1
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Internal Rotation of 2-, 3- and 4-Pyridine Carboxaldehydes and Their Chalcogen Analogues (S and Se) in the Gas and Solution Phases: A Theoretical Investigation. J SOLUTION CHEM 2016. [DOI: 10.1007/s10953-016-0499-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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2
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Umar Y, Tijani J. Density functional theory study of the rotational barriers, conformational preference, and vibrational spectra of 2-formylfuran and 3-formylfuran. J STRUCT CHEM+ 2016. [DOI: 10.1134/s0022476615070112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Bharti A, Banerjee T. Solubility prediction of bio-oil derived chemicals in aqueous media by Localized Molecular Orbital-Energy Decomposition Analysis (LMO-EDA) and COSMO-RS predictions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Hidalgo M, Rivelino R, Canuto S. Origin of the Red Shift for the Lowest Singlet π → π* Charge-Transfer Absorption of p-Nitroaniline in Supercritical CO2. J Chem Theory Comput 2014; 10:1554-62. [DOI: 10.1021/ct401081e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcelo Hidalgo
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP Brazil
| | - Roberto Rivelino
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP Brazil
- Instituto
de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia Brazil
| | - Sylvio Canuto
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP Brazil
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5
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Montaña ÁM, Grima PM, Batalla C, Sanz F, Kociok-Köhn G. Use of thep-Tolylsulfinyl Group as a Chiral Inductor in Stereoselective [4+3] Cycloaddition Reactions: Preparation of Enantiopure Polysubstituted 8-Oxabicyclo[3.2.1]oct-6-en-3-one Systems Having up to Five Stereocenters. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301814] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Santander JE, Tsapatsis M, Auerbach SM. Simulating adsorptive expansion of zeolites: application to biomass-derived solutions in contact with silicalite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4866-4876. [PMID: 23495719 DOI: 10.1021/la300932a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have constructed and applied an algorithm to simulate the behavior of zeolite frameworks during liquid adsorption. We applied this approach to compute the adsorption isotherms of furfural-water and hydroxymethyl furfural (HMF)-water mixtures adsorbing in silicalite zeolite at 300 K for comparison with experimental data. We modeled these adsorption processes under two different statistical mechanical ensembles: the grand canonical (V-Nz-μg-T or GC) ensemble keeping volume fixed, and the P-Nz-μg-T (osmotic) ensemble allowing volume to fluctuate. To optimize accuracy and efficiency, we compared pure Monte Carlo (MC) sampling to hybrid MC-molecular dynamics (MD) simulations. For the external furfural-water and HMF-water phases, we assumed the ideal solution approximation and employed a combination of tabulated data and extended ensemble simulations for computing solvation free energies. We found that MC sampling in the V-Nz-μg-T ensemble (i.e., standard GCMC) does a poor job of reproducing both the Henry's law regime and the saturation loadings of these systems. Hybrid MC-MD sampling of the V-Nz-μg-T ensemble, which includes framework vibrations at fixed total volume, provides better results in the Henry's law region, but this approach still does not reproduce experimental saturation loadings. Pure MC sampling of the osmotic ensemble was found to approach experimental saturation loadings more closely, whereas hybrid MC-MD sampling of the osmotic ensemble quantitatively reproduces such loadings because the MC-MD approach naturally allows for locally anisotropic volume changes wherein some pores expand whereas others contract.
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Affiliation(s)
- Julian E Santander
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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7
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Murugan NA, Kongsted J, Rinkevicius Z, Ågren H. Color modeling of protein optical probes. Phys Chem Chem Phys 2012; 14:1107-12. [DOI: 10.1039/c1cp23060c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Saad ZB, Chong SX, Wong ZX, Abdallah HH, Al-Saadi AA. Structural properties and vibrational spectra of 2-formyloxazole and its 2-thioformyl and 2-selenoformyl derivatives. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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9
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Jaramillo P, Coutinho K, Cabral BJ, Canuto S. Explicit solvent effects on the visible absorption spectrum of a photosynthetic pigment: Chlorophyll-c2 in methanol. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Manzoni V, Lyra ML, Coutinho K, Canuto S. Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: Study of the optical and magnetic properties of diazines in water. J Chem Phys 2011; 135:144103. [DOI: 10.1063/1.3644894] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Oliveira LB, Fonseca TL, Coutinho K, Canuto S. A sequential MC/TD-DFT study of the solvatochromic shift of the pyridinium-N-phenoxide betaine dye in water using standard and long-range corrected functionals. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Murugan NA, Chakrabarti S, Ågren H. Solvent dependence of structure, charge distribution, and absorption spectrum in the photochromic merocyanine-spiropyran pair. J Phys Chem B 2011; 115:4025-32. [PMID: 21417244 DOI: 10.1021/jp2004612] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP)-merocyanine (MC) pair, in chloroform and in water solvents using a combined hybrid QM/MM Car-Parrinello molecular dynamics (CP-QM/MM) and ZINDO approach. We report remarkable differences in the molecular structure and charge distribution of MC between the two solvents; the molecular structure of MC remains in neutral form in chloroform while it becomes charge-separated, zwitterionic, in water. The dipole moment of MC in water is about 50% larger than in chloroform, while the value for SP in water is in between, suggesting that the solvent is more influential than the conformation itself in deciding the dipole moment for the merocyanine-spiropyran pair. The calculations could reproduce the experimentally reported blue shift in the absorption spectra of MC when going from the nonpolar to the polar solvent, though the actual value of the absorption maximum is overestimated in chloroform solvent. We find that the CP-QM/MM approach is appropriate for structure modeling of solvatochromic and thermochromic molecules as this approach is able to capture the solvent and thermal-induced structural changes within the solute important for an accurate assessment of the properties.
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Affiliation(s)
- N Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden.
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13
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Rhyman L, Abdallah HH, Ramasami P. Quantum mechanical study of the syn-anti isomerisation of 2-tellurophenecarboaldehyde: vive la différence. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:258-263. [PMID: 21055998 DOI: 10.1016/j.saa.2010.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 08/23/2010] [Accepted: 10/01/2010] [Indexed: 05/30/2023]
Abstract
The syn- and anti-conformers of 2-tellurophenecarboaldehyde are studied in the gas phase. A transition state is also modelled for the syn-anti isomerisation. Computations are done using different methods namely HF, DFT/B3LYP, MP2 and CCSD(T). The basis set used for all atoms is 6-311++G(d,p) except that LanL2DZ ECP is used for tellurium atom only. The optimised molecular structures and related structural parameters of these conformers are reported. The energy differences between the syn- and anti-conformers, associated rotational barriers and thermodynamic parameters are derived from the computations. The infrared frequencies of these conformers are also reported with appropriate assignments. This study is extended to include solvent effect and the conformers are fully optimised (DFT/B3LYP) using the integral equation formalism in the Polarisable Continuum model. In the gas phase, the theoretical rate constant for the unimolecular conversion, anti conformer to transition state, is reported for the first time; DFT/B3LYP (4.82×10(30) s(-1)) and MP2 (7.81×10(30) s(-1)). It is found that the structures are not much affected by the solvents but energy difference increases and rotational barrier decreases. The results indicate that there is a close agreement with the predictions from the different theoretical methods. The results obtained are critically analysed and compared with the furan, thiophene and selenophene analogues. A major factor affecting conformational preference and the mole fraction is the charge on the chalcogen heteroatom in the ring. An interesting outcome of this work is that in both the gas phase and solutions, the syn conformer is more stable and exists almost exclusively.
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Affiliation(s)
- L Rhyman
- Department of Chemistry, University of Mauritius, Réduit, Mauritius
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14
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Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Mikkelsen KV, Ågren H. Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution. Phys Chem Chem Phys 2011; 13:12506-16. [DOI: 10.1039/c1cp20611g] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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15
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Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques. J Phys Chem B 2010; 114:13349-57. [DOI: 10.1021/jp1060717] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- N. Arul Murugan
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Jacob Kongsted
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Kestutis Aidas
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Hans Ågren
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
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16
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Theoretical study of 2-selenophenecarboaldehyde in the gas and solution phases: Rotational barrier, energy difference and thermodynamic parameters. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Solvation and electronic spectrum of Ni2+ ion in aqueous and ammonia solutions: A sequential Monte Carlo/TD-DFT study. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Fonseca TL, Coutinho K, Canuto S. The isotropic nuclear magnetic shielding constants of acetone in supercritical water: A sequential Monte Carlo/quantum mechanics study including solute polarization. J Chem Phys 2008; 129:034502. [DOI: 10.1063/1.2951995] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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19
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Ashish H, Ramasami P. Rotational barrier and thermodynamical parameters of furfural, thiofurfural, and selenofurfural in the gas and solution phases: theoretical study based on density functional theory method. Mol Phys 2008. [DOI: 10.1080/00268970701881196] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Aguilar CM, De Almeida WB, Rocha WR. The electronic spectrum of Fe2+ ion in aqueous solution: A sequential Monte Carlo/quantum mechanical study. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Malaspina T, Fileti EE, Rivelino R. Structure and UV−Vis Spectrum of C60 Fullerene in Ethanol: A Sequential Molecular Dynamics/Quantum Mechanics Study. J Phys Chem B 2007; 111:11935-9. [PMID: 17892279 DOI: 10.1021/jp0746244] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A molecular dynamics simulation combined with semiempirical quantum mechanics calculations has been performed to investigate the structure, dynamical, and electronic properties of pure C60 in liquid ethanol. The behavior of the fullerene alcoholic solution was obtained by using the NPT ensemble under ambient conditions, including one C60 fullerene immersed in 1000 ethanol molecules. Our analyzed center-of-mass pairwise radial distribution function indicated that, on average, there are 32, 72, 132, and 187 ethanol molecules around, respectively, the first, second, third, and fourth solvation shells of the C60 molecule. To investigate the UV-vis transition energies of C60 in the presence of ethanol, we have considered constituents of the time uncorrelated supramolecular structures of the first solvation shell, i.e., clusters of C60@{EtOH}32 types. The semiempirical calculations were performed at the intermediate neglect of differential overlap level with configuration interaction singles (INDO/CIS). Our results have pointed out that the characteristic C60 UV-vis absorbance peaks are slightly shifted to longer wavelengths, as compared to the isolated molecule. These findings are in connection with the weak donor-acceptor character of the interactions involving electron lone pairs of oxygen atoms on the solvent and the fullerene surface.
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Affiliation(s)
- Thaciana Malaspina
- Instituto de Química, Universidade de São Paulo, 05513-970, São Paulo, SP, Brazil
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22
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Rivelino R, de Brito Mota F. Band gap and density of states of the hydrated C60 fullerene system at finite temperature. NANO LETTERS 2007; 7:1526-31. [PMID: 17508768 DOI: 10.1021/nl070308p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We examine the electronic properties of the hydrated C60 fullerene under ambient conditions using a sequential Monte Carlo/density functional theory scheme. In this procedure, the average electronic properties of the first hydration shell of C60 equilibrate for ca. 40 uncorrelated configurations of the fullerene aqueous solution. We obtain a systematic red-shift of 0.8 eV in the band gap of the hydrated system, which is mainly attributed to the thermal fluctuations of the aqueous environment.
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Affiliation(s)
- Roberto Rivelino
- Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil.
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23
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Georg HC, Coutinho K, Canuto S. Solvent effects on the UV-visible absorption spectrum of benzophenone in water: a combined Monte Carlo quantum mechanics study including solute polarization. J Chem Phys 2007; 126:034507. [PMID: 17249884 DOI: 10.1063/1.2426346] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The entire ultraviolet-visible absorption spectrum of benzophenone in water is studied and compared with the same spectrum in gas phase. Five transitions are considered, and the corresponding solvatochromic shifts are obtained and compared to experiment. Using a sequential procedure of Monte Carlo simulations and quantum mechanical calculations, liquid configurations were generated and an averaged spectrum of the solution was calculated. The solute polarization was included by an iterative procedure where the atomic charges of the solute were obtained as an average with the solvent distribution. The calculated average dipole moment of benzophenone in water, with MP26-31++G(d,p), converges to the value of 5.84+/-0.05 D, 88% larger than the gas-phase value of 3.11 D. Using 100 statistically uncorrelated configurations and solvation shells with 235 explicit water molecules selected by a minimum-distance distribution of solvent shells, instead of the usual radial distribution, the excitation energies were obtained from solute-solvent all-valence-electron INDO/CIS calculations. The shift of the weak n-pi(*) transition is obtained as 2045+/-40 cm(-1) and the strong and broad pi-pi(*) shift as -1790+/-30 cm(-1). These results are in good agreement with the experimental values of 2200 and -1600 cm(-1), respectively. Standard procedure used by common force fields to generate atomic charges to describe the electrostatic moments of the solute, with HF6-31G(d), gives a dipole moment of 3.64 D. Using these standard charges in the simulation, the average shifts are calculated as 1395+/-35 and -1220+/-25 cm(-1), both about 600 cm(-1) smaller in magnitude than those obtained with the average converged fully polarized solute. The influence of the solute polarization in the solute-solvent interaction and, in particular, in solute-solvent hydrogen bonds is analyzed.
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Affiliation(s)
- Herbert C Georg
- Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo, Sao Paulo 05315-970, Brazil.
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24
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Król M, Wrona M, Page CS, Bates PA. Macroscopic pKa Calculations for Fluorescein and Its Derivatives. J Chem Theory Comput 2006; 2:1520-9. [PMID: 26627022 DOI: 10.1021/ct600235y] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcin Król
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK, Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, Kraków 31-501, Poland, and Grey Cancer Insitute, Free Radicals Research Group, Mount Vernon Hospital, P.O. Box 100, Northwood, Middlesex HA6 2JR, UK
| | - Marta Wrona
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK, Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, Kraków 31-501, Poland, and Grey Cancer Insitute, Free Radicals Research Group, Mount Vernon Hospital, P.O. Box 100, Northwood, Middlesex HA6 2JR, UK
| | - Christopher S. Page
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK, Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, Kraków 31-501, Poland, and Grey Cancer Insitute, Free Radicals Research Group, Mount Vernon Hospital, P.O. Box 100, Northwood, Middlesex HA6 2JR, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK, Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, Kraków 31-501, Poland, and Grey Cancer Insitute, Free Radicals Research Group, Mount Vernon Hospital, P.O. Box 100, Northwood, Middlesex HA6 2JR, UK
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25
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Lopes JF, de A Menezes VS, Duarte HA, Rocha WR, De Almeida WB, Dos Santos HF. Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution. J Phys Chem B 2006; 110:12047-54. [PMID: 16800515 DOI: 10.1021/jp057448c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Lennard-Jones (12-6) parameters were obtained for all atoms of cisplatin molecule using the ab initio quantum mechanical potential energy surface for the water-cisplatin interaction as reference data. The parameters found were (epsilon/kcal.mol(-1) and sigma/angstroms) 1.0550, 3.6590 (Pt); 0.0381, 4.6272 (Cl); 0.0455, 3.3783 (N); and 0.0185, 0.0936 (H) and provided very good results for the description of the aqueous solution of cisplatin through Monte Carlo simulation. From statistical analysis of solute-solvent interactions, we observed that the NH3 groups are involved in 53% of the calculated hydrogen bonds with a significant contribution from chlorides (41%) and only 6% involving the Pt center. This is in agreement with the expected behavior for such molecules. Two hydration shells with 22 and 81 water molecules, respectively, centered around 4.6 and 7.3 angstroms were found from the center of mass pair correlation function analysis. The cisplatin atomic Lennard-Jones parameters are reported for the first time, and they might be useful for studying the structure, properties, and processes of cisplatin-like molecules in aqueous solution, including explicitly the solvent effect.
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Affiliation(s)
- Juliana Fedoce Lopes
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Martelos, CEP 36036-900, Juiz de Fora, MG, Brazil
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26
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Maggio AM, Barone G, Bruno M, Duca D, Rosselli S. Conformational analysis and DFT calculations of 8α-hydroxy-germacradiene-6,12-olide derivatives. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.976] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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27
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Affiliation(s)
- Jacopo Tomasi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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28
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Rivelino R, Cabral BC, Coutinho K, Canuto S. Electronic polarization in liquid acetonitrile: A sequential Monte Carlo/quantum mechanics investigation. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.03.049] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Duca D, Bifulco G, Barone G, Casapullo A, Fontana A. SCSA Code: Applications on the Cyclopeptide Renieramide. ACTA ACUST UNITED AC 2004; 44:1024-30. [PMID: 15154771 DOI: 10.1021/ci034258v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SCSA is an algorithm designed to get information on molecular conformational properties. The most stable conformers are determined by the homemade SCSA code, performing a multistep systematic conformational search, which involves energy and structure quantum chemical optimizations at low-level and high-level. The SCSA method was employed to analyze the conformational space of the in vacuo cyclopeptide renieramide at AM1 and B3LYP/6-31G(d) levels. Calculations at B3LYP level of the GIAO (13)C NMR chemical shifts were also performed on the final conformers. In fact, to validate the conformational search results experimental and calculated (13)C NMR spectra of renieramide were compared. Slight disagreements observed between experimental and calculated spectra could be attributed to solute-solvent interactions, which were not taken into account in the algorithm proposed here.
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Affiliation(s)
- Dario Duca
- Dipartimento di Chimica Inorganica e Analitica Stanislao Cannizzaro, Università di Palermo, Viale delle Scienze, Parco d'Orleans II, I-90128 Palermo, Italy.
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30
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Rivelino R, Canuto S. Conformational Stability of Lactonitrile−Water Complexes: An ab Initio Study. J Phys Chem A 2004. [DOI: 10.1021/jp037177a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roberto Rivelino
- Instituto de Física, Universidade de São Paulo, C.P. 66318, 05315-970 São Paulo, SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, C.P. 66318, 05315-970 São Paulo, SP, Brazil
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da Silva CO, Mennucci B, Vreven T. Combining Microsolvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water. J Phys Chem A 2003. [DOI: 10.1021/jp0346918] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clarissa O. da Silva
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, BR456 km 47, Rio de Janeiro, Brazil, Dipartimento di Chimica e Chimica Industriale, Universitá degli Studi di Pisa, via Risorgimento 35, Pisa, Italy, and Gaussian Inc., 140 Washington Avenue, North Haven, Connecticut 06473
| | - Benedetta Mennucci
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, BR456 km 47, Rio de Janeiro, Brazil, Dipartimento di Chimica e Chimica Industriale, Universitá degli Studi di Pisa, via Risorgimento 35, Pisa, Italy, and Gaussian Inc., 140 Washington Avenue, North Haven, Connecticut 06473
| | - Thom Vreven
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, BR456 km 47, Rio de Janeiro, Brazil, Dipartimento di Chimica e Chimica Industriale, Universitá degli Studi di Pisa, via Risorgimento 35, Pisa, Italy, and Gaussian Inc., 140 Washington Avenue, North Haven, Connecticut 06473
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