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Monti M, Brancolini G, Coccia E, Toffoli D, Fortunelli A, Corni S, Aschi M, Stener M. The Conformational Dynamics of the Ligands Determines the Electronic Circular Dichroism of the Chiral Au 38(SC 2H 4Ph) 24 Cluster. J Phys Chem Lett 2023; 14:1941-1948. [PMID: 36787099 PMCID: PMC9940292 DOI: 10.1021/acs.jpclett.2c03923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of the chiral Au38(SC2H4Ph)24 cluster are investigated. We adopt a computational protocol in which ECD spectra are calculated via the first principle polTDDFT approach on a series of conformations extracted from MD simulations by using Essential Dynamics (ED) analysis, and then properly weighted to predict the final spectrum. We find that the experimental spectral features are well reproduced, whereas significant discrepancies arise when the spectrum is calculated using the experimental X-ray structure. This result unambiguously demonstrates the need to account for the conformational effects in the ECD modeling of chiral nanoclusters. The present procedure proved to be able of capturing the essential conformational features of the dynamic Au38(SC2H4Ph)24 system, opening the possibility to model the ECD of soluble chiral nanoclusters in a realistic way.
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Affiliation(s)
- M. Monti
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università
di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - G. Brancolini
- Istituto
Nanoscienze, CNR-NANO, Center S3, Via G. Campi 213/A, 41100 Modena, Italy
| | - E. Coccia
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università
di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - D. Toffoli
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università
di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - A. Fortunelli
- CNR-ICCOM, Consiglio Nazionale delle Ricerche, via G. Moruzzi 1, 56124, Pisa, Italy
| | - S. Corni
- Istituto
Nanoscienze, CNR-NANO, Center S3, Via G. Campi 213/A, 41100 Modena, Italy
- Dipartimento
di Scienze Chimiche, Università di
Padova, Via Francesco Marzolo 1, 35131 Padova, Italy
| | - M. Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Università
dell’Aquila, Via Vetoio, 67100, l’Aquila, Italy
| | - M. Stener
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università
di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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2
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A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238135. [PMID: 36500228 PMCID: PMC9739849 DOI: 10.3390/molecules27238135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy.
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3
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Monti M, Stener M, Aschi M. A computational approach for modeling electronic circular dichroism of solvated chromophores. J Comput Chem 2022; 43:2023-2036. [PMID: 36134712 PMCID: PMC9825941 DOI: 10.1002/jcc.27001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
The present study consists in a novel computational protocol to model the UV-circular dichroism spectra of solvated species. It makes use of quantum-chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG+ and to the aqueous neutral decapeptide (GVGVP)2 . The protocol has proven able to: (i) properly consider the conformational motion of solute in the given environment; (ii) give the actual statistical weight of each conformational state; (iii) provide a reliable quantum mechanical method able to reproduce the spectral features. Temperature effects on conformations and spectral properties are properly taken into account. The role of explicit solvent on the conformational analysis and the spectra calculation is discussed. The comparison of the calculated circular dichroism spectra with experimental ones recorded at different temperatures represents a strict validation test of the method.
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Affiliation(s)
- Marta Monti
- Dipartimento di Scienze Chimiche e FarmaceuticheUniversità di TriesteTriesteItaly
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e FarmaceuticheUniversità di TriesteTriesteItaly
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e ChimicheUniversità dell'AquilaL'AquilaItaly
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4
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Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules 2022; 27:molecules27217408. [DOI: 10.3390/molecules27217408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
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Chen CG, Nardi AN, Giustini M, D'Abramo M. Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study. Phys Chem Chem Phys 2022; 24:12027-12035. [PMID: 35536553 DOI: 10.1039/d1cp05182b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimental absorption measurements in the interval 350-600 nm (Vis), molecular dynamics simulations, quantum-mechanics calculations and an advanced molecular treatment of simulation data are here combined to provide a complete picture of the absorption behavior in the visible portion of the electromagnetic spectrum of the doxorubicin hydrochloride (DX) molecule in different environments. By such an approach, we have shown that it is possible to characterize the effect of the environment on the DX absorption behavior - including the vibronic contributions - as well as to interpret such differences in terms of molecular electronic excited states, which are found to be strongly influenced by the environment.
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Affiliation(s)
| | | | - Mauro Giustini
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.
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Amino Acid Replacement at Position 228 Induces Fluctuation in the Ω-Loop of KPC-3 and Reduces the Affinity against Oxyimino Cephalosporins: Kinetic and Molecular Dynamics Studies. Catalysts 2020. [DOI: 10.3390/catal10121474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
KPC enzymes are the most common class A carbapenemases globally diffused. The peculiarity of this family of β-lactamases is represented by their ability to hydrolyse all classes of β-lactams, including carbapenems, posing a serious problem to public health. In the present study, seven laboratory mutants of KPC-3 (D228S, D228W, D228M, D228K, D228L, D228I and D228G) were generated by site-saturation mutagenesis to explore the role of residue 228, a non-active site residue. Compared to KPC-3, the seven mutants showed evident differences in kcat and Km values calculated for some penicillins, cephalosporins and carbapenems. In particular, D228S and D228M showed a significant increase of Km values for cefotaxime and ceftazidime. Circular dichroism (CD) experiments have demonstrated that substitution at position 228 does not affect the secondary structure of the mutants. Molecular dynamics (MD) simulations were performed on KPC-3, D228S and D228M uncomplexed and complexed with cefotaxime (substrate). Although the residue 228 is located far from the active site, between α11 helix and β7 sheet in the opposite site of the Ω-loop, amino acid substitution at this position generates mechanical effects in the active site resulting in enzyme activity changes.
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Chen Y, Viereck J, Harmer R, Rangan S, Bartynski RA, Galoppini E. Helical Peptides Design for Molecular Dipoles Functionalization of Wide Band Gap Oxides. J Am Chem Soc 2020; 142:3489-3498. [PMID: 31977205 DOI: 10.1021/jacs.9b12001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of helical hexapeptides to establish a surface dipole layer on a TiO2 substrate, with the goal of influencing the energy levels of a coadsorbed chromophore, is explored. Two helical hexapeptides, synthesized from 2-amino isobutyric acid (Aib) residues, were protected at the N-terminus with a carboxybenzyl group (Z) and at the C-terminus carried either a carboxylic acid or an isophthalic acid (Ipa) anchor group to form Z-(Aib)6-COOH or Z-(Aib)6-Ipa, respectively. Using a combination of vibrational and photoemission spectroscopies, bonding of the two peptides to TiO2 surfaces (either nanostructured or single-crystal TiO2(110)) was found to be highly dependent on the anchor group, with Ipa establishing a monolayer much more efficiently than COOH. Furthermore, a monolayer of Z-(Aib)6-Ipa on TiO2(110) was exposed for different binding times to a solution of a zinc tetraphenylporphyrin (ZnTPP) derivative terminated with an Ipa anchor group (ZnTPP-P-Ipa). Photoemission spectroscopy revealed that ZnTPP-P-Ipa partly displaced Z-(Aib)6-Ipa, forming a coadsorbed monolayer on the oxide surface. The presence of the peptide molecular dipole shifted the HOMO levels of the ZnTPP group to lower energy by ∼300 meV, in accordance with a simple parallel plate capacitor model. These results suggest that a mixed-layer approach, involving coadsorption of a strong molecular dipole compound with a chromophore, is a versatile method to shift the energy levels of such chromophores with respect to the band edges of the substrate.
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Affiliation(s)
- Yuan Chen
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Jonathan Viereck
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Ryan Harmer
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Sylvie Rangan
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Robert A Bartynski
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Elena Galoppini
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
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Aschi M, Perini N, Bouchemal N, Luzi C, Savarin P, Migliore L, Bozzi A, Sette M. Structural characterization and biological activity of Crabrolin peptide isoforms with different positive charge. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183055. [DOI: 10.1016/j.bbamem.2019.183055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/20/2019] [Accepted: 08/25/2019] [Indexed: 12/26/2022]
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Kinetic Profile and Molecular Dynamic Studies Show that Y229W Substitution in an NDM-1/L209F Variant Restores the Hydrolytic Activity of the Enzyme toward Penicillins, Cephalosporins, and Carbapenems. Antimicrob Agents Chemother 2019; 63:AAC.02270-18. [PMID: 30917978 DOI: 10.1128/aac.02270-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 01/23/2019] [Indexed: 01/01/2023] Open
Abstract
The New Delhi metallo-β-lactamase-1 (NDM-1) enzyme is the most common metallo-β-lactamase identified in many Gram-negative bacteria causing severe nosocomial infections. The aim of this study was to focus the attention on non-active-site residues L209 and Y229 of NDM-1 and to investigate their role in the catalytic mechanism. Specifically, the effect of the Y229W substitution in the L209F variant was evaluated by antimicrobial susceptibility testing, kinetic, and molecular dynamic (MD) studies. The Y229W single mutant and L209F-Y229W double mutant were generated by site-directed mutagenesis. The Km , k cat, and k cat/Km kinetic constants, calculated for the two mutants, were compared with those of (wild-type) NDM-1 and the L209F variant. Compared to the L209F single mutant, the L209F-Y229W double mutant showed a remarkable increase in k cat values of 100-, 240-, 250-, and 420-fold for imipenem, meropenem, benzylpenicillin, and cefepime, respectively. In the L209F-Y229W enzyme, we observed a remarkable increase in k cat/Km of 370-, 140-, and 80-fold for cefepime, meropenem, and cefazolin, respectively. The same behavior was noted using the antimicrobial susceptibility test. MD simulations were carried out on both L209F and L209F-Y229W enzymes complexed with benzylpenicillin, focusing attention on the overall mechanical features and on the differences between the two systems. With respect to the L209F variant, the L209F-Y229W double mutant showed mechanical stabilization of loop 10 and the N-terminal region. In addition, Y229W substitution destabilized both the C-terminal region and the region from residues 149 to 154. The epistatic effect of the Y229W mutation jointly with the stabilization of loop 10 led to a better catalytic efficiency of β-lactams. NDM numbering is used in order to facilitate the comparison with other NDM-1 studies.
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10
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Amadei A, Aschi M. Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems. RSC Adv 2018; 8:27900-27918. [PMID: 35542751 PMCID: PMC9083445 DOI: 10.1039/c8ra03900c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022] Open
Abstract
In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Universita' di Roma 'Tor Vergata' Roma Italy +390672594905
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Universita' di L'Aquila L'Aquila Italy +390862433775
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Marcoccia F, Leiros HKS, Aschi M, Amicosante G, Perilli M. Exploring the role of L209 residue in the active site of NDM-1 a metallo-β-lactamase. PLoS One 2018; 13:e0189686. [PMID: 29293526 PMCID: PMC5749715 DOI: 10.1371/journal.pone.0189686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/30/2017] [Indexed: 11/28/2022] Open
Abstract
Background New Delhi Metallo-β-Lactamase (NDM-1) is one of the most recent additions to the β-lactamases family. Since its discovery in 2009, NDM-1 producing Enterobacteriaceae have disseminated globally. With few effective antibiotics against NDM-1 producers, there is an urgent need to design new drug inhibitors through the help of structural and mechanistic information available from mutagenic studies. Results/Conclusions In our study we focus the attention on the non-catalytic residue Leucine 209 by changing it into a Phenylalanine. The L209F laboratory variant of NDM-1 displays a drastic reduction of catalytic efficiency (due to low kcat values) towards penicillins, cephalosporins and carbapenems. Thermofluor-based assay demonstrated that NDM-1 and L209F are stable to the temperature and the zinc content is the same in both enzymes as demonstrated by experiments with PAR in the presence of GdnHCL. Molecular Dynamics (MDs) simulations, carried out on NDM-1 and L209F both complexed and uncomplexed with Benzylpenicillin indicate that the point mutation produces a significant mechanical destabilization of the enzyme and also an increase of water content. These observations clearly show that the single mutation induces drastic changes in the enzyme properties which can be related to the observed different catalytic behavior.
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Affiliation(s)
- Francesca Marcoccia
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Hanna-Kirsti S. Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Gianfranco Amicosante
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Mariagrazia Perilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, L’Aquila, Italy
- * E-mail:
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Aschi M, Barone V, Carlotti B, Daidone I, Elisei F, Amadei A. Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model. Phys Chem Chem Phys 2016; 18:28919-28931. [PMID: 27725986 DOI: 10.1039/c6cp06167b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical–computational method is proposed for modelling the complete kinetics – from photo-excitation to relaxation – of a chromophore in solution.
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Affiliation(s)
| | | | - Benedetta Carlotti
- Department of Chemistry
- Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
- University of Perugia
- 06123 Perugia
- Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche
- University of l'Aquila
- Italy
| | - Fausto Elisei
- Department of Chemistry
- Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
- University of Perugia
- 06123 Perugia
- Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche
- Universiy of Roma Tor Vergata
- 00100 Roma
- Italy
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