simulations bond activation, 42 2, 84—107 Quasi-elastic neutron scattering benzene... 

I would like to ask Prof. J. Troe whether he could discuss some typical situations where the SAC approximation may fail. For example, consider the F + HBr — FHBr — HF(u) + Br reaction with energy E just above the potential barrier V41. In this situation, the adiabatic channels in the transition state ( ) should be populated only in the vibrational ground state, and they should, therefore, yield products HF(u = 0) + Br, according to the assumption of adiabatic channels. This is in contrast with population inversion in the experimental results that is, the preferred product channels are HF(i/) + Br, where v = 3, 4 [1] see also the quantum scattering model simulations in Ref. [2]. The fact that dynamics cannot be rigorously adiabatic (as in the most literal interpretation of SAC) has been discussed by Green et al. [3], and the most recent results (for the case of ketene) are in Ref. 4. 

Classical molecular simulation methods such as MC and MD represent atomistic/molecular-level modeling, which discards the electronic degrees of freedom while utilizing parameters transferred from quantum level simulation as force field information. A molecule in the simulation is composed of beads representing atoms, where the interactions are described by classical potential functions. Each bead has a dispersive pair-wise interaction as described by the Lennard-Jones (LJ) potential, ULj(Ly) ... 

The chapter is organized as follows The quantum-classical Liouville dynamics scheme is first outlined and a rigorous surface hopping trajectory algorithm for its implementation is presented. The iterative linearized density matrix propagation approach is then described and an approach for its implementation is presented. In the Model Simulations section the comparable performance of the two methods is documented for the generalized spin-boson model and numerical convergence issues are mentioned. In the Conclusions we review the perspectives of this study. 

An alternative strategy is to synthesize a molecular wave function, on chemical intuition, and progressively modify this function until it solves the molecular wave equation. However, chemical intuition fails to generate molecular wave functions of the required spherical symmetry, as molecules are assumed to have non-spherical three-dimensional structures. The impasse is broken by invoking the Born-Oppenheimer assumption that separates the motion of electrons and nuclei. At this point the strategy ceases to be ab initio and reduces to semi-empirical quantum-mechanical simulation. The assumed three-dimensional nuclear framework is no longer quantum-mechanically defined. The advantage of this model over molecular mechanics is that the electron distribution is defined quantum-mechanically. It has been used to simulate the H2 molecule. 

Bala P, Grochowski P, Lesyng B, McCammon JA (1995) Quantum Classical Molecular Dynamics. Models and Applications. In Field M (ed) Quantum Mechanical Simulation Methods for Studying Biological Systems. Les Houches Physics School Series, Springer Verlag and Les Houches Editions de Physique, 119-156... 

Future directions in the development of polarizable models and simulation algorithms are sure to include the combination of classical or semiempir-ical polarizable models with fully quantum mechanical simulations, and with empirical reactive potentials. The increasingly frequent application of Car-Parrinello ab initio simulations methods " may also influence the development of potential models by providing additional data for the validation of models, perhaps most importantly in terms of the importance of various interactions (e.g., polarizability, charge transfer, partially covalent hydrogen bonds, lone-pair-type interactions). It is also likely that we will see continued work toward better coupling of charge-transfer models (i.e., EE and semiem-pirical models) with purely local models of polarization (polarizable dipole and shell models). 

While the accurate evaluation of electronic coupling (Tj/) among the different chromophores is also very difficult, and is undoubtedly sensitive to uncertainties in the experimental atomic coordinates, several studies (based either on ab initio electronic structure calculations [112e, 154] or a quantum dynamical simulation with parameters adjusted to reproduce experimental kinetic data ]156]) have yielded results in general accord with each other and also with earlier estimates inferred from experimental kinetic data based on a non-adiabatic model [152, 153]. The results are summarized in Table 6, and show two clear trends in coupling magnitudes ... 

ZSM-5 (Al-MFI) is used as a catalyst in petroleum refining, in the production of synthetic fuels, and in other petrochemical processes, whereas TS-1 (Ti-MFI) is applied as a catalyst in fine chemical processes. The orthorhombic MFI structure exhibits 12 crystallographically unique tetrahedral sites. Calculations have been carried out on substitution preferences using classical as well as quantum models. " In most studies 12 simulations were conducted, and in each run, one or more crystallographically equivalent sites of the subsequently crystallographically unique tetrahedral sites were substituted. Energy minimization and molecular dynamics techniques were employed to calculate... 

Quantum dynamics simulations were run within a nine-dimensional model subspace including the nine most important modes displayed on Fig. 10 and a fivedimensional model including only the pseudo-branching-plane modes 1 and 15, and the three out-of-plane photoactive modes 4, 16x, and 16 j [31,53]. The results were interpreted with regard to the topological features of the extended seam of conical intersection and their influence on the photoreactivity. This is illustrated with Fig. 11. 

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