Publication List (Updated 3/31/2008)

 

Hai LIN

 

Papers in Peer-reviewed Journals. 1

Papers Submitted or in Preparation. 7

Peer-reviewed Book Chapters. 8

Conference Contributions. 9

Dissertations. 11

Computational Programs. 11

 

 

Papers in Peer-reviewed Journals

 

58. Zhang, Y.; Lin, H.;

Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems

J. Chem. Theory Comput. 2008, 4, 414-425.

 

57. Ellingson, B. A.; Pu, J.; Lin, H.; Zhao, Y.; Truhlar, D. G.

Multicoefficient Gaussian-3 calculation of the rate constant for the OH + CH4 reaction and its 12C/13C kinetic isotope effect with emphasis on the effects of coordinate system and torsional treatment

J. Phys. Chem. A 2007, 111, 11706-11717.

 

56. Zhang, Y.; Lin, H.; Truhlar, D. G.;

Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum mechanical and molecular mechanical calculations

J. Chem. Theory Comput. 2007, 3, 1378-1398.

 

55. Lin, H.; Truhlar, D. G.;

QM/MM: What have we learned, where are we, and where do we go from here?

Theor. Chem. Acc. 2007, 117, 185-199.

[Invited keynote presentation at the 10th Electronic Computational Chemistry Conference (ECCC10)]

 

54. Heyden, A.; Lin, H.; Truhlar, D. G.

Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

J. Phys. Chem. B 2007, 111, 2231-2241.

 

53. Lin, H.; Zhao, Y.; Tischchenko, O.; Truhlar, D. G.;

Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations.

J. Chem. Theor. Comput. 2006, 2, 1237-1254.

 

52. Chakraborty, A.; Zhao, Y.; Lin, H.; Truhlar, D. G.;

Combined valence bond-molecular mechanics potential energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction.

J. Chem. Phys. 2006, 124, 044315/1-044315/14.

 

51. Yurchenko, S. N.; Zheng, J. J.; Lin, H.;Jensen, P.; Thiel, W.;

Potential energy surface for the electronic ground state of NH3 calculated ab initio up to 20,000 cm-1 above equilibrium.

J. Chem. Phys. 2005, 123, 134308/1-134308/14.

 

50. Lin, H.; Truhlar, D. G.;

Redistributed charge and dipole schemes for combined quantum-mechanical and molecule mechanical calculations.

J. Phys. Chem. A 2005, 109, 3991-4004.

 

49. Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G.;

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change.

J. Am. Chem. Soc. 2005, 127, 2830-2831.

 

48. Yurchenko, S. N.; Carvajal, M.; Lin, H.; Zheng, J.; Thiel, W.; Jensen, P.;

Dipole moment and intensities in the electronic ground state of NH3: bridging the gap between ab initio theory and spectroscopic experiment.

J. Chem. Phys. 2005, 122, 104317/1-104317/14.

 

47. Yurchenko, S. N.; Carvajal, M.; Jensen, P.; Lin, H.; Zheng, J.; Thiel, W.;

Rotation-vibration motion of pyramidal XY3 molecules described in the Eckart frame: theory and application to NH3.

Mol. Phys. 2005, 103, 359-378.

 

46. Lin, H.; Schöneboom, J. C.; Cohen, S.; Shaik, S.; Thiel, W.;

QM/MM study of the product-enzyme complex in P450cam catalysis.

J. Phys. Chem. B 2004, 108, 10083-10088.

 

45. Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G.;

Efficient molecular mechanics for chemical reactions:  multi-configuration molecular mechanics using partial electronic structure Hessians.

J. Phys. Chem. A 2004, 108, 4112-4124.

 

44. Schöneboom, J. C.; Cohen, S.; Lin, H.; Shaik, S.; Thiel, W.

QM/MM investigation of the mechanism of C-H hydroxylation of camphor by Cytochrome  P450cam: theory supports a two-state rebound mechanism.

J. Am. Chem. Soc. 2004, 126, 4017-4034.

 

43. Lin, H.; Thiel, W.; Yurchenko, S. N.; Carvajal, M.; Jensen, P.

Vibrational energies for NH3 based on high level ab initio potential energy surfaces.

J. Chem. Phys. 2002, 117, 11265-11276.

 

42. Schöneboom, J. C.; Lin, H.; Reuter, N.; Thiel, W.; Cohen, S.; Ogliaro, F.; Shaik, S.

The elusive oxidant species of Cytochrome P450 enzymes: characterization by combined quantum mechanical / molecular mechanical (QM/MM) calculations.

J. Am. Chem. Soc. 2002, 124, 8142-8151.

 

41. Reuter, N.; Lin, H.; Thiel, W.;

Green fluorescent proteins: empirical force field for the neutral and deprotonated forms of the chromophore, molecular dynamics simulations of the wild type and S65T mutant.

J. Phys. Chem. B 2002, 102, 6310-6321.

 

40. He, S. G. Liu, A. W.; Lin, H.; Zheng, J. J.; Hu, S. M.; Hao, L. Y.; Zhu, Q. S.;

Stretching vibrational band intensities of XH4 molecules employing four-dimensional ab initio (X = C and Sn) and effective (X = C and Si) dipole moment surfaces.

J. Chem. Phys. 2002, 117, 10073-10080.

 

39. He, S. G.; Lin, H.; Bürger, H.; Thiel, W.; Ding, Y.; Zhu, Q. S.;

Calculation of the Si-H stretching-bending overtones in SiHCl3 empolying ab initio potential energy and dipole moment surfaces.

J. Chem. Phys. 2002, 116, 105-111.

 

38. Hu, S. M.; Ulenikov, O. N.; Bekhtereva, E. S.; Onopenko, G. A.; He, S. G.; Lin, H.; Cheng, J. X.; Zhu, Q. S.;

High resolution Fourier-transform intra-cavity laser absorption spectroscopy of D2O in the region of the 4n1 + n3 band.

J. Mol. Spectrosc. 2002, 212, 89-95.

 

37. He, S. G.; Lin, H.; Thiel, W.; Zhu, Q. S.;

Four-dimensional dipole moment surfaces and local mode vibrational band intensities of GeH4.

Chem. Phys.Lett. 2001, 349, 131-136.

 

36. Lin, H.; He, S.G.; Wang, X.G.; Yuan, L. F.; Bürger, H.; D’Eu, J.-F.; Reuter, N.; Thiel, W.;

The vibrational overtones of SiH4 isotopomers: experimental wavenumbers, assignment, ab initio dipole moment surfaces, and intensities.

Phys. Chem. Chem. Phys. 2001, 3, 3506-3517.

 

35. Lin, H.; Bürger, H.; Mkadmi, E. B.; He, S. G.; Yuan, L. F.; Breidung, J.; Thiel, W.; Huet, T. R.; Demaison, J.;

The Si-H stretching-bending overtone polyads of SiHF3: assignments, band intensities, internal coordinate force field, and ab initio dipole moment surfaces.

J. Chem. Phys. 2001, 115, 1378-1391.

 

34. Lin, H.; Bürger, H.; He, S. G.; Yuan, L. F.; Breidung, J.; Thiel, W.;

Overtones of the Si-H stretching-bending polyad in SiHD3: internal coordinate force field, ab initio dipole moment surfaces, and band intensities.

J. Phys. Chem. A 2001, 105, 6065-6072.

 

33. He, S. G.; Yuan, L. F.; Lin, H.; Wang, X. G.;

Study of the perpendicular band intensities of the CH chromophore in CHCl3, CHBr3, and CHI3 with three-dimensional dipole moment surface from density functional calculations.

J. Phys. Chem. A 2001, 105, 8428-8433.

 

32. Lin, H.; Yuan, L. F.; He, S. G.; Wang, X. G.;

Band strengths for C-H stretching polyads of CHBr3 calculated by use of two-dimensional electric dipole moment surface from density functional theory.

J. Chem. Phys. 2001, 114, 8905-8912.

 

31. He, S. G.; Zheng, J. J.; Hu, S. M.; Lin, H.; Ding, Y.; Wang, X. H.; Zhu, Q. S.;

The stretching vibrational overtone spectra of PH3: local mode vibrational analysis, dipole moment surfaces from density functional theory and band intensities.

J. Chem. Phys. 2001, 114, 7018-7026.

 

30. Zheng, J. J.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; He, S. G.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S.;

Study of the vibration-rotation bands belonging to the n1 + n2 / 2 + n3 = 3.5 polyad of the D2O molecule.

Mol. Phys.2001, 99, 931-937.

 

29. Lin, H.; Yuan, L. F.; He, S. G.; Wang, X. G.; Zhu, Q. S.;

The ab initio calculated dipole moment surface and overtone relative intensities of CH chromophore in CHCl3.

J. Chem. Phys. 2000, 112, 7484-7489.

 

28. Lin, H.; Yuan, L. F.; He, S. G.; Wang, X. G.;

Calculating relative intensities for CH stretching polyads of CHI3 with ab initio dipole moment surface.

Chem. Phys. Lett. 2000, 332, 569-575.

 

27. Hou, J. G.; Yang, J. L.; Wang, H. Q.; Li, Q. X.; Zeng, C. G.; Lin, H.; Chen, D. M.; Zhu, Q. S.;

Comment on “Identifying molecular orientation of individual C60 molecules on Si(111)-(7´7) surfaces” - Hou et al. reply.

Phys. Rev. Lett. 2000, 85, 2654-2654.

 

26. Wang, X. H.; Lin, H.; Chen, X. Y.; Wang, X. G.; Wang, D.; Deng, K.; Zhu, Q. S.;

Coriolis interaction parameters of the (n100;F2) states of GeH4.

Mol. Phys. 2000, 98, 1409-1413.

 

25. Cheng, J. X.; Lin, H.; Hu, S. M.; He, S. G.; Zhu, Q. S.; Kachanov, A. A.;

Infrared intracavity laser absorption spectroscopy with a continuous-scan Fourier transform interferometer.

Appl. Opt. 2000, 39, 2221-2229.

 

24. Chen, X. Y.; Lin, H.; Wang, D.; Wang, X. G.; Zhu, Q. S.;

Spectroscopic study of local mode (4000) overtone of GeH4.

J. Mol. Struct. 2000, 517, 41-51.

 

23. Hu, S. M.; Lin, H.; Cheng, J. X.; He, S. G.; Zhu, Q. S.; Kachanov, A. A.;

High sensitivity and high resolution Fourier-transform intracavity laser absorption spectroscopy (FT-ICLAS).

Proceedings of SPIE, 2000, 4063, 264-268.

 

22. He, S. G.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S.;

High resolution Fourier transform spectrum of the D2O molecule in the region of the second triad of the interacting vibrational states.

J. Mol. Spectrosc. 2000, 200, 34-39.

 

21 Wang, X. H.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; He, S. G.; Hu, S. M.; Lin, H.; Zhu, Q. S.;

High resolution study of the first Hexade of the D2O.

J. Mol. Spectrosc. 2000, 200, 25-33.

 

20. Hu, S. M.; Ulenikov, O. N.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; He, S. G.; Lin, H.; Zhu, Q. S.;

High-resolution study of strongly interacting vibrational bands of HDO in the region 7600 - 8100 cm-1.

J. Mol. Spectrosc. 2000, 203, 228-234.

 

19. Ulenikov, O. N.; He, S. G.; Onopenko, G. A.; Behtereva, E. S.; Wang, X. H.; Hu, S. M.; Lin, H.; Zhu, Q. S.;

High resolution study of the n1 + n2 / 2 + n3 = 3 polyad of strongly interacting vibrational bands of D2O.

J. Mol. Spectrosc.2000, 204, 216-225.

 

18. Lin, H.; Wang, D.; Yuan, L. F.; Zhu, Q. S.;

Nonlinearity of the dipole moment surface and intensities anomaly of CHCl3.

Chinese Phys. Lett. 2000, 17, 13-15.

 

17. Lin, H.; Ulenikov, O. N.; Olechnovitch, I.; Wang, D.; Chen, X. Y.; Hao, L. Y.; Zhu, Q. S.;

Local mode spectroscopic study of the AsH3 molecule: The perturbed (500) local mode overtone.

Chinese Phys. 2000, 9, 113-118.

 

16. Hu, S. M.; He, S. G.; Lin, H.; Cheng, J. X.; Wang, X. H.; Zheng, J. J.; Cheng, G. S.; Zhu, Q. S.;

High-resolution Fourier transform intra-cavity laser absorption spectroscopy: method and application.

Acta Physica Sinica, Chinese Phys. Soc. 2000, 49, 1435-1440.

 

15. Chen, X. Y.; Lin, H.; Wang, D. Zhu, Q. S.;

False Lines due to folding in Fourier transform spectroscopy.

Chinese J. Chem. Phys. 2000, 13, 129-134.

 

14. Hou, J. G.; Yang, J. L.; Wang, H. Q.; Li, Q. X.; Zeng, C. G.; Lin, H.; Chen, D. M.; Zhu, Q. S.;

Identifying molecular orientation of individual C60 molecules on Si(111)-(7´7) surfaces.

Phys. Rev. Lett. 1999, 83, 3001-3004.

 

13. Lin, H.; Yuan, L. F.; Zhu, Q. S.;

Local mode overtone intensities of SiH4 and GeH4 by bond dipole model with ab initio calculated dipole moment surface.

Chem. Phys. Lett. 1999, 308, 137-142.

 

12. Hu, S. M.; Lin, H.; He, S. G.; Cheng, J. X.; Zhu, Q. S.;

Fourier-transform intra-cavity absorption spectroscopy of HOD v(OD) = 5 overtone.

Phys. Chem. Chem. Phys. 1999, 1, 3727-3730.

 

11. Zhou, Z. Y.; Zhu, Q. S.; Lin, H.;

High-resolution spectroscopic study of H280Se in the v(stretch) = 5 and 6 local-mode pairs states.

Mol. Phys. 97, 503-510 (1999).

 

10. Deng, K.; Wang, X. G.; Lin, H.; Wang, D.; Zhu, Q. S.;

High resolution spectroscopic study of CH3D in the region of 5900 - 6100 cm-1.

Mol. Phys. 1999, 97, 787-796.

 

9. Wang, D.; Lin, H, Wang, X. G.; Zhu, Q. S.;

High resolution spectroscopic study of arsine in the region 6000 - 6500 cm-1.

Spectrochim.Acta A 1999, 55, 109-119.

 

8. Lin, H.; Wang, D.; Chen, X. Y.; Wang, X. G.; Zhou, Z. P.; Zhu, Q. S.;

Absorption intensity of stretching vibration states of silane and germane.

J. Mol. Spectrosc.1998, 192, 249-256.

 

7. Yang, S. F.; Lin, H.; Wang, D.; Zhu, Q. S.;

High resolution vibration-rotation spectra of arsine local mode (110 A1/E) band.

J. Chem. Soc. Faraday Trans. 1998, 94, 1397-1402.

 

6. Ulenikov, O. N.; Onopenko, G. A.; Lin, H.; Zhang, J.; Zhou, Z. Y.; Zhu, Q. S.; Tolchenov, R. N.;

Joint rotational analysis of twenty four bands of the H280Se molecule.

J. Mol. Spectrosc. 1998, 189, 29-39.

 

5. Cheng, J. X.; Wang, X. G.; Lin, H.; Zhu, Q. S.;

The high resolution spectrum of AsH3 (400) local mode state: symmetry reduction and rotational re-quantization.

Spectrochim.Acta A 1998, 54, 1947-1960.

 

4. Lin, H.; Wang, X. G.; Yang, S. F.; Hu, S. M.; Zhu, Q. S.;

Study of an intracavity laser absorption spectrometry incorporated with the Fourier transform spectrometry.

Chinese J. Laser A 1998, 25, 1008-1012.

 

3. Cheng, J. X.; Xu, R. X.; Shi, Q.; Lin, H.; Zhu, Q. S.;

Selective bond-breaking in a polyatomic molecule.

Chinese J. Chem. Phys.1998, 11, 516-520.

 

2. Lin, H.; Ulenikov, O. N, Yurchinko, S.; Wang, X. G.; Zhu, Q. S.;

High-resolution spectroscopic study of the local mode (310) combination band system of AsH3.

J. Mol. Spectrosc.1997, 187, 89-96.

 

1. Cheng, J. X.; Wang, X. G.; Lin, H.; Zhu, Q. S.;

Symmetry reduction and rotational re-quantization of symmetric top molecules at the local mode limit.

Chinese Phys. Lett.1997, 14, 656-659.

 

 

Papers Submitted or in Preparation

 

2 Truhlar, D. G.; Gao, J, Ma, S.; Lin, H.; Villà-Freixa, J.

Computational Chemistry in Biology

In Wiley Encyclopedia of Chemical Biology, submitted.

 

1. Zhang, Y.; Lin, H.

Testosterone hydroxylation by cytochrome P450 3A4: 1. Hydrogen abstraction by density functional theory calculations.

In preparation.

 

 

Peer-reviewed Book Chapters

 

2. Yurchenko, S. N.; Zheng, J. J.; Thiel, W.; Carvajal, M.; Lin, H.; Jensen, P.;

Theoretical quantitative spectroscopy: Computer simulation of molecular spectra.

In Perrin, A. et al.(eds.), Remote sensing of the atmosphere for environmental security. 2006, 171-183. Published by Springer.

 

1. Yurchenko, S. N.; Thiel, W.; Carvajal, M.; Lin, H.; Jensen, P.;

Rotation-vibration motion of pyramidal XY3 molecules described in the Eckart frame: the calculation of intensities with application to NH3.

Adv. Quantum Chem. 2005, 48, 209-238.

 

Conference Contributions

 

Oral Presentations:

 

7. Lin, H.; Zhang, Y.; Truhlar, D. G. Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined QM/MM calculations.

234st ACS National Meeting, 2007, Boston, MA, August 19 - 23, 2007.

 

6. Lin, H.; Truhlar, D. G. Toward more realistic simulations for large-size reactive systems by combining quantum mechanics and molecular mechanics.

NWChem Meeting 2007, Richland, WA, January 25 – 26, 2007

 

5. Truhlar, D. G.; Zhao, Y.; Schultz, N.; Cramer, C.; Kelly1, C.; Chamberlin, A.; Tischchenko, O.; Lin, H.; Density Functional Calculations.

AIChE 2006 Annual Meeting, San Francisco, CA, November 11 – 17, 2006

 

4. Lin, H.; Zhao, Y.; Truhlar, D. G. (2006): Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations.

231st ACS National Meeting, 2006, Atlanta, GA, March 26 - 30, 2006.

 

3. Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G. (2004): Carbon-13 kinetic isotope effects of importance to atmospheric science and their temperature dependences.

228th ACS National Meeting, 2004, Philadelphia, PA, August 21 - 26, 2004.

 

2. Lin, H. (2001): Overtone intensities of Si-H stretching-bending polyads of SiHD3 and SiHF3. SPHERS network meeting, Uhldingen-Muehlhofen, Germany, May 27 - 29, 2001.

 

1. Lin, H. (2000): Overtone intensities of XH (X = C and Si) chromophores in some small molecules. Workshop on Reductions of the Rovibrational Hamiltonian, Oberwolfach, Germany, September 28 - October 1, 2000.

 

Posters/Book-abstracts:

 

12. Kim, J.; Morisetti, P.; Lin, H.;

Docking testosterone in the active site of cytochrome P450 3A4: Simulations suggest protein conformational changes are critical to substrate binding.

Rocky Mountain Regional Meeting, Denver, CO, August 29 – September 1, 2007

 

11. Zhang, Y. Lin, H.;

Hydrogen abstraction of testosterone by cytochrome P450 3A4: A computational investigation.
Rocky Mountain Regional Meeting, Denver, CO, August 29 – September 1, 2007

 

10. Yurchenko, S. N.; Carvajal, M.; Jensen, P.; Lin, H.; Thiel, W.;

Vibrational energies of the ammonia molecule and its isotopomers calculated from high level ab initio surfaces.

17th International Conference on High Resolution Molecular Spectroscopy. Czech Republic, Prague (2002).

 

9. Carvajal, M.; Yurchenko, S. N.; Jensen, P.; Lin, H.; Thiel, W.;

Analysis of the ammonia molecule in the MORBID approach based on high level ab initio surfaces.

5th Iberian Joint Meeting on Atomic and Molecular Physics. (2002).

 

8. Schö