Haobin Wang | University of Colorado Denver (original) (raw)
Papers by Haobin Wang
Photochem, 2022
A fundamental goal of photochemistry is to understand how structural features of a chromophore ca... more A fundamental goal of photochemistry is to understand how structural features of a chromophore can make specific bonds within a molecule prone to cleavage by light, or photolabile. The meta effect is an example of a regiochemical explanation for photolability, in which electron donating groups on an aromatic ring cause photolability selectively at the meta position. Here, we show, using a chromophore containing one ring with a meta-methoxy group and one ring with a para-methoxy group, that two stereoisomers of the same compounds can react with light differently, based simply on the three-dimensional positioning of a meta anisyl ring. The result is that the stereoisomers of the compound with the same configuration at both stereogenic centers are photolabile while the stereoisomers with opposite configuration do not react with light. Furthermore, time-dependent density functional theory (TD-DFT) calculations show distinct excitation pathways for each stereoisomer.
Cell Reports, 2020
Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains... more Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains unclear whether and how transcriptional condensates accelerate the search of transcriptional regulatory factors for their target sites. Furthermore, the molecular mechanisms by which regulatory factors nucleate on chromatin to assemble transcriptional condensates remain incompletely understood. The CBX-PRC1 complexes compartmentalize key developmental regulators for repression through phase-separated condensates driven by the chromobox 2 (CBX2) protein. Here, by using live-cell single-molecule imaging, we show that CBX2 nucleates on chromatin independently of H3K27me3 and CBX-PRC1. The interactions between CBX2 and DNA are essential for nucleating CBX-PRC1 on chromatin to assemble condensates. The assembled condensates shorten 3D diffusion time and reduce trials for finding specific sites through revisiting the same or adjacent sites repetitively, thereby accelerating CBX2 in searching for target sites. Overall, our data suggest a generic mechanism by which transcriptional regulatory factors nucleate to assemble condensates that accelerate their target-search process.
Polycomb group (PcG) proteins are master regulators of development and differentiation. Mutation ... more Polycomb group (PcG) proteins are master regulators of development and differentiation. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the nucleus of cells and these condensates are the physical sites of PcG-targeted gene silencing. However, the physiochemical principles underlying the PcG condensate formation remain unknown. Here we show that Polycomb repressive complex 1 (PRC1) protein Cbx2, one member of the Cbx family proteins, contains a long stretch of intrinsically disordered region (IDR). Cbx2 undergoes phase separation to form condensates. Cbx2 condensates exhibit liquid-like properties and can concentrate DNA and nucleosomes. We demonstrate that the conserved residues within the IDR promote the condensate formation in vitro and in vivo. We further indicate that H3K27me3 has minimal effects on the Cbx2 condensate formation while depletion of core PRC1 subunits facilitates the condensate formation. Thus, our r...
arXiv (Cornell University), Feb 10, 2013
The multilayer multiconfiguration time-dependent Hartree method is employed to study vibrationall... more The multilayer multiconfiguration time-dependent Hartree method is employed to study vibrationally coupled charge transport in models of single molecule junctions. To increase the efficiency of the simulation method, a representation of the Hamiltonian in terms of the scattering states of the underlying electronic Hamiltonian is used. It is found that with an appropriate choice of the scattering states the artificial electron correlation present in the original representation of the model is greatly reduced. This allows efficient simulation of the steady-state currents in a wide physical parameter space, which is demonstrated by several numerical examples.
Advances in Gas Phase Ion Chemistry, 1998
Chemical Physics, 2004
A detailed study of photoinduced electron transfer reactions from an electronically excited state... more A detailed study of photoinduced electron transfer reactions from an electronically excited state of a dye molecule to the conduction band of a semiconductor substrate is presented. Adopting a generic model for electronic–vibrational coupling in heterogeneous electron transfer reactions, the quantum dynamics of the electron injection process is simulated employing the recently proposed self-consistent hybrid method. The results reveal the
The Journal of Physical Chemistry A
Nanoscale
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.
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.
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.
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.
Entropy
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.
The Journal of Chemical Physics
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.
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.
Chinese Journal of Chemical Physics
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.
Physical Chemistry Chemical Physics
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.
Journal of Biological Chemistry
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 ...
Nature communications, May 25, 2018
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.
Photochem, 2022
A fundamental goal of photochemistry is to understand how structural features of a chromophore ca... more A fundamental goal of photochemistry is to understand how structural features of a chromophore can make specific bonds within a molecule prone to cleavage by light, or photolabile. The meta effect is an example of a regiochemical explanation for photolability, in which electron donating groups on an aromatic ring cause photolability selectively at the meta position. Here, we show, using a chromophore containing one ring with a meta-methoxy group and one ring with a para-methoxy group, that two stereoisomers of the same compounds can react with light differently, based simply on the three-dimensional positioning of a meta anisyl ring. The result is that the stereoisomers of the compound with the same configuration at both stereogenic centers are photolabile while the stereoisomers with opposite configuration do not react with light. Furthermore, time-dependent density functional theory (TD-DFT) calculations show distinct excitation pathways for each stereoisomer.
Cell Reports, 2020
Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains... more Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains unclear whether and how transcriptional condensates accelerate the search of transcriptional regulatory factors for their target sites. Furthermore, the molecular mechanisms by which regulatory factors nucleate on chromatin to assemble transcriptional condensates remain incompletely understood. The CBX-PRC1 complexes compartmentalize key developmental regulators for repression through phase-separated condensates driven by the chromobox 2 (CBX2) protein. Here, by using live-cell single-molecule imaging, we show that CBX2 nucleates on chromatin independently of H3K27me3 and CBX-PRC1. The interactions between CBX2 and DNA are essential for nucleating CBX-PRC1 on chromatin to assemble condensates. The assembled condensates shorten 3D diffusion time and reduce trials for finding specific sites through revisiting the same or adjacent sites repetitively, thereby accelerating CBX2 in searching for target sites. Overall, our data suggest a generic mechanism by which transcriptional regulatory factors nucleate to assemble condensates that accelerate their target-search process.
Polycomb group (PcG) proteins are master regulators of development and differentiation. Mutation ... more Polycomb group (PcG) proteins are master regulators of development and differentiation. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the nucleus of cells and these condensates are the physical sites of PcG-targeted gene silencing. However, the physiochemical principles underlying the PcG condensate formation remain unknown. Here we show that Polycomb repressive complex 1 (PRC1) protein Cbx2, one member of the Cbx family proteins, contains a long stretch of intrinsically disordered region (IDR). Cbx2 undergoes phase separation to form condensates. Cbx2 condensates exhibit liquid-like properties and can concentrate DNA and nucleosomes. We demonstrate that the conserved residues within the IDR promote the condensate formation in vitro and in vivo. We further indicate that H3K27me3 has minimal effects on the Cbx2 condensate formation while depletion of core PRC1 subunits facilitates the condensate formation. Thus, our r...
arXiv (Cornell University), Feb 10, 2013
The multilayer multiconfiguration time-dependent Hartree method is employed to study vibrationall... more The multilayer multiconfiguration time-dependent Hartree method is employed to study vibrationally coupled charge transport in models of single molecule junctions. To increase the efficiency of the simulation method, a representation of the Hamiltonian in terms of the scattering states of the underlying electronic Hamiltonian is used. It is found that with an appropriate choice of the scattering states the artificial electron correlation present in the original representation of the model is greatly reduced. This allows efficient simulation of the steady-state currents in a wide physical parameter space, which is demonstrated by several numerical examples.
Advances in Gas Phase Ion Chemistry, 1998
Chemical Physics, 2004
A detailed study of photoinduced electron transfer reactions from an electronically excited state... more A detailed study of photoinduced electron transfer reactions from an electronically excited state of a dye molecule to the conduction band of a semiconductor substrate is presented. Adopting a generic model for electronic–vibrational coupling in heterogeneous electron transfer reactions, the quantum dynamics of the electron injection process is simulated employing the recently proposed self-consistent hybrid method. The results reveal the
The Journal of Physical Chemistry A
Nanoscale
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.
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.
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.
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.
Entropy
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.
The Journal of Chemical Physics
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.
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.
Chinese Journal of Chemical Physics
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.
Physical Chemistry Chemical Physics
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.
Journal of Biological Chemistry
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 ...
Nature communications, May 25, 2018
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.