Hua, Weijie

o 2007-2011, PhD in Biotechnology (theoretical chemistry direction), Department of theoretical Chemistry, School of Biotechnology, KTH Royal Institute of Technology, Sweden.

Supervisor: Prof. Yi Luo

Thesis: Structure and spectroscopy of bio- and nano-materials from first-principles simulations.

o 2004-2010, PhD in Chemistry (theoretical chemistry direction), Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, China.

Supervisor: Prof. Shuhua Li

Thesis: Approximate methods for calculating ground-state electronic structure and properties of large molecules: methodological developments and applications.

o 2000-2004, B.S. in Chemistry, School of Chemistry and Chemical Engineering, Nanjing University.

  2000-2002, also selected in School of Intensitive Instructions for Sciences and Arts (now named Kuang Yaming Hornors School) of the same university for intensive training in math and physics.

Undergraduate thesis: Monte Carlo simulations of polymer configurations in dilute solution (supervised by Profs. Shuhua Li and Jing Ma)

o Professor, Department of Applied Physics, Nanjing University of Science and Technology, China, 2016.12-present

o PostDoc with Prof. Yi Luo, Royal Institute of Technology, Sweden, 2015.5-2016.12

o PostDoc with Prof. Shaul Mukamel, Department of Chemistry, School of Physical Sciences, Universty of California, Irvine, USA, 2013.4-2015.4       

o PostDoc with Prof. Yi Luo, Royal Institute of Technology, Sweden, 2011.5-2013.3

(please ignore the formatted purple headings above)

• Contents

I. Softwares

   A. Code contributions to spectroscopy calculations

      1. MCNOX

      2. PSSXS

      3. XspecTime

      4. Specryst

      5. DynaVib

      6. LSQC

   B. Other programs coded

II. Databases

   A. N1s Binding energies

   B. Vibrationally-resolved high-resolution X-ray spectra

------------------------------------------------------------------------------------------------------------------------------------------

I. Softwares

A. Code contributions to spectroscopy calculations

1. MCNOX

Citation: W. Hua, Y. Luo, S. Mukamel, Multi-Configurational methods for ultrafast NOlinear X-ray spectra (MCNOX), version 1.0, 2019, https://jszy.njust. edu.cn/lxy/hwj_en/list.psp

BibTeX format:

@misc{mcnox,

Author = {Hua, Weijie and Luo, Yi and Mukamel, Shaul},

    Title = {\uppercase{M}ulti-\uppercase{C}onfigurational methods for ultrafast \uppercase{NO}linear X-ray spectra (\uppercase{MCNOX}), version 1.0, http://jszy.njust.edu.cn/lxy/hwj\_en/list.psp},

Year= {2019},

}

@article{hua_mcnox_2024,

title = {{MCNOX}: {A} code for computing and interpreting ultrafast nonlinear {X}-ray spectra of molecules at the multiconfigurational level},

volume = {296},

doi = {10.1016/j.cpc.2023.109016},

journal = {Comput. Phys. Commun.},

author = {Hua, Weijie},

month = mar,

year = {2024},

pages = {109016},

}

Descreption: The MCNOX package was devloped by

Weijie Hua (wjhua@njust.edu.cn, Nanjing University of Science and Technology, China),

Yi Luo (yiluo@ustc.edu.cn, University of Science and Technology of China, China), and

Shaul Mukamel (smukamel@uci.edu, University of California, Irvine, USA),

which is capable of computing ultrafast (attosecond and femtosecond) nonlinear X-ray spectra of molecules at the multiconfigurational quantum chemistry level. It is aimed at cutting-edge current and future applications on photo-physics and photochemistry enabled by X-ray free electron lasers (XFELs) and high harmonic generation (HHG) light sources. Three types of signals can be simulated, including the transient X-ray absorption spectroscopy (TXAS), all-X-ray four-wave mixing (FWM), and stimulated Raman (SR) types. It is especially capable of analyses on major electronic transitions and further visualization of transitions in terms of the natural transition orbitals (NTOs), which is helpful for extracting the physical and chemical insights from complex signals. It was implemented to be interfaced with the Molpro software for electronic structure (integrals, molecular orbital coefficients, and configuration amplitudes) calculations and to print Molden format files for visualizing transition orbitals. A manual is still under development. An introduction paper to the package has been recently published on the "Attosecond Chemistry software" special issue of Computer Physics Communications[1].

Code capability:

- Steady-state XAS

- Transient XAS

- Four-wave mixing signals

- Stimulated Raman signals

- Natural transition orbital analysis

Publications using the code:

[1] W. Hua*, MCNOX: A code for computing and interpreting ultrafast nonlinear X-ray spectra of molecules at the multiconfigurational level, Comput. Phys. Commun., 2024, 296, 109016.

(published on Attosecond Chemistry software special issue)

[3]W. Hua, S. Oesterling, J. D. Biggs, Y. Zhang, H. Ando, R. de Vivie-Riedle*, B. P. Fingerhut, and S. Mukamel*, Monitoring conical intersections in the ring opening of furan by Attosecond Stimulated X-ray Raman Spectroscopy, Struct. Dyn.2016, 3, 023601

[4] W. Hua, K. Bennett, Y. Zhang, Y. Luo, S. Mukamel*, Study of double core hole excitations in molecules by X-ray double-quantum-coherence signals: a multi-configuration simulation, Chem. Sci., 2016, 7, 5922-5933

[5] W. Hua*, S. Mukamel*, Y. Luo, Transient X-ray absorption spectral fingerprints of the S1 dark state in uracil, J. Phys. Chem. Lett. 2019, 10, 7172-7178,

Code availability: To request a copy of MCNOX program, please complete the LICENSE FORM, MCNOX_User_License_Agreement_202305.pdf, and send its photo-copy to the maintainer at wjhua@njust.edu.cn.

2. PSSXS

Citation: W. Hua, Y. Luo, Platform for simulation of soft X-ray spectroscopy (PSSXS), version 1.0, 2023, https://jszy.njust. edu.cn/lxy/hwj_en/list.psp

BibTeX format:

@misc{PSSXS,

author = {Weijie Hua and Yi Luo},

note = {Platform for simulation of soft X-ray spectroscopy (PSSXS),  version 1.0, 2023, http://jszy.njust.edu.cn/lxy/hwj\_en/list.psp},

}

Descreption: The PSSXS package was devloped by Weijie Hua and Yi Luo. Its main body was developed during 2011-2013 and during 2015-2016, when Weijie Hua was a postdoc in the group of Prof. Yi Luo, and the code was used in several publications without the name (mentioned as our "in-house" code). It was reorganized and coined the name PSSXS in 2023.

The code was indended for soft X-ray spectroscopy simulations of large molecules and materials, and most applications are for 2D materials.

Code capability:

- Linear X-ray absorption spectroscopy (XAS) 

- Linear X-ray emission spectroscopy (XES), 

- Resonant inelastic X-ray scattering (RIXS)

- Shake-up satellites in X-ray photoelectron spectroscopy 

The code is interfaced to Gamess-US/Gaussian/NWChem.

Publications using the code:

[1] X. Li, W. Hua*, J. Guo, Y. Luo, Electronic Structure of Nitrogen-Doped Graphene in the Ground and Core-Excited States from First-Principles Simulations, J. Phys. Chem. C 2015, 119, 16660

[2] X. Li, W. Hua*, B.-Y. Wang, W.-F. Pong, P.-A. Glans, J. Guo*, and Y Luo, Effects of domain size on x-ray absorption spectra of boron nitride doped graphenes, Appl. Phys. Lett. 2016, 109, 081601

[3] Y. Ma, J. Lin, X.-N. Song, C.-K. Wang, W. Hua*, Yi Luo*, Local structures of nitrogen-doped graphdiynes determined by computational X-ray spectroscopy, Carbon 2019, 149, 672

[4] J.-R. Zhang, Y. Ma, S.-Y. Wang, J. Ding, B. Gao, E. Kan, W. Hua*, Accurate K-edge X-ray photoelectron and absorption spectra of g-C3N4 nanosheets by first-principles simulations and reinterpretations, PCCP 2019, 21, 22819

[5] G. Ge, J.-R. Zhang, S.-Y. Wang, M Wei, W. Hua*, A QM/MM Study on the X‑ray Spectra of Organic Proton Transfer Crystals of Isonicotinamides, J.Phys. Chem. C 2022,126,15849

[6] J.-R. Zhang, S.-Y. Wang, G. Ge, M. Wei*, Y. Ma*, on the choice of shape and size for truncated cluster-based x-ray spectral simulations of 2D materials, J. Chem. Phys. 2022, 157, 094704

[7] B.-B. Zhang, J. Lin, X.-N. Song, C.-K. Wang, W. Hua, Yong Ma*, Identification of oxidation states in gamma-graphyne by computational XPS and NEXAFS spectra, Appl. Surf. Sci. 2023, 609, 155134

[8] B.-B. Zhang, J. Ming, H.-Q. Li, X.-N. Song*, C.-K. Wang, W. Hua, Y. Ma*, Structural characterization of nitrogen-doped gamma-graphynes by computational X-ray spectroscopy, Carbon  2023, 214, 118301

[9] F. Pan, K. Ni, T. Xu, et al. R. S. Ruoff, Y. Zhu, Long-range ordered porous carbons produced from C60, Nature  2023, 614, 95-101

[10] J. Ming, J.-R. Zhang, X.-N. Song, X. Li, W. Hua, Y. Ma, First-principles simulation of X-ray spectra of graphdiyne and graphdiyne oxides at the carbon K-edge, PCCP2023, 25, 32421-32429

[11] J. Qi, Q. Ge, Z. Wang, J. Wu, Y. Wang, T. Gao, Theoretical study of Sulfur-Doped Graphdiynes by X-ray Spectroscopy, Inorg. Chem. 2024, 63, 766

3. W. Hua, M. Wei, XspecTime, version 0.9, Nanjing University of Science and Technology, 2023

XspecTime is a package under development to calculate X-ray spectra of molecules and ions by using wavepacket simulations, currently only valid for vibrationally-resolved XAS of diatomic systems.

Publications using the code

[1] L. Zhang, M. Wei*, G. Ge*, W. Hua*, Franck-Condon Simulation of Vibrationally-Resolved X-ray Spectra for Diatomic Systems: Validation of Harmonic Approximation and Density Functional Theory, Phys. Rev. A 2024, 00, 0000

4. G. Ge., J. Zhang, W. Hua,  Specryst, ver.1.0; Nanjing University of Science and Technology: Nanjing, 2022.

This is a MATLAB script program to construct QM/MM models of crystals for  X-ray spectra (XPS/XAS) calculations. 

Publications using the code

[1] G. Ge, J.-R. Zhang, S.-Y. Wang, M Wei, W. Hua*, A QM/MM Study on the X‑ray Spectra of Organic Proton Transfer Crystals of Isonicotinamides, J.Phys. Chem. C 2022,126,15849

5. G. Tian, S. Duan, W. Hua, Y. Luo∗, DynaVib, version 1.0, Royal Institute of Technology, 2012.

DynaVib is a package which can calculate various vibrationally-resolved high-resolution electronic spectra from the optical to the X-ray regimes.  Please contact Prof. Guangjun Tian at Yanshan University (tian@ysu.edu.cn) for a license.

Publications using the code (incomplete; only those with WH involved):

[1] W. Hua*, G. Tian*, Y. Luo, Theoretical assessment of vibrationally resolved C1s X-ray photoelectron spectra of simple cyclic molecules, PCCP 2020, 22, 20014

[2]L. Sun#, W. Hua#, Y. Liu, G. Tian, M. Chen, M. Chen, F. Yang, S. Wang, X. Zhang, Y. Luo, W. Hu*,Thermally Activated Delayed Fluorescence in an Organic Cocrystal: Narrowing the Singlet‐Triplet, Energy Gap via Charge Transfer, Angew. Chem. Int. Ed. 2019, 58, 11311-11316; Angew. Chem. 2019, 131, 11433 –11438

[3] M. Wei, X. Cheng, L. Zhang, J.-R. Zhang, S.-Y. Wang, G. Ge, G. Tian, W. Hua*, Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulation. Azines, Phys. Rev. A 2022, 106, 022811

[4] M. Wei, L. Zhang, G. Tian, W. Hua*,Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulation. II. Indoles, Phys. Rev. A 2023, 108, 022816

[5] X. Cheng, M. Wei, G. Tian, Y. Luo, W. Hua*, Vibrationally-Resolved X‑ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations, J. Phys. Chem. A 2022,126, 5582

6. S. Li∗, W. Li, T. Fang, J. Ma, W. Hua, S. Hua, and Y. Jiang, Lower Scaling Quantum Chemistry (LSQC) Program, version 2, Nanjing University 2010

LSQC is a package which can do low-scaling quantum chemistry calculations based on the generalized energy-based fragmentation (GEBF) method and the cluster in molecule (CIM) method. Please visit http://itcc.nju.edu.cn/lsqcto request a license for the latest version of LSQC.

Publications using the code (incomplete; only those with WH involved):

[1] W. Hua, T. Fang, W. Li, J.-G. Yu, and S. Li, Geometry Optimizations and Vibrational Spectra of Large Molecules from a Generalized Energy-Based Fragmentation Approach, J. Phys. Chem. A 2008, 112, 10864

[2] S. Hua, W. Hua, S. Li, An Efficient Implementation of the Generalized Energy-Based Fragmentation 

Approach for General Large Molecules, J. Phys. Chem. A 2010, 114, 31, 8126

[3] W. Li, W. Hua, F. Tao, S. Li, The energy-based fragmentation approach for computing total energies, structures, and molecular properties of large systems at the ab initio levels,in Jeffrey R. Reimers (ed.), Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, ISBN: 978-0-470-48788-4, John Wiley & Sons Inc., 2011, pp. 182-210 (book chapter, our optimized peptide appears in the book cover)

B. Other programs coded

7. W. Hua, S. Li∗, a matlab package for model Hamiltonian of single molecular magnets

8. W. Hua, L. Xu, S. Hua, S. Li∗, a package to dock a guest into cavity by Monte Carlo (interfaced to Amber for energy calculations)

9. A modified version of the fDynamo package (by Martin J. Field) to do ab initio and ONIOM QM/MM Born-Oppenheimer molecular dynamics (interfaced to LSQC and Gaussian).

II. Databases

A. N1s Binding energies

[1] Du et al., A theoretical library of N1s core binding energies of polynitrogen molecules and ions in the gas phase, PCCP 2022, 24, 8196

Optimized Cartesian coordinates : xyz_Du_PCCP2022.tgz). 

Theoretical IP data：(see supporting information)

B. Vibrationally-resolved high-resolution X-ray spectra (under development).

Method and program development:

[1] W. Hua*, G. Tian*, Y. Luo, Theoretical assessment of vibrationally resolved C1s X-ray photoelectron spectra of simple cyclic molecules, PCCP 2020, 22, 20014

[2] L. Zhang, M. Wei*, G. Ge*, W. Hua*, Franck-Condon Simulation of Vibrationally-Resolved X-ray Spectra for Diatomic Systems: Validation of Harmonic Approximation and Density Functional Theory, Phys. Rev. A 2024, 00, 0000

Applications:

[3] M. Wei, X. Cheng, L. Zhang, J.-R. Zhang, S.-Y. Wang, G. Ge, G. Tian, W. Hua*, Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulation. Azines, Phys. Rev. A 2022, 106, 022811

Optimized Cartesian coordinates: SuppInfo1_Coordinates.pdf

Raw spectral data:SuppInfo2_XPSpectra.txt

[4] M. Wei, L. Zhang, G. Tian, W. Hua*,Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulation. II. Indoles, Phys. Rev. A 2023, 108, 022816

Optimized Cartesian coordinates: data1.XYZ.zip

Raw spectral data:data2.Spectra.zip

Supporting Information:si_indole.pdf

[5] M. Wei, L. Zhang, G. Tian, W. Hua*,Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulation. III. Rules for amine and imine N atoms in small N-heterocycles, Phys. Rev. A 2024, 109, 022820

Optimized Cartesian coordinates: data1.XYZ.zip

Raw spectral data: data2.Spectra.zip

Supporting Information:SuppInfo3.pdf

[6] X. Cheng, M. Wei, G. Tian, Y. Luo, W. Hua*, Vibrationally-Resolved X‑ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations, J. Phys. Chem. A 2022,126, 5582

Resarch Field

Our major research interests are theory and simulations of traditional X-ray spectroscopy (XAS, XES, XPS, XPS shake-up, RIXS) and ultrafast nonlinear X-ray spectroscopy (stimulated Raman, four-wave-mixing, etc) by combing quantum chemistry, solid state physics, molecular dynamics, and nonlinear optics. Our theoretical work aims to help spectral interpretation of important materials and uncover the physical and chemical insights, and to suggest new time-resolved nonlinear x-ray experiments for x-ray free electron (XFEL) facilities. We develop in-house codes for spectroscopic calculations at the density functional theory and multi-configurational levels, taking advantage of the integrals and wave functions read from common electronic structure softwares.

Group

Prof. Weijie Hua

Assoc. Prof. Junxiang Zuo

PhD students

Sheng-Yu Wang (PhD 2019, joint student 2018) Metallo-enzymes, XAS

Jun-Rong Zhang ( PhD 2020, joint student 2018-2019) XPS

Guoyan Ge (PhD2020, Master 2019) QM/MM, transient spectroscopy

Minrui Wei (PhD2020, Master 2019) Vibronic coupling

Master students

Yang Xiao (Master 2018) 2D materials

Lu Zhang (Master 2021) Wavepacket dynamics

Jinyu Li (Master 2022) Potential energy surface and X-ray spectra (co-supervised by JZ)

Ying Xin (Master 2023) Potential energy surface (co-supervised by JZ) 

Research Grants

2023.1-2026.12, National NSF of China, 12274229

2018.1-2021.12, National NSF of China, 11774174

2018.1-2020.12, National NSF of China, 21703105

2017.7-2020.6, NSF of Jiangsu Province of China, BK20170833

2017-2020 Shuangchuang program of Jiangsu Province of China

2016-2019 Swedish Research Concil, co-PI

Dynamics of x-ray-matter interaction with free-electron laser applications

2012, Lars Hierta memorial foundation (Stiftelsen Lars Hiertas Minne), Sweden (FO2012-1039)

First-Principles Simulation of L-edge XAS of Fe(II) Spin Crossover Complexes'

Courses (in Chinese)

1. Modern Electronic Structure Theory

 (48 hours, doctoral students)

2. Selected Topics of Nobel Prizes in Physics and Chemistry: Light, Quantum, and Structure

(16 hours, undergraduate students)

(please ignore the formatted purple headings above)

Representative Publications

[1] Transient X-ray absorption spectral fingerprints of the S1 dark state in uracil

W. Hua*, S. Mukamel*, Y. Luo, J. Phys. Chem. Lett. 2019, 10, 7172-7178

 [Highlighted in supplementary journal cover]

 [Highlighted by ACS Live Slides] (Vedeo in MP4 format)

[2] MCNOX: A code for computing and interpreting ultrafast nonlinear X-ray spectra of molecules at the multiconfigurational level

W. Hua*, Comput. Phys. Commun. 2024, 296, 109016

[3] Study of double core hole excitations in molecules by X-ray double-quantum-coherence signals: a multi-configuration simulation,

W. Hua, K. Bennett, Y. Zhang, Y. Luo, S. Mukamel, Chem. Sci. 2016, 7, 5922-5933

[4] Interpreting the Cu−O2 Antibonding Nature in Two Cu−O2 Complexes from Cu L‑Edge X‑ray Absorption Spectra

 S.-Y. Wang, J.-R. Zhang, M. Guo, and W. Hua*, Inorg. Chem .2023, 62,17115

[5] Thermally Activated Delayed Fluorescence in an Organic Cocrystal: Narrowing the Singlet‐Triplet Energy Gap via Charge Transfer

L. Su#, W. Hua#, Y. Liu, G. Tian, M. Chen, M. Chen, F. Yang, S. Wang, X. Zhang, Y. Luo, W. Hu*

Angew. Chem. Int. Ed. 2019, 58, 11311-11316

[6] Manipulating Spatial Alignment of Donor and Acceptor in Host-Guest MOF for TADF

X. Liu#, W. Hua#, H. X. Nie, M. Chen, Z. Chang*, X. H. Bu*, Natl. Sci. Rev. 2022, 9, nwab222

[7] Local structures of nitrogen doped graphdiynes determined by computational X-ray spectroscopy

Y Ma, J Lin, XN Song, CK Wang, W Hua*, Y Luo*, Carbon 2019, 149, 672-678

[8] Accurate K-edge X-ray photoelectron and absorption spectra of g-C3N4 nanosheet by first-principles simulations and reinterpretations, 

J. Zhang#, Y. Ma#, S. Wang, J. Ding, B. Gao, E. Kan, W. Hua*, PCCP 2019, 21, 22819

    [2019 Hot PCCP Article]

[9] Monitoring conical intersections in the ring opening of furan by Attosecond Stimulated X-ray Raman Spectroscopy,

    W. Hua#, S. Oesterling#, J. D. Biggs, Y. Zhang, H. Ando, R. de Vivie-Riedle, B. P. Fingerhut, and S. Mukamel, Struct. Dyn. 2016, 3, 023601.  

    [Most Read Articles in Structural Dynamics in 2016]

[10] Geometry optimizations and vibrational spectra of large molecules from a generalized energy-based fragmentation approach, 

    W. Hua, T. Fang, W. Li, J. G. Yu, S. Li*,  J. Phys. Chem. A 2008, 112, 10864. 

#共同一作  *通讯作者