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Computational, Investigational Explorations on Structural, Electro-Optic Behavior of Pelargonidin Organic Colorant for TiO2 Based DSSCs. Symmetry (Basel) 2022. [DOI: 10.3390/sym15010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In an expedition for green-energy generation and to lower the cost per watt of solar energy, environmentally friendly biotic colorants were separated from Tectona grandis seeds. The prime colorant in the extract is pelargonidin which sensitizes titanium dioxide (TiO2)-based photo anodes. The pelargonidin-sensitized TiO2 nanomaterials endured structural, photosensitive, spectral and current-voltage interpretations. Frontier molecular orbital analysis, physicochemical and electronic parameter computation, UV–visible and DOS spectral analysis, van der Waals prediction and molecular electrostatic potential map were performed theoretically with Gaussian tools, and IR symmetry response was computed using the crystal maker software package. The pelargonidin-sensitized TiO2-created dye-sensitized solar cells which exhibited capable solar light energy to photon conversion proficiency. For comparative purposes, the commercial P25 Degussa TiO2-based DSSC was also fabricated and its proficiency was analyzed. The commercial TiO2 exhibited 57 % higher proficiency in comparison to the sol-gel-derived TiO2-based DSSC.
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:319505. [PMID: 25977746 PMCID: PMC4419266 DOI: 10.1155/2015/319505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 01/03/2023]
Abstract
Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Joaquín Ortega-Castro
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Juan Frau
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Francisco Muñoz
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
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Comparative Study of Vibrational Spectra of Two Bioactive Natural Products Lupeol and Lupenone Using MM/QM Method. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/486304] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This work deals with the theoretical study on the molecular structure and vibrational spectra of two well-known natural products: lupeol and lupenone. The spectra were interpreted with the aid of normal mode analysis following full-structure optimization carried out with the hybrid two-level ONIOM (B3LYP/6-31G: PM3) method. A detailed interpretation of the infrared spectra of Lupeol and Lupenone is also reported in the present work. The similarities and differences between the vibrational spectra of the two molecules studied have been highlighted. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The thermodynamic calculations related to the title compounds were also performed at B3LYP/6-31G: PM3 level of theory. Quantum chemical calculations have been carried out to understand the dynamical behavior of the bioactive molecules Lupeol and Lupenone.
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Allis DG, Korter TM. DEVELOPMENT OF COMPUTATIONAL METHODOLOGIES FOR THE PREDICTION AND ANALYSIS OF SOLID-STATE TERAHERTZ SPECTRA. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s0129156407004436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The analytical applications of terahertz (THz) spectroscopy for the characterization of molecular solids have been limited by the lack of information concerning the assignment of observed spectral features to specific internal (intramolecular) and external (intermolecular) atomic motions. Computational methodologies addressing the assignment of spectral data are the enabling technology for moving THz spectroscopy to the forefront of available detection methods for both imaging and spectroscopic applications. Solid-state density functional theory (DFT) studies have been performed on the high explosives cyclotetramethylenetetranitramine (HMX) and pentaerythritol tetranitrate (PETN) in order to address the dependencies of the predictions of solid-state vibrations in the terahertz (3 to 120 cm−1) region on the choice of basis set and integration grid size, building on previous work that examined this dependency on the choice of density functional. DFT THz simulations reveal that both the choice of basis set and grid size have important influences on the reproduction of spectral features. The sensitivity to basis set choice is most pronounced in the calculation of vibrational intensities, where it is found that THz absorption intensities are most accurately reproduced when derived from basis set-sensitive Mulliken atomic charges as opposed to basis set-insensitive atomic charges generated by the Hirshfeld partitioning method.
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Affiliation(s)
- Damian G. Allis
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
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DFT study of H-bonds in the peptide secondary structures: The backbone–side-chain and polar side-chains interactions. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.01.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hakey PM, Hudson MR, Allis DG, Ouellette W, Korter TM. Examination of Phencyclidine Hydrochloride via Cryogenic Terahertz Spectroscopy, Solid-State Density Functional Theory, and X-ray Diffraction. J Phys Chem A 2009; 113:13013-22. [DOI: 10.1021/jp907083u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick M. Hakey
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| | - Matthew R. Hudson
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| | - Damian G. Allis
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| | - Wayne Ouellette
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
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Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum. Int J Mol Sci 2009; 10:3358-3370. [PMID: 20111685 PMCID: PMC2812828 DOI: 10.3390/ijms10083358] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/21/2009] [Accepted: 07/27/2009] [Indexed: 11/29/2022] Open
Abstract
Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ɛ-polylysine (ɛ-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and α-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6°. The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.
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Vener MV, Egorova AN, Fomin DP, Tsirelson VG. Hierarchy of the non-covalent interactions in the alanine-based secondary structures. DFT study of the frequency shifts and electron-density features. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1445] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Allis DG, Zeitler JA, Taday PF, Korter TM. Theoretical analysis of the solid-state terahertz spectrum of the high explosive RDX. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Serrano V, Liu W, Franzen S. An infrared spectroscopic study of the conformational transition of elastin-like polypeptides. Biophys J 2007; 93:2429-35. [PMID: 17545236 PMCID: PMC1965438 DOI: 10.1529/biophysj.106.100594] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The infrared spectroscopy of elastin-like polypeptides and the relation to the inverse thermal transition are discussed. To correlate the spectroscopic observations with structure a density function theory model was created that captures the essential hydrogen bonding and packing of the beta-spiral structure proposed for elastin and elastin-like polypeptides. The infrared spectrum was calculated using periodic boundary conditions and a method for estimating the difference dipole moment permits both frequencies and intensities to be obtained for the modeling of spectra. The two observed amide I bands at 1615 cm(-1) and 1656 cm(-1) are shown to arise from the beta-spiral structure. The increase in intensity of these bands with increasing salt concentration and temperature is assigned to the closer association of strands of the beta-spiral. The sharp inverse temperature transition is observed within 1 degrees C and involves a change in secondary structure that involves formation of interstrand beta-sheets for approximately 25% of the amino acids. This conclusion is consistent with available data and simulations that have been reported to date.
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Affiliation(s)
- Vesna Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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Allis DG, Korter TM. Theoretical Analysis of the Terahertz Spectrum of the High Explosive PETN. Chemphyschem 2006; 7:2398-408. [PMID: 17042039 DOI: 10.1002/cphc.200600456] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The experimental solid-state terahertz (THz) spectrum (3 to 120 cm(-1)) of the high explosive pentaerythritol tetranitrate (PETN, C(5)H(6)N(4)O(12)) has been modeled using solid-state density functional theory (DFT) calculations. Solid-state DFT, employing the BP density functional, is in best qualitative agreement with the features in the previously reported THz spectrum. The crystal environment of PETN includes numerous intermolecular hydrogen-bonding interactions that contribute to large (up to 80 cm(-1)) calculated shifts in molecular normal-mode positions in the solid state. Comparison of the isolated-molecule and solid-state normal-mode calculations for a series of density functionals reveals the extent to which the inclusion of crystal-packing interactions and the relative motions between molecules are required for correctly reproducing the vibrational structure of solid-state THz spectra. The THz structure below 120 cm(-1) is a combination of both intermolecular (relative rotations and translations) and intramolecular (torsions, large amplitude motions) vibrational motions. Vibrational-mode analyses indicate that the first major feature (67.2 cm(-1)) in the PETN THz spectrum contains all of the optical rotational and translational cell modes and no internal (molecular) vibrational modes.
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Affiliation(s)
- Damian G Allis
- Department of Chemistry, Syracuse University, 111 College Place; Syracuse, New York 13244-4100, USA
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Allis DG, Prokhorova DA, Korter TM. Solid-State Modeling of the Terahertz Spectrum of the High Explosive HMX. J Phys Chem A 2006; 110:1951-9. [PMID: 16451029 DOI: 10.1021/jp0554285] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The experimental solid-state terahertz (THz) spectrum (3-120 cm(-1)) of the beta-crystal form of the high explosive octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been analyzed using solid-state density functional theory calculations. Various density functionals (both generalized gradient approximation and local density approximation) are compared in terms of their abilities to reproduce the experimentally observed solid-state structure and low-frequency vibrational motions. Good-to-excellent agreement between solid-state theory and experiment can be achieved in the THz region where isolated-molecule calculations fail to reproduce the observed spectral features, demonstrating a clear limitation of using isolated-molecule calculations for the assignment of THz frequency motions in molecular solids. The deficiency of isolated-molecule calculations is traced to modification of the molecular structure in the solid state through crystal packing effects and the formation of weak C-H...O hydrogen bonds.
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Affiliation(s)
- Damian G Allis
- 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, USA
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Ismer L, Ireta J, Boeck S, Neugebauer J. Phonon spectra and thermodynamic properties of the infinite polyalanine alpha helix: a density-functional-theory-based harmonic vibrational analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:031911. [PMID: 15903463 DOI: 10.1103/physreve.71.031911] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 01/10/2005] [Indexed: 05/02/2023]
Abstract
We have performed a density-functional theory harmonic vibrational analysis of the infinite polyalanine alpha helix. The calculated phonon dispersion spectrum shows excellent agreement to available experimental data, except for the high frequency hydrogen stretching modes which show characteristic shifts due to anharmonic effects. A major advantage compared to previously performed empirical force field studies is that long range effects such as electrostatic interaction and polarization are intrinsically taken into account for characterizing hydrogen bond formation in the helix. Our results indicate that these effects are crucial to accurately describe the low frequency acoustical branches and lead to a significantly better agreement with experiment for the specific heat in the low temperature range.
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Affiliation(s)
- Lars Ismer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
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