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Article ; Online: A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data.

Bazayeva, Milana / Giachetti, Andrea / Pagliai, Marco / Rosato, Antonio

International journal of molecular sciences

2023 Volume 24, Issue 6

Abstract: Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been ... ...

Abstract	Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S
MeSH term(s)	Zinc/metabolism ; Molecular Dynamics Simulation ; Metalloproteins/metabolism ; Magnetic Resonance Spectroscopy ; Metals
Chemical Substances	Zinc (J41CSQ7QDS) ; Metalloproteins ; Metals
Language	English
Publishing date	2023-03-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24065440
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes.

Macchiagodena, Marina / Pagliai, Marco / Procacci, Piero

Journal of computational chemistry

2023 Volume 44, Issue 12, Page(s) 1221–1230

Abstract: We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology ... ...

Abstract	We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host-guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb_gromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932.
Language	English
Publishing date	2023-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.27077
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Article ; Online: Exploring High-Pressure Polymorphism in Carbonic Acid through Direct Synthesis from Carbon Dioxide Clathrate Hydrate.

Berni, Selene / Scelta, Demetrio / Romi, Sebastiano / Fanetti, Samuele / Alabarse, Frederico / Pagliai, Marco / Bini, Roberto

Angewandte Chemie (International ed. in English)

2024 , Page(s) e202403953

Abstract: Carbon dioxide ( ... ...

Abstract	Carbon dioxide (CO
Language	English
Publishing date	2024-03-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202403953
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Article ; Online: Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution.

Barone, Vincenzo / Carnimeo, Ivan / Mancini, Giordano / Pagliai, Marco

ACS omega

2022 Volume 7, Issue 15, Page(s) 13382–13394

Abstract: A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit ...

Abstract	A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution.
Language	English
Publishing date	2022-04-06
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c01110
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Article: Adsorption Geometry of Alizarin on Silver Nanoparticles: A Computational and Spectroscopic Study.

Gellini, Cristina / Macchiagodena, Marina / Pagliai, Marco

Nanomaterials (Basel, Switzerland)

2021 Volume 11, Issue 4

Abstract: The knowledge of the adsorption geometry of an analyte on a metal substrate employed in surface enhanced Raman scattering (SERS) spectroscopy is important information for the correct interpretation of experimental data. The adsorption geometry of ... ...

Abstract	The knowledge of the adsorption geometry of an analyte on a metal substrate employed in surface enhanced Raman scattering (SERS) spectroscopy is important information for the correct interpretation of experimental data. The adsorption geometry of alizarin on silver nanoparticles was studied through ab initio calculations in the framework of density functional theory (DFT) by modeling alizarin taking into account all the different charged species present in solution as a function of pH. The calculations allowed a faithful reproduction of the measured SERS spectra and to elucidate the adsorption geometry of this dye on the silver substrate.
Language	English
Publishing date	2021-03-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano11040860
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Article ; Online: Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.

Macchiagodena, Marina / Karrenbrock, Maurice / Pagliai, Marco / Procacci, Piero

Journal of chemical information and modeling

2021 Volume 61, Issue 11, Page(s) 5320–5326

Abstract: We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational ...

Abstract	We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational protocol has been automated through an open source Python middleware (HPC_Drug) which allows one to set up the GROMACS/PLUMED input files for execution on high performing computing facilities. The proposed protocol, by exploiting its inherent parallelism and the power of the GROMACS code on graphical processing units, has the potential to afford accurate and precise estimates of the dissociation constants in drug-receptor systems described at the atomistic level. The procedure has been applied to the calculation of the absolute dissociation free energy of PF-07321332, an oral antiviral proposed by Pfizer, with the main protease (3CL
MeSH term(s)	Antiviral Agents ; COVID-19 ; Entropy ; Lactams ; Leucine ; Molecular Dynamics Simulation ; Nitriles ; Proline ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Lactams ; Nitriles ; nirmatrelvir (7R9A5P7H32) ; Proline (9DLQ4CIU6V) ; Leucine (GMW67QNF9C)
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c00909
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Article ; Online: Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease.

Macchiagodena, Marina / Pagliai, Marco / Procacci, Piero

Journal of molecular graphics & modelling

2021 Volume 110, Page(s) 108042

Abstract: We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical ... ...

Abstract	We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical structure has been recently disclosed, is a promising oral antiviral clinical candidate with well-established anti-SARS-CoV-2 activity in vitro. The drug, currently in phase III clinical trials in combination with ritonavir, relies on the electrophilic attack of a nitrile warhead to the catalytic cysteine of the protease. Nonbonded interaction between the inhibitor and the residues of the binding pocket, as well as with water molecules on the protein surface, have been characterized using two different force fields and the two possible protonation states of the main protease catalytic dyad HIS41-CYS145. When the catalytic dyad is in the neutral state, the non-covalent binding is likely to be stronger. Molecular dynamics simulations seems to lend support for an inhibitory mechanism in two steps: a first non-covalent addition with the dyad in neutral form and then the formation of the thiolate-imidazolium ion pair and the ligand relocation for finalising the electrophilic attack.
MeSH term(s)	Antiviral Agents/therapeutic use ; COVID-19 ; Coronavirus 3C Proteases ; Humans ; Lactams ; Leucine ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nitriles ; Proline ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Lactams ; Nitriles ; Protease Inhibitors ; nirmatrelvir (7R9A5P7H32) ; Proline (9DLQ4CIU6V) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Leucine (GMW67QNF9C)
Language	English
Publishing date	2021-10-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.108042
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Article ; Online: The Smart Drifter Cluster: Monitoring Sea Currents and Marine Litter Transport Using Consumer IoT Technologies.

Merlino, Silvia / Calabrò, Vincenzo / Giannelli, Carlotta / Marini, Lorenzo / Pagliai, Marco / Sacco, Lorenzo / Bianucci, Marco

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 12

Abstract: The study of marine Lagrangian transport holds significant importance from a scientific perspective as well as for practical applications such as environmental-pollution responses and prevention (e.g., oil spills, dispersion/accumulation of plastic ... ...

Abstract	The study of marine Lagrangian transport holds significant importance from a scientific perspective as well as for practical applications such as environmental-pollution responses and prevention (e.g., oil spills, dispersion/accumulation of plastic debris, etc.). In this regard, this concept paper introduces the Smart Drifter Cluster: an innovative approach that leverages modern "consumer" IoT technologies and notions. This approach enables the remote acquisition of information on Lagrangian transport and important ocean variables, similar to standard drifters. However, it offers potential benefits such as reduced hardware costs, minimal maintenance expenses, and significantly lower power consumption compared to systems relying on independent drifters with satellite communication. By combining low power consumption with an optimized, compact integrated marine photovoltaic system, the drifters achieve unlimited operational autonomy. With the introduction of these new characteristics, the Smart Drifter Cluster goes beyond its primary function of mesoscale monitoring of marine currents. It becomes readily applicable to numerous civil applications, including recovering individuals and materials at sea, addressing pollutant spills, and tracking the dispersion of marine litter. An additional advantage of this remote monitoring and sensing system is its open-source hardware and software architecture. This fosters a citizen-science approach, enabling citizens to replicate, utilize, and contribute to the improvement of the system. Thus, within certain constraints of procedures and protocols, citizens can actively contribute to the generation of valuable data in this critical field.
MeSH term(s)	Environmental Monitoring/instrumentation ; Environmental Monitoring/methods ; Oceans and Seas ; Electrochemical Techniques/instrumentation ; Electrochemical Techniques/methods ; Water Pollutants, Chemical/chemistry ; Temperature ; Software Design
Chemical Substances	Water Pollutants, Chemical
Language	English
Publishing date	2023-06-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23125467
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Article ; Online: Concerted versus stepwise proton transfer reactions in the [2, 2'-bipyridyl]-3-3'-diol molecule: A static and dynamic ab-initio investigation.

Briccolani-Bandini, Lorenzo / Brémond, Eric / Pagliai, Marco / Cardini, Gianni / Ciofini, Ilaria / Adamo, Carlo

Journal of computational chemistry

2023 Volume 44, Issue 30, Page(s) 2308–2318

Abstract: The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, ...

Abstract	The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free-energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange-correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature.
Language	English
Publishing date	2023-08-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.27198
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Article: Exploring the effect of Mg2+ substitution on amorphous calcium phosphate nanoparticles

Gelli, Rita / Briccolani-Bandini, Lorenzo / Pagliai, Marco / Cardini, Gianni / Ridi, Francesca / Baglioni, Piero

Journal of colloid and interface science. 2022 Jan. 15, v. 606

2022

Abstract: The study of Amorphous Calcium Phosphate (ACP) has become a hot topic due to its relevance in living organisms and as a material for biomedical applications. The preparation and characterization of Mg-substituted ACP nanoparticles (AMCP) with tunable Ca/ ... ...

Abstract	The study of Amorphous Calcium Phosphate (ACP) has become a hot topic due to its relevance in living organisms and as a material for biomedical applications. The preparation and characterization of Mg-substituted ACP nanoparticles (AMCP) with tunable Ca/Mg ratio is reported in the present study to address the effect of Mg²⁺ on their structure and stability.AMCPs particles were synthesized by precipitation of the precursors from aqueous solutions. The particles were analyzed in terms of morphology, crystallinity, and thermal stability, to get a complete overview of their physico-chemical characteristics. Computational methods were also employed to simulate the structure of ACP clusters at different levels of Mg²⁺ substitution.Our results demonstrate that AMCP particles with tunable composition and crystallinity can be obtained. The analysis of the heat-induced crystallization of AMCP shows that particles’ stability depends on the degree of Mg²⁺ substitution in the cluster, as confirmed by computational analyses. The presented results shed light on the effect of Mg²⁺ on ACP features at different structural levels and may be useful guidelines for the preparation and design of AMCP particles with a specific Ca/Mg ratio.
Keywords	calcium phosphates ; crystal structure ; crystallization ; thermal stability
Language	English
Dates of publication	2022-0115
Size	p. 444-453.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2021.08.033
Database	NAL-Catalogue (AGRICOLA)

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