Publications



    Years 1995 to 2001

  1. S. A. Nizkorodov, O. Dopfer, T. Ruchti, M. Meuwly, J. P. Maier, E. J. Bieske
    Size Effects in Cluster Infrared Spectra. The n1 Band of Ar n-HCO+ (n=1-13)
    J. Phys. Chem. 99, 17118 (1995)

  2. M. Meuwly, S. A. Nizkorodov, J. P. Maier, E. J. Bieske
    Mid-infrared spectra of He-HN2+ and He2-HN2+
    J. Chem. Phys. 104, 3876 (1995)

  3. S.A. Nizkorodov, O. Dopfer, M. Meuwly, E.J. Bieske, J.P. Maier
    Mid-infrared spectra of the proton-bound complexes Nen-HCO+ (n=1-13)
    J. Chem. Phys. 105, 1770 (1996)

  4. O. Dopfer, S. A. Nizkorodov, M. Meuwly, E.J. Bieske, J.P. Maier
    The n3 infrared spectrum of the He-NH4+ complex
    Chem. Phys. Lett. 260, 545 (1996)

  5. O. Dopfer, S. A. Nizkorodov, M. Meuwly, E.J. Bieske, J. P. Maier
    Microsolvation of the Ammonium Ion in Ar: Mid-infrared Spectra of NH4+-Arn Complexes (n=1-7)
    Int. J. Mass. Spectr. Ion Proc. 167/168, 637 (1997)

  6. M. Meuwly, S.A. Nizkorodov, E.J. Bieske, J.P. Maier, O. Dopfer
    Reply to Comment on "The n3 infrared spectrum of the He-NH4+ complex"
    Chem. Phys. Lett. 270, 252 (1997)

  7. M. Meuwly, R. Bemish
    Adiabatic Correction of the N2H+-He Intermolecular Potential Energy Surface
    J. Chem. Phys. 106 8672 (1997)

  8. S. A. Nizkorodov, M. Meuwly, J.P. Maier, O. Dopfer, E.J. Bieske
    Infrared predissociation spectra of Nen-HN2+ clusters (n=1-5)
    J. Chem. Phys. 108, 8964 (1998)

  9. M. Meuwly, J. P. Maier, P. Rosmus
    Vibrational state in the electronic ground state of the OH+-He and OH+-Ne complexes
    J. Chem. Phys., 109, 3850 (1998)

  10. M. Meuwly and J. M. Hutson
    The potential energy surface and near-dissociation states of He-H2+
    J. Chem. Phys., 110, 3418 (1999)

  11. M. Meuwly and J. M. Hutson
    Predictions of microwave transitions in He-H2+
    Monthly Notices of the Royal Astronomical Society (1999)

  12. M. Meuwly and J. M. Hutson
    Morphing ab initio potentials: a systematic study of Ne-HF
    J. Chem. Phys., 110, 8338 (1999)

  13. M. Meuwly
    Structures and energetics of
    Nen-HN2+ clusters
    J. Chem. Phys., 111, 2633 (1999)

  14. J.P. Connelly, M. Meuwly, A.R. Auty, B.J. Howard
    The dynamics of N2-O3 and N2-SO2 probed by microwave spectroscopy
    J. Mol. Spec., 199, 205 (2000)

  15. M. Meuwly and J. M. Hutson
    Intermolecular potential energy surfaces and bound states in F-HF
    J. Chem. Phys., 112, 592 (2000)

  16. M. Meuwly and J. M. Hutson
    Potential energy surfaces and properties of the Br-HBr complex
    PCCP, 2, 441 (2000)

  17. M. Meuwly and N. J. Wright
    The potential energy surface and ro-vibrational states of He-CH+
    J. Phys. Chem. A, 104, 1271 (2000)

  18. N.M. Lakin, O. Dopfer, M. Meuwly, B.J. Howard, J.P. Maier
    The intermolecular potential of NH4+-Ar 1. Calculations for the internal rotor structure of the
    n3 band
    Mol. Phys., 2, 63 (2000)

  19. M. Meuwly
    Quantum simulations of Nen-OH+ clusters
    J. Phys. Chem. A, 104, 7144 (2000)

  20. S. Coussan, M. Meuwly, S. Leutwyler
    Proton transfer and tautomerisation in 7-Hydroxyquinoline-(NH3)n clusters: Structure and energetics at the SCF level
    J. Chem. Phys., 114, 3524 (2001)

  21. M. Meuwly, A. Bach, S. Leutwyler
    Grotthus proton translocation along ammonia wires in 7-Hydroxyquinoline-(NH3)n clusters
    J. Am. Chem. Soc., 123, 11446 (2001)


  22. Year 2002

  23. M. Meuwly and M. Karplus
    Simulation of Proton Transfer along Ammonia Wires: A ab initio DFT and SCC Classical Molecular Dynamics Study
    J. Chem. Phys., 116, 2572 (2002)

  24. M. Meuwly, P. Peter Wolynek, E. J. Bieske
    The potential energy surface and lower bound states of HCCH-Cl-
    J. Chem. Phys., 116, 4948 (2002)

  25. M. Meuwly, O. Becker, R. H. Stote, M. Karplus
    NO Rebinding in Myoglobin: A Reactive Molecular Dynamics Study
    Biophys. Chem., 98,183 (2002)

  26. M. Meuwly and J. D. Doll
    Dynamical studies of mixed rare-gas clusters: Collision-induced absorption of (Ne)n-(Ar)m (n+m < 100)
    Phys. Rev. A66, 023202 (2002)


  27. Year 2003

  28. M. Meuwly, A. Müller and S. Leutwyler
    Energetics, Dynamics and Infrared Spectra of the DNA Base-Pair Analogue 2-Pyridone 2-Hydroxypyridine
    PCCP, 5, 2663 (2003)

  29. M. Meuwly and M. Karplus
    Theoretical Investigations of Ferredoxin I:
    The Possible Role of Internal Water Molecules on the Coupled Electron Proton Transfer Reaction
    Farad. Disc. 124, 297 (2003)

  30. M. Lochner, M. Meuwly, and W.-D. Woggon
    The origin of the low-spin resting state of cytochrome P450cam investigated by means of active site analogues
    ChemComm, 12, 1330, (2003)

  31. M. Meuwly and J. M. Hutson
    Potential energy surfaces and bound states for the open-shell Van der Waals cluster Br-HF
    J. Chem. Phys., 119, 8873 (2003)

  32. D. R. Nutt and M. Meuwly
    Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin
    Biophys. J., 85, 3612 (2003)


  33. Year 2004

  34. M. Meuwly and M. Karplus
    Theoretical Investigations on Azotobacter Vinelandii Ferredoxin I: Effects of Electron Transfer on Protein Dynamics
    Biophys. J., 86, 1987 (2004)

  35. V. Zoete, M. Meuwly and M. Karplus
    Investigation of glucose binding sites on insulin
    Proteins, Structure, Function and Bioinformatics, 55, 568 (2004)

  36. D. R. Nutt and M. Meuwly
    CO Migration in Native and Mutant Myoglobin: Atomistic Simulations for the Understanding of Protein Function
    Proc. Natl. Acad. Sci., 101, 5998 (2004)

  37. V. Zoete and M. Meuwly
    On the Influence of Semirigid Environments on Proton Transfer along Molecular Chains
    J. Chem. Phys., 120, 7085 (2004)

  38. V. Zoete and M. Meuwly
    Double proton transfer in the isolated and DNA embedded guanine-cytosine base pair
    J. Chem. Phys., 121, 4377 (2004)

  39. F. Daniel, M.-L. Dubernet and M. Meuwly
    Selective hyperfine excitation of N2H+ by He : new potential energy surface, cross-sections and propensity rules
    J. Chem. Phys., 232, 4540 (2004)

  40. V. Zoete, M. Meuwly and M. Karplus
    A comparison of the dynamic behavior of monomeric and dimeric insulin shows structural rearrangements in the active monomer
    J. Mol. Biol, 342, 913 (2004)

  41. D. R. Nutt and M. Meuwly
    Ligand dynamics in myoglobin: Calculation of infrared spectra for photodissociated NO
    Chem. Phys. Chem., 5, 1710 (2004)

  42. X. Zhang, M. Meuwly and W.-D. Woggon
    The first supramolecular orthovanadate receptor - Structural mimics of vanadium haloperoxidase
    J. Inorg. Biochem., 98, 1967 (2004)

  43. C. Mazet, S. P. Smidt, M. Meuwly and A. Pfaltz
    A combined experimental and computational study of dihydrido(phosphinooxazoline)iridium complexes
    J. Am. Chem. Soc., 43, 14176 (2004)

  44. A. Robin, M. Meuwly, K. M. Fromm, H. Grossmann and G. Bernardinelli
    How many structures are there for {[AgL](NO3)(H2O)n}? Water-content dependent variations in the structure of [AgL](NO3)(H2O)n}, n=0,1,2; L=ethanediyl bis(isonicotinate)
    CrystEngComm., 6, 336 (2004)

  45. S. Lammers and M. Meuwly
    Double Proton Transfer Reactions using Dissociable Force Fields
    J. Aust. Chem. Soc., 12, 1223 (2004)


  46. Year 2005

  47. B. Ladinig, M. Respondek, W. Leupin, M. Meuwly, J. Wirz, and V. Zoete
    Protonation Equilibria of Hoechst 33258 in Aqueous Solution
    Helv. Chim. Acta, 88, 53 (2005)

  48. V. Zoete, M. Meuwly and M. Karplus
    Study of the insulin dimerization: Binding free energy calculations and per-residue free energy decomposition
    Proteins, Structure, Function and Bioinformatics, 61, 79 (2005)

  49. P. Banushkina and M. Meuwly
    Hierarchical Numerical Solution of Smoluchowski Equations with Rough Potentials
    J. Chem. Theory Comp., 1, 208 (2005)

  50. D. R. Nutt, P. Banushkina and M. Meuwly
    Computational Chemistry for Elucidating Protein Function: Energetics and Dynamics of Myoglobin-Ligand Systems
    Chimia, 59, 517 (2005)

  51. P. Banushkina, O. Schenk and M. Meuwly
    Efficiency considerations in solving Smoluchowksi equations for rough potentials
    Lecture Notes in Computer Sciences, LNBI 3695, 208 (2005)

  52. P. Banushkina and M. Meuwly
    Free Energy Barriers in MbCO Rebinding
    J. Phys. Chem. B, 109, 16911 (2005)

  53. M. Meuwly
    Reactions in Complex Biologically Relevant Systems: Challenges for Computational Approaches
    Future Generation Computer Systems, 21, 1285 (2005)

  54. D. R. Nutt, M. Karplus and M. Meuwly
    Potential energy surface and molecular dynamics of MbNO: Existence of an unsuspected FeON minimum
    J. Phys. Chem. B, 109, 21118 (2005)

  55. A. Fouqueau and M. Meuwly
    Structures and Dynamics of Protonated Ammonia Clusters
    J. Chem. Phys., 123, 244308 (2005)

  56. F. Daniel, M.-L. Dubernet, M. Meuwly, J. Cernicharo and L. Pagani
    Collisional Rate Excitation Rate Coefficients of N2H+ by He
    Mon. Not. R. Astron. Soc., 363, 1083 (2005)


  57. Year 2006

  58. D. R. Nutt and M. Meuwly
    Studying Reactive Processes with Classical Dynamics: Rebinding Dynamics in MbNO
    Biophys. J., 90, 1191 (2006)

  59. G. Buffa, L. Dore, F. Tinti and M. Meuwly
    New experimental and theoretical results for Argon broadening and shift of HCO+ rotational lines
    Chem. Phys. Chem., 7, 1764 (2006)

  60. V. Zoete and M. Meuwly
    On the importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer
    J. Comp. Chem., 27, 1843 (2006)

  61. H. Thorsteinsdottir, V. Zoete, T. Schwede and M. Meuwly
    How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding
    Proteins, Structure, Function and Bioinformatics, 65, 407 (2006)

  62. J. Danielsson, P. Banushkina, D. R. Nutt and M. Meuwly
    Computer Simulations of structures, energetics and dynamics of myoglobin--ligand complexes
    Int. Rev. Phys. Chem., 25, 407 (2006)

  63. M. Meuwly
    On the Influence of the Local Environment on the CO Stretching Frequencies in Native Myoglobin: Assignment of the B-states in MbCO
    Chem. Phys. Chem., 7, 2061 (2006)

  64. M. Koch, Franziska F.-F. Schmid, V. Zoete and M. Meuwly
    Insulin: A Model System for Nanomedicine?
    Nanomedicine, 1, 373 (2006)

  65. B. Christen, M. Christen, R. Paul, F. Schmid, M. Folcher, P. Jenoe, M. Meuwly and U. Jenal
    Allosteric Control of Cyclic di-GMP Signalling
    J. Biol. Chem., 281, 32015 (2006)


  66. Year 2007

  67. J. Danielsson and M. Meuwly
    Energetics and Dynamics in MbCN: CN---Vibrational Relaxation from Molecular Dynamics Simulations
    J. Phys. Chem. B, 111, 218 (2007)

  68. D. R. Nutt and M. Meuwly
    Ferric and Ferrous Iron in Nitroso-Myoglobin: Computer Simulations of Stable and Metastable States and Their Infrared Spectra
    ChemPhysChem, 8, 527 (2007)

  69. S. Lammers and M. Meuwly
    On the Relationship between Infrared Spectra of Shared Protons in Different Chemical Environments: A Comparison of protonated diglyme and protonated water dimer
    J. Phys. Chem. A, 111, 1638 (2007)

  70. M. Meuwly
    Using Small Molecules to Probe Protein Cavities: The Myoglobin-XO (X=C,N) Family of Systems
    Eur. Phys. J., 141, 209 (2007)

  71. J. Danielsson and M. Meuwly
    Molecular Dynamics Simulations of CN--- Dynamics and Spectroscopy in Myoglobin
    ChemPhysChem, 8, 1077 (2007)

  72. A. Fouqueau, R. J. Bemish and M. Meuwly
    Adsorption of Acridine Orange at a C8, 18/water/acetonitrile interface
    J. Phys. Chem. B, 111, 10208 (2007)

  73. C. Markert, M. Neuburger, K. Kulicke, M. Meuwly and A. Pfaltz
    Palladium-Catalyzed Allylic Substitution: Reversible Formation of Allyl-Bridged Dinuclear Palladium(I) Complexes
    Angew. Chem. Int. Ed., 46, 5892 (2007)

  74. W. Maudez, M. Meuwly and K. M. Fromm
    Analogy of the Coordination Chemistry of Alkaline Earch Metal and Lanthanide Ln2+ Ions
    Chem. Eur. J., 13, 8302 (2007)

  75. P. Banushkina and M. Meuwly
    Diffusive Dynamics on Multidimensional Rough Free Energy Surfaces
    J. Chem. Phys., 127, 135101 (2007)

  76. F.-F. Schmid and M. Meuwly
    All-atom Simulations of Structures and Energetics of c-di-GMP-bound and free PleD
    J. Mol. Biol., 374, 1270 (2007)


  77. Year 2008

  78. S. Lammers, S. Lutz and M. Meuwly
    Reactive Force Fields for Proton Transfer Dynamics
    J. Comp. Chem., 29, 1048 (2008)

  79. N. Plattner and M. Meuwly
    The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin
    Biophys. J., 94, 2505 (2008)

  80. D. Sabo, M. Meuwly, D. L. Freeman and J. D. Doll
    A constant entropy increase model for the selection of parallel tempering ensembles
    J. Chem. Phys., 128, 174109 (2008)

  81. N. Plattner and M. Meuwly
    Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry
    ChemPhysChem, 9, 1271 (2008)

  82. J. Danielsson and M. Meuwly
    Atomistic Simulation of Adiabatic Reactive Processes Based on Multi-State Potential Energy Surfaces
    J. Chem. Theory Computing, 4, 1083 (2008)

  83. J. Braun, A. Fouqueau, R. J. Bemish and M. Meuwly
    Solvent Structures of Mixed Water/Acetonitrile Mixtures at Chromatographic Interfaces from Computer Simulations
    PCCP, 10, 4765 (2008)

  84. N. Plattner, T. Bandi, J. D. Doll, D. L. Freeman and M. Meuwly
    MD Simulations using Distributed Multipole Electrostatics: Structural and Spectroscopic Properties of CO- and Methane-Containing Clathrates
    Mol. Phys., 106, 1675 (2008)

  85. G. Buffa, L. Dore, F. Tinti and M. Meuwly
    Experimental and theoretical study of Helium broadening and shift of HCO+ rotational lines
    ChemPhysChem, 9, 2237 (2008)

  86. F.-F. Schmid and M. Meuwly
    Direct Comparison of Experimental and Calculated NMR-Scalar Coupling Constants for Force Field Validation and Adaptation
    JCTC, 4, 1949 (2008)

  87. J. L. Sague, M. Meuwly and K. M. Fromm
    Counterion effect on the formation of coordination polymer networks between AgNO3 and L(2,2'-oxybis(ethane-2,1-diyl)diisonicotinate). Part 2
    CrystEngComm, 10, 1542 (2008)


  88. Year 2009

  89. I. Tubert-Brohman, M. Schmid and M. Meuwly
    A molecular mechanics force field for octahedral organometallic compounds with inclusion of the trans influence
    JCTC, 5, 530 (2009)

  90. N. Plattner and M. Meuwly
    Higher order multipole moments for MD simulations
    J. Mol. Mod., 15, 687 (2009)

  91. S. Mishra and M. Meuwly
    Nitric Oxide Dynamics in Truncated Hemoglobin: Docking Sites, Migration Pathways, and Vibrational Spectroscopy from Molecular Dynamics Simulations
    Biophys. J., 96, 2105 (2009)

  92. M. Devereux and M. Meuwly
    Structural Assignment of Spectra by Characterization of Conformational Substates in Bound MbCO
    Biophys. J., 96, 4363 (2009)

  93. G. Buffa, L. Dore, and M. Meuwly
    State-to-state rotational transition rates of the HCO+ ion by collisions with helium
    Monthly Notices of the Royal Astronomical Society, 397, 1909 (2009)

  94. M. Devereux, N. Plattner and M. Meuwly
    Application of Multipolar Charge Models and Molecular Dynamics Simulations to Study Stark Shifts in Inhomogeneous Electric Fields
    J. Phys. Chem. A, 113, 13199 (2009)

  95. M. Devereux and M. Meuwly
    Anharmonic Coupling in Molecular Dynamics Simulations of Ligand Vibrational Relaxation in Bound Carbonmonoxy Myoglobin
    J. Phys. Chem. B, 113, 13061 (2009)

  96. J. D. Doll, J. E. Gubernatis, N. Plattner, M. Meuwly, P. Dupuis and H. Wang
    A Spatial Averaging Approach to Rare-Event Sampling
    J. Chem. Phys., 131, 104107 (2009)

  97. S. Lutz, K. Nienhaus, G. U. Nienhaus and M. Meuwly
    Pocket Dynamics of Photodissociated Carbonmonoxy Neuroglobin
    J. Phys. Chem. B, 113, 15334 (2009)


  98. Year 2010

  99. K. Nienhaus, S. Lutz, M. Meuwly and G. U. Nienhaus
    Structural Identification of Spectroscopic Substates in Neuroglobin
    ChemPhysChem, 11, 119 (2010)

  100. J. Huang and M. Meuwly
    Explicit Hydrogen-bond Potentials and their Application to NMR Scalar Couplings in Proteins
    JCTC, 6, 467 (2010)

  101. S. Mishra and M. Meuwly
    Atomistic Simulation of NO Dioxygenation in Group~I Truncated Hemoglobin
    J. Am. Chem. Soc., 132, 2968 (2010)

  102. M. Devereux and M. Meuwly
    Force Field Optimization using Dynamics and Ensemble-Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO
    J. Chem. Inf. Model., 50, 349 (2010)

  103. N. Plattner, M. W. Lee and M. Meuwly
    Structural and Spectroscopic Characterization of Mixed Planetary Ices
    Faraday Discuss., 147, 217 (2010)

  104. J. D. Doll and M. Meuwly
    Finite-Temperature Quantum Simulations of Mixed Rare Gas Clusters
    J. Chem. Phys., 132, 234315 (2010)

  105. G. Buffa, O. Tarrini, L. Dore, and M. Meuwly
    Experimental and theoretical study of broadening and shift of N2H+ rotational lines by Helium
    ChemPhysChem., 11, 3141 (2010)

  106. J. L. Sague, T. Vig Slenters, P. S. Brunetto, S. Zuber, A. Fleury, L. Mirolo, A. Y. Robin, M. Meuwly, O. Gordon, R. Landmann, A. U. Daniels, and K. M. Fromm
    Of Chains and Rings: Synthetic Strategies and Theoretical Investigations for Tuning the Structure of Silver Coordination Compounds and Their Applications
    Materials, 3, 3407 (2010)

  107. Y. Yang and M. Meuwly
    A Generalized Reactive Force Field for Nonlinear Hydrogen Bonds: Hydrogen Dynamics and Transfer in Malonaldehyde
    J. Chem. Phys., 133, 064503 (2010)

  108. N. Plattner, J. D. Doll and M. Meuwly
    Spatial Averaging for Small Molecule Diffusion in Condensed Phase Environments
    J. Chem. Phys., 133, 044506 (2010)

  109. M. Orzechowski and M. Meuwly
    Dynamics of Water Filaments in Disordered Environments
    J. Phys. Chem. B, 114, 12203 (2010)

  110. S. Mishra and M. Meuwly
    Quantitative Analysis of Ligand Migration from Transition Networks
    Biophys. J., 99, 3969 (2010)


  111. Year 2011

  112. L. Zhang and M. Meuwly
    Stability and Dynamics of c-di-GMP in Solution
    ChemPhysChem, 12, 295 (2011)

  113. U. Gellrich, W. Seiche, M. Keller, B. Breit, J. Huang and M. Meuwly
    On the Origin of Ligand Self-Assembling Through Complementary Hydrogen-Bonding in the Coordination Sphere of a Transition Metal Center: The 6-Diphenylphosphanylpyridin-2(1H)-one system
    J. Am. Chem. Soc., 133, 964 (2011)

  114. S. Lutz and M. Meuwly
    Structural Characterization of Spectroscopic Substates in Carbonmonoxy Neuroglobin
    Faraday Discuss., 150, 375 (2011)

  115. P.-A. Cazade, S. Lutz, M. W. Lee and M. Meuwly
    Computational Spectroscopy and Reaction Dynamics
    Chimia, 65, 326 (2011)

  116. M. W. Lee and M. Meuwly
    On the Role of Nonbonded Interactions in Vibrational Energy Relaxation of Cyanide in Water
    J. Phys. Chem. A, 115, 5053 (2011)

  117. S. Lutz, Y. Yang, I. Tubert-Brohman and M. Meuwly
    Water-assisted proton transfer in ferredoxin I
    J. Biol. Chem., 286, 23679 (2011)

  118. J. Yosa and M. Meuwly
    Vibrationally Induced Dissociation of Sulfuric Acid (H2SO4)
    J. Phys. Chem. B, 115, 14350 (2011)


  119. Year 2012

  120. S. Lutz and M. Meuwly
    Photodissociation Dynamics of ClCN at Different Wavelengths
    ChemPhysChem, 13, 305 (2012)

  121. M Schmid, E. S. Nogueira F. W. Monnard, T. R. Ward and M. Meuwly
    Arylsulfonamides as Inhibitors for Carbonic Anhydrase: Prediction & Validation
    Chem. Soc., 3, 690 (2012)

  122. N. Plattner and M. Meuwly
    Quantifying the importance of protein conformation on ligand migration in Myoglobin
    Biophys. J., 102, 333 (2012)

  123. J. Helbing, M. Devereux, K. Nienhaus, G. U. Nienhaus, P. Hamm and M. Meuwly
    Temperature Dependence of the Heat Diffusivity of Proteins
    J. Phys. Chem. B, 116, 2620 (2012)

  124. M. Meuwly
    Reaction Dynamics: Rules Change with Molecular Size
    Chem. Phys. Chem, 13, 684 (2012)

  125. J. Huang and M. Meuwly
    Force Field Refinement from NMR Scalar Couplings
    Chem. Phys., 396, 116 (2012)

  126. Q. Cui and M. Meuwly
    Editorial to Special Issue "Protein Dynamics"
    Chem. Phys., 396, 1 (2012)

  127. M. W. Lee and M. Meuwly
    Molecular Dynamics Simulation of Nitric Oxide in Myoglobin
    J. Phys. Chem. B, 116, 4154 (2012)

  128. C. Kramer, P. Gedeck and M. Meuwly
    Atomic Multipoles: Electrostatic Potential Fit, Local Reference Axis Systems and Conformational Dependence
    J. Comp. Chem., 33, 1673 (2012)

  129. P.-A. Cazade, J. Huang, J. Yosa, J. J. Szymczak and M. Meuwly
    Atomistic Simulations of Reactive Processes in the Gas- and Condensed-Phase
    Intern. Rev. Phys. Chem., 31, 235 (2012)

  130. X. Tong, T. Nagy, J. Yosa, M. Germann, M. Meuwly, and S. Willitsch
    State-selected ion-molecule reactions with Coulomb-crystallized molecular ions in traps
    Chem. Phys. Lett., 547, 1 (2012)

  131. P. K. Gupta and M. Meuwly
    Dynamics of water/methanol mixtures at functionalized chromatographic interfaces
    J. Phys. Chem. B, 116, 10951 (2012)

  132. B. Bozic-Weber, V. Chaurin, E. C. Constable, C. E. Housecroft, M. Meuwly, M. Neuburger, J. A. Rudd, E. Schönhofer, and L. Siegfried
    Exploring copper(I)-based dye-sensitized solar cells: a complementary experimental and TD-DFT investigation
    Dalton Trans., 41, 14157 (2012)

  133. Y. Yang, X. Liu, M. Meuwly, L. Xiao, and S. Jia
    Harmonic Bath Averaged Hamiltonian: An efficient Tool to Capture Quantum effects of Large Systems
    J. Phys. Chem. A, 116, 11134 (2012)

  134. P.-A. Cazade and M. Meuwly
    Oxygen Migration Pathways in NO-bound Truncated Hemoglobin (TrHbN)
    Chem. Phys. Chem., 13, 4276-4286 (2012)

  135. M. W. Lee, N. Plattner and M. Meuwly
    Structure, Spectroscopy and Dynamics of layered H2O and CO2 ices
    PCCP, 14, 15464 (2012)

  136. J. Huang, D. Häussinger, U. Gellrich, W. Seiche, B. Breit and M. Meuwly
    Hydrogen-Bond and Solvent Dynamics in Transition Metal Complexes: A Combined Simulation and NMR-Investigation
    J. Phys. Chem. B, 116, 14406 (2012)


  137. Year 2013

  138. Laurent Mirolo, Tobias Schmidt, Sonja Eckhardt, Markus Meuwly, and Katharina M. Fromm
    pH-Dependent Coordination of Ag(I) Ions by Histidine: Experiment, Theory, and a Model for SilE
    Chem. Eur. J., 19, 1754 (2013)

  139. K. Nienhaus, S. Lutz, M. Meuwly and G. U. Nienhaus
    Reaction Pathway Selection in the Structural Dynamics of a Heme Protein
    Chem. Eur. J., 19, 3558 (2013)

  140. C. Kramer, P. Gedeck, and M. Meuwly
    Multipole-based Force Fields from ab initio Interaction Energies and the Need for Jointly Refitting all Intermolecular Parameters
    J. Chem. Theo. Chem., 9, 1499 (2013)

  141. J. J. Szymczak, F. Hofmann, and M. Meuwly
    Structure and Dynamics of Solvent Shells around Photoexcited Metal Complexes
    PCCP, 15, 6268 (2013)

  142. M. H. Schmid, T. R. Ward and M. Meuwly
    Towards a Broadly Applicable Force Field for d6-Piano Stool Complexes
    J. Chem. Theo. Comp., 9, 2313 (2013)

  143. T. Bereau, C. Kramer, F. W. Monnard, E. S. Nogueira, T. R. Ward and M. Meuwly
    Scoring multipole electrostatics in condensed-phase atomistic simulations
    J. Phys. Chem. B, 117, 5460 (2013)

  144. P. K. Gupta and M. Meuwly
    Dynamics and vibrational spectroscopy of water at hydroxylated silica surface
    Farad. Disc., 167, 329-346 (2013)

  145. M. W. Lee, J. K. Carr, M. Goellner, P. Hamm and M. Meuwly
    2D IR Spectra of Cyanide in Water Investigated by Molecular Dynamics Simulations
    J. Chem. Phys., 139, 054506 (2013)

  146. U. Gellrich, D. Himmel, M. Meuwly, and B. Breit
    Realistic Energy Surfaces for Real World Systems: An IMOMO CCSD(T):DFT scheme for the Rhodium Catalyzed Hydroformylation with the 6-DPPon ligand
    Chem. Eur. J., 19, 16272-16281 (2013)

  147. M. W. Lee and M. Meuwly
    Hydration Free Energies of Cyanide and Hydroxide Ions from Molecular Dynamics Simulations with Accurate Force Fields
    PCCP, 15, 20303 (2013)

  148. T. Bereau, C. Kramer and M. Meuwly
    Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations
    J. Chem. Theo. Comp., 9, 5450-5459 (2013)

  149. C. Kramer, T. Bereau, A. Spinn, K. R. Liedl, P. Gedeck and M. Meuwly
    Deriving Static Atomic Multipoles from the Electrostatic Potential
    J. Chem. Inf. Model., 53, 3410-3417 (2013)


  150. Year 2014

  151. J. Huang, M. Buchowiecki, T. Nagy, J. Vanicek and M. Meuwly
    Kinetic isotope effect in malonaldehyde from path integral Monte Carlo simulations
    PCCP, 16, 204-211 (2014)

  152. F. Hofmann, M. Devereux, A. Pfaltz and M. Meuwly
    Towards Force Fields for Atomistic Simulations of Iridium-Containing Complexes
    J. Comp. Chem., 35, 18-29 (2014)

  153. N. Plattner and M. Meuwly
    The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates
    J. Chem. Phys., 140, 024311 (2014)

  154. M. W. Lee and M. Meuwly
    Diffusion of Atomic Oxygen Relevant to Water Formation in Amorphous Interstellar Ices
    Faraday Disc., 168, 205-222 (2014)

  155. T. Nagy, J. Y. Reyes and M. Meuwly
    Multi-Surface Adiabatic Reactive Molecular Dynamics
    J. Chem. Theo. Comp., 10, 1366-1375 (2014)

  156. P.-A. Cazade, T. Bereau and M. Meuwly
    Computational Two-Dimensional Infrared Spectroscopy without Maps: N-methylacetamide in water
    J. Phys. Chem. B (J. L. Skinner Festschrift), 118, 8135-8147 (2014)

  157. M. Soloviov and M. Meuwly
    CO-Dynamics in the Active Site of Cytochrome c Oxidase
    J. Chem. Phys., 140, 45101 (2014)

  158. T. Schmidt, T. Schwede and M. Meuwly
    Computational Analysis of Methyltransfer Reactions in Dengue Virus Methyltransferase
    J. Phys. Chem. B, 118, 5882-5890 (2014)

  159. M. Devereux, N. Gresh, J. P. Piquemal and M. Meuwly
    A Supervised Fitting Approach to Force Field Parametrization with Application to the SIBFA Polarizable Force Field
    J. Comput. Chem., 35, 1577-1591 (2014)

  160. J. Y. Reyes, T. Nagy and M. Meuwly
    Competitive Reaction Pathways in Vibrationally Induced Photodissociation of H2SO4
    PCCP, 16, 18533-18544 (2014)

  161. M. Meuwly
    Quantitative Atomistic Simulations of Reactive and Non-Reactive Processes
    Chimia, 68, 592-595 (2014)

  162. M. Devereux, S. Raghunathan, D. G. Fedorov and M. Meuwly
    A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulation
    J. Chem. Theo. Comput., 10, 4229-4241 (2014)

  163. F. Hedin, N. Plattner, J. D. Doll and M. Meuwly
    Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules
    J. Chem. Theo. Comput., 10, 4284-4296 (2014)

  164. J. C. Castro-Palacio, T. Nagy, R. J. Bemish and M. Meuwly
    Computational study of collisions between O(3P) and NO(2Π) at temperatures relevant to the Hypersonic Flight Regime
    J. Chem. Phys., 141, 164319 (2014)


  165. Year 2015

  166. P. A. Cazade, W. Zhang, D. Prada-Gracia, G. Berezovska, F. Rao, C. Clementi and M. Meuwly
    A Comparative Analysis of Clustering Algorithms: O2 Migration in truncated Hemoglobin I from Transition Networks
    J. Chem. Phys., 142, 025103 (2015)

  167. P. A. Cazade, G. Berezovska and M. Meuwly
    Coupled Protein-Ligand Dynamics in Truncated Hemoglobin N from Atomistic Simulations and Transition Networks
    BBA - General Subjects, 1850, 996-1005 (2015)

  168. T. Dudev, M. Devereux, M. Meuwly, C. Lim, J.-P. Piquemal and N. Gresh
    Quantum-chemistry based calibration of the alkali metal cation series (Li(+) to Cs(+) ) for large-scale polarizable molecular mechanics/dynamics simulations.
    J. Comp. Chem., 36, 285-302 (2015)

  169. P. A. Cazade, F. Hedin, Z.-H. Xu and M. Meuwly
    Vibrational Relaxation and Energy Migration of N-methylacetamide in Water: The Role of Nonbonded Interactions
    J. Phys. Chem. B, 119, 3112-3122 (2015)

  170. S. Jacobsen, T. Bereau and M. Meuwly
    Multipolar Force Fields and Their Effects on Solvent Dynamics Around Simple Solutes
    J. Phys. Chem. B, 119, 3034-3045 (2015)

  171. J. C. Castro-Palacio, R. J. Bemish and M. Meuwly
    Equilibrium Rate Coefficients from Atomistic Simulations: The O(3P) + NO(2Π) → O2g-) + O(4S) Reaction at Temperatures Relevant to the Hypersonic Flight Regime
    J. Chem. Phys., 142, 091104 (2015)

  172. P.-A. Cazade, H. Tran, T. Bereau, A. K. Das, F. Klasi, P. Hamm and M. Meuwly
    Solvation of Fluoro-Acetonitrile in Water by 2D-IR Spectroscopy: A Combined Experimental-Computational Study
    J. Chem. Phys., 142, 212415 (2015)

  173. D. L. Howard, H. G. Kjaergaard, J. Huang and M. Meuwly
    Infrared and Near Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone
    J. Phys. Chem. A, 119, 7980 (2015)

  174. M. Soloviov and M. Meuwly
    Reproducing Kernel Potential Energy Surfaces in Biomolecular Simulations: Nitric Oxide Binding to Myoglobin
    J. Chem. Phys., 143, 105103 (2015)

  175. O. Unke and M. Meuwly
    Kernel Density Estimation-based Solution of the Nuclear Schrodinger Equation
    Chem. Phys. Lett., 639, 52 (2015)


  176. Year 2016

  177. H. Schmidt, M. Spulber, M. Neuburger, C. Palivan, M. Meuwly and O. Wenger
    Charge Transfer Pathways in Three Isomers of Naphthalene-Bridged Organic Mixed Valence Compounds
    J. Org. Chem., 81, 595 (2016)

  178. A. K. Das, R. V. Solomon, F. Hofmann and M. Meuwly
    Inner-Shell Water Rearrangement Following Photo-Excitation of Tris(2,2'-bipyridine)iron(II)
    J. Phys. Chem. B, 120, 206 (2016)

  179. J. Y. Reyes, S. Brickel, O. Unke, T. Nagy and M. Meuwly
    HSOH3Cl: A Prototype Molecule for Studying OH-stretching Overtone Induced Photodissociation
    PCCP, 18, 6780 (2016)

  180. H. Jin, P. Gojal, A. K. Das, M. Gaus, M. Meuwly and Q. Cui
    Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations
    J. Phys. Chem. B, 120, 1894 (2016)

  181. P. K. Gupta and M. Meuwly
    Ligand and Interfacial Dynamics in a Homodimeric Hemoglobin
    Struc. Dyn., 3, 012003 (2016)

  182. L. MacAleese, S. Hermelin, K. ElHage, P. Chouzenoux, A. Kulesza, R. Antoine, L. Bonacina, M. Meuwly, J.-P. Wolf and P. Dugourd
    Sequential Proton Coupled Electron Transfer (PCET): Dynamics Observed over 8 Orders of Magnitude in Time
    J. Am. Chem. Soc., 138, 4401 (2016)

  183. K. ElHage, T. Bereau, S. Jakobsen and M. Meuwly
    Impact of Quadrupolar Electrostatics on Atoms Adjacent to the Sigma-Hole in Condensed-Phase Simulations
    J. Chem. Theo. Comput., 12, 3008 (2016)

  184. P. K. Gupta and M. Meuwly
    Structure and Dynamics of Water/Methanol Mixtures at Hydroxylated Silica Interfaces Relevant to Chromatography
    ChemPhysChem, 17, 2938 (2016)

  185. O. T. Unke, R. J. Bemish, J. C. Castro-Palacio, and M. Meuwly
    Collision-Induced Rotational Excitation in N2+( 2Σg+, v=0)--Ar: Comparison of Computations and Experiment
    J. Chem. Phys., 144, 224307 (2016)

  186. K. Mackeprang, Z.-H. Xu, Z. Maroun, M. Meuwly and H. Kjaergaard
    Spectroscopy and Dynamics of Double Proton Transfer in F ormic Acid Dimer
    PCCP, 18, 24654 (2016)

  187. F. Hedin, K. ElHage and M. Meuwly
    A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations
    J. Chem. Inf. Model., 56, 1479 (2016)

  188. M. Soloviov, A. K. Das and M. Meuwly
    Structural Interpretation of Metastable States in MbNO
    Angew. Chem. Int. Ed., 55, 10126 (2016)

  189. K. El Hage, V. Pandyarajan, N. B. Phillips, B. J. Smith, J. G. Menting, J. Whittaker, M. C. Lawrence, M. Meuwly and M. A. Weiss
    Extending Halogen-Based Medicinal Chemistry to Proteins: Iodo-Insulin as a Case Study
    J. Biol. Chem., 291, 27023 (2017))


  190. Year 2017

  191. O. Denis-Alpizar, R. J. Bemish and M. Meuwly
    Reactive Collisions for NO(2Π)+N(4S) at Temperatures Relevant to the Hypersonic Flight Regime
    PCCP, 19, 2392 (2017)

  192. S. Brickel and M. Meuwly
    OH-Stretching Overtone Induced Dynamics in HSO3F from Reactive Molecular Dynamics Simulations
    J. Phys. Chem. A, 121, 5079 (2017)

  193. Z.-H. Xu and M. Meuwly
    Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate
    J. Phys. Chem. A, 121, 5389 (2017)

  194. O. T. Unke and M. Meuwly
    Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces
    J. Chem. Inf. Model., 57, 1923 (2017)

  195. O. T. Unke, M. Devereux and M. Meuwly
    Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics
    J. Chem. Phys., in print (2017)

  196. P. Diamantis, O. T. Unke and M. Meuwly
    Migration of Small Ligands in Globins: Xe Diffusion in Truncated Hemoglobin N
    PLoS Comput. Biol., 13, e1005450 (2017)

  197. U. Gonzalez, M. Meuwly and S. Willitsch
    A Computational Study of the Diels-Alder Reactions Between 2,3-Dibromo-1,3-Butadiene and Maleic Anhydride
    Chem. Phys. Lett., 684, 598 (2017)

  198. K. El Hage, P. K. Gupta, R. J. Bemish and M. Meuwly
    Molecular Mechanisms Underlying Solute Retention at Heterogeneous Interfaces
    J. Phys. Chem. Lett., 8, 4600 (2017)

  199. K. Karandashev, Z.-H. Xu, M. Meuwly, J. Vanicek, and J. O. Richardson
    Kinetic Isotope Effects and How to Describe Them
    Struct. Dyn., in print (2017)

  200. K. El Hage, S. Brickel, S. Hermelin, G. Gaulier, C. Schmidt, L. Bonacina, S. C. van Keulen, S. Bhattacharyya, M. Chergui, P. Hamm, U. Roethlisberger, J.-P. Wolf, and M. Meuwly
    Implications of Short Time Scale Dynamics on Long Time Processes
    Struct. Dyn., in print (2017)

  201. S. V. Antipov, S. Bhattacharyya, K. El Hage, Z.-H. Xu, M. Meuwly, U. Roethlisberger, and J. Vanicek
    Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches
    Struct. Dyn., in print (2017)

  202. O. Denis-Alpizar, O. T. Unke, R. J. Bemish, and M. Meuwly
    Quantum and quasiclassical trajectory studies of rotational relaxation in N2+--Ar collisions
    PCCP, in print (2017)

  203. Book Chapters

  204. M. Meuwly
    Atomistic Simulations of Reactions and Transition States
    Computational Structural Biology, Ed. T. Schwede and M. Peitsch, Wiley (2008)

  205. S. Mishra and M. Meuwly
    Reactive Processes with Molecular Simulations
    Kinetics and Dynamics: from Nano- to Bio-Scale, Challenges and Advances in Computational Chemistry and Physics, Ed. P. Paneth and A. Dybala-Defratyka, Springer (2010)

  206. J. Huang, M. Devereux, F. Hofmann and M. Meuwly
    Computational Organometallic Chemistry with Force Fields
    Chapter 2 in "Computational Organometallic Chemistry", Ed: O. Wiest and Y. Wu, Springer, 19-46 (2012)

  207. J. Huang and M. Meuwly
    Force Field Treatment of Proton and Hydrogen Transfer in Molecular Systems
    Chapter 10 in "Tautomerism: Methods and Theories", Ed: L. Antonov, Wiley-VCH, (2014)

  208. T. Bereau and M. Meuwly
    Multipolar Force Fields for Atomistic Simulations
    Many-body effects and electrostatics in multi-scale computations of Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly, Springer (2015)

  209. A. K. Das and M. Meuwly
    Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins
    Methods in Enzymology, Ed. G. A. Voth, (2016)