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Bartocci A, Dumont E. Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations. J Chem Phys 2024; 160:105101. [PMID: 38465686 DOI: 10.1063/5.0198522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
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Affiliation(s)
- Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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Cappelletti D, Falcinelli S, Pirani F. The dawn of hydrogen and halogen bonds and their crucial role in collisional processes probing long-range intermolecular interactions. Phys Chem Chem Phys 2024; 26:7971-7987. [PMID: 38411471 DOI: 10.1039/d3cp05871a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
This perspective review focuses on the results of an internally consistent study developed in the Perugia laboratory, centered on the fundamental interaction components that, at large intermolecular distances, determine the formation of weak intermolecular hydrogen (HB) and halogen (XB) bonds. This investigation exploits old and novel molecular beam scattering experiments involving several gaseous prototypical systems. In particular, we focus on the kinetic energy dependence of the total (elastic + inelastic) integral cross-sections. Of particular interest is the measure of quantum interference patterns in the energy dependence of cross-sections of targeted systems and their shift compared to that of known reference systems. We interpreted these findings as interaction energy stabilization components, such as charge transfer, σ-hole, and polar flattening, that emerge at intermediate separation distance ranges and selectively manifest for specific geometries of collision complexes. Another significant observable we discuss is the absolute value of the cross-section and its dependence on permanent multipole moments of the collisional partners. Specifically, we show how the spontaneous orientation of rotationally cold and polar molecules, due to the electric field gradient associated with the interaction between permanent multipole moments, can significantly modify the magnitude of the total cross-section, even at high values of the impact parameter. We are confident that the present results can help extend the force field formulation to various interacting systems and carry out molecular dynamics simulations under conditions of application interest.
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Affiliation(s)
- David Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Stefano Falcinelli
- Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia, via G. Duranti 93, 06215 Perugia, Italy
| | - Fernando Pirani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
- Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia, via G. Duranti 93, 06215 Perugia, Italy
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Dagdigian PJ. Interaction of the H 2S molecule with molecular hydrogen: Ab initio potential energy surface and scattering calculations. J Chem Phys 2020; 152:074307. [PMID: 32087660 DOI: 10.1063/1.5144604] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The potential energy surface describing the interaction of H2S with molecular hydrogen has been computed through explicitly correlated coupled cluster calculations including single, double, and (perturbative) triple excitations [CCSD(T)-F12a], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate coefficients. Representative sets of energy dependent state-to-state rotationally inelastic cross sections and rate coefficients are presented and discussed.
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Affiliation(s)
- Paul J Dagdigian
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218-2685, USA
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Nunzi F, Cesario D, Belpassi L, Tarantelli F, Roncaratti LF, Falcinelli S, Cappelletti D, Pirani F. Insight into the halogen-bond nature of noble gas-chlorine systems by molecular beam scattering experiments, ab initio calculations and charge displacement analysis. Phys Chem Chem Phys 2019; 21:7330-7340. [PMID: 30896694 DOI: 10.1039/c9cp00300b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have carried out molecular-beam scattering experiments and high-level ab initio investigations on the potential energy surfaces of a series of noble-gas-Cl2 adducts. This effort has permitted the construction of a simple, reliable and easily generalizable analytical model potential formulation, which is based on a few physically meaningful parameters of the interacting partners and transparently shows the origin, strength, and stereospecificity of the various interaction components. The results demonstrate quantitatively beyond doubt that the interaction between a noble-gas (Ng) atom - even He - and Cl2 in a collinear configuration is characterized by weak halogen bond (XB) formation, accompanied by charge transfer (CT) from the Ng to chlorine. This characteristic, which stabilizes the adduct, rapidly disappears on going towards the T-shaped configuration, dominated by pure van der Waals (vdW) forces. Similarly, a pure vdW interaction takes place - with no CT component in any configuration - if Cl2 is present in the lowest πg* → σu* excited state, because the change in electron density that accompanies the excitation eliminates the Cl2 polar flattening and σ hole, making the XB interaction inaccessible.
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Affiliation(s)
- Francesca Nunzi
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy.
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Wang C, Danovich D, Shaik S, Mo Y. Halogen Bonds in Novel Polyhalogen Monoanions. Chemistry 2017; 23:8719-8728. [DOI: 10.1002/chem.201701116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Changwei Wang
- College of Science; China University of Petroleum (East China); Changjiangxi Road 66 266580 Tsingtao P. R. China
| | - David Danovich
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University; Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University; Jerusalem 91904 Israel
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo MI 49008 USA
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Cappelletti D, Falcinelli S, Pirani F. The intermolecular interaction in D2 − CX4 and O2 − CX4 (X = F, Cl) systems: Molecular beam scattering experiments as a sensitive probe of the selectivity of charge transfer component. J Chem Phys 2016; 145:134305. [DOI: 10.1063/1.4964092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, Perugia 06123, Italy
| | - Stefano Falcinelli
- Dipartimento di Ingegneria Civile ed Ambientale, Università di Perugia, Via G. Duranti 93, Perugia 06125, Italy
| | - Fernando Pirani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, Perugia 06123, Italy
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Lao KU, Herbert JM. Energy Decomposition Analysis with a Stable Charge-Transfer Term for Interpreting Intermolecular Interactions. J Chem Theory Comput 2016; 12:2569-82. [PMID: 27049750 DOI: 10.1021/acs.jctc.6b00155] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many schemes for decomposing quantum-chemical calculations of intermolecular interaction energies into physically meaningful components can be found in the literature, but the definition of the charge-transfer (CT) contribution has proven particularly vexing to define in a satisfactory way and typically depends strongly on the choice of basis set. This is problematic, especially in cases of dative bonding and for open-shell complexes involving cation radicals, for which one might expect significant CT. Here, we analyze CT interactions predicted by several popular energy decomposition analyses and ultimately recommend the definition afforded by constrained density functional theory (cDFT), as it is scarcely dependent on basis set and provides results that are in accord with chemical intuition in simple cases, and in quantitative agreement with experimental estimates of the CT energy, where available. For open-shell complexes, the cDFT approach affords CT energies that are in line with trends expected based on ionization potentials and electron affinities whereas some other definitions afford unreasonably large CT energies in large-gap systems, which are sometimes artificially offset by underestimation of van der Waals interactions by density functional theory. Our recommended energy decomposition analysis is a composite approach, in which cDFT is used to define the CT component of the interaction energy and symmetry-adapted perturbation theory (SAPT) defines the electrostatic, polarization, Pauli repulsion, and van der Waals contributions. SAPT/cDFT provides a stable and physically motivated energy decomposition that, when combined with a new implementation of open-shell SAPT, can be applied to supramolecular complexes involving molecules, ions, and/or radicals.
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Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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Cappelletti D, Aquilanti V, Bartocci A, Nunzi F, Tarantelli F, Belpassi L, Pirani F. Interaction of O2 with CH4, CF4, and CCl4 by Molecular Beam Scattering Experiments and Theoretical Calculations. J Phys Chem A 2016; 120:5197-207. [PMID: 26938313 DOI: 10.1021/acs.jpca.6b00948] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique by measuring both the integral cross section value, Q, and its dependence on the collision velocity, v. The adopted experimental conditions have been appropriate to resolve the oscillating "glory" pattern, a quantum interference effect controlled by the features of the intermolecular interaction, for all the three case studies. The analysis of the Q(v) data, performed by adopting a suitable representation of the intermolecular potential function, provided the basic features of the anisotropic potential energy surfaces at intermediate and large separation distances and information on the relative role of the physically relevant types of contributions to the global interaction. The present work demonstrates that while O2-CH4 and O2-CF4 are basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreaciable intermolecular bond stabilization by charge transfer is operative in O2-CCl4. Ab initio calculations of the strength of the interaction, coupled with detailed analysis of electronic charge displacement promoted by the formation of the dimer, fully rationalizes the experimental findings. This investigation indicates that the interactions of O2, when averaged over its relative orientations, are similar to that of a noble gas (Ng), specifically Ar. We also show that the binding energy in the basic configurations of the prototypical Ng-CF4,CCl4 systems [ Cappelletti , D. ; Chem. Eur. J. 2015 , 21 , 6234 - 6240 ] can be reconstructed by using the interactions in Ng-F and Ng-Cl systems, previously characterized by molecular beam scattering experiments of state-selected halogen atom beams. This information is fundamental to approach the modeling of the weak intermolecular halogen bond. On the basis of the electronic polarizability, this also confirms [ Aquilanti , V. ; Angew. Chem., Int. Ed. 2005 , 44 , 2356 - 2360 ] that O2 can be taken as a proper reference partner for simulating the behavior of some basic noncovalent components of the interactions involving water. Present results are of fundamental relevance to build up the force field controlling the hydrophobic behavior of prototypical apolar CX4 (X = H, F, Cl) molecules.
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Affiliation(s)
- David Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Alessio Bartocci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Francesca Nunzi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy.,CNR-Istituto di Scienze e Tecnologie Molecolari, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Francesco Tarantelli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy.,CNR-Istituto di Scienze e Tecnologie Molecolari, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Leonardo Belpassi
- CNR-Istituto di Scienze e Tecnologie Molecolari, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Fernando Pirani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
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Bartocci A, Frati F, Roncaratti LF, Cappelletti D, Tarantelli F, Belpassi L, Pirani F. Anab initioelectronic density study of the CH4–Ar, CH4–Xe, CH4–H2O and CH4–H2S complexes: insights into the nature of the intermolecular interaction. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1100344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Bartocci A, Belpassi L, Cappelletti D, Falcinelli S, Grandinetti F, Tarantelli F, Pirani F. Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases. J Chem Phys 2015; 142:184304. [DOI: 10.1063/1.4919692] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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11
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Bistoni G, Rampino S, Tarantelli F, Belpassi L. Charge-displacement analysis via natural orbitals for chemical valence: Charge transfer effects in coordination chemistry. J Chem Phys 2015; 142:084112. [DOI: 10.1063/1.4908537] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Giovanni Bistoni
- Istituto di Tecnologie e Scienze Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Sergio Rampino
- Istituto di Tecnologie e Scienze Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Francesco Tarantelli
- Istituto di Tecnologie e Scienze Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Leonardo Belpassi
- Istituto di Tecnologie e Scienze Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
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Cappelletti D, Bartocci A, Frati F, Roncaratti LF, Belpassi L, Tarantelli F, Lakshmi PA, Arunan E, Pirani F. H2O–CH4and H2S–CH4complexes: a direct comparison through molecular beam experiments and ab initio calculations. Phys Chem Chem Phys 2015; 17:30613-23. [DOI: 10.1039/c5cp03704b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron density redistribution upon the formation of the water–methane complex arises from polarisation and charge transfer effects.
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Affiliation(s)
- David Cappelletti
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- Italy
| | - Alessio Bartocci
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- Italy
| | - Federica Frati
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- Italy
| | - Luiz F. Roncaratti
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- Italy
| | | | | | | | - Elangannan Arunan
- Indian Institute of Science
- Dept. Inorgan. & Phys. Chem
- Bangalore 560012
- India
| | - Fernando Pirani
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- Italy
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