Yihan Shao Ph.D.

 


Principal Scientist for Q-Chem, Inc.

Head of Developer Relations

yihan

Dr. Shao obtained his B.Sc. in Chemistry from Nanjing University in 1993, where he studied the topology and electronic structure of carbon clusters under the supervision of Prof. Yuansheng Jiang. In 2002, he received his Ph.D. in Theoretical Chemistry from the University of California at Berkeley, where he studied linear-scaling algorithms (especially the J engine method, publications 13-14) in density functional calculations under the supervision of Prof. Martin Head-Gordon. With Prof. Head-Gordon and Prof. Anna Krylov (USC), he also developed the spin-flip density functional theory (publication 17) for studying radicals and diradicals. He joined Q-Chem in September 2002 as a staff scientist and became a senior scientist in 2010 and a principal scientist in 2012. Over the years, he enjoyed (and benefited from) working with dozens of Q-Chem developers and numerous Q-Chem users.

His research interests include: QM/MM methods (publications 27, 33, 38, 42, 50) and applications (publications 28, 36, 49); excited state methods and applications (publications 17, 24, 25, 41, 43, 46, 47, 48); assisting new functional development (publications 40, 44, 51, 52); perturbation theory methods (publications 23, 26, 30-35, 53); GPU acceleration of QM calculations (publications 37, 39); linear-scaling electrostatics (publications 13, 14, 45); linear-scaling diagonalization (publications 16, 18-22); and nanoclusters (publications 1-5, 7-11), etc.

Yihan Shao's publications include:

53. Yuanhang Huang, Yihan Shao, and Gregory J. O. Beran, "Accelerating MP2C dispersion corrections for dimers and molecular crystals", J. Chem. Phys. 138, 224112 (2013).

52. Seoin Back, Johan A. Schmidt, Hyunjun Ji, Jiyoung Heo, Yihan Shao, and Yousung Jung, "On the structure of Si(100) surface: Importance of higher order correlations for buckled dimer", J. Chem. Phys. 138, 204709 (2013).

51. Hyunjun Ji, Yihan Shao, William A. Goddard, and Yousung Jung, "Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Complexes", J. Chem. Theory Comput. 9, 1971 (2013).

50. Debashree Ghosh, Dmytro Kosenkov, Vitalii Vanovschi, Joanna Flick, Ilya Kaliman, Yihan Shao, Andrew T.B. Gilbert, Anna I. Krylov, and Lyudmila V. Slipchenko, "Effective fragment potential method in Q-CHEM: A guide for users and developers", J. Comput. Chem. 34, 1060 (2013).

49. Peng Tao, Milan Hodoscek, Joseph D. Larkin, Yihan Shao, and Bernard R. Brooks, "Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints", J. Chem. Theory Comput. 8, 5035 (2012).

48. Shushu Zhang, Zexing Qu, Peng Tao, Bernard Brooks, Yihan Shao, Xiaoyuan Chen, and Chungen Liu, "Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes", J. Phys. Chem. C, 116, 12434 (2012).

47. Yves A. Bernard, Yihan Shao, and Anna I. Krylov, "General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: Theory, implementation, and benchmarks", J. Chem. Phys. 136, 204103 (2012).

46. Xinle Liu, Shervin Fatehi, Yihan Shao, Brad S. Veldkamp, and Joseph E. Subotnik, "Adjusting charge transfer state energies for configuration interaction singles: Withoua any parameterization and with minimal cost", J. Chem. Phys. 136, 161101 (2012).

45. Chun-Min Chang, Yihan Shao, and Jing Kong, "Ewald mesh method for quantum mechanical calculations" , J. Chem. Phys. 136, 114112 (2012).

44. Emil Proynov, Fenglai Liu, Yihan Shao and Jing Kong, "Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation" , J. Chem. Phys. 136, 034102 (2012).

43. Shervin Fatehi, Ethan Alguire, Yihan Shao and Joseph E. Subotnik, "Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance", J. Chem. Phys. 135, 234105 (2011).

42. An Ghysels, H. Lee Woodcock III, Joseph D. Larkin, Benjamin T. Miller, Yihan Shao, Jing Kong, Dimitri Van Neck, Veronique Van Speybroeck, Michel Waroquier and Bernard R. Brooks, "Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian", J. Chem. Theory Comput. 7, 496 (2011).

41. Fenglai Liu, Zhengting Gan, Yihan Shao, Chao-Ping Hsu, Andreas Dreuw, Martin Head-Gordon, Benjamin T. Miller, Bernard R. Brooks, Jian-Guo Yu, Thomas R. Furlani and Jing Kong, "A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm-Dancoff approximation", Mol. Phys. 108, 2791 (2010).

40. Emil Proynov, Yihan Shao and Jing Kong, "Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method", Chem. Phys. Lett. 493, 381 (2010).

39. Roberto Olivares-Amaya, Mark A. Watson, Richard G. Edgar, Leslie Vogt, Yihan Shao and Alan Aspuru-Guzik, "Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library", J. Chem. Theory Comput. 6, 135 (2010).

38. H. Lee Woodcock, Wenjun Zheng, An Ghysels, Yihan Shao, Jing Kong and Bernard R. Brooks, "Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit", J. Chem. Phys. 129, 214109 (2008).

37. Leslie Vogt, Roberto Olivares-Amaya, Sean Kermes, Yihan Shao, Carlos Amador-Bedolla and Alan Aspuru-Guzik, "Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Unit", J. Phys. Chem. A, 112, 2049 (2008).

36. Marek Freindorf, Yihan Shao, Jing Kong, Thomas R. Furlani, "Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin", J. Inorg. Chem. 102, 427 (2008).

35. Yousung Jung, Yihan Shao and Martin Head-Gordon, "Fast evaluation of scaled opposite spin second-order Moller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity", J. Comput. Chem. 28, 1953 (2007).

34. Rohini C. Lochan, Yihan Shao and Martin Head-Gordon, "Quartic-Scaling Analytical Energy Gradient of Scaled Opposite-Spin Second-Order Moller-Plesset Perturbation Theory", J. Chem. Theory Comput. 3, 988 (2007).

33. Yihan Shao and Jing Kong, "YinYang Atom: A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model", J. Phys. Chem. A, 111, 3661 (2007).

32. Robert A. Distasio Jr., Ryan P. Steele, Young Min Rhee, Yihan Shao and Martin Head-Gordon, "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis", J. Comput. Chem. 28, 839 (2007).

31. Ryan P. Steele, Yihan Shao, Robert A. DiStasio Jr. and Martin Head-Gordon, "Dual-Basis Analytic Gradients. 1. Self-Consistent Field Theory", J. Phys. Chem. A, 110, 13915 (2006).

30. Ryan P. Steele, Robert A. DiStasio, Yihan Shao, Jing Kong and Martin Head-Gordon, "Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations", J. Chem. Phys. 125, 074108 (2006).

29. Yihan Shao, Laszlo Fusti Molnar, Yousung Jung, Joerg Kussmann, Christian Ochsenfeld, Shawn T. Brown, Andrew T.B. Gilbert, Lyudmila V. Slipchenko, Sergey V. Levchenko, Darragh P. O'Neill, Robert A. DiStasio Jr, Rohini C. Lochan, Tao Wang, Gregory J.O. Beran, Nicholas A. Besley, John M. Herbert, Ching Yeh Lin, Troy Van Voorhis, Siu Hung Chien, Alex Sodt, Ryan P. Steele, Vitaly A. Rassolov, Paul E. Maslen, Prakashan P. Korambath, Ross D. Adamson, Brian Austin, Jon Baker, Edward F. C. Byrd, Holger Dachsel, Robert J. Doerksen, Andreas Dreuw, Barry D. Dunietz, Anthony D. Dutoi, Thomas R. Furlani, Steven R. Gwaltney, Andreas Heyden, So Hirata, Chao-Ping Hsu, Gary Kedziora, Rustam Z. Khalliulin, Phil Klunzinger, Aaron M. Lee, Michael S. Lee, WanZhen Liang, Itay Lotan, Nikhil Nair, Baron Peters, Emil I. Proynov, Piotr A. Pieniazek, Young Min Rhee, Jim Ritchie, Edina Rosta, C. David Sherrill, Andrew C. Simmonett, Joseph E. Subotnik, H. Lee Woodcock III, Weimin Zhang, Alexis T. Bell, Arup K. Chakraborty, Daniel M. Chipman, Frerich J. Keil, Arieh Warshel, Warren J. Hehre, Henry F. Schaefer III, Jing Kong, Anna I. Krylov, Peter M. W. Gill and Martin Head-Gordon, "Advances in methods and algorithms in a modern quantum chemistry program package", Phys. Chem. Chem. Phys. 8, 3172 (2006).

28. Marek Freindorf, Yihan Shao, Shawn T. Brown, Jing Kong, Thomas R. Furlani, "A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin", Chem. Phys. Lett. 419, 563 (2006).

27. Marek Freindorf, Yihan Shao, Thomas R. Furlani and Jing Kong, "Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential", J. Comput. Chem. 26, 1270 (2005).

26. Paul E. Maslen, Anthony D. Dutoi, Michael S. Lee, Yihan Shao and Martin Head-Gordon, "Accurate local approximations to the triples correlation energy: formulation, implementation and tests of 5th-order scaling models", Mol. Phys. 103, 425 (2005).

25. Zhi-Qiang You, Yihan Shao and Chao-Ping Hsu, "Calculating electron transfer couplings by the Spin-Flip approach: energy splitting and dynamical correlation effects", Chem. Phys. Lett. 390, 116 (2004).

24. Ana-Maria C. Cristian, Yihan Shao and Anna I. Krylov, "Bonding Patterns in Benzene Triradicals from Structural, Spectroscopic, and Thermochemical Perspectives", J. Phys. Chem. A, 108, 6581 (2004).

23. Joseph E. Subotnik, Yihan Shao, WanZhen Liang and Martin Head-Gordon, "An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: Applications to localized occupied orbitals", J. Chem. Phys. 121, 9220 (2004).

22. WanZhen Liang, Roi Baer, Chandra Saravanana, Yihan Shao, Alexis T Bell and Martin Head-Gordon, "Fast methods for resumming matrix polynomials and Chebyshev matrix polynomials", J. Comput. Phys. 194, 575 (2004).

21. Yousung Jung, Yihan Shao, Mark S. Gordon, Douglas J. Doren and Martin Head-Gordon, "Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations", J. Chem. Phys. 119, 10917 (2003).

20. Yihan Shao, Chandra Saravanan, Martin Head-Gordon and Christopher A. White, "Curvy steps for density matrix-based energy minimization: Application to large-scale self-consistent-field calculations", J. Chem. Phys. 118, 6144 (2003).

19. Martin Head-Gordon, Yihan Shao, Chandra Saravanan and Christopher A. White, "Curvy steps for density matrix based energy minimization: tensor formulation and toy applications", Mol. Phys. 101, 37 (2003).

18. Chandra Saravanan, Yihan Shao, Roi Baer, Philip N. Ross, Martin Head-Gordon, "Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks", J. Comput. Chem. 24, 618 (2003).

17. Yihan Shao, Martin Head-Gordon and Anna I. Krylov, "The spin-flip approach within time-dependent density functional theory: Theory and applications to diradicals", J. Chem. Phys. 118, 4807 (2003).

16. WanZhen Liang, Chandra Saravanan, Yihan Shao, Roi Baer, Alexis T. Bell and Martin Head-Gordon, "Improved Fermi operator expansion methods for fast electronic structure calculations", J. Chem. Phys. 119, 4117 (2003).

15. WanZhen Liang, Yihan Shao, Christian Ochsenfeld, Alexis T. Bell and Martin Head-Gordon, "Fast evaluation of a linear number of local exchange matrices", Chem. Phys. Lett. 358, 43 (2002).

14. Yihan Shao, Christopher A. White and Martin Head-Gordon, "Efficient evaluation of the Coulomb force in density-functional theory calculations", J. Chem. Phys. 114, 6572 (2001).

13. Yihan Shao and Martin Head-Gordon, "An improved J matrix engine for density functional theory calculations", Chem. Phys. Lett. 323, 425 (2000).

12. Jing Kong, Christopher A. White, Anna I. Krylov, David Sherrill, Ross D. Adamson, Thomas R. Furlani, Michael S. Lee, Aaron M. Lee, Steven R. Gwaltney, Terry R. Adams, Christian Ochsenfeld, Andrew T. B. Gilbert, Gary S. Kedziora, Vitaly A. Rassolov, David R. Maurice, Nikhil Nair, Yihan Shao, Nicholas A. Besley, Paul E. Maslen, Jeremy P. Dombroski, Holger Daschel, Weimin Zhang, Prakashan P. Korambath, Jon Baker, Edward F. C. Byrd, Troy Van Voorhis, Manabu Oumi, So Hirata, Chao-Ping Hsu, Naoto Ishikawa, Jan Florian, Arieh Warshel, Benny G. Johnson, Peter M. W. Gill, Martin Head-Gordon and John A. Pople, "Q-Chem 2.0: a high-performance ab initio electronic structure program package", J. Comput. Chem. 21, 1532 (2000).

11. Yihan Shao, Jian Wu and Yuansheng Jiang, "Enumeration and Symmetry of Substitution Isomers", J. Phys. Chem. 100, 15064 (1996).

10. Yihan Shao and Yuansheng Jiang, "Enumeration of B24-mNm Cages", J. Phys. Chem. 100, 1554 (1996).

9. Yihan Shao, Jian Wu and Yuansheng Jiang, "Isomer counting and isomer permutation representation", Chem. Phys. Lett. 248, 366 (1996).

8. Chungen Liu, Yihan Shao and Yuansheng Jiang, "Factorization of the Hueckel Hamiltonian matrix for highly symmetrical molecules", Croat. Chem. Acta, 69, 201 (1996).

7. Yihan Shao and Yuansheng Jiang, "Symmetry of hydrogenated C60", Chem. Phys. Lett. 242, 191 (1995).

6. Yuansheng Jiang, Xiaoliang Qian and Yihan Shao, "The evaluation of moments for benzenoid hydrocarbons", Theoret. Chim. Acta, 90, 135 (1995).

5. Yuansheng Jiang, Chungen Liu and Yihan Shao, "Analyitcal solution of graph spectra for fullerenes", Prog. in Phys. (in Chinese), 15, 307 (1995).

4. Chungen Liu, Yihan Shao and Yuansheng Jiang "Analytical solution of graph spectra for fullerenes", Chem. Phys. Lett. 228, 131 (1994).

3. Chungen Liu, Miaomiao Wang, Yihan Shao and Yuansheng Jiang, "Factorization of the Hueckel Hamiltonian matrix for C-540", Phys. Lett. A, 196, 120 (1994).

2. Yuansheng Jiang, Yihan Shao and Edward C. Kirby, "Topology and Stability of Trivalent Polyhedral Clusters", Fullerene Sci. Tech. 2, 481 (1994).

1. Jun Liu, Yihan Shao and Yuansheng Jiang, "Exact solution of graph spectrum of C60", Chem. Phys. Lett. 210, 149 (1993).