Dynamical Simulation of Electron Transfer Processes in Alkanethiolate Self-Assembled Monolayers at the Au(111) Surface
The Journal of Physical Chemistry C, 2013
ABSTRACT Electron transfer is investigated in a series of self-assembled monolayers (SAMs) consis... more ABSTRACT Electron transfer is investigated in a series of self-assembled monolayers (SAMs) consisting of nitrile-substituted short chain alkanethiolate molecules adsorbed at the Au(111) surface. Using first-principles methods and a model electron transfer Hamiltonian, we analyze the main factors controlling, at the molecular level, the electron injection times from donor states localized at the tail group of the SAM into the Au(111) substrate. We show that the donor–acceptor electronic couplings depend significantly on the orbital symmetry of the donor state and the length of the aliphatic spacer chain of the SAM. The dependence on the donor state symmetry and on the molecular structure of the linker can be used to control the electron injection times even in situations where the energy separation between the donor states is smaller than their width.
Femtosecond charge-transfer dynamics in self-assembled monolayers of cyano-terminated ethane-thio... more Femtosecond charge-transfer dynamics in self-assembled monolayers of cyano-terminated ethane-thiolate on gold substrates was investigated with the core hole clock method. By exploiting symmetry selection rules rather than energetic selection, electrons from the nitrogen K-shell are state-selectively excited into the two symmetry-split π* orbitals of the cyano end group with X-ray photons of well-defined polarization. The charge-transfer times from these temporarily occupied orbitals to the metal substrate differ significantly. Theoretical calculations show that these two π* orbitals extend differently onto the alkane backbone and the anchoring sulfur atom, thus causing the observed dependence of the electron-transfer dynamics on the symmetry of the orbital.
Janus nanoparticles self-assemble into chiral vesicle-like hollow nanostructures due to the forma... more Janus nanoparticles self-assemble into chiral vesicle-like hollow nanostructures due to the formation of a dipole vertex.
Quantum Phase Transition in the Spin-Boson Model: A Multilayer Multiconfiguration Time-Dependent Hartree Study
The Journal of Physical Chemistry A
The multilayer improved relaxation is applied to study the delocalization-localization transition... more The multilayer improved relaxation is applied to study the delocalization-localization transition in the spin-boson model at zero temperature-a well-known example of quantum phase transition. Calculations of energy eigenstates are obtained by iteratively diagonalizing the matrix of the Boltzmann operator in the top layer representation, using a Lanczos/Arnoldi method while relaxing the single particle functions of all layers using the multilayer multiconfiguration time-dependent Hartree imaginary time propagation. Two properties are used to examine the quantum phase transition: the energy splitting for the lowest pair of eigenstates and the magnetic susceptibility. Consistent findings are obtained with appropriate scaling parameters.
Direct Aryloxylation/Alkyloxylation of Dialkyl Phosphonates for the Synthesis of Mixed Phosphonates
Angewandte Chemie (International ed. in English), Jan 16, 2018
A strategy for the direct functionalization strategy of inertial dialkyl phosphonates with hydrox... more A strategy for the direct functionalization strategy of inertial dialkyl phosphonates with hydroxy compounds to afford diverse mixed phosphonates with good yields and functional-group tolerance has been developed. Mechanistic investigations involving both NMR studies and DFT studies suggest that an unprecedented highly reactive P species (phosphoryl pyridin-1-ium salt), a key intermediate for this new synthetic transformation, is generated in situ from dialkyl phosphonate in the presence of Tf O/pyridine.
Quantum dynamical simulation of photoinduced electron transfer processes in dye-semiconductor systems: theory and application to coumarin 343 at TiO2
Journal of physics. Condensed matter : an Institute of Physics journal, Jan 10, 2015
A recently developed methodology to simulate photoinduced electron transfer processes at dye-semi... more A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.
Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8‐oxo ‐7,8‐dihydropurine, and 8‐bromopurine analogues within A‐form duplexes of RNA
Extending our previous work, quantum dynamic simulations are performed to study low temperature h... more Extending our previous work, quantum dynamic simulations are performed to study low temperature heat transport in a spin-boson model where a two-level subsystem is coupled to two independent harmonic baths. Multilayer multiconfiguration time-dependent Hartree theory is used to numerically evaluate the thermal flux, for which the bath is represented by hundreds to thousands of modes. The simulation results are compared with the approximate Redfield theory approach, and the physics is analyzed versus different physical parameters.
Stochastic differential equation is a powerful tool for describing the dynamics of a dissipative ... more Stochastic differential equation is a powerful tool for describing the dynamics of a dissipative system, in which noise characterizes the influence of the environment. For the Ornstein-Uhlenbeck noise both the formula of differentiation and the hierarchy approach provide efficient numerical simulations, with the stochastic differential equation transformed into a set of coupled, linear ordinary differential equations. We show that while these two deterministic schemes result in different sets of equations, they can be regarded as two representations of an underlying linear-dynamics. Moreover, by manipulating the involved Ornstein-Uhlenbeck noise, we propose a unified algorithm that may reduce to the hierarchy approach or the formula of differentiation in different limit. We further analyze the numerical performance of this algorithm and find that the hierarchy approach appears to be more efficient for our numerical model studies.
Modeling of canonical and C2′-O-thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability
New Journal of Chemistry
Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal ... more Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal stabilization of the duplex. Predicting the effects that modifications will have on structure of RNA is of importance in the development of new RNA technologies.
An efficient and accurate method for computing the equilibrium reduced density matrix is presente... more An efficient and accurate method for computing the equilibrium reduced density matrix is presented for treating open quantum systems characterized by the system-bath model. The method employs the multilayer multiconfiguration time-dependent Hartree theory for imaginary time propagation and an importance sampling procedure for calculating the quantum mechanical trace. The method is applied to the spin-boson Hamiltonian, which leads to accurate results in agreement with those produced by the multi-electronic-state path integral molecular dynamics method.
Polycomb group (PcG) proteins repress master regulators of development and differentiation throug... more Polycomb group (PcG) proteins repress master regulators of development and differentiation through organization of chromatin structure. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the cell nucleus, and these condensates are the physical sites of PcG-targeted gene silencing via formation of facultative heterochromatin. However, the physiochemical principles underlying the formation of PcG condensates remain unknown, and their determination could shed light on how these condensates compact chromatin. Using fluorescence live-cell imaging, we observed that the Polycomb repressive complex 1 (PRC1) protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. Using site-directed mutagenesis, we demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region ...
Over 80% of diffuse intrinsic pontine gliomas (DIPGs) harbor a point mutation in histone H3.3 whe... more Over 80% of diffuse intrinsic pontine gliomas (DIPGs) harbor a point mutation in histone H3.3 where lysine 27 is substituted with methionine (H3.3K27M); however, how the mutation affects kinetics and function of PcG proteins remains elusive. We demonstrate that H3.3K27M prolongs the residence time and search time of Ezh2, but has no effect on its fraction bound to chromatin. In contrast, H3.3K27M has no effect on the residence time of Cbx7, but prolongs its search time and decreases its fraction bound to chromatin. We show that increasing expression of Cbx7 inhibits the proliferation of DIPG cells and prolongs its residence time. Our results highlight that the residence time of PcG proteins directly correlates with their functions and the search time of PcG proteins is critical for regulating their genomic occupancy. Together, our data provide mechanisms in which the cancer-causing histone mutation alters the binding and search dynamics of epigenetic complexes.
Car--Parrinello Molecular Dynamics Study of Base-Catalyzed Hydrolysis Reactions
We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello... more We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello molecular dynamics package to study the base-catalyzed hydrolysis of N-methylacetamide in aqueous solution. Our calculations are carried out in the framework of density functional theory combined with the hybrid BLYP exchange-correlation functional The free energy surfaces and hydrolysis reaction pathways for N-methylacetamide are examined in the presence of a hydroxide ion, and 4, 32, and 64 water molecules. We find that at least 32 water molecules must be explicitly included in metadynamics simulations to accurately describe the mechanism of the hydrolysis reaction of N-Methylacetamide. Our theoretical estimate for the dissociation energy of N-Methylacetamide is in good agreement with the results of previous experimental and theoretical studies.
Four types of density functional theory (DFT)-based approaches are assessed in this work for the ... more Four types of density functional theory (DFT)-based approaches are assessed in this work for the approximate construction of diabatic states and evaluation of the electronic couplings between these states.
The accuracy of the noninteracting electron approximation is examined for a model of vibrationall... more The accuracy of the noninteracting electron approximation is examined for a model of vibrationally coupled electron transport in single molecule junction. In the absence of electronicvibrational coupling, steady state transport in this model is described exactly by Landauer theory. Including coupling, both electronic-vibrational and vibrationally induced electron-electron correlation effects may contribute to the real time quantum dynamics. Using the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory to describe nuclear dynamics exactly while maintaining the noninteracting electron approximation for the electronic dynamics, the correlation effects are analyzed in different physical regimes. It is shown that although the noninteracting electron approximation may be reasonable for describing short time dynamics, it does not give the correct long time limit for certain initial conditions.
Dynamical Simulation of Electron Transfer Processes in Alkanethiolate Self-Assembled Monolayers at the Au(111) Surface
The Journal of Physical Chemistry C, 2013
ABSTRACT Electron transfer is investigated in a series of self-assembled monolayers (SAMs) consis... more ABSTRACT Electron transfer is investigated in a series of self-assembled monolayers (SAMs) consisting of nitrile-substituted short chain alkanethiolate molecules adsorbed at the Au(111) surface. Using first-principles methods and a model electron transfer Hamiltonian, we analyze the main factors controlling, at the molecular level, the electron injection times from donor states localized at the tail group of the SAM into the Au(111) substrate. We show that the donor–acceptor electronic couplings depend significantly on the orbital symmetry of the donor state and the length of the aliphatic spacer chain of the SAM. The dependence on the donor state symmetry and on the molecular structure of the linker can be used to control the electron injection times even in situations where the energy separation between the donor states is smaller than their width.
Femtosecond charge-transfer dynamics in self-assembled monolayers of cyano-terminated ethane-thio... more Femtosecond charge-transfer dynamics in self-assembled monolayers of cyano-terminated ethane-thiolate on gold substrates was investigated with the core hole clock method. By exploiting symmetry selection rules rather than energetic selection, electrons from the nitrogen K-shell are state-selectively excited into the two symmetry-split π* orbitals of the cyano end group with X-ray photons of well-defined polarization. The charge-transfer times from these temporarily occupied orbitals to the metal substrate differ significantly. Theoretical calculations show that these two π* orbitals extend differently onto the alkane backbone and the anchoring sulfur atom, thus causing the observed dependence of the electron-transfer dynamics on the symmetry of the orbital.
Janus nanoparticles self-assemble into chiral vesicle-like hollow nanostructures due to the forma... more Janus nanoparticles self-assemble into chiral vesicle-like hollow nanostructures due to the formation of a dipole vertex.
Quantum Phase Transition in the Spin-Boson Model: A Multilayer Multiconfiguration Time-Dependent Hartree Study
The Journal of Physical Chemistry A
The multilayer improved relaxation is applied to study the delocalization-localization transition... more The multilayer improved relaxation is applied to study the delocalization-localization transition in the spin-boson model at zero temperature-a well-known example of quantum phase transition. Calculations of energy eigenstates are obtained by iteratively diagonalizing the matrix of the Boltzmann operator in the top layer representation, using a Lanczos/Arnoldi method while relaxing the single particle functions of all layers using the multilayer multiconfiguration time-dependent Hartree imaginary time propagation. Two properties are used to examine the quantum phase transition: the energy splitting for the lowest pair of eigenstates and the magnetic susceptibility. Consistent findings are obtained with appropriate scaling parameters.
Direct Aryloxylation/Alkyloxylation of Dialkyl Phosphonates for the Synthesis of Mixed Phosphonates
Angewandte Chemie (International ed. in English), Jan 16, 2018
A strategy for the direct functionalization strategy of inertial dialkyl phosphonates with hydrox... more A strategy for the direct functionalization strategy of inertial dialkyl phosphonates with hydroxy compounds to afford diverse mixed phosphonates with good yields and functional-group tolerance has been developed. Mechanistic investigations involving both NMR studies and DFT studies suggest that an unprecedented highly reactive P species (phosphoryl pyridin-1-ium salt), a key intermediate for this new synthetic transformation, is generated in situ from dialkyl phosphonate in the presence of Tf O/pyridine.
Quantum dynamical simulation of photoinduced electron transfer processes in dye-semiconductor systems: theory and application to coumarin 343 at TiO2
Journal of physics. Condensed matter : an Institute of Physics journal, Jan 10, 2015
A recently developed methodology to simulate photoinduced electron transfer processes at dye-semi... more A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.
Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8‐oxo ‐7,8‐dihydropurine, and 8‐bromopurine analogues within A‐form duplexes of RNA
Extending our previous work, quantum dynamic simulations are performed to study low temperature h... more Extending our previous work, quantum dynamic simulations are performed to study low temperature heat transport in a spin-boson model where a two-level subsystem is coupled to two independent harmonic baths. Multilayer multiconfiguration time-dependent Hartree theory is used to numerically evaluate the thermal flux, for which the bath is represented by hundreds to thousands of modes. The simulation results are compared with the approximate Redfield theory approach, and the physics is analyzed versus different physical parameters.
Stochastic differential equation is a powerful tool for describing the dynamics of a dissipative ... more Stochastic differential equation is a powerful tool for describing the dynamics of a dissipative system, in which noise characterizes the influence of the environment. For the Ornstein-Uhlenbeck noise both the formula of differentiation and the hierarchy approach provide efficient numerical simulations, with the stochastic differential equation transformed into a set of coupled, linear ordinary differential equations. We show that while these two deterministic schemes result in different sets of equations, they can be regarded as two representations of an underlying linear-dynamics. Moreover, by manipulating the involved Ornstein-Uhlenbeck noise, we propose a unified algorithm that may reduce to the hierarchy approach or the formula of differentiation in different limit. We further analyze the numerical performance of this algorithm and find that the hierarchy approach appears to be more efficient for our numerical model studies.
Modeling of canonical and C2′-O-thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability
New Journal of Chemistry
Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal ... more Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal stabilization of the duplex. Predicting the effects that modifications will have on structure of RNA is of importance in the development of new RNA technologies.
An efficient and accurate method for computing the equilibrium reduced density matrix is presente... more An efficient and accurate method for computing the equilibrium reduced density matrix is presented for treating open quantum systems characterized by the system-bath model. The method employs the multilayer multiconfiguration time-dependent Hartree theory for imaginary time propagation and an importance sampling procedure for calculating the quantum mechanical trace. The method is applied to the spin-boson Hamiltonian, which leads to accurate results in agreement with those produced by the multi-electronic-state path integral molecular dynamics method.
Polycomb group (PcG) proteins repress master regulators of development and differentiation throug... more Polycomb group (PcG) proteins repress master regulators of development and differentiation through organization of chromatin structure. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the cell nucleus, and these condensates are the physical sites of PcG-targeted gene silencing via formation of facultative heterochromatin. However, the physiochemical principles underlying the formation of PcG condensates remain unknown, and their determination could shed light on how these condensates compact chromatin. Using fluorescence live-cell imaging, we observed that the Polycomb repressive complex 1 (PRC1) protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. Using site-directed mutagenesis, we demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region ...
Over 80% of diffuse intrinsic pontine gliomas (DIPGs) harbor a point mutation in histone H3.3 whe... more Over 80% of diffuse intrinsic pontine gliomas (DIPGs) harbor a point mutation in histone H3.3 where lysine 27 is substituted with methionine (H3.3K27M); however, how the mutation affects kinetics and function of PcG proteins remains elusive. We demonstrate that H3.3K27M prolongs the residence time and search time of Ezh2, but has no effect on its fraction bound to chromatin. In contrast, H3.3K27M has no effect on the residence time of Cbx7, but prolongs its search time and decreases its fraction bound to chromatin. We show that increasing expression of Cbx7 inhibits the proliferation of DIPG cells and prolongs its residence time. Our results highlight that the residence time of PcG proteins directly correlates with their functions and the search time of PcG proteins is critical for regulating their genomic occupancy. Together, our data provide mechanisms in which the cancer-causing histone mutation alters the binding and search dynamics of epigenetic complexes.
Car--Parrinello Molecular Dynamics Study of Base-Catalyzed Hydrolysis Reactions
We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello... more We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello molecular dynamics package to study the base-catalyzed hydrolysis of N-methylacetamide in aqueous solution. Our calculations are carried out in the framework of density functional theory combined with the hybrid BLYP exchange-correlation functional The free energy surfaces and hydrolysis reaction pathways for N-methylacetamide are examined in the presence of a hydroxide ion, and 4, 32, and 64 water molecules. We find that at least 32 water molecules must be explicitly included in metadynamics simulations to accurately describe the mechanism of the hydrolysis reaction of N-Methylacetamide. Our theoretical estimate for the dissociation energy of N-Methylacetamide is in good agreement with the results of previous experimental and theoretical studies.
Four types of density functional theory (DFT)-based approaches are assessed in this work for the ... more Four types of density functional theory (DFT)-based approaches are assessed in this work for the approximate construction of diabatic states and evaluation of the electronic couplings between these states.
The accuracy of the noninteracting electron approximation is examined for a model of vibrationall... more The accuracy of the noninteracting electron approximation is examined for a model of vibrationally coupled electron transport in single molecule junction. In the absence of electronicvibrational coupling, steady state transport in this model is described exactly by Landauer theory. Including coupling, both electronic-vibrational and vibrationally induced electron-electron correlation effects may contribute to the real time quantum dynamics. Using the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory to describe nuclear dynamics exactly while maintaining the noninteracting electron approximation for the electronic dynamics, the correlation effects are analyzed in different physical regimes. It is shown that although the noninteracting electron approximation may be reasonable for describing short time dynamics, it does not give the correct long time limit for certain initial conditions.
Uploads
Papers by Haobin Wang