Marco Pagliai - Publication list
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- Marco Pagliai, Simone Raugei, Gianni Cardini, Vincenzo Schettino
Ab-initio molecular dynamics study of the SN2 reaction Cl- + ClCH2CN
Phys. Chem. Chem. Phys., 3 (2001) 2559-2566
DOI: 10.1039/B101560P
- Vincenzo Schettino, Marco Pagliai, Lucia Ciabini, Gianni
Cardini
The Vibrational Spectrum of Fullerene C60
J. Phys. Chem. A, 105 (2001) 11192-11196
DOI: 10.1021/jp012874t
- Marco Pagliai, Simone Raugei, Gianni Cardini, Vincenzo Schettino
Car-Parrinello molecular dynamics of the SN2 reaction Cl- + Cl2CH2
Phys Chem. Chem. Phys., 3 (2001) 4870-4873
DOI: 10.1039/B105617B
- Vincenzo Schettino, Marco Pagliai, Gianni Cardini
The Infrared and Raman Spectra of Fullerene C70. DFT Calculations and Correlation with C60
J. Phys. Chem. A, 106 (2002) 1815-1823
DOI: 10.1021/jp012680d
- Marco Pagliai, Simone Raugei, Gianni Cardini, Vincenzo Schettino
Thermal effects on the Cl- + ClCH2CN reaction by Car-Parrinello molecular dynamics
J. Chem. Phys., 117 (2002) 2199-2204
DOI: 10.1063/1.1489904
- Marco Pagliai, Simone Raugei, Gianni Cardini, Vincenzo Schettino
Car-Parrinello molecular dynamics on the SN2 reaction Cl- + CH3Br in water
J. Mol. Struct. (Theochem), 630 (2003) 141-149
DOI: 10.1016/S0166-1280(03)00162-3
- Marco Pagliai, Gianni Cardini, Roberto Righini, Vincenzo
Schettino
Hydrogen bond dynamics in liquid methanol
J. Chem. Phys., 119 (2003) 6655-6662
DOI: 10.1063/1.1605093
- Marco Pagliai, Simone Raugei, Gianni Cardini, Vincenzo Schettino
Intramolecular solvation effects in the SN2 reaction Cl- + Cl(CH2)nCN
J. Chem. Phys., 119 (2003) 9063-9072
DOI: 10.1063/1.1613940
- Riccardo Chelli, Marco Pagliai, Piero Procacci, Gianni Cardini, Vincenzo Schettino
Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: Implications for charge transfer
J. Chem. Phys., 122 (2005) 074504
DOI: 10.1063/1.1851504
- Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Solvation Dynamics of Li+ and Cl- Ions in Liquid Methanol
J. Phys. Chem. B, 109 (2005) 7475-7481
DOI: 10.1021/jp050428q
- Marco Pagliai, Luca Bellucci, Maurizio Muniz-Miranda, Gianni Cardini, Vincenzo Schettino
A combined Raman, DFT and MD study of the solvation dynamics and the adsorption process of pyridine in silver hydrosols
Phys. Chem. Chem. Phys., 8 (2006) 171-178
DOI: 10.1039/B509976E
- Marco Pagliai, Marcella Iannuzzi, Gianni Cardini, Michele Parrinello, Vincenzo Schettino
Lithium Hydroxide Phase Transition under High Pressure: An Ab Initio Molecular Dynamics Study
ChemPhysChem, 7 (2006) 141-147
DOI: 10.1002/cphc.200500272
- Elisa Di Pietro, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Solid-State Phase Transition Induced by Pressure in LiOH·H2O
J. Phys. Chem. B, 110 (2006) 13539-13546
DOI: 10.1021/jp061620a
- Cristian Faralli, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Structure and Dynamics of Br- Ion in Liquid Methanol
J. Phys. Chem. B., 110 (2006) 14923-14928
DOI: 10.1021/jp061230o
- Gianni Cardini, Maurizio Muniz-Miranda, Marco Pagliai, Vincenzo Schettino
A density functional study of the SERS spectra of pyridine adsorbed on silver clusters
Theor. Chem. Acc., 117 (2007) 451-458
DOI: 10.1007/s00214-006-0176-3
- Vincenzo Schettino, Riccardo Chelli, Simone Marsili, Alessandro Barducci, Cristian Faralli, Marco Pagliai, Piero Procacci, Gianni Cardini
Problems in molecular dynamics of condensed phases
Theor. Chem. Acc., 117 (2007) 1105-1120
DOI: 10.1007/s00214-006-0223-0
- Maurizio Muniz-Miranda, Gianni Cardini, Marco Pagliai, Vincenzo Schettino
DFT investigation on the SERS band at ~ 1025 cm-1 of pyridine adsorbed on silver
Chem. Phys. Lett., 436 (2007) 179-183
DOI: 10.1016/j.cplett.2007.01.020
- Cristian Faralli, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
The solvation dynamics of Na+ and K+ ions in liquid methanol
Theor. Chem. Acc., 118 (2007) 417-423
DOI: 10.1007/s00214-007-0286-6
- Vincenzo Schettino, Marco Pagliai, Gianni Cardini
Molecular dynamics of chemical reactions and phase transitions
at high pressure
Chimica Oggi / Chem. Today, 25 (2007) 42-44
- Marco Pagliai, Carlo Cavazzoni, Gianni Cardini, Giovanni Erbacci, Michele Parrinello, Vincenzo Schettino
Calcolo di Spettri Vibrazionali di Cristalli da Principi Primi
notizie dal CINECA, 58 (2007) 7-9
DOI: 10.1388/notizie-58-03
- Cristian Faralli, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Ab Initio Molecular Dynamics Study of Mg2+ and Ca2+ Ions in Liquid Methanol
J. Chem. Theory Comput., 4 (2008) 156-163
DOI: 10.1021/ct700209v
- Maurizio Muniz-Miranda, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Role of Surface Metal Clusters in SERS Spectra of Ligands Adsorbed on Ag Colloidal Nanoparticles
J. Phys. Chem. C, 112 (2008) 762-767
DOI: 10.1021/jp073914h
- Maurizio Muniz-Miranda, Marco Pagliai, Gianni Cardini, Luigi Messori, Bruno Bruni, Angela Casini, Massimo Di Vaira, Vincenzo Schettino
A multi-technique approach to predicting the molecular structure of cuprizone in the gas phase and in the crystalline state
CrystEngComm, 10 (2008) 416-422
DOI: 10.1039/B715131D
- Martina Mugnai, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Mechanism of the Ethylene Polymerization at Very High Pressure
J. Chem. Theory Comput., 4 (2008) 646-651
DOI: 10.1021/ct700275v
- Marco Pagliai, Carlo Cavazzoni, Gianni Cardini, Giovanni Erbacci, Michele Parrinello, Vincenzo Schettino
Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations
J. Chem. Phys., 128 (2008) 224514
DOI: 10.1063/1.2936988
- V. Schettino, R. Bini, G. Cardini, M. Ceppatelli, M. Citroni, M. Pagliai
Solid-state transitions and chemical reactions at high pressure
Nuovo Cimento B, 123 (2008) 1399-1414
DOI: 10.1393/ncb/i2008-10716-2
- Vincenzo Schettino, Roberto Bini, Gianni Cardini, Matteo Ceppatelli, Margherita Citroni, Marco Pagliai
Spectroscopy and monitoring of high pressure phenomena
J. Mol. Struct., 924-926 (2009) 2-8
DOI: 10.1016/j.molstruc.2008.10.067
- Marco Candelaresi, Marco Pagliai, Manuela Lima, Roberto Righini
Chemical Equilibrium Probed by Two-Dimensional IR Spectroscopy: Hydrogen Bond Dynamics of Methyl Acetate in Water
J. Phys. Chem. A, 113 (2009) 12783-12790
DOI: 10.1021/jp906072w
- Marco Pagliai, Maurizio Muniz-Miranda, Gianni Cardini, Vincenzo Schettino
Solvation Dynamics and Adsorption on Ag Hydrosols of Oxazole: A Raman and Computational Study
J. Phys. Chem. A, 113 (2009) 15198-15205
DOI: 10.1021/jp905530x
- Maurizio Muniz-Miranda, Cristina Gellini, Pier Remigio Salvi, Marco Pagliai
Surface-enhanced Raman micro-spectroscopy of DNA/RNA bases adsorbed on pyroxene rocks as a test of in situ search for life traces on Mars
J. Raman Spectrosc., 41 (2010) 12-15
DOI: 10.1002/jrs.2398
- Margherita Citroni, Roberto Bini, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Nitromethane Decomposition under High Static Pressure
J. Phys. Chem. B, 114 (2010) 9420-9428
DOI: 10.1021/jp1035508
- Maurizio Muniz-Miranda, Cristina Gellini, Marco Pagliai, Massimo Innocenti, Pier Remigio Salvi, Vincenzo Schettino
SERS and Computational Studies on MicroRNA Chains Adsorbed on Silver Surfaces
J. Phys. Chem. C., 114 (2010) 13730-13735
DOI: 10.1021/jp103304r
- Marco Pagliai, Francesco Muniz-Miranda, Gianni Cardini, Roberto Righini, Vincenzo Schettino
Hydrogen Bond Dynamics of Methyl Acetate in Methanol
J. Phys. Chem. Lett., 1 (2010) 2951-2955
DOI: 10.1021/jz1010994
- Maurizio Muniz-Miranda, Marco Pagliai, Francesco Muniz-Miranda, Vincenzo Schettino
Raman and computational study of solvation and chemisorption of thiazole in silver hydrosol
Chem. Commun., 47 (2011) 3138-3140
DOI: 10.1039/C0CC05217E
- Francesco Muniz-Miranda, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Wavelet Transform for Spectroscopic Analysis: Application to Diols in Water
J. Chem. Theory Comput., 7 (2011) 1109-1118
DOI: 10.1021/ct100625e
- Marco Pagliai, Maurizio Muniz-Miranda, Gianni Cardini, Vincenzo Schettino
Raman and infrared spectra of minerals from ab initio molecular dynamics simulations: The spodumene crystal
J. Mol. Struct., 993 (2011) 151-154
DOI: 10.1016/j.molstruc.2010.12.064
- Marco Pagliai, Francesco Muniz-Miranda, Gianni Cardini, Roberto Righini, Vincenzo Schettino
Spectroscopic properties with a combined approach of ab initio molecular dynamics and wavelet analysis
J. Mol. Struct., 993 (2011) 438-442
DOI: 10.1016/j.molstruc.2011.02.007
- Marco Pagliai, Paola Bonazzi, Luca Bindi, Maurizio Muniz-Miranda, Gianni Cardini
Structural and Vibrational Properties of Arsenic Sulfides: Alacranite (As8S9)
J. Phys. Chem. A, 115 (2011) 4558-4562
DOI: 10.1021/jp201097k
- S. Caporali, M. Pagliai, G. Pratesi, V. Schettino
Surface-Enhanced Raman Scattering Investigation of Nucleobases Adsorbed on Samples of Martian Analogue Material
Spectrosc. Lett., 44 (2011) 580-584
DOI: 10.1080/00387010.2011.611572
- Maurizio Muniz-Miranda, Cristina Gellini, Pier Remigio Salvi, Vincenzo Schettino, Marco Pagliai, Massimo Innocenti
Nanostructured Ag Platforms as Biosensors of Nucleobase Chains
J. Nanosci. Nanotechnol., 11 (2011) 8763-8767
DOI: 10.1166/jnn.2011.3448
- Maurizio Muniz-Miranda, Cristina Gellini, Pier Remigio Salvi, Massimo Innocenti, Marco Pagliai, Vincenzo Schettino
Fabrication of nanostructured silver substrates for surface-enhanced Raman spectroscopy
J. Nanopart. Res., 13 (2011) 5863-5871
DOI: 10.1007/s11051-011-0493-x
- Marco Pagliai, Stefano Caporali, Maurizio Muniz-Miranda, Giovanni Pratesi, Vincenzo Schettino
SERS, XPS, and DFT Study of Adenine Adsorption on Silver and Gold Surfaces
J. Phys. Chem. Lett., 3 (2012) 242-245
DOI: 10.1021/jz201526v
- Francesco Muniz-Miranda, Marco Pagliai, Gianni Cardini, Roberto Righini
Bifurcated Hydrogen Bond in Lithium Nitrate Trihydrate Probed by ab Initio Molecular Dynamics
J. Phys. Chem. A, 116 (2012) 2147-2153
DOI: 10.1021/jp2120115
- Marco Pagliai, Francesco Muniz-Miranda, Vincenzo Schettino, Maurizio Muniz-Miranda
Competitive Solvation and Chemisorption in Silver Colloidal Suspensions
Progr. Colloid. Polym. Sci., 139 (2012) 39-44
DOI: 10.1007/978-3-642-28974-3_8
- Stefano Caporali, Vanni Moggi-Cecchi, Maurizio Muniz-Miranda, Marco Pagliai, Giovanni Pratesi, Vincenzo Schettino
SERS investigation of possible extraterrestrial life traces: Experimental adsorption of adenine on a Martian meteorite
Meteorit. Planet. Sci., 47 (2012) 853-860
DOI: 10.1111/j.1945-5100.2012.01361.x
- Francesco Muniz-Miranda, Marco Pagliai, Gianni Cardini, Roberto Righini
Hydrogen bond effects in the vibrational spectra of 1,3-propanediol in acetonitrile: Ab initio and experimental study
J. Chem. Phys., 137 (2012) 244501
DOI: 10.1063/1.4770499
- Maurizio Muniz-Miranda, Marco Pagliai
Positively Charged Active Sites for the Adsorption of Five-Membered Heterocycles on Silver Colloids
J. Phys. Chem. C, 117 (2013) 2328-2333
DOI: 10.1021/jp309600p
- Samuele Fanetti, Andrea Lapini, Marco Pagliai, Margherita Citroni, Mariangela Di
Donato, Sandro Scandolo, Roberto Righini, Roberto Bini
Structure and Dynamics of Low-Density and High-Density Liquid Water at High Pressure
J. Phys. Chem. Lett., 5 (2014) 235-240
DOI: 10.1021/jz402302z
- Marco Pagliai, Gianni Cardini, Roberto Cammi
Vibrational Frequencies of Fullerenes C60 and C70 under Pressure Studied with a Quantum Chemical Model Including Spatial Confinement Effects
J. Phys. Chem. A, 118 (2014) 5098-5111
DOI: 10.1021/jp504173k
- Samuele Fanetti, Marco Pagliai, Margherita Citroni, Andrea Lapini,
Sandro Scandolo, Roberto Righini, Roberto Bini
Connecting the Water Phase Diagram to the Metastable Domain: High-Pressure Studies in the Supercooled Regime
J. Phys. Chem. Lett., 5 (2014) 3804-3809
DOI: 10.1021/jz501971h
- Matteo Ceppatelli, Marco Pagliai, Roberto Bini, Hans J. Jodl
High-Pressure Photoinduced Synthesis of Polynitrogen in δ and ε Nitrogen Crystals
Substitutionally Doped with CO
J. Phys. Chem. C, 119 (2015) 130-140
DOI: 10.1021/jp510228t
- Pauline Delcroix, Marco Pagliai, Gianni Cardini, Didier Bégué, Benjamin Hanoune
Structural and Spectroscopic Properties of Methanediol in Aqueous Solutions from Quantum Chemistry Calculations and Ab Initio Molecular Dynamics Simulations
J. Phys. Chem. A, 119 (2015) 290-298
DOI: 10.1021/jp510759r
- Pauline Delcroix, Marco Pagliai, Gianni Cardini, Didier Bégué, Benjamin Hanoune
Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab Initio Molecular Dynamics Simulations and Quantum Chemistry Calculations
J. Phys. Chem. A, 119 (2015) 9785-9793
DOI: 10.1021/acs.jpca.5b06293
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Margherita Citroni, Samuele Fanetti, Carla Bazzicalupi, Kamil
Dziubek, Marco Pagliai, Marcelo Medre Nobrega, Mohamed Mezouar,
Roberto Bini
Structural and Electronic Competing Mechanisms in the
Formation of Amorphous Carbon Nitride by Compressing s-triazine
J. Phys. Chem. C, 119 (2015) 28560-28569
DOI: 10.1021/acs.jpcc.5b09538
- Marco Pagliai, Roberto Cammi, Gianni Cardini, Vincenzo Schettino
XP-PCM Calculations of High Pressure Structural and Vibrational Properties of P4S3
J. Phys. Chem. A, 120 (2016) 5136-5144
DOI: 10.1021/acs.jpca.6b00590
- Andrea Salvadori, Gianluca Del Frate, Marco Pagliai, Giordano Mancini, Vincenzo Barone
Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data
Int. J. Quantum Chem., 116 (2016) 1731-1746
DOI: 10.1002/qua.25207
www.chemistryviews.org
Scuola Normale Superiore
Cover Image
- Marina Macchiagodena, Giordano Mancini, Marco Pagliai, Vincenzo Barone
Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies
Phys. Chem. Chem. Phys., 18 (2016), 25342-25354
DOI: 10.1039/C6CP04666E
- Andrea Lapini, Marco Pagliai, Samuele Fanetti, Margherita Citroni, Sandro Scandolo, Roberto Bini, Roberto Righini
Pressure Dependence of Hydrogen-Bond Dynamics in Liquid Water Probed by Ultrafast Infrared Spectroscopy
J. Phys. Chem. Lett., 7 (2016) 3579-3584
DOI: 10.1021/acs.jpclett.6b01375
- Marco Pagliai, Giordano Mancini, Ivan Carnimeo, Nicola De Mitri, Vincenzo Barone
Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach
J. Comput. Chem., 38 (2017) 319-335
DOI: 10.1002/jcc.24683
- Marina Macchiagodena, Giordano Mancini, Marco Pagliai, Gianluca Del Frate, Vincenzo Barone
Fine-tuning of atomic point charges: Classical simulations of pyridine
in different environments
Chem. Phys. Lett., 677 (2017) 120-126
DOI: 10.1016/j.cplett.2017.04.004
- Laura Moroni, Marco Pagliai, Riccardo Chelli, Giangaetano Pietraperzia, Pier Remigio Salvi, Cristina Gellini
Photochemical Reactivity of 1,6-Methano[10]annulene
J. Phys. Chem. A, 121 (2017) 4412-4421
DOI: 10.1021/acs.jpca.7b01635
- Chiara Caratelli, Roberto Cammi, Riccardo Chelli, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Insights on the Realgar Crystal Under Pressure from XP-PCM and Periodic Model Calculations
J. Phys. Chem. A, 121 (2017) 8825-8834
DOI:10.1021/acs.jpca.7b08868
- Edoardo Giovannelli, Piero Procacci, Gianni Cardini, Marco Pagliai, Victor Volkov, Riccardo Chelli
Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical
Framework
J. Chem. Theory Comput., 13 (2017) 5874-5886
DOI:10.1021/acs.jctc.7b00594
- Edoardo Giovannelli, Matteo Cioni, Piero Procacci, Gianni Cardini, Marco Pagliai, Victor Volkov, Riccardo Chelli
Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative calculations and numerical validation
J. Chem. Theory Comput., 13 (2017) 5887-5899
DOI:10.1021/acs.jctc.7b00595
- Marina Macchiagodena, Giordano Mancini, Marco Pagliai, Gianni Cardini, Vincenzo Barone
New atomistic model of pyrrole with improved liquid state properties and structure
Int. J. Quantum Chem., 118 (2018) e25554
DOI: 10.1002/qua.25554
Cover Image
- Marco Pagliai, Iacopo Osticioli, Austin Nevin, Salvatore Siano, Gianni Cardini, Vincenzo Schettino
DFT Calculations of the IR and Raman Spectra of Anthraquinone Dyes and Lakes
J. Raman Spectrosc., 49 (2018) 668-683
DOI: 10.1002/jrs.5334
- Edoardo Giovannelli, Cristina Gellini, Giangaetano Pietraperzia, Gianni Cardini, Piero Procacci, Marco Pagliai, Victor Volkov, Riccardo Chelli
Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states
J. Chem. Phys., 149 (2018) 084101
DOI:10.1063/1.5028116
- Dario Vassetti, Marco Pagliai, Piero Procacci
Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules
J. Chem. Theory Comput., 15 (2019) 1983-1995
DOI:10.1021/acs.jctc.8b01039
- Marco Pagliai, Giada Funghi, Dario Vassetti, Piero Procacci, Riccardo Chelli, Gianni Cardini
Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration
J. Phys. Chem. B, 123 (2019) 4055-4064
DOI:10.1021/acs.jpcb.9b01611
- Lorenzo Briccolani-Bandini, Alberto Brandi, Gianni Cardini, Riccardo Chelli, Franca M. Cordero, Cristina Gellini, Marco Pagliai
Computational Investigation of the Selective Cleavage of Diastereotopic Cyclopropane Bonds in 5-Spirocyclopropane Isoxazolidines Rearrangement
J. Org. Chem., 84 (2019) 6757-6764
DOI:10.1021/acs.joc.9b00499
- Iacopo Osticioli, Marco Pagliai, Daniela Comelli, Vincenzo Schettino, Austin Nevin
Red Lakes from Leonardo's Last Supper and other Old Master Paintings: micro-Raman spectroscopy of anthraquinone pigments in paint cross-sections
Spectrochim. Acta, Part A, 222 (2019) 117273
DOI:10.1016/j.saa.2019.117273
- Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci
Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands
J. Chem. Inf. Model., 59 (2019) 3803-3816
DOI:10.1021/acs.jcim.9b00407
- Marco Pagliai, Marina Macchiagodena, Piero Procacci, Gianni Cardini
Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics Study
J. Phys. Chem. Lett., 10 (2019) 6414-6418
DOI:10.1021/acs.jpclett.9b02724
- Marina Macchiagodena, Marco Pagliai, Piero Procacci
Identification of Potential Binders of the Main Protease 3CLpro of the COVID-19 via Structure-Based Ligand Design and Molecular Modeling
Chem. Phys. Lett., 750 (2020) 137489
DOI:10.1016/j.cplett.2020.137489
Inhibiting the Coronavirus
- Anna Ranzenico, Chiara Mercurio, Maurice Karrenbrock, Franca M. Cordero, Gianni Cardini, Marco Pagliai, Alberto Brandi
Regioselective Deuteration of a 3,4-Dialkoxypyrroline N-Oxide and Synthesis of 8a-d-Indolizidines
Eur. J. Org. Chem., 23 (2020) 3423-3429
DOI:10.1002/ejoc.202000402
- Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci
Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins
ACS Omega, 5 (2020) 15301-15310
DOI:10.1021/acsomega.0c01337
- Piero Procacci, Marina Macchiagodena, Marco Pagliai, Guido Guarnieri, Francesco Iannone
Interaction of Hydroxychloroquine with SARS-CoV2 Functional Proteins Using All-atoms Non-equilibrium Alchemical Simulations
Chem. Commun., 56 (2020) 8854-8856
DOI:10.1039/D0CC03558K
- Giordano Mancini, Sara Del Galdo, Balasubramanian Chandramouli, Marco Pagliai, Vincenzo Barone
Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics
J. Chem. Theory Comput., 16 (2020) 5747-5761
DOI:10.1021/acs.jctc.0c00454
- Marina Macchiagodena, Marco Pagliai, Maurice Karrenbrock, Guido Guarnieri, Francesco Iannone, Piero Procacci
Virtual Double-System-Single-Box: a Nonequilibrium
Alchemical Technique for Absolute Binding Free Energy Calculations.
Application to Ligands of the SARS-CoV-2 Main Protease
J. Chem. Theory Comput., 16 (2020) 7160-7172
DOI:10.1021/acs.jctc.0c00634
- Cristina Gellini, Maurizio Muniz-Miranda, Marco Pagliai, Pier Remigio Salvi
Spectroscopic studies on antimalarial Artesunate: Raman and surface-enhanced Raman scattering and adsorption geometries of Artesunate on silver nanoparticles
J. Mol. Struct., 1224 (2021) 129020
DOI:10.1016/j.molstruc.2020.129020
- Hasret Subaka, Giulia Selvolini, Marina Macchiagodena, Dilsat Ozkan-Ariksoysal, Marco Pagliai, Piero Procacci, Giovanna Marrazza
Mycotoxins aptasensing: from molecular docking to electrochemical detection of deoxynivalenol
Bioelectrochemistry 138 (2021) 107691
DOI:10.1016/j.bioelechem.2020.107691
- Luca Conti, Nicola Flore, Mauro Formica, Luca Giorgi, Marco Pagliai, Luca Mancini, Vieri Fusi, Barbara Valtancoli, Claudia Giorgi
Glyphosate and AMPA binding by two polyamino-phenolic ligands and their dinuclear Zn(II) complexes
Inorg. Chim. Acta 519 (2021) 120261
DOI:10.1016/j.ica.2021.120261
- Cristina Gellini, Marina Macchiagodena, Marco Pagliai
Adsorption Geometry of Alizarin on Silver Nanoparticles: A Computational and Spectroscopic Study
Nanomaterials 11 (2021) 860
DOI:10.3390/nano11040860
- Chiara Calvagna,
Andrea Lapini, Andrea Taschin, Samuele Fanetti, Marco Pagliai, Paolo Bartolini, Roberto Bini,
Roberto Righini and Renato Torre
Modification of local and collective dynamics of water in perchlorate solution, induced by pressure and concentration
J. Mol. Liq. 337 (2021) 116273
DOI:10.1016/j.molliq.2021.116273
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Lorenzo Briccolani Bandini, Marco Pagliai, Franca M. Cordero, Alberto Brandi, Gianni Cardini
The "Cyclopropylidene Effect" in the 1,3-Dipolar Cycloaddition of Nitrones to Alkylidene cyclopropanes. A Computational Rationalization
J. Phys. Chem. A 125 (2021) 3892-3899
DOI:10.1021/acs.jpca.1c02204
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Matteo Boccalini, Roberto Cammi, Marco Pagliai, Gianni Cardini, Vincenzo Schettino
Towards an Understanding of the Pressure Effect on the Intramolecular Vibrational Frequencies of Sulfur Hexafluoride
J. Phys. Chem. A 125 (2021) 6362-6373
DOI:10.1021/acs.jpca.1c02595
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Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Piero Procacci
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS
J. Chem. Inf. Model. 61 (2021) 5320-5326
DOI:10.1021/acs.jcim.1c00909
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Nuno Barbosa, Marco Pagliai, Sourab Sinha, Vincenzo Barone, Dario Alfè, Giuseppe Brancato
Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case
J. Phys Chem. A 125 (2021) 10475-10484
DOI:10.1021/acs.jpca.1c07576
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Rita Gelli, Lorenzo Briccolani-Bandini, Marco Pagliai, Gianni Cardini, Francesca Ridi, Piero Baglioni
Exploring the effect of Mg2+ substitution on amorphous calcium phosphate nanoparticles
J. Colloid Interface Sci. 606 (2022) 444-453
DOI:10.1016/j.jcis.2021.08.033
- Marina Macchiagodena, Marco Pagliai, Piero Procacci
Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease
110 (2022) 109042
DOI:10.1016/j.jmgm.2021.108042
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Gina Elena Giacomazzo, Luca Conti, Annalisa Guerri, Marco Pagliai, Camilla Fagorzi, Patrick Severin Sfragano, Ilaria Palchetti, Giangaetano Pietraperzia, Alessio Mengoni, Barbara Valtancoli, Claudia Giorgi
Nitroimidazole-Based Ruthenium(II) Complexes: Playing with Structural Parameters to Design Photostable and Light-Responsive Antibacterial Agents
Inorg. Chem., 61 (2022) 6689-6694
DOI:10.1021/acs.inorgchem.1c03032
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Vincenzo Barone, Ivan Carnimeo, Giordano Mancini, Marco Pagliai
Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution
ACS Omega, 7 (2022) 13382-13394
DOI:10.1021/acsomega.2c01110
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Jonathan Campeggio, Victor Volkov, Massimo Innocenti, Walter Giurlani, Claudio Fontanesi, Mirco Zerbetto, Marco Pagliai, Alessandro Lavacchi, Riccardo Chelli
Ethanol electro-oxidation reaction on the Pd(111) surface in alkaline media: insights from quantum and molecular mechanics
Phys. Chem. Chem. Phys., 24 (2022) 12569-12579
DOI:10.1039/D2CP00909A
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Irene Vettori, Marina Macchiagodena, Marco Pagliai, Gavino Bassu, Emiliano Fratini, Piero Baglioni
Conformational and solvent effects in structural and spectroscopic properties of 2-hydroxyethyl methacrylate and acrylic acid
J. Mol. Liq, 360 (2022) 119428
DOI:10.1016/j.molliq.2022.119428
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Sandra Doria, Mariangela Di Donato, Raffaele Borrelli, Maxim F. Gelin, Justin Caram, Marco Pagliai, Paolo Foggi, Andea Lapini
Vibronic coherences in light harvesting nanotubes: unravelling the role of dark states
J. Mater. Chem. C, 10 (2022) 7216-7226
DOI:10.1039/d2tc00203e
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Silvia Di Grande, Ilaria Ciofini, Carlo Adamo, Marco Pagliai, Gianni Cardini
Absorption Spectra of Flexible Fluorescent Probes by a Combined Computational Approach: Molecular Dynamics Simulations and Time-Dependent Density Functional Theory
J. Phys. Chem. A, 126 (2022) 8809-8817
DOI:10.1021/acs.jpca.2c04637
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Marina Macchiagodena, Gavino Bassu, Irene Vettori, Emiliano Fratini, Piero Procacci, Marco Pagliai
2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study
J. Phys. Chem. A, 126 (2022) 8826-8833
DOI:10.1021/acs.jpca.2c05708
- Margherita Verrucchi, Gina Elena Giacomazzo, Patrick Severin Sfragano, Serena Laschi, Luca Conti, Marco Pagliai, Cristina Gellini, Marilena Ricci, Enrico Ravera, Barbara Valtancoli, Caludia Giorgi,
Ilaria Palchetti
Characterization of a Ruthenium(II) Complex in Singlet Oxygen-Mediated Photoelectrochemical Sensing
Langmuir, 39 (2023) 679-689
DOI:10.1021/acs.langmuir.2c03042
- Marina Macchiagodena, Marco Pagliai, Piero Procacci
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes
J. Comp. Chem., (2023) in press
DOI:10.1002/jcc.27077
- Milana Bazayeva, Andrea Giachetti, Marco Pagliai, Antonio Rosato
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data
Int. J. Mol. Sci., 24 (2023) 5440
DOI:10.3390/ijms24065440
- Matteo Savastano, María Dolores Lòpez de la Torre, Marco Pagliai, Giovanna Poggi, Francesca Ridi, Carla Bazzicalupi, Manuel Melguizo, Antonio Bianchi
Crystal engineering of high explosives through lone pair-π interactions: Insights for improving thermal safety
iScience, 26 (2023) 107330
DOI:10.1016/j.isci.2023.107330
- Lorenzo Briccolani-Bandini, Eric Br$eacute;mond, Marco Pagliai, Gianni Cardini, Ilaria Ciofini, Carlo Adamo
Concerted versus stepwise proton transfer reactions in the [2,2'-bipyridyl]-3-3'-diol molecule: A static and dynamic ab-initio investigation
J. Comput. Chem., (2023) in press
DOI:10.1002/jcc.27198