Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics
نویسندگان
چکیده
s the hydrogen atom from the other, the products would be HC(O)OH and CO2. If the two HOCO radicals form an intermediate oxalic acid (HOC(O)C(O)OH) complex, the products could be H2O, CO and CO2, or two CO2 and H2. The dynamics will be carried out using a dual level ab initio method. The aim of this research is to determine the mechanism and product branching ratio as well as rate coefficients. A new direction in the study of combustion-related radical reactions using the direct ab initio molecular dynamics program will focus on the kinetics and dynamics of cyclic, Nand O-containing fuel molecules. The concentration of cyclic compounds in diesels and other future transportation fuels, produced largely from non-traditional sources such as oil shales and sand oils, are much higher than those in current fuels. There are only limited kinetics data on cyclic fuel molecules, yet they are required to design future internal combustion engines using such fuels. A new unique step in the chemistry is the ring-opening processes resulting in, for example cyclopentoxy (cyc-C5H9O) radicals discussed by us before. Such radicals may well contribute to enhanced formation of soot without a ring-opening reaction. In this work, we will start this project with the reactions of morpholine (1-oxa-4-aza-cyclohexane, i.e. cyclic −OCH2CH2NHCH2CH2−) and its derivatives with small radicals such as O2, HO2 and OH. Westmoreland et al. have recently demonstrated that morpholine is an ideal compound for modeling those hydrocarbon, oxygenated and N-containing fuels. Here, we will address the energies, geometries, and vibrational frequencies of the stationary points on the ground-state surfaces, and the reaction mechanism. The dynamics will be carried out using the DualOrthGT program, together with variational RRKM theory. Vibronic spectrum calculations of CH2 and its interactions with He In our GPMD group, Sears and Hall have observed rich and complicated rovibronic levels of CH2 near the C + H2 and CH + H dissociation limits. They provide a challenge for multiple surface dynamics theory, with relevance to the reactive system as well as CH2 spectroscopy. We have calculated five low-lying electronic potential energy surfaces of CH2 using a multireference CI (MRCI) method. The adiabatic surfaces will be transformed into a set of diabatic ones using the quasi-adiababatic approximation of Koppel et al. Full-dimensional quantum dynamics will then be performed on the five coupled surfaces. The principal interest is in the energy levels and non-adiadiabatic coupling effects, for detailed comparison with experimental observations. In addition, we also plan to calculate the singlet and triplet potential energy surfaces of the He-CH2 (X/A) interaction system using the CCSD(T)/aug-cc-pVQZ level of theory. The surfaces will be used for investigating the dynamics of singlet and triplet states of CH2 in collaboration with Tscherbul at Harvard, and rotationally inelastic scattering calculations in collaboration with Dagdigian and Alexander at Johns Hopkins and Maryland. Non-adiabatic molecular dynamics studies of polyatomic molecular reactions Electronically excited species such as CH2 also play an important role in combustion chemistry. However, the studies of their reactivity are rather limited, partially due to the non-adiabatic dynamics effects because those reactions often occur on multiple potential energy surfaces. In this research, we will extend the surface hopping direct ab initio molecular dynamics algorithm, developed for the SECH MD studies, to simulate the bimolecular reactions and the photo-dissociation chemistry. The first application would be the photodissociation dynamics of acetone at 193-230 nm. This system has been investigated by Suits et al. using an universal ion imaging technique. The photon excited acetones produce two major types of products: CH3CO + CH3 and CO + 2CH3. The latter products result from poorly understood dissociation mechanisms. Here we will attempt to explore the dissociation pathways of acetone on its three low-lying electronic states. Publications since 2008 H.-G. Yu, G. Poggi, J.S. Francisco and J. T. Muckerman, Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals, J. Chem. Phys. 129, 214307 (2008). H.-G. Yu, J.S. Francisco and J. T. Muckerman, Ab initio and direct dynamics study of the reaction of Cl atoms with HOCO, J. Chem. Phys. 129, 064301 (2008). H.-G. Yu and J.S. Francisco, Energetics and kinetics of the reaction of HOCO with hydrogen atoms, J. Chem. Phys. 128, 244315 (2008). H.-G. Yu, A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination, J. Chem. Phys. 128, 194106 (2008). B.J. Braams and H.-G. Yu, Potential energy surface and quantum dynamics study of rovibrational states of HO3(XA”), Phys. Chem. Chem. Phys. 10, 3150 (2008). W.-Q. Han, H.-G. Yu, C. Zhi, J. Wang, Z. Liu, T. Sekiguchi and Y. Bando, Isotope effect on band gap and radiative transitions properties of boron nitride nanotubes, Nano Lett. 10, 491 (2008). H.-G. Yu and J.S. Francisco, A theoretical study of the reaction of CH3 with HOCO radicals , J. Phys. Chem. A, 113, 3844 (2009). H.-G. Yu and J.S. Francisco, Ab initio and RRKM study of the reaction of ClO with HOCO radicals, J. Phys. Chem. A, 113, 12932 (2009). H.-G. Yu, Product branching ratios of the reaction of CO with H3 and H2D, Astrophys. J. Lett., 706, L52 (2009). H.-G. Yu, Spherical electron cloud hopping molecular dynamics simulation on dissociative recombination of protonated water, J. Phys. Chem. A, 113, 6555 (2009). H.-G. Yu, A general rigorous quantum dynamics algorithm to calculate vibrational energy levels of pentaatomic molecules, J. Mol. Spectrosc. 256, 287 (2009).
منابع مشابه
Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...
متن کاملA DFT and Molecular Dynamics Study on Inhibitory Action of Three Amine Derivatives on Corrosion of Carbon Steel
Inhibition efficiencies of three amine derivatives (Diethylenetriamine (I), Triethylenetetramine (II), and Pentaethylenehexamine (III)) have been studied on corrosion of carbon steel using density functional theory (DFT) method in gas phase. Quantum chemical parameters such as EHOMO (highest occupied molecular orbital energy), ELUMO (lowest unoccupied molecular orbital energy), hardness (η), po...
متن کاملStudies of Interaction between Propranolol and Human Serum Albumin in the Presence of DMMP by Molecular Spectroscopy and Molecular Dynamics Simulation
The interaction between propranolol (PROP) and human serum albumin (HSA) was studied in the presence of dimethyl methylphosphonate (DMMP). DMMP is usually considered as a simulant for chemical warfare agents (CWAs). For this purpose fluorescence quenching, resonance light scattering (RLS), synchronous, three-dimensional fluorescence spectroscopy and molecular dynamics (MD) simulation were emplo...
متن کاملMolecular dynamics simulation of interaction of Melittin and DMPC bilayer: Temperature dependence
The interaction between proteins and membranes has an important role in biological pro-cesses.We have calculated energies of interaction between Melittin and DMPC bilayer in differenttemperatures. We have used the CHARMM software for MD simulation under the canonical (N,V, E) ensemble at different temperatures. The computations have shown that water moleculeshave more penetration into the bilay...
متن کاملEnergy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...
متن کاملMolecular dynamics studies on the denaturation of polyalanine in the presence of guanidinium chloride at low concentration
Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...
متن کامل