Xiujun Wang - Academia.edu (original) (raw)

Papers by Xiujun Wang

Research paper thumbnail of Nutrient utilization ratios in the Polar Frontal Zone in the Australian sector of the Southern Ocean: A model

Global Biogeochemical Cycles, 2003

[1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the So... more [1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Southern Ocean, we simulated the seasonal nitrate, phosphate, and silicate cycle in the upper ocean with a biophysical model. Total phytoplankton biomass was prescribed from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) estimates, and we included two phytoplankton types, diatoms and nondiatoms. We set the nondiatoms N/P uptake ratio to 16 while the diatoms N/P and N/Si ratios were determined by fitting the observed seasonal nitrate, phosphate, and silicate cycle in the mixed layer. The best model fit to the observations required an annual N/P utilization ratio of 13.2, but this low N/P ratio still overestimated the nitrate utilization during the summer. We considered three mechanisms for improving the simulated nitrate cycle: (1) seasonal variation in the N/P ratio of the horizontal nutrient supply to the PFZ, (2) different remineralization length scales for particulate organic nitrogen (PON) and particulate organic phosphorus (POP), and (3) seasonal accumulation and decomposition of labile dissolved and suspended organic matter (OM). Model simulations showed that the seasonal variability in the N/P ratio of horizontal supply failed to reduce the simulated excess nitrate utilization in summer. Preferential recycling of PON compared to POP below the mixed layer degrades the simulation and cannot produce results that satisfy both the observed seasonal nitrate and phosphate cycle in the mixed layer. The most realistic model simulation was obtained with preferential recycling of POP over PON, but this mechanism alone was incapable of satisfying the summer nitrate and phosphate data. With the inclusion of an OM pool in our model we were able to reproduce the observed seasonal mixed layer nitrate and phosphate cycles. Satisfactory results can be achieved through various combinations of the N/P ratio of OM and the lifetime of the OM. Seasonal observations of dissolved and suspended organic phosphorus, nitrogen and carbon are needed to confirm their role. The important conclusion of our model study is that in the PFZ the annual nutrient utilization ratio of nitrate to phosphate is considerably less than the classical Redfield value of 16.

Research paper thumbnail of Nutrient utilization ratios in the Polar Frontal Zone in the Australian sector of the Southern Ocean: A model

Global Biogeochemical Cycles, 2003

1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Sou... more 1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Southern Ocean, we simulated the seasonal nitrate, phosphate, and silicate cycle in the upper ocean with a biophysical model. Total phytoplankton biomass was prescribed from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) estimates, and we included two phytoplankton types, diatoms and nondiatoms. We set the nondiatoms N/P uptake ratio to 16 while the diatoms N/P and N/Si ratios were determined by fitting the observed seasonal nitrate, phosphate, and silicate cycle in the mixed layer. The best model fit to the observations required an annual N/P utilization ratio of 13.2, but this low N/P ratio still overestimated the nitrate utilization during the summer. We considered three mechanisms for improving the simulated nitrate cycle: (1) seasonal variation in the N/P ratio of the horizontal nutrient supply to the PFZ, (2) different remineralization length scales for particulate organic nitrogen (PON) and particulate organic phosphorus (POP), and seasonal accumulation and decomposition of labile dissolved and suspended organic matter (OM). Model simulations showed that the seasonal variability in the N/P ratio of horizontal supply failed to reduce the simulated excess nitrate utilization in summer. Preferential recycling of PON compared to POP below the mixed layer degrades the simulation and cannot produce results that satisfy both the observed seasonal nitrate and phosphate cycle in the mixed layer. The most realistic model simulation was obtained with preferential recycling of POP over PON, but this mechanism alone was incapable of satisfying the summer nitrate and phosphate data. With the inclusion of an OM pool in our model we were able to reproduce the observed seasonal mixed layer nitrate and phosphate cycles. Satisfactory results can be achieved through various combinations of the N/P ratio of OM and the lifetime of the OM. Seasonal observations of dissolved and suspended organic phosphorus, nitrogen and carbon are needed to confirm their role. The important conclusion of our model study is that in the PFZ the annual nutrient utilization ratio of nitrate to phosphate is considerably less than the classical Redfield value of 16.

Research paper thumbnail of Modeling the upper ocean dynamics in the Subantarctic and Polar Frontal Zones in the Australian sector of the Southern Ocean

Journal of Geophysical Research, 2001

A one-dimensional (l-D) mixed layer model (the Chen scheme) was applied in the Subantarctic Zone ... more A one-dimensional (l-D) mixed layer model (the Chen scheme) was applied in the Subantarctic Zone (SAg) and the Polar Frontal Zone (PFZ) to simulate the upper ocean dynamics. The model was forced with 4 years data of the heat fluxes, freshwater fluxes, and wind stresses from the National Centers for Environmental Prediction. In both the SAZ and PFZ, the 1-D model was capable of reproducing the amplitude of the seasonal sea surface temperature (SST) and the seasonality of the mixed layer depth (MLD). The shallowest MLD was found in January-Febm• (20 m in the SAZ, 35 m in the PFZ), and the deepest MLD was found between August and October (600 m in the SAZ, 160 m in the PFZ). The summer MLD was shallower in the SAZ than in the PFZ due to the lower wind stress. However, the shallower winter MLD in the PFZ than in the SAZ was due to the strong stratification in the water below the mixed layer. In the SAZ, variability in the wind stress was the dominant term driving the fluctuation in MLD in the summer, but variability in the heat flux was the major factor controlling the timing of the deepening and shoaling of the mixed layer in the winter. In the PFZ both the variability in the wind stress and the heat flux dominated the variability of the MLD in both the sintuner and the winter.

Research paper thumbnail of Modeling seasonal phosphate export and resupply in the Subantarctic and Polar Frontal Zones in the Australian sector of the Southern Ocean

Journal of Geophysical Research, 2001

We developed and applied a one-dimensional (z) biophysical model to the Subantarctic Zone (SAZ) a... more We developed and applied a one-dimensional (z) biophysical model to the Subantarctic Zone (SAZ) and the Polar Frontal Zone (PFZ) to simulate seasonal phosphate export production and resupply. The physical component of our model was capable of reproducing the observed seasonal amplitude of sea surface temperature and mixed layer depth. In the biological component of the model we used incident light, mixed layer depth, phosphate availability, and estimates of phytoplankton biomass from the Sea-viewing Wide Field-of-view Sensor to determine production and tuned the model to reproduce the observed seasonal cycle of phosphate. We carried out a series of sensitivity studies, taking into account uncertainties in both physical fields and biological formulations (including potential influence of iron limitation), which led to several robust conclusions (as represented by the ranges below). The major growing season contributed 66-76% of the annual export production in both regions. The simulated annual export production was significantly higher in the PFZ (68-83 mmol P m 2) than in the SAZ (52-61 mmol P m -2) despite the PFZ's having lower seasonal nutrient depletion. The higher export production in the PFZ was due to its greater resupply of phosphate to the upper ocean during 2 the September to March period (27-37 mmol P m 2) relative to that in the SAZ (8-15 mmol P m-). Hence seasonal nutrient depletion was a better estimate of seasonal export production in the SAZ, as demonstrated by its higher ratio of seasonal depletion/export (64-78%) relative to that in the PFZ (34-47%). In the SAZ, vertical mixing was the dominant mechanism for supplying phosphate to the euphotic zone, whereas in the PFZ, vertical mixing supplied only 37% of the phosphate to the euphotic zone and horizontal transport supplied the remaining 63%.

Research paper thumbnail of Practical synthesis and mechanistic study of polysubstituted tetrahydropyrimidines with use of domino multicomponent reactions

Tetrahedron, 2009

The practical synthesis of polysubstituted tetrahydropyrimidines 4 from but-2-ynedioates 1, amine... more The practical synthesis of polysubstituted tetrahydropyrimidines 4 from but-2-ynedioates 1, amines 2, and formaldehyde 3 through a domino process of one-pot multicomponent reactions (MCRs) and the detailed mechanistic studies are described. The MCRs were performed under extremely mild reaction conditions and offered the desired products in excellent yields. The detailed studies on the mechanism of the MCRs proved that: (1)

Research paper thumbnail of Electronic structure and charge distribution of potassium iodide intercalated single-walled carbon nanotubes

Applied Physics Letters, 2004

Recently, potassium iodide was inserted into single-walled carbon nanotubes. We present here a fi... more Recently, potassium iodide was inserted into single-walled carbon nanotubes. We present here a first-principles density-functional theory calculation of the electronic and optical properties of a potassium iodide intercalated (10,10) nanotube. Band structure, density of states, and charge distribution of the intercalated nanotube are determined. Significant changes in the electronic structure of carbon nanotube are found upon the intercalation. In particular, the electron distribution on the tube becomes more diffusive, and one out of every four K 4s electrons transfers to the tube wall, while the other three go to I 5p orbitals.

Research paper thumbnail of Absorption-spectral features of single-walled carbon nanotubes

Chemical Physics Letters, 2004

We present a visual, intuitive connection between optical absorption line shapes and the underlyi... more We present a visual, intuitive connection between optical absorption line shapes and the underlying carbon nanotube structures. Within the tight-binding model, the absorption spectra can be linked directly to plots of energy contours and transition dipoles of a graphene sheet. Via two additional approaches, spectral features are shown only slightly altered by electronic correlations and σ–π orbital rehybridization. Despite dependence

Research paper thumbnail of Development, Scope and Mechanisms of Multicomponent Reactions of Asymmetric Electron-Deficient Alkynes with Amines and Formaldehyde

Chemistry-a European Journal, 2008

Based on the reactive behaviour of the substrates, two synthetic routes to polysubstituted pyrimi... more Based on the reactive behaviour of the substrates, two synthetic routes to polysubstituted pyrimidine derivatives are presented herein: 1) A catalyst-free multicomponent reaction of electron-deficient alkynes, aliphatic amines and formaldehyde and 2) AgI-catalyzed synthesis of pyrimidines from electron-deficient alkynes, anilines and formaldehyde by a domino reaction. Under optimized conditions, the multicomponent reactions were accomplished with high regioselectivity and excellent yields. A computational study was carried out by using the B3LYP density functional theory to elucidate the mechanisms of the catalyst-free hydroamination reaction. Calculations showed the activation free energies of aliphatic amines were lower than those of anilines, which is consistent with the experimental results.

Research paper thumbnail of Improving the accuracy of density-functional theory calculation: The genetic algorithm and neural network approach

Chemical Physics, 2007

The combination of genetic algorithm and neural network approach ͑GANN͒ has been developed to imp... more The combination of genetic algorithm and neural network approach ͑GANN͒ has been developed to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation and GANN correction approach has been applied to evaluate the optical absorption energies of 150 organic molecules. The neural network approach reduces the root-mean-square ͑rms͒ deviation of the calculated absorption energies of 150 organic molecules from 0.47 to 0.22 eV for the TDDFT/ B3LYP/ 6-31G͑d͒ calculation, and the newly developed GANN correction approach reduces the rms deviation to 0.16 eV.

Research paper thumbnail of Combined first-principles calculation and neural-network correction approach for heat of formation

Chemical Physics, 2003

Despite their success, the results of first-principles quantum mechanical calculations contain in... more Despite their success, the results of first-principles quantum mechanical calculations contain inherent numerical errors caused by various intrinsic approximations. We propose here a neural-network-based algorithm to greatly reduce these inherent errors. As a demonstration, this combined quantum mechanical calculation and neural-network correction approach is applied to the evaluation of standard heat of formation ⌬ f H for 180 small-to medium-sized organic molecules at 298 K. A dramatic reduction of numerical errors is clearly shown with systematic deviation being eliminated. For example, the root-mean-square deviation of the calculated ⌬ f H for the 180 molecules is reduced from 21.4 to 3.1 kcal mol Ϫ1 for B3LYP/6-311ϩG(d, p) and from 12.0 to 3.3 kcal mol Ϫ1 for B3LYP/6-311ϩG(3d f ,2p) before and after the neural-network correction.

Research paper thumbnail of Linear scaling time-dependent density-functional tight-binding method for absorption spectra of large systems

Physical Review B, 2007

We present an implementation of time-dependent density-functional theory (TDDFT) in the linear re... more We present an implementation of time-dependent density-functional theory (TDDFT) in the linear response formalism enabling the calculation of low energy optical absorption spectra for large molecules and nanostructures. The method avoids any explicit reference to canonical representations of either occupied or virtual Kohn-Sham states and thus achieves linear-scaling computational effort with system size. In contrast to conventional localised orbital formulations, where a single set of localised functions is used to span the occupied and unoccupied state manifold, we make use of two sets of in situ optimised localised orbitals, one for the occupied and one for the unoccupied space. This double representation approach avoids known problems of spanning the space of unoccupied Kohn-Sham states with a minimal set of localised orbitals optimised for the occupied space, while the in situ optimisation procedure allows for efficient calculations with a minimal number of functions. The method is applied to a number of medium sized organic molecules and a good agreement with traditional TDDFT methods is observed. Furthermore, linear scaling of computational cost with system size is demonstrated on (10,0) carbon nanotubes of different lengths. * Electronic address: tjz07@imperial.ac.uk

Research paper thumbnail of A generalized exchange-correlation functional: the Neural-Networks approach

Chemical Physics Letters, 2004

A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation func... more A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation functional for density functional theory. It is applied to improve B3LYP functional by taking into account of high-order contributions to the exchange-correlation functional. The improved B3LYP functional is based on a neural network whose structure and synaptic weights are determined from 116 known experimental atomization energies, ionization potentials, proton affinities or total atomic energies which were used by Becke in his pioneer work on the hybrid functionals [J. Chem. Phys. 98, 5648 (1993)]. It leads to better agreement between the first-principles calculation results and these 116 experimental data. The new B3LYP functional is further tested by applying it to calculate the ionization potentials of 24 molecules of the G2 test set. The 6-311+G(3df,2p) basis set is employed in the calculation, and the resulting root-mean-square error is reduced to 2.2 kcal·mol −1 in comparison to 3.6 kcal·mol −1 of conventional B3LYP/6-311+G(3df,2p) calculation.

Research paper thumbnail of Localized-density-matrix method and its application to nanomaterials

Pure and Applied Chemistry, 2000

The localized-density-matrix (LDM) method has been developed to calculate the excited state prope... more The localized-density-matrix (LDM) method has been developed to calculate the excited state properties of very large systems containing thousands of atoms. It is particularly suitable for simulating the dynamic electronic processes in nanoscale materials, and has been applied to poly(p-phenylenevynelene) (PPV) aggregates and carbon nanotubes. Absorption spectra of PPVs and carbon nanotubes have been calculated and compared to the experiments. 290 G. CHEN et al. © 2000 IUPAC, Pure and Applied Chemistry 72, 281-291

Research paper thumbnail of Nutrient utilization ratios in the Polar Frontal Zone in the Australian sector of the Southern Ocean: A model

Global Biogeochemical Cycles, 2003

[1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the So... more [1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Southern Ocean, we simulated the seasonal nitrate, phosphate, and silicate cycle in the upper ocean with a biophysical model. Total phytoplankton biomass was prescribed from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) estimates, and we included two phytoplankton types, diatoms and nondiatoms. We set the nondiatoms N/P uptake ratio to 16 while the diatoms N/P and N/Si ratios were determined by fitting the observed seasonal nitrate, phosphate, and silicate cycle in the mixed layer. The best model fit to the observations required an annual N/P utilization ratio of 13.2, but this low N/P ratio still overestimated the nitrate utilization during the summer. We considered three mechanisms for improving the simulated nitrate cycle: (1) seasonal variation in the N/P ratio of the horizontal nutrient supply to the PFZ, (2) different remineralization length scales for particulate organic nitrogen (PON) and particulate organic phosphorus (POP), and (3) seasonal accumulation and decomposition of labile dissolved and suspended organic matter (OM). Model simulations showed that the seasonal variability in the N/P ratio of horizontal supply failed to reduce the simulated excess nitrate utilization in summer. Preferential recycling of PON compared to POP below the mixed layer degrades the simulation and cannot produce results that satisfy both the observed seasonal nitrate and phosphate cycle in the mixed layer. The most realistic model simulation was obtained with preferential recycling of POP over PON, but this mechanism alone was incapable of satisfying the summer nitrate and phosphate data. With the inclusion of an OM pool in our model we were able to reproduce the observed seasonal mixed layer nitrate and phosphate cycles. Satisfactory results can be achieved through various combinations of the N/P ratio of OM and the lifetime of the OM. Seasonal observations of dissolved and suspended organic phosphorus, nitrogen and carbon are needed to confirm their role. The important conclusion of our model study is that in the PFZ the annual nutrient utilization ratio of nitrate to phosphate is considerably less than the classical Redfield value of 16.

Research paper thumbnail of Nutrient utilization ratios in the Polar Frontal Zone in the Australian sector of the Southern Ocean: A model

Global Biogeochemical Cycles, 2003

1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Sou... more 1] To investigate the non-Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Southern Ocean, we simulated the seasonal nitrate, phosphate, and silicate cycle in the upper ocean with a biophysical model. Total phytoplankton biomass was prescribed from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) estimates, and we included two phytoplankton types, diatoms and nondiatoms. We set the nondiatoms N/P uptake ratio to 16 while the diatoms N/P and N/Si ratios were determined by fitting the observed seasonal nitrate, phosphate, and silicate cycle in the mixed layer. The best model fit to the observations required an annual N/P utilization ratio of 13.2, but this low N/P ratio still overestimated the nitrate utilization during the summer. We considered three mechanisms for improving the simulated nitrate cycle: (1) seasonal variation in the N/P ratio of the horizontal nutrient supply to the PFZ, (2) different remineralization length scales for particulate organic nitrogen (PON) and particulate organic phosphorus (POP), and seasonal accumulation and decomposition of labile dissolved and suspended organic matter (OM). Model simulations showed that the seasonal variability in the N/P ratio of horizontal supply failed to reduce the simulated excess nitrate utilization in summer. Preferential recycling of PON compared to POP below the mixed layer degrades the simulation and cannot produce results that satisfy both the observed seasonal nitrate and phosphate cycle in the mixed layer. The most realistic model simulation was obtained with preferential recycling of POP over PON, but this mechanism alone was incapable of satisfying the summer nitrate and phosphate data. With the inclusion of an OM pool in our model we were able to reproduce the observed seasonal mixed layer nitrate and phosphate cycles. Satisfactory results can be achieved through various combinations of the N/P ratio of OM and the lifetime of the OM. Seasonal observations of dissolved and suspended organic phosphorus, nitrogen and carbon are needed to confirm their role. The important conclusion of our model study is that in the PFZ the annual nutrient utilization ratio of nitrate to phosphate is considerably less than the classical Redfield value of 16.

Research paper thumbnail of Modeling the upper ocean dynamics in the Subantarctic and Polar Frontal Zones in the Australian sector of the Southern Ocean

Journal of Geophysical Research, 2001

A one-dimensional (l-D) mixed layer model (the Chen scheme) was applied in the Subantarctic Zone ... more A one-dimensional (l-D) mixed layer model (the Chen scheme) was applied in the Subantarctic Zone (SAg) and the Polar Frontal Zone (PFZ) to simulate the upper ocean dynamics. The model was forced with 4 years data of the heat fluxes, freshwater fluxes, and wind stresses from the National Centers for Environmental Prediction. In both the SAZ and PFZ, the 1-D model was capable of reproducing the amplitude of the seasonal sea surface temperature (SST) and the seasonality of the mixed layer depth (MLD). The shallowest MLD was found in January-Febm• (20 m in the SAZ, 35 m in the PFZ), and the deepest MLD was found between August and October (600 m in the SAZ, 160 m in the PFZ). The summer MLD was shallower in the SAZ than in the PFZ due to the lower wind stress. However, the shallower winter MLD in the PFZ than in the SAZ was due to the strong stratification in the water below the mixed layer. In the SAZ, variability in the wind stress was the dominant term driving the fluctuation in MLD in the summer, but variability in the heat flux was the major factor controlling the timing of the deepening and shoaling of the mixed layer in the winter. In the PFZ both the variability in the wind stress and the heat flux dominated the variability of the MLD in both the sintuner and the winter.

Research paper thumbnail of Modeling seasonal phosphate export and resupply in the Subantarctic and Polar Frontal Zones in the Australian sector of the Southern Ocean

Journal of Geophysical Research, 2001

We developed and applied a one-dimensional (z) biophysical model to the Subantarctic Zone (SAZ) a... more We developed and applied a one-dimensional (z) biophysical model to the Subantarctic Zone (SAZ) and the Polar Frontal Zone (PFZ) to simulate seasonal phosphate export production and resupply. The physical component of our model was capable of reproducing the observed seasonal amplitude of sea surface temperature and mixed layer depth. In the biological component of the model we used incident light, mixed layer depth, phosphate availability, and estimates of phytoplankton biomass from the Sea-viewing Wide Field-of-view Sensor to determine production and tuned the model to reproduce the observed seasonal cycle of phosphate. We carried out a series of sensitivity studies, taking into account uncertainties in both physical fields and biological formulations (including potential influence of iron limitation), which led to several robust conclusions (as represented by the ranges below). The major growing season contributed 66-76% of the annual export production in both regions. The simulated annual export production was significantly higher in the PFZ (68-83 mmol P m 2) than in the SAZ (52-61 mmol P m -2) despite the PFZ's having lower seasonal nutrient depletion. The higher export production in the PFZ was due to its greater resupply of phosphate to the upper ocean during 2 the September to March period (27-37 mmol P m 2) relative to that in the SAZ (8-15 mmol P m-). Hence seasonal nutrient depletion was a better estimate of seasonal export production in the SAZ, as demonstrated by its higher ratio of seasonal depletion/export (64-78%) relative to that in the PFZ (34-47%). In the SAZ, vertical mixing was the dominant mechanism for supplying phosphate to the euphotic zone, whereas in the PFZ, vertical mixing supplied only 37% of the phosphate to the euphotic zone and horizontal transport supplied the remaining 63%.

Research paper thumbnail of Practical synthesis and mechanistic study of polysubstituted tetrahydropyrimidines with use of domino multicomponent reactions

Tetrahedron, 2009

The practical synthesis of polysubstituted tetrahydropyrimidines 4 from but-2-ynedioates 1, amine... more The practical synthesis of polysubstituted tetrahydropyrimidines 4 from but-2-ynedioates 1, amines 2, and formaldehyde 3 through a domino process of one-pot multicomponent reactions (MCRs) and the detailed mechanistic studies are described. The MCRs were performed under extremely mild reaction conditions and offered the desired products in excellent yields. The detailed studies on the mechanism of the MCRs proved that: (1)

Research paper thumbnail of Electronic structure and charge distribution of potassium iodide intercalated single-walled carbon nanotubes

Applied Physics Letters, 2004

Recently, potassium iodide was inserted into single-walled carbon nanotubes. We present here a fi... more Recently, potassium iodide was inserted into single-walled carbon nanotubes. We present here a first-principles density-functional theory calculation of the electronic and optical properties of a potassium iodide intercalated (10,10) nanotube. Band structure, density of states, and charge distribution of the intercalated nanotube are determined. Significant changes in the electronic structure of carbon nanotube are found upon the intercalation. In particular, the electron distribution on the tube becomes more diffusive, and one out of every four K 4s electrons transfers to the tube wall, while the other three go to I 5p orbitals.

Research paper thumbnail of Absorption-spectral features of single-walled carbon nanotubes

Chemical Physics Letters, 2004

We present a visual, intuitive connection between optical absorption line shapes and the underlyi... more We present a visual, intuitive connection between optical absorption line shapes and the underlying carbon nanotube structures. Within the tight-binding model, the absorption spectra can be linked directly to plots of energy contours and transition dipoles of a graphene sheet. Via two additional approaches, spectral features are shown only slightly altered by electronic correlations and σ–π orbital rehybridization. Despite dependence

Research paper thumbnail of Development, Scope and Mechanisms of Multicomponent Reactions of Asymmetric Electron-Deficient Alkynes with Amines and Formaldehyde

Chemistry-a European Journal, 2008

Based on the reactive behaviour of the substrates, two synthetic routes to polysubstituted pyrimi... more Based on the reactive behaviour of the substrates, two synthetic routes to polysubstituted pyrimidine derivatives are presented herein: 1) A catalyst-free multicomponent reaction of electron-deficient alkynes, aliphatic amines and formaldehyde and 2) AgI-catalyzed synthesis of pyrimidines from electron-deficient alkynes, anilines and formaldehyde by a domino reaction. Under optimized conditions, the multicomponent reactions were accomplished with high regioselectivity and excellent yields. A computational study was carried out by using the B3LYP density functional theory to elucidate the mechanisms of the catalyst-free hydroamination reaction. Calculations showed the activation free energies of aliphatic amines were lower than those of anilines, which is consistent with the experimental results.

Research paper thumbnail of Improving the accuracy of density-functional theory calculation: The genetic algorithm and neural network approach

Chemical Physics, 2007

The combination of genetic algorithm and neural network approach ͑GANN͒ has been developed to imp... more The combination of genetic algorithm and neural network approach ͑GANN͒ has been developed to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation and GANN correction approach has been applied to evaluate the optical absorption energies of 150 organic molecules. The neural network approach reduces the root-mean-square ͑rms͒ deviation of the calculated absorption energies of 150 organic molecules from 0.47 to 0.22 eV for the TDDFT/ B3LYP/ 6-31G͑d͒ calculation, and the newly developed GANN correction approach reduces the rms deviation to 0.16 eV.

Research paper thumbnail of Combined first-principles calculation and neural-network correction approach for heat of formation

Chemical Physics, 2003

Despite their success, the results of first-principles quantum mechanical calculations contain in... more Despite their success, the results of first-principles quantum mechanical calculations contain inherent numerical errors caused by various intrinsic approximations. We propose here a neural-network-based algorithm to greatly reduce these inherent errors. As a demonstration, this combined quantum mechanical calculation and neural-network correction approach is applied to the evaluation of standard heat of formation ⌬ f H for 180 small-to medium-sized organic molecules at 298 K. A dramatic reduction of numerical errors is clearly shown with systematic deviation being eliminated. For example, the root-mean-square deviation of the calculated ⌬ f H for the 180 molecules is reduced from 21.4 to 3.1 kcal mol Ϫ1 for B3LYP/6-311ϩG(d, p) and from 12.0 to 3.3 kcal mol Ϫ1 for B3LYP/6-311ϩG(3d f ,2p) before and after the neural-network correction.

Research paper thumbnail of Linear scaling time-dependent density-functional tight-binding method for absorption spectra of large systems

Physical Review B, 2007

We present an implementation of time-dependent density-functional theory (TDDFT) in the linear re... more We present an implementation of time-dependent density-functional theory (TDDFT) in the linear response formalism enabling the calculation of low energy optical absorption spectra for large molecules and nanostructures. The method avoids any explicit reference to canonical representations of either occupied or virtual Kohn-Sham states and thus achieves linear-scaling computational effort with system size. In contrast to conventional localised orbital formulations, where a single set of localised functions is used to span the occupied and unoccupied state manifold, we make use of two sets of in situ optimised localised orbitals, one for the occupied and one for the unoccupied space. This double representation approach avoids known problems of spanning the space of unoccupied Kohn-Sham states with a minimal set of localised orbitals optimised for the occupied space, while the in situ optimisation procedure allows for efficient calculations with a minimal number of functions. The method is applied to a number of medium sized organic molecules and a good agreement with traditional TDDFT methods is observed. Furthermore, linear scaling of computational cost with system size is demonstrated on (10,0) carbon nanotubes of different lengths. * Electronic address: tjz07@imperial.ac.uk

Research paper thumbnail of A generalized exchange-correlation functional: the Neural-Networks approach

Chemical Physics Letters, 2004

A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation func... more A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation functional for density functional theory. It is applied to improve B3LYP functional by taking into account of high-order contributions to the exchange-correlation functional. The improved B3LYP functional is based on a neural network whose structure and synaptic weights are determined from 116 known experimental atomization energies, ionization potentials, proton affinities or total atomic energies which were used by Becke in his pioneer work on the hybrid functionals [J. Chem. Phys. 98, 5648 (1993)]. It leads to better agreement between the first-principles calculation results and these 116 experimental data. The new B3LYP functional is further tested by applying it to calculate the ionization potentials of 24 molecules of the G2 test set. The 6-311+G(3df,2p) basis set is employed in the calculation, and the resulting root-mean-square error is reduced to 2.2 kcal·mol −1 in comparison to 3.6 kcal·mol −1 of conventional B3LYP/6-311+G(3df,2p) calculation.

Research paper thumbnail of Localized-density-matrix method and its application to nanomaterials

Pure and Applied Chemistry, 2000

The localized-density-matrix (LDM) method has been developed to calculate the excited state prope... more The localized-density-matrix (LDM) method has been developed to calculate the excited state properties of very large systems containing thousands of atoms. It is particularly suitable for simulating the dynamic electronic processes in nanoscale materials, and has been applied to poly(p-phenylenevynelene) (PPV) aggregates and carbon nanotubes. Absorption spectra of PPVs and carbon nanotubes have been calculated and compared to the experiments. 290 G. CHEN et al. © 2000 IUPAC, Pure and Applied Chemistry 72, 281-291