1
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Mendolicchio M, Barone V. Accurate Vibrational and Ro-Vibrational Contributions to the Properties of Large Molecules by a New Engine Employing Curvilinear Internal Coordinates and Vibrational Perturbation Theory to Second Order. J Chem Theory Comput 2024. [PMID: 39215708 DOI: 10.1021/acs.jctc.4c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The unbiased comparison between theory and experiment requires approaches more sophisticated than the basic harmonic-oscillator rigid-rotor model, for taking into account vibrational averaging effects and ro-vibrational couplings in molecules of increasing size. Second-order vibrational perturbation theory based on curvilinear internal coordinates (ICs) offers a remarkable compromise between accuracy and computational cost, thanks to the reduction of mode-mode couplings with respect to their counterparts based on Cartesian coordinates. Therefore, we have developed, implemented, and validated a general engine employing ICs, which allows the accurate evaluation of vibrational averages and ro-vibrational couplings for molecules containing up to about 50 atoms beyond the harmonic approximation. After validation of the new tool for relatively small molecules, the effectiveness of ICs has been demonstrated for some flexible and/or quite large molecular bricks of life.
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2
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Lehtola S, Karttunen AJ. Free and open source software for computational chemistry education. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Susi Lehtola
- Molecular Sciences Software Institute Blacksburg Virginia USA
| | - Antti J. Karttunen
- Department of Chemistry and Materials Science Aalto University Espoo Finland
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3
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Tasinato N, Pietropolli Charmet A, Ceselin G, Salta Z, Stoppa P. In Vitro and In Silico Vibrational-Rotational Spectroscopic Characterization of the Next-Generation Refrigerant HFO-1123. J Phys Chem A 2022; 126:5328-5342. [PMID: 35930010 PMCID: PMC9393866 DOI: 10.1021/acs.jpca.2c04680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Very short-lived substances have recently been proposed as replacements for hydrofluorocarbons (HFCs), in turn being used in place of ozone-depleting substances, in refrigerant applications. In this respect, hydro-fluoro-olefins (HFOs) are attracting particular interest because, due to their reduced global warming potential, they are supposed to be environmentally friendlier. Notwithstanding this feature, they represent a new class of compounds whose spectroscopic properties and reactivity need to be characterized to allow their atmospheric monitoring and to understand their environmental fate. In the present work, the structural, vibrational, and ro-vibrational properties of trifluorothene (HFO-1123, F2C = CHF) are studied by state-of-the-art quantum chemical calculations. The equilibrium molecular structure has an expected error within 2 mÅ and 0.2° for bond lengths and angles, respectively. This represents the first step toward the computation of highly accurate rotational constants for both the ground and first excited fundamental vibrational levels, which reproduce the available experimental data well within 0.1%. Centrifugal distortion parameters and vibrational-rotational coupling terms are computed as well and used to solve some conflicting experimental results. Simulation of the vibrational transition frequencies and intensities beyond the double harmonic approximation and up to three quanta of vibrational excitation provides insights into the couplings ruling the vibrational dynamics and guides the characterization of the gas-phase infrared spectrum experimentally recorded in the range of 200-5000 cm-1. The full characterization of the IR features is completed with the experimental determination of the absorption cross sections over the 400-5000 cm-1 region from which the radiative forcing and global warming potential of HFO-1123 are derived.
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Affiliation(s)
- Nicola Tasinato
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Andrea Pietropolli Charmet
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari Venezia, Via Torino 155, I-30172 Mestre, Italy
| | - Giorgia Ceselin
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Zoi Salta
- Scuola
Normale Superiore, SMART Laboratory, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Paolo Stoppa
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari Venezia, Via Torino 155, I-30172 Mestre, Italy
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4
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Ceselin G, Salta Z, Bloino J, Tasinato N, Barone V. Accurate Quantum Chemical Spectroscopic Characterization of Glycolic Acid: A Route Toward its Astrophysical Detection. J Phys Chem A 2022; 126:2373-2387. [PMID: 35384666 PMCID: PMC9036519 DOI: 10.1021/acs.jpca.2c01419] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Indexed: 11/29/2022]
Abstract
The first step to shed light on the abiotic synthesis of biochemical building blocks, and their further evolution toward biological systems, is the detection of the relevant species in astronomical environments, including earthlike planets. To this end, the species of interest need to be accurately characterized from structural, energetic, and spectroscopic viewpoints. This task is particularly challenging when dealing with flexible systems, whose spectroscopic signature is ruled by the interplay of small- and large-amplitude motions (SAMs and LAMs, respectively) and is further tuned by the conformational equilibrium. In such instances, quantum chemical (QC) calculations represent an invaluable tool for assisting the interpretation of laboratory measurements or even observations. In the present work, the role of QC results is illustrated with reference to glycolic acid (CH2OHCOOH), a molecule involved in photosynthesis and plant respiration and a precursor of oxalate in humans, which has been detected in the Murchison meteorite but not yet in the interstellar medium or in planetary atmospheres. In particular, the equilibrium structure of the lowest-energy conformer is derived by employing the so-called semiexperimental approach. Then, accurate yet cost-effective QC calculations relying on composite post-Hartree-Fock schemes and hybrid coupled-cluster/density functional theory approaches are used to predict the structural and ro-vibrational spectroscopic properties of the different conformers within the framework of the second-order vibrational perturbation theory. A purposely tailored discrete variable representation anharmonic approach is used to treat the LAMs related to internal rotations. The computed spectroscopic data, particularly those in the infrared region, complement the available experimental investigations, thus enhancing the possibility of an astronomical detection of this molecule.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Zoi Salta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
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5
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The Spectroscopic Characterization of Halogenated Pollutants through the Interplay between Theory and Experiment: Application to R1122. Molecules 2022; 27:molecules27030748. [PMID: 35164013 PMCID: PMC8839295 DOI: 10.3390/molecules27030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 01/30/2023] Open
Abstract
In the last decade, halogenated ethenes have seen an increasing interest for different applications; in particular, in refrigeration, air-conditioning and heat pumping. At the same time, their adverse effects as atmospheric pollutants require environmental monitoring, especially by remote sensing spectroscopic techniques. For this purpose, an accurate characterization of the spectroscopic fingerprint—in particular, those of relevance for rotational–vibrational spectroscopy—of the target molecules is strongly needed. This work provides an integrated computational–theoretical investigation on R1122 (2-Chloro-1,1-difluoro-ethylene, ClHC=CF2), a compound widely employed as a key intermediate in different chemical processes. State-of-the-art quantum chemical calculations relying on CCSD(T)-based composite schemes and hybrid CCSD(T)/DFT approaches are used to obtain an accurate prediction of the structural, rotational and vibrational spectroscopic properties. In addition, the equilibrium geometry is obtained by exploiting the semi-experimental method. The theoretical predictions are used to guide the analysis of the experimentally recorded gas-phase infrared spectrum, which is assigned in the 400–6500 cm−1 region. Furthermore, absorption cross sections are accurately determined over the same spectral range. Finally, by using the obtained spectroscopic data, a first estimate of the global warming potential of R1122 vibrational spectra is obtained.
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6
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Debefve LM, Pollock CJ. Systematic assessment of DFT methods for geometry optimization of mononuclear platinum-containing complexes. Phys Chem Chem Phys 2021; 23:24780-24788. [PMID: 34714314 DOI: 10.1039/d1cp01851e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platinum is used extensively as a catalyst for a wide variety of chemical reactions, though its scarcity and price present limitations to expansions of its use. To understand the origin of platinum's versatility-with the goals of both improving the efficiency of existing catalysts and mimicking its reactivity with more abundant metals-the mechanisms of platinum-catalyzed chemical reactions must be understood via structural and spectroscopic characterization of these catalysts under operando conditions. Such data, typically consisting of complex mixtures of species, often prove challenging to interpret, inviting the aid of chemical theory. DFT calculations in particular have proven successful at predicting structural and spectroscopic parameters of transition metal species, though a thorough investigation of how these methods perform for platinum-based complexes has yet to be undertaken. Herein, we evaluated the performance of geometry optimization for five commonly used functionals (BP86, PBE, B3LYP, PBE0, and TPSSh) in combination with various ligand basis sets, relativistic approximations, and solvation and dispersion models. We applied these DFT methods to a training set of 14 platinum-containing complexes with varying sizes, oxidation states, and number and type of ligands and determined that the best-performing method was the PBE0 functional together with the def2-TZVP basis set for the ligand atoms, the ZORA relativistic approximation, and solvation and dispersion corrections. The ability of this DFT methodology to accurately predict metrical parameters was confirmed using two case studies, most notably by comparing the DFT optimized geometry of a previously uncharacterized complex to newly collected EXAFS data, which showed excellent agreement.
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Affiliation(s)
- Louise M Debefve
- Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, New York 14853, USA.
| | - Christopher J Pollock
- Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, New York 14853, USA.
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7
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Ceselin G, Barone V, Tasinato N. Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry. J Chem Theory Comput 2021; 17:7290-7311. [PMID: 34666488 PMCID: PMC8582257 DOI: 10.1021/acs.jctc.1c00788] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The determination
of accurate equilibrium molecular structures
plays a fundamental role for understanding many physical–chemical
properties of molecules, ranging from the precise evaluation of the
electronic structure to the analysis of the role played by dynamical
and environmental effects in tuning their overall behavior. For small
semi-rigid systems in the gas phase, state-of-the-art quantum chemical
computations rival the most sophisticated experimental (from, for
example, high-resolution spectroscopy) results. For larger molecules,
more effective computational approaches must be devised. To this end,
we have further enlarged the compilation of available semi-experimental
(SE) equilibrium structures, now covering the most important fragments
containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new
SE100 database. Next, comparison with geometries optimized by methods
rooted in the density functional theory showed that the already remarkable
results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals
can be further improved by a linear regression (LR) approach. Use
of template fragments (taken from the SE100 library) together with
LR estimates for the missing interfragment parameters paves the route
toward accurate structures of large molecules, as witnessed by the
very small deviations between computed and experimental rotational
constants. The whole approach has been implemented in a user-friendly
tool, termed nano-LEGO, and applied to a number of demanding case
studies.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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8
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Tchounwou PB, Dasari S, Noubissi FK, Ray P, Kumar S. Advances in Our Understanding of the Molecular Mechanisms of Action of Cisplatin in Cancer Therapy. J Exp Pharmacol 2021; 13:303-328. [PMID: 33776489 PMCID: PMC7987268 DOI: 10.2147/jep.s267383] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Cisplatin and other platinum-based chemotherapeutic drugs have been used extensively for the treatment of human cancers such as bladder, blood, breast, cervical, esophageal, head and neck, lung, ovarian, testicular cancers, and sarcoma. Cisplatin is commonly administered intravenously as a first-line chemotherapy for patients suffering from various malignancies. Upon absorption into the cancer cell, cisplatin interacts with cellular macromolecules and exerts its cytotoxic effects through a series of biochemical mechanisms by binding to Deoxyribonucleic acid (DNA) and forming intra-strand DNA adducts leading to the inhibition of DNA synthesis and cell growth. Its primary molecular mechanism of action has been associated with the induction of both intrinsic and extrinsic pathways of apoptosis resulting from the production of reactive oxygen species through lipid peroxidation, activation of various signal transduction pathways, induction of p53 signaling and cell cycle arrest, upregulation of pro-apoptotic genes/proteins, and down-regulation of proto-oncogenes and anti-apoptotic genes/proteins. Despite great clinical outcomes, many studies have reported substantial side effects associated with cisplatin monotherapy, while others have shown substantial drug resistance in some cancer patients. Hence, new formulations and several combinational therapies with other drugs have been tested for the purpose of improving the clinical utility of cisplatin. Therefore, this review provides a comprehensive understanding of its molecular mechanisms of action in cancer therapy and discusses the therapeutic approaches to overcome cisplatin resistance and side effects.
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Affiliation(s)
- Paul B Tchounwou
- Cellomics and Toxicogenomics Research Laboratory, NIH-RCMI Center for Health Disparities Research, Jackson State University, Jackson, MS, USA
| | - Shaloam Dasari
- Cellomics and Toxicogenomics Research Laboratory, NIH-RCMI Center for Health Disparities Research, Jackson State University, Jackson, MS, USA
| | - Felicite K Noubissi
- Cellomics and Toxicogenomics Research Laboratory, NIH-RCMI Center for Health Disparities Research, Jackson State University, Jackson, MS, USA
| | - Paresh Ray
- Department of Chemistry and Biochemistry, College of Science, Engineering and Technology, Jackson State University, Jackson, MS, USA
| | - Sanjay Kumar
- Department of Life Sciences, School of Earth, Biological, and Environmental Sciences, Central University of South Bihar, Gaya, India
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9
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Kaspi-Kaneti AW, Bhandari S, Schubert A, Huang SD, Dunietz BD. Cyanide Bridged Platinum-Iron Complexes as Cisplatin Prodrug Systems: Design and Computational Study. Chemphyschem 2020; 22:106-111. [PMID: 33098742 DOI: 10.1002/cphc.202000748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/13/2020] [Indexed: 11/09/2022]
Abstract
The potential role of cyanide-bridged platinum-iron complexes as an anti-cancer Pt(IV) prodrug is studied. We present design principles of a dual-function prodrug that can upon reduction dissociate and release concurrently six cisplatin units and a ferricyanide anion per prodrug unit. The prodrug molecule is a unique complex of hepta metal centers consisting of a ferricyanide core with six Pt(IV) centers each bonded to the Fe(III) core through a cyano ligand. The functionality of the prodrug is addressed through density functional theory (DFT) calculations.
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Affiliation(s)
- Ariela W Kaspi-Kaneti
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Srijana Bhandari
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Alexander Schubert
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.,Present address: Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Songping D Huang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
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10
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Barone V, Ceselin G, Fusè M, Tasinato N. Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals. Front Chem 2020; 8:584203. [PMID: 33195078 PMCID: PMC7645164 DOI: 10.3389/fchem.2020.584203] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.
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Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Giorgia Ceselin
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
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11
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DFT meets the segmented polarization consistent basis sets: Performances in the computation of molecular structures, rotational and vibrational spectroscopic properties. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127886] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Sohn H, Shin HW, Lee SM. Metal-Mediated Morphology Regulation of Self-Assembled Double-Hydrophilic Block Copolymers. ACS Macro Lett 2020; 9:600-605. [PMID: 35648493 DOI: 10.1021/acsmacrolett.0c00120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report a nanoscale morphology-regulation strategy of self-assembled double-hydrophilic block copolymers with square planar PtII compounds. The selective coordination of PtII on the chelating blocks of poly(acrylic acid)-b-poly(ethylene glycol) (PAA-b-PEG) induced the self-association of metal-chelated unimers by the known cohesive force of PtII. The block-length variation of PAA with constant PEG led to the shape transition from normal core/shell and crew-cut spheres to anisotropic pearl-string structures. On the other hand, PtII adsorption on PEG blocks by extensive hydrogen bonding can further modify the molecular geometry of metal-chelated unimers by decreasing the volume of hydrophilic segments, eventually leading to the shape transition to vesicular structures. This result was well correlated to the structural constraint of PEG conformation estimated by the quantitative 1H NMR analysis. The vesicles also exhibited the enclosing nature for the fluorescent guest molecules, which demonstrated the promising potential for the encapsulating delivery vehicle.
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Affiliation(s)
- Hyerin Sohn
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, Korea
| | - Hyeon-Woo Shin
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, Korea
| | - Sang-Min Lee
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, Korea
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13
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Boussessi R, Tasinato N, Pietropolli Charmet A, Stoppa P, Barone V. Sextic centrifugal distortion constants: interplay of density functional and basis set for accurate yet feasible computations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1734678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | - Paolo Stoppa
- Università Ca’ Foscari Venezia, Dipartimento di Scienze Molecolari e Nanosistemi, Mestre Venezia, Italy
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14
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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15
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Gwee EH, Seeger ZL, Appadoo DRT, Wood BR, Izgorodina EI. Influence of DFT Functionals and Solvation Models on the Prediction of Far-Infrared Spectra of Pt-Based Anticancer Drugs: Why Do Different Complexes Require Different Levels of Theory? ACS OMEGA 2019; 4:5254-5269. [PMID: 31459697 PMCID: PMC6649127 DOI: 10.1021/acsomega.8b03455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/25/2019] [Indexed: 05/06/2023]
Abstract
Computational modeling was applied to far-infrared (FIR) spectra of Pt-based anticancer drugs to study the hydrolysis of these important molecules. Here, we present a study that investigates the influence of different factors-basis sets on non-Pt atoms, relativistic effective core potentials (RECPs) on the Pt atom, density functional theory (DFT) functionals, and solvation models-on the prediction of FIR spectra of two Pt-based anticancer drugs, cisplatin and carboplatin. Geometry optimizations and frequency calculations were performed with a range of functionals (PBE, PBE0, M06-L, and M06-2X), Dunning's correlation-consisted basis sets (VDZ, VTZ, aVDZ, and aVTZ), RECPs (VDZ-pp, VTZ-pp, aVDZ-pp, and aVTZ-pp), and solvation models (IEFPCM, CPCM, and SMD). The best combination of the basis set/DFT functional/solvation model was identified for each anticancer drug by comparing with experimentally available FIR spectra. Different combinations were established for cisplatin and carboplatin, which was rationalized by means of the partial atomic charge scheme, ChelpG, that was utilized to study the charge transfer between the Pt ion and ligands in both cisplatin and carboplatin.
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Affiliation(s)
- Eunice
S. H. Gwee
- Monash
Computational Chemistry Group, School of Chemistry and Centre for Biospectroscopy,
School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, Victoria 3800, Australia
| | - Zoe L. Seeger
- Monash
Computational Chemistry Group, School of Chemistry and Centre for Biospectroscopy,
School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, Victoria 3800, Australia
| | | | - Bayden R. Wood
- Monash
Computational Chemistry Group, School of Chemistry and Centre for Biospectroscopy,
School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, Victoria 3800, Australia
| | - Ekaterina I. Izgorodina
- Monash
Computational Chemistry Group, School of Chemistry and Centre for Biospectroscopy,
School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, Victoria 3800, Australia
- E-mail:
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16
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Malik-Gajewska M, Trynda J, Zierkiewicz W, Helios K, Latajka R, Wietrzyk J, Michalska D. Picoplatin-based complexes with the bioactive orotate and 5-fluoroorotate ligands: Synthesis, DFT calculations, structure, spectroscopic characterization and in vitro cytotoxicity. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Torres M, Khan S, Duplanty M, Lozano HC, Morris TJ, Nguyen T, Rostovtsev YV, DeYonker NJ, Mirsaleh-Kohan N. Raman and Infrared Studies of Platinum-Based Drugs: Cisplatin, Carboplatin, Oxaliplatin, Nedaplatin, and Heptaplatin. J Phys Chem A 2018; 122:6934-6952. [PMID: 30071735 DOI: 10.1021/acs.jpca.8b04023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Marjorie Torres
- Department of Chemistry & Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Sidrah Khan
- Department of Chemistry & Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Michael Duplanty
- Department of Chemistry & Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Hannah C. Lozano
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Tyree J. Morris
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Trang Nguyen
- Department of Chemistry & Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
| | - Yuri V. Rostovtsev
- Center for Nonlinear Sciences and Department of Physics, University of North Texas, Denton, Texas 76203, United States
| | - Nathan J. DeYonker
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Nasrin Mirsaleh-Kohan
- Department of Chemistry & Biochemistry, Texas Woman’s University, Denton, Texas 76204, United States
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18
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Gorle AK, Zhang J, Liu Q, Berners‐Price SJ, Farrell NP. Structural Factors Affecting Binding of Platinum Anticancer Agents with Phospholipids: Influence of Charge and Phosphate Clamp Formation. Chemistry 2018; 24:4643-4652. [DOI: 10.1002/chem.201705822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Anil Kumar Gorle
- Institute for Glycomics Griffith University, Gold Coast Campus Southport Queensland 4222 Australia
| | - Junyong Zhang
- School of Biomedical, Biomolecular & Chemical Sciences University of Western Australia Crawley WA 6009 Australia
- Present address: College of Biological Chemical Science and Engineering, Jiaxing University Jiaxing 314001 P. R. China
| | - Qin Liu
- Department of Chemistry and The Massey Cancer Center Virginia Commonwealth University Richmond 23284 Virginia USA
- Present address: College of Food Science and Engineering Nanjing University of Finance and Economics Nanjing 210023 P. R. China
| | - Susan J. Berners‐Price
- Institute for Glycomics Griffith University, Gold Coast Campus Southport Queensland 4222 Australia
- School of Biomedical, Biomolecular & Chemical Sciences University of Western Australia Crawley WA 6009 Australia
| | - Nicholas P. Farrell
- Institute for Glycomics Griffith University, Gold Coast Campus Southport Queensland 4222 Australia
- Department of Chemistry and The Massey Cancer Center Virginia Commonwealth University Richmond 23284 Virginia USA
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Puzzarini C, Barone V. Diving for Accurate Structures in the Ocean of Molecular Systems with the Help of Spectroscopy and Quantum Chemistry. Acc Chem Res 2018; 51:548-556. [PMID: 29400950 DOI: 10.1021/acs.accounts.7b00603] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The prediction and interpretation of structural properties are the starting points for a deep understanding of thermochemistry, kinetics, and spectroscopic signatures of molecular systems. To give an example, detailed knowledge of the conformational behavior of the main building blocks of biomolecules in the gas phase (i.e., without the perturbing effect of the environment) is a mandatory prerequisite toward the understanding of the role played by different interactions in determining the biological activity in terms of structure-activity relationships. The first step to take is an unambiguous definition of molecular structure. We address the so-called Born-Oppenheimer equilibrium structure, which is defined in a rigorous manner and isotopically independent, and the target accuracy. For the latter, we aim at so-called "spectroscopic" accuracy, which implies uncertainties of a few milliangstroms for bond lengths and smaller than a tenth of degree for angles. If on one side the continuous enhancements of the experimental techniques give access to new and unprecedented spectroscopic determinations, on the other side they require increasing efforts for an unbiased interpretation and analysis. Among the pieces of information, accurate molecular structures play a particularly important role. Indeed, there is a strong relationship between the experimental outcome and the electronic structure of the system. Spectroscopic techniques, in particular those exploited in the gas phase, are therefore accurate and reliable sources for structural information. However, it is seldom straightforward to derive molecular structures directly from the experimental information. Indeed, even in the favorable case of investigations in the gas phase, vibrational effects are always present, and disentangling their contributions requires collection of information for all vibrational modes, a nearly impossible task. To overcome these limitations, joint theory-spectroscopy strategies can be identified, which are referred to as "top-down" and "bottom-up". The first approach, denoted as the semiexperimental approach, relies on extracting from experimental outcomes the equilibrium structure by using quantum-chemical computations to recover vibrational effects. The bottom-up approach consists in verifying the computed equilibrium geometry by means of a comparison between calculated and experimental spectroscopic parameters that probe structural characteristics. In this contribution, we try to review the most important challenges in accurate molecular structure determinations, with particular emphasis on the "solution" provided by a joint theoretical-experimental approach and on the current state of the art. Starting from the illustration of different strategies, we proceed by addressing the increasing complexity in the derivation of equilibrium geometries: we start from the construction of a database of accurate structures, we then face the problem of extending the dimension of the systems amenable to accurate structural determinations, and finally we move to the challenge of understanding the nature of intermolecular interactions.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di
Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei
Cavalieri 7, I-56126 Pisa, Italy
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20
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Tasinato N, Puzzarini C, Barone V. Correct Modeling of Cisplatin: a Paradigmatic Case. Angew Chem Int Ed Engl 2017; 56:13838-13841. [PMID: 28857397 PMCID: PMC5656895 DOI: 10.1002/anie.201707683] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Indexed: 01/20/2023]
Abstract
Quantum chemistry is a useful tool in modern approaches to drug and material design, but only when the adopted model reflects a correct physical picture. Paradigmatic is the case of cis‐diaminodichloroplatinum(II), cis‐[Pt(NH3)2Cl2], for which the correct simulation of the structural and vibrational properties measured experimentally still remains an open question. By using this molecule as a proof of concept, it is shown that state‐of‐the‐art quantum chemical calculations and a simple model, capturing the basic physical flavors, a cis‐[Pt(NH3)2Cl2] dimer, can provide the accuracy required for interpretative purposes. The present outcomes have fundamental implications for benchmark studies aiming at assessing the accuracy of a given computational protocol.
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Affiliation(s)
- Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126, Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126, Pisa, Italy
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