Likai Du

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tullys surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Theoretical Analysis of Excited States and Energy Transfer Mechanism in Conjugated Dendrimers (vol 36, pg 151, 2015)

The excited states of the phenylene ethynylene dendrimer are investigated comprehensively by various electronic‐structure methods. Several computational methods, including SCS‐ADC(2), TDHF, TDDFT with different functionals (B3LYP, BH&HLYP, CAM‐B3LYP), and DFT/MRCI, are applied in systematic calculations. The theoretical approach based on the one‐electron transition density matrix is used to understand the electronic characters of excited states, particularly the contributions of local excitations and charge‐transfer excitations within all interacting conjugated branches. Furthermore, the potential energy curves of low‐lying electronic states as the functions of ethynylene bonds are constructed at different theoretical levels. This work provides us theoretical insights on the intramolecular excited‐state energy transfer mechanism of the dendrimers at the state‐of‐the‐art electronic‐structure theories.

Water-dependent reaction pathways: an essential factor for the catalysis in HEPD enzyme.

The hydroxyethylphosphonate dioxygenase (HEPD) catalyzes the critical carbon-carbon bond cleavage step in the phosphinothricin (PT) biosynthetic pathway. The experimental research suggests that water molecules play an important role in the catalytic reaction process of HEPD. This work proposes a water involved reaction mechanism where water molecules serve as an oxygen source in the generation of mononuclear nonheme iron oxo complexes. These molecules can take part in the catalytic cycle before the carbon-carbon bond cleavage process. The properties of trapped water molecules are also discussed. Meanwhile, water molecules seem to be responsible for converting the reactive hydroxyl radical group ((-)OH) to the ferric hydroxide (Fe(III)-OH) in a specific way. This converting reaction may prevent the enzyme from damages caused by the hydroxyl radical groups. So, water molecules may serve as biological catalysts just like the work in the heme enzyme P450 StaP. This work could provide a better interpretation on how the intermediates interact with water molecules and a further understanding on the O(18) label experimental evidence in which only a relatively smaller ratio of oxygen atoms in water molecules (∼40%) are incorporated into the final product HMP.

QM/MM study on the reaction mechanism of O6-alkylguanine-DNA alkyltransferase.

Combined quantum-mechanical/molecular-mechanical (QM/MM) approaches have been applied to investigate the detailed reaction mechanism of human O(6)-alkylguanine-DNA alkyltransferase (AGT). AGT is a direct DNA repair protein that is capable of repairing alkylated DNA by transferring the methyl group to the thiol group of a cysteine residue (Cys145) in the active site in an irreversible and stoichiometric reaction. Our QM/MM calculations reveal that the methyl group transferring step is expected to occur through two steps, in which the methyl carbocation generating step is the rate-determining step with an energy barrier of 14.4 kcal/mol at the QM/MM B3LYP/6-31G(d,p)//CHARMM22 level of theory. It is different from the previous theoretical studies based on QM calculations by using a cluster model in which the methyl group transferring step is a one-step process with a higher energy barrier.

Application of Polarizable Ellipsoidal Force Field Model to Pnicogen Bonds

Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono‐ and polysubstituted PH3–NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self‐assembly structures.

Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers.

The excited states of the phenylene ethynylene dendrimer are investigated comprehensively by various electronic-structure methods. Several computational methods, including SCSADC(2), TDHF, TDDFT with different functionals (B3LYP, BH&HLYP, CAM-B3LYP), and DFT/MRCI, are applied in systematic calculations. The theoretical approach based on the oneelectron transition density matrix is used to understand the electronic characters of excited states, particularly the contributions of local excitations and charge-transfer excitations within all interacting conjugated branches. Furthermore, the potential energy curves of low-lying electronic states as the functions of ethynylene bonds are constructed at different theoretical levels. This work provides us theoretical insights on the intramolecular excited-state energy transfer mechanism of the dendrimers at the state-of-the-art electronic-structure theories. VC 2014 Wiley Periodicals, Inc.

Photoinduced Ultrafast Intramolecular Excited-State Energy Transfer in the Silylene-Bridged Biphenyl and Stilbene (SBS) System: A Nonadiabatic Dynamics Point of View

The photoinduced intramolecular excited-state energy-transfer (EET) process in conjugated polymers has received a great deal of research interest because of its important role in the light harvesting and energy transport of organic photovoltaic materials in photoelectric devices. In this work, the silylene-bridged biphenyl and stilbene (SBS) system was chosen as a simplified model system to obtain physical insight into the photoinduced intramolecular energy transfer between the different building units of the SBS copolymer. In the SBS system, the vinylbiphenyl and vinylstilbene moieties serve as the donor (D) unit and the acceptor (A) unit, respectively. The ultrafast excited-state dynamics of the SBS system was investigated from the point of view of nonadiabatic dynamics with the surface-hopping method at the TDDFT level. The first two excited states (S1 and S2) are characterized by local excitations at the acceptor (vinylstilbene) and donor (vinylbiphenyl) units, respectively. Ultrafast S2-S1 decay is responsible for the intramolecular D-A excitonic energy transfer. The geometric distortion of the D moiety play an essential role in this EET process, whereas the A moiety remains unchanged during the nonadiabatic dynamics simulation. The present work provides a direct dynamical approach to understand the ultrafast intramolecular energy-transfer dynamics in SBS copolymers and other similar organic photovoltaic copolymers.

Atomic Resolution Insights into the Structural Aggregations and Optical Properties of Neat Imidazolium-Based Ionic Liquids.

A fundamental understanding of the structural heterogeneity and optical properties of ionic liquids is crucial for their potential applications in catalysis, optical measurement, and solar cells. Herein, a synergistic approach combining molecular dynamics simulations, excited-state calculations, and statistical analysis was used to explore the explicit correlation between the structural and optical properties of one imidazolium amino acid-based ionic liquid, 1-butyl-3-methylimidazolium glycine. The estimated absorption spectrum successfully rationalizes the unusual and non-negligible absorption band beyond 300 nm for the neat imidazolium-based ionic liquid. The absorption behavior of imidazolium-based ionic liquids is shown to be sensitive to the details of their locally heterogeneous environments. We quantitatively highlight the imidazolium moiety and its various molecular aggregations, rather than the monomeric imidazolium moiety, that are responsible for the absorption characteristics. These results would improve our understanding of the preliminary interplay between structural heterogeneity and optical properties for neat imidazolium-based ionic liquids.

Theoretical studies on nonadiabatic process in chemical dynamics

Electronic transitions induced by nuclear motions are called nonadiabatic processes. In recent years, numerous experimental studies showed ultrafast nonadiabatic processes widely exist in molecular systems. The theoretical treatment of nonadiabatic dynamics is extremely challenging, because electron-nuclei coupled motions induce the breakdown of the Born-Oppenheimer approximation. We try to summarize the state-of-art theoretical understanding of nonadiabatic dynamics in recent years. Particularly, we wish to briefly discuss the development of theoretical methods (nonadiabatic dynamics approaches and electronic-structure methods) and review the theoretical understanding of nonadiabatic dynamics of various typical systems (photostability of biological molecules, photoisomerization, intersystem crossing, excited-state energy and electron transfers). Although the great progress has been achieved in the theoretical treatment of nonadiabatic dynamics, it is still very challenging to investigate complex systems with large number of degrees of freedom. In the future, the further development in this field should largely rely on the joint progress of dynamics theory, quantum chemistry and computer technology.