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85 Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II
Daniele Narzi, Emanuele Coccia, Marco Manzoli, Leonardo Guidoni, published online on Biophysical Chemistry (2017)
84 A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem II
Daniele Narzi, Giuseppe Mattioli, Daniele Bovi and Leonardo Guidoni, published online on Chemistry - A European Journal (2017)

One-Electron Oxidation of Methionine-Containing Dipeptides of 2
Reverse Sequence: Sulfur versus Sulfoxide Characterized by IRMPD:
Spectroscopy and Static and Dynamics DFT Simulations

Barbara Gregori, Leonardo Guidoni, Maria Elisa Crestoni, Pedro de
Oliveira, Chantal Houee-Levin,  and Debora Scuderi, J. Phys Chem B (2017)

82. Contact Ion Pairs on a Protonated Azamacrocycle: the Role of the Anion Basicity
C. Fraschetti, A. Filippi, M. E. Crestoni, E. Marcantoni, M. Glucini, L. Guarcini, M. Montagna, L. Guidoni, Maurizio Speranza, published online on J. Am. Soc. Mass S (2016)
81. The role of Electron Correlation along the Water Splitting Reaction
S. Chu, E. Coccia, M. Barborini, and L. Guidoni, published online on JCTC (2016)
Geometries of Low Spin states of Multi-Centre Transition Metal Complexes through Extended Broken Symmetry Variational Monte Carlo
M. Barborini, and L. Guidoni, J. Chem. Phys. 145, 124107 (2016)
79. QM/MM dynamics of a Peridinin model in triplet state in three prototypical solvents.
D. Bovi, A. Mezzetti, L. Guidoni, Vibrational Spectroscopy 87, 182–192 (2016)
78. Vibrational fingerprints of the Mn4CaO5 cluster in Photosystem II by mixed quantum-classical dynamics.
D. Bovi, M. Capone, D. Narzi, and L. Guidoni, BBA-Bioenergetics 1857, 1669–1677 (2016)
77. Structural and Vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): interpretation of experimental results with ab initio molecular dynamics.
M. Campetella, D. Bovi, R. Caminiti, L. Guidoni, L. Bencivenni, and L. Gontrani, J. Chem. Phys. 145, 024507 (2016)
76. Mechanism of Water Delivery to the Active Site of Photosystem II along the S2 to S3 Transition.
M. Capone, D. Narzi, D. Bovi, L. GuidoniJ. Phys. Chem. Lett. 7, 592-596 (2016)
75. Dynamics of the special pair of chlorophylls of Photosystem II.
D. Narzi, D. Bovi, P. De Gaetano, L. Guidoni,  JACS 138, 257-264 (2016)
74. The Hidden Hydration Structure of Halide Ions: an Insight into the Importance of Lone Pairs.
F. Sessa, P. D'Angelo, L. Guidoni, V. Migliorati, J. Phys. Chem B, 119, 15729-37 (2015)
73. Reorganization of Substrate Waters between the Closed and Open Cubane Conformers during the S2 to S3 Transition in the Oxygen Evolving Complex.
M. Capone, D. Bovi, D. Narzi, L. Guidoni, Biochemistry 54, 6439-6442 (2015) 
72. Characterization of the Sr2+- and Cd2+-Substituted Oxygen-Evolving Complex of Photosystem II by Quantum Mechanics/Molecular Mechanics Calculations.
F. Pitari, D. Bovi, D. Narzi, L. Guidoni, Biochemistry 54, 5959–5968 (2015)
71. Ground State Geometries of Polyacetylene Chains from Many-Particle Quantum Mechanics.
M. BarboriniL. Guidoni, JCT11, 4109-4118 (2015) 
70. Atomistic Texture of Amorphous Manganese Oxides for Electrochemical Water Splitting Revealed by Ab Initio Calculations Combined with X-ray Spectroscopy
G. Mattioli, I. Zaharieva, H. Dau, L. Guidoni, J. Am. Chem. Soc., 137, 10254-10267 (2015) 
69. Protonated hexaazamacrocycles as selective K+ receptor.
C. Fraschetti, A. Filippi,  M.E. Crestoni, E. Marcantoni, M. Glucini, L. Guarcini, M. Montagna, L. Guidoni, M. Speranza, J. Am. Soc. Mass. Spectrom., 26, 1186-1190 (2015)  
68. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo.
A. Zen, Y. Luo, G. Mazzola, L. Guidoni, S. Sorella, J. Chem. Phys. 142, 144111 (2015),
67. π-Conjugation in trans-1,3-Butadiene: Static and Dynamical Electronic Correlations Described through Quantum Monte Carlo 
M. Barborini, L. Guidoni, JCTC, 11, 508-517 (2015)
66. Quantum Monte Carlo Treatment of the Charge Transfer and Diradical Electronic Character in a Retinal Chromophore Minimal Model.  
A. Zen, E. Coccia, S. Gozem, M. Olivucci, L. Guidoni, JCTC, 11, 992-1005 (2015)  
65. Competing factors on the frequency separation between the OH stretching modes in water.
C. Zhang, L. Guidoni, T. D. Kühne, J. Mol. Liquids. 205, 42-45 (2015)
64. Vibrational Signatures of S-Nitroso Glutathione as Gaseous, Protonated Species.
B. Gregori, L. Guidoni, B. Chiavarino, D. Scuderi, E. Nicol, G. Frison, S. Fornarini, M. Crestoni, J. Phys. Chem. B, 118, 12371-12382 (2014)
63. Spectroscopic evidence for a gas-phase librating G-quartet/Na+ complex.
C. Fraschetti, M. Montagna, L. Guarcini, L. Guidoni, A. Filippi, Chem. Commun., 50, 14767-14770 (2014)
62. The origin of the chemoselectivity in the Cp2TiCl2/MAO catalyst for the polymerization of 1,3-butadiene explored by Density Functional Theory.  
M. Montagna, G. Ricci, G. Leone, F. Masi, L. Guidoni, Materials Today Communications, 1, 42-47 (2014) 
doi: 10.1016/j.mtcomm.2014.09.004 
61. Asymmetric environmental effects on the structure and vibrations of cis-Pt(NH3)_2Cl_2 in condensed phases  
C. Zhang, E. Baribefe Naziga, L. Guidoni, J. Phys. Chem. B, 118, 11487-11495 (2014). doi: 
60. Properties of Reactive Oxygen Species by Quantum Monte Carlo  
A. Zen, B. Trout, L. Guidoni, J. Chem. Phys., 141, 014305 (2014). doi:
59. Pathway for Mn cluster oxidation by Tyrosine-Z in the S2 state of Photosystem II  
D. Narzi, D. Bovi, L. Guidoni, Proc. Natl. Acad.Sci. USA, 111, 8723-8728 (2014). doi: 10.1073/pnas.1401719111
58. Fermi Resonance as a Tool for Probing Peridinin Environment  
M.M. Mendes Pinto, D. Bovi, M. Basire, L. Guidoni, R. Vuilleumier, B. Robert, R. Spezia, A. Mezzetti, E. Kish, J. Phys Chem. B, 118, 5873-5881 (2014). doi: 
57. Ground state structures and electronic excitations of biological chromophores at Quantum Monte Carlo /Many Body Green's Function Theory level  
D. Varsano, E. Coccia, L. Guidoni, Excited States Special Issue of Computational and Theoretical Chemistry (2014). 
56. Static and dynamical correlation in diradical molecules by Quantum Monte Carlo using the Jastrow Antisymmetrized Geminal Power ansatz  
A. Zen, E. Coccia, Y. Luo, S. Sorella, L. Guidoni, J. Chem. Theory Comput., 10, 1048-1061 (2014). (PDF)
55. Kohn-Sham orbitals and potentials from Quantum Monte Carlo molecular Densities  
D. Varsano, M. Barborini, L. Guidoni, J. Chem. Phys., 140, 054102 (2014).
54. Ab initio geometry and bright excitation of carotenoids: Quantum Monte Carlo and Many Body Green’s Function Theory calculations on peridinin  
E. Coccia, D. Varsano, L. Guidoni, J. Chem. Theory Comput., 10, 501-506 (2014). 
53. Magnetic interactions in the catalyst used by nature to split water: a DFT+U multiscale study on the Mn4CaO5 core in Photosystem II  
D. Bovi, D. Narzi and L. Guidoni, New Journal of Physics, 16, 015020 (2013)
52. Reaction Pathways for Oxygen Evolution Promoted by Cobalt Catalyst  
G. Mattioli, P. Giannozzi, A. Amore Bonapasta, L. Guidoni, J. Am. Chem. Soc., 135, 15353–15363 (2013) 
51. Vibrational Signature of Water Molecules in Asymmetric Hydrogen Bonding Environments  
C. Zhang, R. Khaliullin, D. Bovi, L. Guidoni, T. Kuhne, J. Phys. Chem. Lett., 4, 3245–3250. (2013) 
50. Molecular properties by Quantum Monte Carlo: an investigation on the role of the wave function ansatz and the basis set in the water molecule  
A. Zen, Y. Luo, S. Sorella, and L. Guidoni, J. Chem. Theory Comput.9, 4332–4350. (2013) 
49. The S2 state of the Oxygen-Evolving Complex of Photosystem II explored by QM/MM dynamics: spin surfaces and metastable states suggest a reaction path towards the S3 state  
D. Bovi, D. Narzi and L. Guidoni, Angewandte Chemie (VIP article) 125, 11960-11965. (2013) 
48. The Impact of Nitric Oxide Toxicity on the Evolution of the Glutathione Transferase Superfamily. A proposal for an evolutionary driving force  
A. Bocedi, R. Fabrini, A. Farrotti, L. Stella, A. J. Ketterman, J. Z. Pedersen, N. Allocati, P. C. K. Lau, S. Grosse, L. D. Eltis, A. Ruzzini, T. E. Edwards, L. Morici, E. Del Grosso, L. Guidoni, D. Bovi, M. Lo Bello, G. Federici, M. W. Parker, P. G. Board, and G. Ricci, J. Biol. Chem., 288, 24936-24947 (2013) (PDF)
47. Protonated Pyrimidine Nucleosides probed by IRMPD  Spectroscopy  
A.    Filippi, C. Fraschetti, F. Rondino, S. Piccirillo, V. Steinmetz, L. Guidoni, and M. SperanzaInternational Journal of Mass Spectrometry, 354–355, 54– 61 (2013) (PDF)
46. Theoretical optical spectroscopy of complex systems  
A. Mosca Conte, C. Violante, M. Missori, F. Bechstedt, L. Teodonio, E. Ippoliti, P. Carloni, L. Guidoni, O. PulciJ. Electron Spectrosc. Relat. Phenom., 189S, 46– 55 (2013) (PDF)
45. Tautomerism in liquid 1,2,3-triazole: a combined Energy-Dispersive X-Ray Diffraction, Molecular Dynamics and FTIR study  
M. Bellagamba, L. Bencivenni, L. Gontrani, L. Guidoni, C. Sadun, Struct. Chem., 24, 933–943 (2013).
44. Protein field effect on the dark state of 11-cis Retinal in Rhodopsin by Quantum Monte Carlo / Molecular Mechanics  
E. Coccia, D. Varsano, L. Guidoni, J. Chem. Theory Comput., 9, 8-12 (2013). (PDF)
43. Reaction pathways by Quantum Monte Carlo: insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene  
M. Barborini, L. Guidoni, J. Chem. Phys.137, 224309 (2012). (PDF)
42. Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation  
L. Tanzi, F. Ramondo, L. Guidoni, J. Phys. Chem. A, 116,10160–10171 (2012). (PDF)

41. Optimized structure and vibrational properties by error affected potential energy surfaces 
A. Zen, D. Zhelyazov, L. Guidoni, J. Chem. Theory Comput., 8, 4204–4215 (2012).  (PDF)
40. Structural and Spectroscopic Properties of Water Around Small Hydrophobic Solutes 
M. Montagna, F. Sterpone, L. Guidoni, J. Phys. Chem. B, 116, 11695-11700 (2012). (PDF)
39. Magnetic coupling constants and vibrational frequencies by Extended Broken Symmetry approach with hybrid functionals 
D. Bovi, L. Guidoni, J. Chem. Phys., 137, 114107 (2012). (PDF)
38. Quantum monte carlo study of the retinal minimal model C5H6NH2+ 
E. Coccia, L. Guidoni, J. Comput. Chem., 33, 2332-2339 (2012).  (PDF)
37. Molecular electrical properties from Quantum Monte Carlo calculations: application to ethyne 
E. Coccia, O. Chernomor, M. Barborini, S. Sorella, L. Guidoni, J. Chem. Theory Comput., 8, 1952-1962 (2012). (PDF)
36. Structural optimization by Quantum Monte Carlo: investigating the low-lying excited states of Ethylene 
M. Barborini, S. Sorella, L. Guidoni, J. Chem. Theory Comput., 8, 1260-1269 (2012). (PDF)  
35. Bathochormic shift in Green Fluorescent Protein: A puzzle for QM/MM approaches 
C. Filippi, F. Buda, L. Guidoni, and A. Sinicropi, J. Chem. Theory Comput., 8,112-124 (2012). (PDF)  
34. Environmental Effects on Vibrational Properties of Carotenoids:
Experiments and Calculations on Peridinin

D. Bovi, A. Mezzetti, R. Vuilleumier, M.-P. Gaigeot, B. Chazallon, R. Spezia and L. Guidoni, Phys. Chem. Chem. Phys., 13, 20954-20964 (2011). (PDF)
Many-Body study of the photoisomerization of the protonated Schiff Base Minimal Mode
A. Mosca Conte, L. Guidoni, R. Del Sole and O. Pulci, Chemical Physics Letters, 515, 290-295 (2011). (PDF)
Protonation States in a Cobalt-Oxide Catalyst for Water Oxidation: Fine Comparison of Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy Results
G. Mattioli, M. Risch, A. Amore Bonapasta, H. Dau and L. Guidoni, Phys. Chem. Chem. Phys., 15437, 13 (2011). (PDF)
Hydration structure of the quaternary ammonium cations
W. I. Babiaczyk, S. Bonella, L. Guidoni and G. Ciccotti, Journal of Phys. Chem. B 15018, 114 (2010). (PDF)
On the hydration properties of the bromide aqua ion: the interplay of first principle and classical Molecular Dynamics, and X-ray absorption spectroscopy
P. D'Angelo, V. Migliorati and L. Guidoni, Journal of Inorganic Chemistry 4224, 49 (2010). (PDF)


Coordination numbers of K+ and Na+ ions inside the selectivity filter of the KcsA potassium channel: Insights from first principles molecular dynamics
D. Bucher, L. Guidoni, P. Carloni and U. Röthlisberger,  Biophysical Journal 98, L47 (2010). (PDF)


Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potential
D. Bucher, L. Guidoni, P. Maurer and U. Röthlisberger, J. Chem. Theory Comput. 5, 2173 (2009). (PDF)


Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study
E. M. Gonzalez, L. Guidoni and C. Molteni, Phys. Chem. Chem. Phys. 11, 4556 (2009). (PDF)


Overcoming the Inadequacy of X-ray Powder Diffraction in Reliable Hydrogen Location with the Aid of First Principles Calculations: Crystal Structure Determination of Orotaldehyde Monohydrate
L. Guidoni, L. Gontrani, L. Bencivenni, C. Sadun and P. Ballirano, J. Phys. Chem. A 113, 353 (2009). (PDF)


Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach
F. Sterpone, L. Spanu, L. Ferraro, S. Sorella and L. Guidoni, J. Chem. Theory Comput. 4, 1428 (2008). (PDF)


Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study
M. C. Colombo, J. VandeVondele, S. Van Doorslaer, A. Laio, L. Guidoni and U. Röthlisberger, Proteins 70, 1084 (2008). (PDF)


The protonation state of the Glu-71/Asp-80 residues in the KcsA Potassium Channel. A first-principles QM/MM Molecular Dynamics Study
D. Bucher, L. Guidoni  and U. Röthlisberger, Biophys. J. 93, 2315 (2007). (PDF)


Protonation of the chromophore in the photoactive yellow protein
E. J. M. Leenders, L. Guidoni , U. Röthlisberger, J. Vreede, P. G. Bolhuis and E. J. Meijer, J. Phys. Chem B 111, 3765 (2007). (PDF)
21. Polarization effects and charge transfer in the Kcsa Potassium Channel 
D. Bucher, L. Guidoni, S. Raugei, M. Dal Peraro, U. Röthlisberger, P. Carloni and M. Klein, Biophys. Chem. 124, 292 (2006). (PDF)
Quantum Mechanical/Molecular Mechanical (QM/MM) Car-Parrinello Simulations in Excited States
M.-E. Moret, E. Tapavizca, L. Guidoni, U. Röhrig, M. Sulpizi, I. Taverneli
and U. Röthlisberger, Chimia 59, 493 (2005). (PDF)
Experimental and theoretical study of intramolecular exchange in Ir2Rh2(CO)12 and Ir4(CO)11(µ-SO2)
Z. Beni, L. Guidoni, G. Laurenczy, U. Röthlisberger and R. Roulet, Dalton Trans. 310 (2005). (PDF)
Scanning Reactive Pathways with Orbital Biased Molecular Dynamics
L. Guidoni and U. Röthlisberger,  J. Chem. Theory Comput. 1, 554560 (2005). (PDF)
Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore
U. Röhrig, L. Guidoni and U. Röthlisberger, ChemPhysChem 6, 1836 (2005).(PDF) 
16. QM/MM Simulation of the first step of vision
U. Röhrig, S. Grimm, I. Frank, L. Guidoni, A. Laio and U.Röthlisberger. In High Performance Computing in Science and Engineering, edited by S. Wagner, W. Hanke, A. Bode, and F. Durst, Springer-Verlag, Berlin (2004). (PDF)
15. QM/MM study of rhodopsin
U. Röhrig, C. Nonnenberg, I. Frank, L. Guidoni and U.Röthlisberger. In High Performance Computing in Science and Engineering, edited by S. Wagner, W. Hanke, A. Bode, and F. Durst, Springer-Verlag, Berlin (2003). (PDF)
A Molecular Spring for Vision
U. F. Röhrig, L. Guidoni, A. Laio, I. Frank and U. Röthlisberger, J. Am. Chem. Soc. 126(47), 15328 (2004). (PDF)
Green Oxidation Catalysts: Computational Design of High-Efficiency Models of Galactose Oxidase
L. Guidoni, K. Spiegel, M. Zumstein and U. Röthlisberger, Angew. Chem. Int. Ed. 43, 3286 (2004). (PDF)
Multiple Steering Molecular Dynamics Applied to Water at Alkali Ions
M. Cascella , L. Guidoni, A. Maritan, U. Röthlisberger and P. Carloni, J. Phys. Chem. B 106, 13027 (2002). (PDF)
Hybrid Car-Parrinello/Molecular Mechanics Modelling of Transition Metal Complexes: Structure, Dynamics and Reactivity
L. Guidoni, P. Maurer, S. Piana and U. Röthlisberger, Quant. Struct.-Act. Relat. 21, 173 (2002). (PDF)
Early Steps of the Intramolecular Signaling Pathway in Rhodopsin Explored by Molecular Dynamics Simulations
U. Röhrig, L. Guidoni and U.Röthlisberger, Biochemistry  41, 10799 (2002). (PDF
Potassium permeation through the KcsA channel: a density functional study
L. Guidoni and P. Carloni, Biochimica et Biophysica Acta - Biomembranes 1563, 1 (2002). (PDF)
Hybrid QM/MM Car-Parrinello Simulations of Catalytic and Enzymatic Reactions
M. C. Colombo, L. Guidoni, A. Laio, A. Magistrato, P. Maurer, S. Piana, U. Röhrig, K. Spiegel, M. Sulpizi, J. VandeVondele, M. Zumstein and U. Röthlisberger, Chimia 56, 13 (2002). (PDF)
Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: implications for ion permeation
L. Guidoni and P. Carloni, Journal of Receptors and Signal Transduction Research 22, 315 (2002). (PDF)
Water and potassium dynamics inside the KcsA K + channe
L. Guidoni, V. Torre and P. Carloni, FEBS Letters 477, 37 (2000). (PDF)
Potassium and sodium binding to the outer mouth of the K+ channel
L. Guidoni, V. Torre and P. Carloni, Biochemistry 38, 8599 (1999). (PDF)
Spin liquid ground state in a two dimensional non-frustrated spin model
G. Santoro, S. Sorella, L. Guidoni, A. Parola and E. Tosatti. Phys. Rev. Lett. 83, 3065 (1999). (PDF)
Spin gap in low-dimensional Mott insulators with orbital degeneracy

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