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Article ; Online: Tuning the low-temperature phase behavior of aqueous ionic liquids.

Bachler, Johannes / Daidone, Isabella / Zanetti-Polzi, Laura / Loerting, Thomas

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 12, Page(s) 9741–9753

Abstract: Water's anomalous behavior is often explained using a two-liquid model, where two types of water, high-density liquid (HDL) and low-density liquid (LDL), can be ... ...

Abstract	Water's anomalous behavior is often explained using a two-liquid model, where two types of water, high-density liquid (HDL) and low-density liquid (LDL), can be separated
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp06101a
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A statistical mechanical model of supercooled water based on minimal clusters of correlated molecules.

Daidone, Isabella / Foffi, Riccardo / Amadei, Andrea / Zanetti-Polzi, Laura

The Journal of chemical physics

2023 Volume 159, Issue 9

Abstract: ... critical fluid water [Zanetti-Polzi et al., J. Chem. Phys. 156(4), 44506 (2022)], is based on a combination ...

Abstract	In this paper, we apply a theoretical model for fluid state thermodynamics to investigate simulated water in supercooled conditions. This model, which we recently proposed and applied to sub- and super-critical fluid water [Zanetti-Polzi et al., J. Chem. Phys. 156(4), 44506 (2022)], is based on a combination of the moment-generating functions of the enthalpy and volume fluctuations as provided by two gamma distributions and provides the free energy of the system as well as other relevant thermodynamic quantities. The application we make here provides a thermodynamic description of supercooled water fully consistent with that expected by crossing the liquid-liquid Widom line, indicating the presence of two distinct liquid states. In particular, the present model accurately reproduces the Widom line temperatures estimated with other two-state models and well describes the heat capacity anomalies. Differently from previous models, according to our description, a cluster of molecules that extends beyond the first hydration shell is necessary to discriminate between the statistical fluctuation regimes typical of the two liquid states.
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0157505
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Article ; Online: Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin.

Zanetti-Polzi, Laura / Daidone, Isabella / Iacobucci, Claudio / Amadei, Andrea

The protein journal

2023 Volume 42, Issue 3, Page(s) 219–228

Abstract: Metamorphic, or fold-switching, proteins feature different folds that are physiologically relevant. The human chemokine XCL1 (or Lymphotactin) is a metamorphic protein that features two native states, an [Formula: see text] and an all[Formula: see text] ... ...

Abstract	Metamorphic, or fold-switching, proteins feature different folds that are physiologically relevant. The human chemokine XCL1 (or Lymphotactin) is a metamorphic protein that features two native states, an [Formula: see text] and an all[Formula: see text] fold, which have similar stability at physiological condition. Here, extended molecular dynamics (MD) simulations, principal component analysis of atomic fluctuations and thermodynamic modeling based on both the configurational volume and free energy landscape, are used to obtain a detailed characterization of the conformational thermodynamics of human Lymphotactin and of one of its ancestors (as was previously obtained by genetic reconstruction). Comparison of our computational results with the available experimental data show that the MD-based thermodynamics can explain the experimentally observed variation of the conformational equilibrium between the two proteins. In particular, our computational data provide an interpretation of the thermodynamic evolution in this protein, revealing the relevance of the configurational entropy and of the shape of the free energy landscape within the essential space (i.e., the space defined by the generalized internal coordinates providing the largest, typically non-Gaussian, structural fluctuations).
MeSH term(s)	Humans ; Thermodynamics ; Lymphokines/chemistry ; Lymphokines/metabolism ; Sialoglycoproteins/chemistry ; Sialoglycoproteins/metabolism ; Molecular Dynamics Simulation
Chemical Substances	lymphotactin ; Lymphokines ; Sialoglycoproteins
Language	English
Publishing date	2023-05-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-023-10123-7
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Article ; Online: A general statistical mechanical model for fluid system thermodynamics: Application to sub- and super-critical water.

Zanetti-Polzi, Laura / Daidone, Isabella / Amadei, Andrea

The Journal of chemical physics

2022 Volume 156, Issue 4, Page(s) 44506

Abstract: We propose in this paper a theoretical model for fluid state thermodynamics based on modeling the fluctuation distributions and, hence, the corresponding moment generating functions providing the free energy of the system. Using the relatively simple and ...

Abstract	We propose in this paper a theoretical model for fluid state thermodynamics based on modeling the fluctuation distributions and, hence, the corresponding moment generating functions providing the free energy of the system. Using the relatively simple and physically coherent gamma model for the fluctuation distributions, we obtain a complete theoretical equation of state, also giving insight into the statistical/molecular organization and phase or pseudo-phase transitions occurring under the sub- and super-critical conditions, respectively. Application to sub- and super-critical fluid water and a comparison with the experimental data show that this model provides an accurate description of fluid water thermodynamics, except close to the critical point region where limited but significant deviations from the experimental data occur. We obtain quantitative evidence of the correspondence between the sub- and super-critical thermodynamic behaviors, with the super-critical water pseudo-liquid and pseudo-gas phases being the evolution of the sub-critical water liquid and gas phases, respectively. Remarkably, according to our model, we find that for fluid water the minimal subsystem corresponding to either the liquid-like or the gas-like condition includes an infinite number of molecules in the sub-critical regime (providing the expected singularities due to macroscopic phase transitions) but only five molecules in the super-critical regime (coinciding with the minimal possible hydrogen-bonding cluster), thus suggesting that the super-critical regime be characterized by the coexistence of nanoscopic subsystems in either the pseudo-liquid or the pseudo-gas phase with each subsystem fluctuating between forming and disrupting the minimal hydrogen-bonding network.
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0079206
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Article ; Online: Origins of the pH-Responsive Photoluminescence of Peptide-Functionalized Au Nanoclusters.

Zanetti-Polzi, Laura / Charchar, Patrick / Yarovsky, Irene / Corni, Stefano

ACS nano

2022 Volume 16, Issue 12, Page(s) 20129–20140

Abstract: Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with ... ...

Abstract	Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au
MeSH term(s)	Metal Nanoparticles/chemistry ; Peptides ; Gold/chemistry ; Amines ; Hydrogen-Ion Concentration
Chemical Substances	Peptides ; Gold (7440-57-5) ; Amines
Language	English
Publishing date	2022-10-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.2c04335
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Article ; Online: Segregation on the nanoscale coupled to liquid water polyamorphism in supercooled aqueous ionic-liquid solution.

Zanetti-Polzi, Laura / Amadei, Andrea / Daidone, Isabella

The Journal of chemical physics

2021 Volume 155, Issue 10, Page(s) 104502

Abstract: The most intriguing hypothesis explaining many water anomalies is a metastable liquid-liquid phase transition (LLPT) at high pressure and low temperatures, experimentally hidden by homogeneous nucleation. Recent infrared spectroscopic experiments showed ... ...

Abstract	The most intriguing hypothesis explaining many water anomalies is a metastable liquid-liquid phase transition (LLPT) at high pressure and low temperatures, experimentally hidden by homogeneous nucleation. Recent infrared spectroscopic experiments showed that upon addition of hydrazinium trifluoroacetate to water, the supercooled ionic solution undergoes a sharp, reversible LLPT at ambient pressure, possible offspring of that in pure water. Here, we calculate the temperature-dependent signature of the OH-stretching band, reporting on the low/high density phase of water, in neat water and in the same experimentally investigated ionic solution. The comparison between the infrared signature of the pure liquid and that of the ionic solution can be achieved only computationally, providing insight into the nature of the experimentally observed phase transition and allowing us to investigate the effects of ionic compounds on the high to low density supercooled liquid water transition. We show that the experimentally observed crossover behavior in the ionic solution can be reproduced only if the phase transition between the low- and high-density liquid states of water is coupled to a mixing-unmixing transition between the water component and the ions: at low temperatures, water and ions are separated and the water component is a low density liquid. At high temperatures, water and ions get mixed and the water component is a high-density liquid. The separation at low temperatures into ion-rich and ion-poor regions allows unveiling the polyamorphic nature of liquid water, leading to a crossover behavior resembling that observed in supercooled neat water under high pressure.
Language	English
Publishing date	2021-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0061659
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Article ; Online: Fully Atomistic Multiscale Approach for p

Zanetti-Polzi, Laura / Daidone, Isabella / Amadei, Andrea

The journal of physical chemistry. B

2020 Volume 124, Issue 23, Page(s) 4712–4722

Abstract: The ionization state of titratable amino acids strongly affects proteins structure and functioning in a large number of biological processes. It is therefore essential to be able to characterize the ... ...

Abstract	The ionization state of titratable amino acids strongly affects proteins structure and functioning in a large number of biological processes. It is therefore essential to be able to characterize the p
MeSH term(s)	Amino Acids ; Entropy ; Hydrogen-Ion Concentration ; Lysine ; Proteins
Chemical Substances	Amino Acids ; Proteins ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2020-06-02
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c01752
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Article ; Online: Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study.

Zanetti-Polzi, Laura / Aschi, Massimiliano / Daidone, Isabella

Physical chemistry chemical physics : PCCP

2020 Volume 22, Issue 35, Page(s) 19975–19981

Abstract: We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the ... ...

Abstract	We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the energy variation upon PT, and from that we also calculate the PT reaction free energy, making use of a hybrid quantum mechanics/molecular dynamics approach. In agreement with the experimental data, we obtain that the reaction free energy is basically the same in the two systems. Yet, we show that the instantaneous PT energy is on average lower in the mutant possibly contributing to the faster PT rate. Analysis of the contribution to the PT energetics of the solvent and of each protein residue, also not in the vicinity of the active site, provides evidence for electrostatic tuning of the PT energy arising from the combined effect of the solvent and the protein environment. These findings open up a way to the more general task of the rational design of mutants with either enhanced or reduced PT rate.
MeSH term(s)	Carbonic Anhydrase II/chemistry ; Carbonic Anhydrase II/genetics ; Catalytic Domain ; Humans ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Mutation ; Protons ; Quantum Theory ; Thermodynamics
Chemical Substances	Protons ; Carbonic Anhydrase II (EC 4.2.1.-) ; CA2 protein, human (EC 4.2.1.1)
Language	English
Publishing date	2020-08-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp03652h
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Article ; Online: Evidence for a high pK

Capone, Matteo / Zanetti-Polzi, Laura / Leonzi, Ilenia / Spreti, Nicoletta / Daidone, Isabella

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 11, Page(s) 4949–4956

Abstract: ... Candida ... ...

Abstract	Candida antarctica
MeSH term(s)	Aspartic Acid ; Catalytic Domain ; Fungal Proteins/chemistry ; Lipase/chemistry
Chemical Substances	lipase B, Candida antarctica (EC 3.1.1.3) ; Aspartic Acid (30KYC7MIAI) ; Fungal Proteins ; Lipase (EC 3.1.1.3)
Language	English
Publishing date	2022-05-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2077834
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Article ; Online: Mechanism and Dynamics of Photodecarboxylation Catalyzed by Lactate Monooxygenase.

Li, Xiankun / Page, Claire G / Zanetti-Polzi, Laura / Kalra, Aarat P / Oblinsky, Daniel G / Daidone, Isabella / Hyster, Todd K / Scholes, Gregory D

Journal of the American Chemical Society

2023 Volume 145, Issue 24, Page(s) 13232–13240

Abstract: Photoenzymes are a rare class of biocatalysts that use light to facilitate chemical reactions. Many of these catalysts utilize a flavin cofactor to absorb light, suggesting that other flavoproteins might have latent photochemical functions. Lactate ... ...

Abstract	Photoenzymes are a rare class of biocatalysts that use light to facilitate chemical reactions. Many of these catalysts utilize a flavin cofactor to absorb light, suggesting that other flavoproteins might have latent photochemical functions. Lactate monooxygenase is a flavin-dependent oxidoreductase previously reported to mediate the photodecarboxylation of carboxylates to afford alkylated flavin adducts. While this reaction holds a potential synthetic value, the mechanism and synthetic utility of this process are unknown. Here, we combine femtosecond spectroscopy, site-directed mutagenesis, and a hybrid quantum-classical computational approach to reveal the active site photochemistry and the role the active site amino acid residues play in facilitating this decarboxylation. Light-induced electron transfer from histidine to flavin was revealed, which has not been reported in other proteins. These mechanistic insights enable the development of catalytic oxidative photodecarboxylation of mandelic acid to produce benzaldehyde, a previously unknown reaction for photoenzymes. Our findings suggest that a much wider range of enzymes have the potential for photoenzymatic catalysis than has been realized to date.
MeSH term(s)	Mixed Function Oxygenases/chemistry ; Lactic Acid ; Oxidation-Reduction ; Catalysis ; Flavins/metabolism
Chemical Substances	Mixed Function Oxygenases (EC 1.-) ; Lactic Acid (33X04XA5AT) ; Flavins
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c02446
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