Publications of Ralph A. Wheeler

2008

 

new.gif (1150 bytes)74. Annual Reports in Computational Chemistry, Volume 4; R.A. Wheeler and D. Spellmeyer, eds.; Elsevier and ACS Computers in Chemistry Division: Amsterdam, 2008; In press.

 

new.gif (1150 bytes)73. Bender, Shana L.; Keough, James, M.; Boesch, Scott E.; Wheeler, Ralph A.; Barry, Bridgette; “The vibrational spectrum of the secondary electron acceptor, A1, in photosystem I”; J. Phys. Chem B 2008; 112; 3844-3852.

 

new.gif (1150 bytes)72. Huang, Zunnan; Wong, Chung; Wheeler, R.A.; “Flexible protein-flexible ligand docking with disrupted velocity simulated annealing”; Proteins: Structure, function, bioinformatics 2008, 71, 440-454.

 

2007

 

  1. Annual Reports in Computational Chemistry, Volume 3; D. Spellmeyer and R.A. Wheeler, eds.; Elsevier and ACS Computers in Chemistry Division: Amsterdam, 2007.

 

2006

 

  1. Yoneda, Juliane D.; Albuquerque, M.G.; Leal, Katia Z.; Seidl, Peter R.; Wheeler, R.A.; Boesch, Scott E.; de Alencastro, R.B.; de Souza, M.C.B.V.; Ferreira, Vitor F.; “Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent:  conformational studies in vacuum and in water”; J. Molec. Struc. (Theochem) 2006, 778, 97-103.

 

  1. Carter, Shawn M.; Lee, Jonghyuk; Hixson, Christopher Adam; Powell, Douglas R.; Wheeler, R.A.; Shaw, Michael J.; Richter-Addo, George B.; “Fiber-optic infrared reflectance spectroelectrochemical studies osmium and ruthenium nitrosyl porphyrins containing alkoxide and thiolate ligands”; J. Chem. Soc. Dalton Trans. 2006, 1338-1346.

 

2005

 

  1. Rahaman, Asif; Wheeler, R.A.; “Wavelet Transforms for Determining Time-Dependent Vibrational Frequencies”; J. Chem. Theory Comput. 2005, 1, 769-771.

 

One of the most frequently accessed papers from J. Chem. Theory Comput. during 3rd and 4th quarters of 2005: http://pubs.acs.org/journals/jctcce/promo/most_accessed/index.html

 

  1. Dong, Haitao; Wheeler, R.A.; “Ultrafast Vibrational Energy Transfer from O-H Stretching Vibrations of Liquid Water”; Chem. Phys. Lett. 2005, 413, 176-181.

2004

  1. Protein Bioenergetics:  Simulations of Electron, Proton, and Energy Transfer; R. A. Wheeler, ed.; ACS Symposium Series: Washington, DC, 2004.

 

  1. Sinha, Pankaj; Boesch, Scott E.; Gu, Changming; Wheeler, R.A.; Wilson, Angela K.; “Harmonic Vibrational Frequencies: Scaling Factors for HF, B3LYP, and MP2 Methods in Combination with Correlation-Consistent Basis Sets”; J. Phys. Chem. A 2004, 108, 9213-9217.

 

  1. Wheeler, R.A.; “Simulating Thermochemistry of p-Benzoquinone Reduction in Water and Ubiquinone Binding in the Photosynthetic Reaction Center” in Molecular Bioenergetics:  Simulations of Electron, Proton, and Energy Transfer; R.A. Wheeler, ed.; ACS Symposium Series: Washington, DC, 2004, pp. 51-69.

 

63. Hixson, Christopher Adam; Chen, Jermont; Huang, Zunnan; Wheeler, R.A.; “New Perspectives on Multiple-Copy Mean-Field Molecular

      Dynamics Methods”; J. Molec. Graphics and Modeling 2004, 22, 349-357 (invited review).

 

62. Hixson, Christopher Adam; Wheeler, R.A.; “Practical Multiple-Copy Methods for Sampling Classical Statistical Mechanical Ensembles”;

      Chem. Phys. Lett. 2004, 386, 330-335.

 

61. Rahaman, Asif; Wheeler, R.A.; “Potential Energy Landscape for Conformationally Gated, Secondary Ubiquinone Binding in the

      Photosynthetic Reaction Center of Rhodobacter sphaeroides”; ChemPhysChem 2004, 5, 249-252.                                                                                                                                                                                                                                                                                            

   2003

60. York, Shawna; Boesch, Scott E.; Wheeler, R.A.; Frech, Roger; “Vibrational Assignments of High Molecular Weight Linear Polyethylenimine (LPEI) Based on Monomeric and Tetrameric Model Compounds”; Macromolecules 2003, 36, 7348-7351.

59. Wheeler, R.A.; Dong, Haitao; “Optimal Spectrum Estimation in Statistical Mechanics”; ChemPhysChem 2003, 4, 1227-1230.

Featured in Chemical & Engineering News, February 9, 2004, pp. 30-31.

58. Wheeler, R.A.; Dong, Haitao; Boesch, Scott E.; “Quasiharmonic Vibrations of Water, Water Dimer, and Liquid Water from Principal Component Analysis of Quantum or QM/MM Trajectories”; ChemPhysChem 2003, 4, 382-384.

Featured in Chemical & Engineering News, February 9, 2004, pp. 30-31.

57. Sanders, Rebecca A.; Boesch, Scott E.; Snow, Albert G.; Hu, Lieyu (Richard); Frech, Roger; Wheeler, R.A.; Glatzhofer, Daniel T.; “N, N, N’, N’, N”-Pentamethyldiethyltriamine (PMDETA) as a Model Compound for Linear Poly(N-Methylethylenimine), LPMEI”; Polym. Preprints 2003, 44, 966-967.

2002

56. Boesch, Scott E.; York, Shawna; Frech, Roger; Wheeler, R.A.; "Effect of Lithium Triflate and Lithium Bromide on the Vibrational Frequencies of Dimethylethylenediamine (DMEDA)"; J. Chem. Soc., Phys. Chem. Commun. 2002; 5, 99-111.

55. Dong, Haitao; Hyun, Jin-Kee; Rhodes, Christopher P.; Frech, Roger; Wheeler, R.A.; "Molecular Dynamics Simulations and Vibrational Spectroscopic Studies of Local Structure in Tetraglyme:Sodium Triflate (CH3O(CH2CH2O)4CH3:NaCF3SO3) Solutions"; J. Phys. Chem. B 2002, 106, 4878-4885.

54. Walden, Susan E.; Wheeler, R.A.; "Protein Conformational Gate Controlling Binding Site Preference and Migration of Ubiquinone-B in the Photosynthetic Reaction Center of Rhodobacter sphaeroides"; J. Phys. Chem. B 2002, 106, 3001-3006.

2001

53. Hixson, Christopher Adam; Wheeler, R.A.; "Rigorous Classical-Mechanical Derivation of a Multiple-Copy Algorithm for Sampling Statistical Mechanical Ensembles"; Phys. Rev. E 2001, 64, 026701/1-026701/6.

52. Richter-Addo, George B.; Wheeler, R.A.; Hixson, Christopher Adam; Chen, Li; Khan, Masood A.; Ellison, Mary K.; Schulz, Charles E.; Scheidt, W. Robert; "Unexpected Nitrosyl Group Bending in Six-Coordinate {MNO}6 s-Bonded Aryl-(iron) and -(ruthenium) Porphyrins"; J. Am. Chem. Soc. 2001, 123, 6314-6326.

51. Dong, Haitao; Hyun, Jin-Kee; Durham, Curtis; Wheeler, R.A.; "Molecular Dynamics Simulations and Structural Comparisons of Amorphous Poly(ethylene oxide) and Poly(ethylenimine) Models"; Polymer 2001, 42, 7809-7817.

50. Hyun, Jin-Kee; Dong, Haitao; Rhodes, Christopher P.; Frech, Roger; Wheeler, R.A.; "Molecular Dynamics Simulations and Spectroscopic Studies of Structure in Amorphous Tetraglyme (CH3O(CH2CH2O)4CH3) and Tetraglyme:LiCF3SO3"; J. Phys. Chem. A 2001, 105, 3329-3337.

49. Wheeler, R.A.; "Quinones and Quinoidal Radicals in Photosynthesis" in Theoretical Biochemistry--Processes and Properties; L.A. Eriksson, ed.; Elsevier:   Amsterdam, 2001; pp. 655-690.

48. Matthäus, Christian; Wheeler, R.A.; "Fragment Mode Analysis and its Application to the Vibrational Normal Modes of Boron Trichloride-Ammonia and Boron Trichloride-Pyridine Complexes"; Spectrochim. Acta A 2001, 57, 523-536.

2000

47. Boesch, Scott E.; York, Shawna; Frech, Roger; Wheeler, R. A.; "Experimental and Computational Investigation of the Structure and Vibrations of Dimethylethylenediamine, a Model for Poly(ethylenimine)"; J. Chem. Soc., Phys. Chem. Commun. 2001, 1 (electronic publication).

46. Skokov, Sergei; Wheeler, R.A.; "Ab initio Molecular Dynamics Shows Low-Frequency Mode Manifolds Mediate Electron Transfer in CO+ + CO --> CO + CO+ Electron Exchange"; J. Phys. Chem. A 2000, 104, 6413-6423.

1999

45. Razeghifard, M. Reza; Kim, Sunyoung; Patzlaff, Jason; Hutchison, Ronald, S.; Krick, Thomas; Ayala, Idelisa; Steenhuis, Jacqueline J.; Boesch, Scott E.; Wheeler, R. A.; Barry, Bridgette, A.; "In vivo, In vitro, and Calculated Vibrational Spectra of Plastoquinone and Plastoquinone Anion Radical"; J. Phys. Chem. B 1999, 103,  9790-9800.

44. Wise, Kristopher E.; Wheeler, R.A.; "Donor-Acceptor Assisted Diels-Alder Reaction of Anthracene and Tetracyanoethylene (TCNE)"; J. Phys. Chem. A 1999, 103, 8279-8287.

43. Grafton, Anthony Kurt; Wheeler, R.A.; "Amino Acid Protonation States Determine Binding Sites of the Secondary Ubiquinone and its Anion in the Rhodobacter sphaeroides Photosynthetic Reaction Center; J. Phys. Chem. B 1999, 103, 5380-5387.

Highlighted in NSF publicity magazine Access Fall/Winter 1998, pp. 41-43.

42. Wise, Kristopher E.; Pate, J. Brett; Wheeler, R.A.; "Phenoxyl, (Methylthio)phenoxyl, and (Methylthio)cresyl Radical Models for the Structures, Vibrations, and Spin Properties of the Cysteine-Linked Tyrosyl Radical in Galactose Oxidase"; J. Phys. Chem. B 1999, 103, 4764-4772.

41. Skokov, Sergei; Wheeler, R.A.; "Oxidative Aromatic Substitution: Hartree-Fock/Density Functional and Ab Initio Molecular Orbital Studies of Benzene and Toluene Nitrosation"; J. Phys. Chem. A 1999, 103, 4261-4269.

40. Raymond, Kevin S.; Wheeler, R.A.; "Compatibility of Correlation-Consistent Basis Sets with the Becke3LYP Hybrid Hartree-Fock/Density Functional"; J. Comput. Chem. 1999, 20, 207-216.

1998

39. Grafton, Anthony Kurt; Wheeler, R.A.; "Vibrational Projection Analysis: A New Tool for Comparing Normal Vibrational Modes of Similar Molecules"; J. Comput. Chem. 1998, 19, 1663-1674.

38. Grafton, Anthony Kurt; Wheeler, R.A.; "ViPA: A Computer Program for Vector Projection Analysis of Normal Vibrational Modes of Molecules"; Comput. Phys. Commun. 1998; 113, 78-84.

1997

37. Boesch, Scott E.; Wheeler, R.A.; "Pi-Donor Substituent Effects on Calculated Structures, Spin Properties, and Vibrations of Radical Anions of p-Chloranil, p-Fluoranil, and p-Benzoquinone"; J. Phys. Chem. A 1997, 101, 8351-8359.

36. Grafton, Anthony Kurt; Wheeler, R.A.; "Comparison of the Properties of Various Fused-Ring Quinones and Their Radical Anions Using Hartree-Fock and Hybrid Hartree-Fock/Density Functional Methods"; J. Phys. Chem. A 1997, 101, 7154-7166.

35. Boesch, Scott E.; Wheeler, R.A.; "Structures and Properties of Ubiquinone-1 and its Radical Anion Predicted from a Hybrid Hartree-Fock/Density Functional Method"; J. Phys. Chem. A 1997, 101, 5799-5804.

34. Grafton, Anthony Kurt; Boesch, Scott E.; Wheeler, R.A.; "Structures and Properties of Vitamin K and its Radical Anion Predicted by Hybrid Hartree-Fock/Density Functional Theory"; J. Mol. Struc. (Theochem) 1997, 392, 1-11.

33. Skokov, Sergei; Wheeler, R.A.; "Study of Hydrogen Abstraction Reactions by Hybrid Hartree-Fock/Density Functional Methods"; Chem. Phys. Lett. 1997, 271, 251-258.

32. Walden, Susan E.; Wheeler, R.A.; "First Evidence of Anchimeric Spin Delocalization in Tryptophan Radical Cation"; J. Am. Chem. Soc.; 1997, 119, 3175-3176.

Highlighted in Chemical & Engineering News, "Science/Technology Concentrates" for April 7, 1997, p. 49.

31. Wise, Kristopher E.; Grafton, Anthony Kurt; Wheeler, R.A.; "Trimethyl-p-Benzoquinone Provides Excellent Structural, Spectroscopic, and Thermochemical Models for Plastoquinone-1 and its Radical Anion"; J. Phys. Chem. A 1997, 101, 1160-1165.

30. Raymond, Kevin S.; Grafton, Anthony Kurt; Wheeler, R.A.; "Calculated One-Electron Reduction Potentials and Solvation Structures for Selected p-Benzoquinones in Water"; J. Phys. Chem. B 1997, 101, 623-631.

1996

29. Walden, Susan E.; Wheeler, R.A.; "Structural and Vibrational Analysis of Indolyl Radical and Indolyl Radical Cation by Density Functional Methods"; J. Chem. Soc., Perkin Trans. 2 1996, 2663-2672.

28. Walden, Susan E.; Wheeler, R.A.; "Structural and Vibrational Analysis of Indole by Density Functional and Hybrid Hartree-Fock/Density Functional Methods"; J. Chem. Soc., Perkin Trans. 2 1996, 2653-2662.

27. Qin, Yue; Wheeler, R.A.; "Density-Functional-Derived Structures, Spin Properties, and Vibrations of Phenol Radical Cation"; J. Phys. Chem. 1996, 100, 10554-10563.

26. Boesch, Scott E.; Grafton, Anthony Kurt; Wheeler, R.A.; "Electron Affinities for Substituted p-Benzoquinones From Hybrid Hartree-Fock/Density-Functional Calculations"; J. Phys. Chem. 1996, 100, 10083-10087.

25. Walden, Susan E.; Wheeler, R.A.; "Distinguishing Features of Indolyl Radical and Radical Cation: Implications for Tryptophan Radical Studies"; J. Phys. Chem. 1996, 100, 1530-1535.

1995

24. Qin, Yue; Wheeler, R.A.; "Similarities and Differences Between Phenoxyl and Tyrosine Phenoxyl Radical Structures, Vibrational Frequencies, and Spin Densities"; J. Am. Chem. Soc. 1995, 117, 6083-6092.

23. Boesch, Scott E.; Wheeler, R.A.; "Pi-Donor Substituent Effects on Calculated Structures and Vibrational Frequencies for p-Benzoquinone, p-Fluoranil, and p-Chloranil"; J. Phys. Chem. 1995, 99, 8125-8134.

22. Qin, Yue; Wheeler, R.A.; "Density-Functional Methods Give Accurate Vibrational Frequencies and Spin Densities for Phenoxyl Radical"; J. Chem. Phys. 1995, 102, 1689-1698.

1994

21. Wheeler, R.A.; "A Method for Computing One-Electron Reduction Potentials and its Application to p-Benzoquinone in Water at 300 K"; J. Am. Chem. Soc. 1994, 116, 11048-11051.

20. Huang, Weiwei; Wheeler, R.A.; Frech, Roger; "Vibrational Spectroscopic and Ab Initio Molecular Orbital Studies of the Normal and 13C-Labeled Trifluoromethanesulfonate Anion"; Spectrochimica Acta, Part A 1994, 50, 985-996.

19. Huang, Weiwei; Frech, Roger; Wheeler, R.A.; "Molecular Structures and Normal Vibrations of CF3SO3- and its Lithium Ion Pairs and Aggregates"; J. Phys. Chem. 1994, 98, 100-110.

1993

18. Wheeler, R.A.; "Low Energy, Doublet States of p-Benzosemiquinone Radical Anion From SCF-CI and CASSCF Calculations"; J. Phys. Chem. 1993, 97, 1533-1537.

17. Raymond, Kevin S.; Wheeler, R.A.; "Structure, Bonding, and Vibrational Modes of the p-Aminophenoxyl Radical and p-Benzosemiquinone Anion Radical From Ab Initio Molecular Orbital Calculations"; J. Chem. Soc., Faraday Trans. 1993, 88, 665-670.

1992

16. Wheeler, R.A.; Pavan Kumar, P. N. V.; "Stereochemically Active or Inactive Lone-Pair Electrons in Some Six-Coordinate, Group 15 Halides"; J. Am. Chem. Soc. 1992, 114, 4776-4784.

1991

15. Tsai, Jing-Cherng; Wheeler, R.A.; Khan, Masood A.; Nicholas, Kenneth M.; "Structure and Bonding in the Unsymmetrically Hydrido-Bridged Heterobimetallic Complex (h5-C5H5)2Mo(m-H)(m-CO)Co(CO)3"; Organometallics, 1991, 10, 1344-1350 .

1990

14. Wheeler, R.A.; "Bonding to Intersitital Main Group or Transition-Metal Atoms in Cubic Clusters Related to Ni9(m4-Te)6(PEt3)8". J. Am. Chem. Soc. 1990, 112, 8737-8741; 1991, 113, 4046.

13. Wheeler, R.A.; McCammon, J. Andrew; "Pi Orbitals in Quantum Path Integral Simulations of Electron Transfer Paths". Chem. Phys. Lett. 1990, 174, 369-375.

1989

12. Neithamer, David R.; LaPointe, Robert E.; Wheeler, R.A.; Richeson, Darren S.; Van Duyne, Gregory D.; Wolczanski, Peter T.; "Carbon Monoxide Cleavage by (silox)3Ta (silox=t-Bu3SiO-): Physical, Theoretical, and Mechanistic Investigations". J. Am. Chem. Soc. 1989, 111, 9056-9072.

1988

11. Wheeler, R.A.; Hoffmann, Roald; "Trans-Edge-Sharing Molybdenum Octahedra: A Reciprocal Space Approach to Metal-Metal Bonding in Finite Chains". J. Am. Chem. Soc. 1988, 110, 7315-7325.

Highlighted in Nachrich. Chem., Technik, Lab. Vol. 37, Number. 2, p. 116; 1989 (Significant Advances in Inorganic Chemistry for 1988).

10. Wheeler, R.A.; Piela, Lucjan; Hoffmann, Roald; "A Reciprocal Space Approach to the Orbitals of Truncated Crystals". J. Am. Chem. Soc. 1988, 110, 7302-7315.

Highlighted in Nachrich. Chem., Technik, Lab. Vol. 37, Number. 2, p. 116; 1989 (Significant Advances in Inorganic Chemistry for 1988).

9. Burk, Mark J.; McGrath, Mark P.; Wheeler, R.A.; Crabtree, Robert H.; "The Origin of the Directing Effect in H2 Addition to Square-Planar d8 Complexes". J. Am. Chem. Soc. 1988, 110, 5034-5039.

1987

8. Hoffmann, Roald; Li, Jing; Wheeler, R.A.; "YCoC, A Simple Organometallic Polymer in the Solid State with Strong Co-C Pi Bonding". J. Am. Chem. Soc. 1987, 109, 6600-6602.

7. Jørgensen, Karl-Anker; Wheeler, R.A.; Hoffmann, Roald; "Electronic and Steric Factors Determining the Asymmetric Epoxidation of Allylic Alcohols by Titanium-Tartrate Complexes (The Sharpless Epoxidation)". J. Am. Chem. Soc. 1987, 109, 3240-3246.

6. Chandrasekhar, P.; Wheeler, R.A.; Hoffmann, Roald; "Sigma Bond Cleavage in Coordinated Dioxygen: The Case of the m-Peroxo Complex [((THF)3Cl2VIII)2(m-O22-)] and Vanadyl Formation in Solution". Inorg. Chim. Acta 1987, 122, 51-59.

1986

5. Wheeler, R.A.; Hoffmann, Roald; "A New Magic Cluster Electron Count and Metal-Metal Multiple Bonding". J. Am. Chem. Soc. 1986, 108, 6605-6610.

Highlighted in Nachrich. Chem., Technik, Lab. Vol. 35, Number. 2, p. 109; 1987 (Significant Advances in Inorganic Chemistry for 1986).

4. Wheeler, R.A.; Hoffmann, Roald; Strähle, Joachim; "Transition Metal Nitrides, Organic Polyenes, and Phosphazenes: A Structural and Orbital Analogy" J. Am. Chem. Soc. 1986, 108, 5381-5387.

3. Wheeler, R.A.; Hoffmann, Roald; "A Novel Electron Count and Metal-Metal Multiple Bonding in Trigonal Prismatic Clusters". Angew. Chem. 1986, 98, 828-829. Angew. Chem. Int. Ed. Engl. 1986, 25, 822-823.

Highlighted in Nachrich. Chem., Technik, Lab. Vol. 35, Number. 2, p. 109; 1987 (Significant Advances in Inorganic Chemistry for 1986).

2. Wheeler, R.A.; Whangbo, Myung-Hwan; Hughbanks, Timothy; Hoffmann, Roald; Burdett, Jeremy K.; Albright, Thomas A.; "Symmetric vs. Asymmetric Linear M-X-M Linkages in Molecules, Polymers, and Extended Networks" J. Am. Chem. Soc. 1986, 108, 2222-2236.

1984

1. Wheeler, R.A.; Van Hecke, Gerald R.; "Application of Regular Solution Theory to Discotic Mesophases: Calculation of Phase Diagrams Exhibiting Minima" in "Liquid Crystals and Ordered Fluids ", vol. 4; A.C. Griffin, J.F. Johnson, eds.; Plenum: New York, 1984; pp. 283-292.