Development of a Hybrid Quantum Chemical and Molecular Mechanics Method with Application to Solvent Effects on the Electronic Spectra of Uracil and Uracil Derivatives

Abstract

A method for molecular dynamics (MD), Monte Carlo (MC), and energy minimization simulation utilizing a Hamiltonian that is divided into two parts is described. One part is treated with a quantum mechanical Hamiltonian, typically a small part of the simulated system that comprises the chromophore. The other part is treated with a classical mechanical Hamiltonian. This partitioning of the system allows us to simulate, for example, not only electronic spectroscopy but also chemical reactions where a bond is broken or to explore the excited state potential energy surface. The particular choice of the quantum mechanical Hamiltonian, the intermediate neglecting of differential overlap (INDO) model Hamiltonian, also offers the possibility of simulating systems that contain a transition metal, which only rarely have been accessible with traditional MD and MC methods. Test calculations on small systems are presented together with an investigation of the photophysics of uracil and 1,3-dimethyluracil.

Vibrational properties of thymine, uracil and their isotopomers

“…For example, the calculations predict 153 and 208 cm 1 upshifts for 13 of the 1,3-d 2 and 5,6-d 2 isotopomers compared to observed values of 63 and 99 cm 1 , respectively. For example, the calculations predict 153 and 208 cm 1 upshifts for 13 of the 1,3-d 2 and 5,6-d 2 isotopomers compared to observed values of 63 and 99 cm 1 , respectively.…”

A multiconfiguration self-consistent field/molecular dynamics study of the (n→π*)1 transition of carbonyl compounds in liquid water

“…[20][21][22][23][24][25] These kinds of methods, denoted as QM/MM ͑quantum-mechanics/molecular me-chanics͒, can in turn be classified into two groups, which we here term coupled and noncoupled, depending on whether the classical field force is modified ͑coupled methods͒ or not ͑noncoupled͒ during the process. In the latter case the quantum calculations are performed only for a limited number of configurations when the simulation has finished.…”

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications

“…[67] Among the participants was Michael Zerner who contributed enthusiastically to the scientific discussion and development of QM/MM models, particularly for simulations of electronic spectroscopy in solution. [69,70] In fact, soon after the 1992 publication, [6] he invited one of the authors (JG) to present a plenary talk on QM/MM methods at the 33 rd Sanibel Symposium in Florida. [71] The advice that he had provided, on both personal and professional levels, proved to be extremely valuable to the young scientist who had just begun venturing into a competitive, but rewarding field.…”

“…Zerner and coworkers proposed a perturbation approach based on the Thomas-Reiche-Kuhn sum rule to model the dispersion red-shifts for conjugated compounds. [69,70,146] The method makes use of separate calculations for solute and solvent molecules, and was shown to yield excellent results for a range of conjugated compounds.…”