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La Penna G, Tiana D, Giannozzi P. Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function. Molecules 2021; 26:molecules26134044. [PMID: 34279382 PMCID: PMC8271441 DOI: 10.3390/molecules26134044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions.
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Affiliation(s)
- Giovanni La Penna
- Institute of Chemistry of Organometallics Compounds (ICCOM), National Research Council (CNR), via Madonna Del Piano 10, I-50019 Sesto Fiorentino, Italy;
- National Institute of Nuclear Physics (INFN), Section of Roma-Tor Vergata, via Della Ricerca Scientifica 1, I-00133 Roma, Italy
| | - Davide Tiana
- School of Chemistry, University College Cork, T12 YN60 Cork, Ireland;
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science, and Physics, University of Udine, Via Delle Scienze 206, I-33100 Udine, Italy
- Istituto Officina dei Materiali (IOM), National Research Council (CNR), SISSA-ISAS, I-34136 Trieste, Italy
- Correspondence:
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2
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Car–Parrinello molecular dynamics study of the melting behaviors of n -atom (n=6,10) graphene quantum dots. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Mosconi E, Etienne T, De Angelis F. Rashba Band Splitting in Organohalide Lead Perovskites: Bulk and Surface Effects. J Phys Chem Lett 2017; 8:2247-2252. [PMID: 28467716 DOI: 10.1021/acs.jpclett.7b00328] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A Rashba/Dresselhaus band splitting has been recently measured in organohalide perovskites and invoked in various experiments as a possible cause for the reduced electron-hole recombination rates observed in this class of materials. In this Perspective, we discuss the interplay of electronic and nuclear degrees of freedom in defining such an effect in realistic methylammonium lead iodide (MAPbI3) models. We distinguish between bulk and surface effects and find that, while a spatially local (in time and space) effect may be at work in the bulk, a "static" band-splitting effect is found at surfaces due to structural distortion. The proposed surface effect is consistent with the low surface recombination reported for MAPbI3 single crystals and might contribute to the success of organohalide perovskites.
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Affiliation(s)
- Edoardo Mosconi
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), CNR-ISTM, via Elce di Sotto, I-06123, Perugia, Italy
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Thibaud Etienne
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), CNR-ISTM, via Elce di Sotto, I-06123, Perugia, Italy
- Institut Charles Gerhardt - CNRS and Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Filippo De Angelis
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), CNR-ISTM, via Elce di Sotto, I-06123, Perugia, Italy
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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Novir SB, Hashemianzadeh SM. Computational study of new azo dyes with different anchoring groups for dye-sensitised solar cells. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1110629] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Azpiroz JM, De Angelis F. Ligand Induced Spectral Changes in CdSe Quantum Dots. ACS APPLIED MATERIALS & INTERFACES 2015; 7:19736-19745. [PMID: 26289823 DOI: 10.1021/acsami.5b05418] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The rational design of ligand molecules has earned lots of attention as an elegant means to tailor the electronic and optical properties of semiconductor quantum dots (QDs). Aromatic dithiocarbamate molecules, in particular, are known to greatly influence the optoelectronic properties of CdSe QDs, red-shifting the absorption features and enhancing the photoluminescence. Here, we present an integrated computational study, which combines ab initio molecular dynamics and excited state calculations including thousands of excitations, aimed at understanding the impact of this kind of surface ligand on the optoelectronic properties of CdSe QDs. We demonstrate that the valence electronic states of the dithiocarbamate molecules, mostly localized in the anchoring moiety, are responsible for the red-shift of the absorption features of capped CdSe QDs. Ligands develop interfacial electronic states close to the band edges of the CdSe, which enhance the absorption features of the QD and might open new channels for the radiative decay from the excited state, improving optical emission. Hybridized QD/ligand states could also funnel interfacial charge transfer between the inorganic core and surface molecules, a process that lies at the heart of many photovoltaic and photocatalytic devices. This work may pave the way toward the design of new capping ligands that, adsorbed on the QD surface, could provide control over the optoelectronic properties of the semiconductor core.
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Affiliation(s)
- Jon M Azpiroz
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari (ISTM-CNR) , Via Elce di Sotto 8, 06123, Perugia, Italy
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain
| | - Filippo De Angelis
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari (ISTM-CNR) , Via Elce di Sotto 8, 06123, Perugia, Italy
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Bagheri Novir S, Hashemianzadeh SM. Density functional theory study of new azo dyes with different π-spacers for dye-sensitized solar cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 143:20-34. [PMID: 25710111 DOI: 10.1016/j.saa.2015.02.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
Some of new azo-based metal-free dyes with different π-conjugation spacers, such as carbazole, fluorene, pyrrole, thiophene, furan and thiazole, have been investigated with density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. Theoretical calculations allow us to quantify factors such as light harvesting efficiency (LHE), electron injection driving force (ΔG(inject)) and the weight of the LUMO orbital on the carboxylic group (QLUMO) related to the short-circuit photocurrent density (Jsc), and to evaluate both charge recombination between the semiconductor conduction band electrons and the oxidized dyes and/or electrolyte, and also the shift of the conduction band of the semiconductor as a result of the adsorption of the dyes onto the semiconductor surface, associated with the open-circuit photovoltage (Voc). According to the results, we could predict that how the π-conjugation spacers influence the Jsc as well as the Voc of DSSCs. Among these dyes, the carbazole and fluorene-based dyes (dyes 1 and 2) show the highest LHE, ΔG(inject), QLUMO, and the slowest recombination rate. Consequently, the obtained results show that the carbazole and fluorene-based dyes could have the better Jsc and Voc compared to the other dyes.
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Affiliation(s)
- Samaneh Bagheri Novir
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran, Iran
| | - Seyed Majid Hashemianzadeh
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran, Iran.
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Rangel E, Magana LF, Sansores LE. A Theoretical Study of the Interaction of Hydrogen and Oxygen with Palladium or Gold Adsorbed on Pyridine-Like Nitrogen-Doped Graphene. Chemphyschem 2014; 15:4042-8. [DOI: 10.1002/cphc.201402532] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Indexed: 11/07/2022]
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La Penna G, Hureau C, Andreussi O, Faller P. Identifying, by first-principles simulations, Cu[amyloid-β] species making Fenton-type reactions in Alzheimer's disease. J Phys Chem B 2013; 117:16455-67. [PMID: 24313818 DOI: 10.1021/jp410046w] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
According to the amyloid cascade hypothesis, amyloid-β peptides (Aβ) play a causative role in Alzheimer's disease (AD), of which oligomeric forms are proposed to be the most neurotoxic by provoking oxidative stress. Copper ions seem to play an important role as they are bound to Aβ in amyloid plaques, a hallmark of AD. Moreover, Cu-Aβ complexes are able to catalyze the production of hydrogen peroxide and hydroxyl radicals, and oligomeric Cu-Aβ was reported to be more reactive. The flexibility of the unstructured Aβ peptide leads to the formation of a multitude of different forms of both Cu(I) and Cu(II) complexes. This raised the question of the structure-function relationship. We address this question for the biologically relevant Fenton-type reaction. Computational models for the Cu-Aβ complex in monomeric and dimeric forms were built, and their redox behavior was analyzed together with their reactivity with peroxide. A set of 16 configurations of Cu-Aβ was studied and the configurations were classified into 3 groups: (A) configurations that evolve into a linearly bound and nonreactive Cu(I) coordination; (B) reactive configurations without large reorganization between the two Cu redox states; and (C) reactive configurations with an open structure in the Cu(I)-Aβ coordination, which have high water accessibility to Cu. All the structures that showed high reactivity with H2O2 (to form HO(•)) fall into class C. This means that within all the possible configurations, only some pools are able to produce efficiently the deleterious HO(•), while the other pools are more inert. The characteristics of highly reactive configurations consist of a N-Cu(I)-N coordination with an angle far from 180° and high water crowding at the open side. This allows the side-on entrance of H2O2 and its cleavage to form a hydroxyl radical. Interestingly, the reactive Cu(I)-Aβ states originated mostly from the dimeric starting models, in agreement with the higher reactivity of oligomers. Our study gives a rationale for the Fenton-type reactivity of Cu-Aβ and how dimeric Cu-Aβ could lead to a higher reactivity. This opens a new therapeutic angle of attack against Cu-Aβ-based reactive oxygen species production.
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Affiliation(s)
- Giovanni La Penna
- CNR - National Research Council of Italy , ICCOM - Institute for Chemistry of Organo-Metallic Compounds, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
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Pastore M, De Angelis F. Modeling Materials and Processes in Dye-Sensitized Solar Cells: Understanding the Mechanism, Improving the Efficiency. Top Curr Chem (Cham) 2013; 352:151-236. [DOI: 10.1007/128_2013_468] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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10
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Giannozzi P, Jansen K, Penna GL, Minicozzi V, Morante S, Rossi G, Stellato F. Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements. Metallomics 2012; 4:156-65. [DOI: 10.1039/c2mt00148a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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A computational approach to the electronic and optical properties of Ru(II) and Ir(III) polypyridyl complexes: Applications to DSC, OLED and NLO. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.03.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Furlan S, La Penna G. The mechanism of hydrogen uptake in [NiFe] hydrogenase: first-principles molecular dynamics investigation of a model compound. J Biol Inorg Chem 2011; 17:149-64. [DOI: 10.1007/s00775-011-0838-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
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13
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Pastore M, Angelis FD. Computational Modeling of Stark Effects in Organic Dye-Sensitized TiO2 Heterointerfaces. J Phys Chem Lett 2011; 2:1261-1267. [PMID: 26295419 DOI: 10.1021/jz200443w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a computational modeling study, based on DFT and time-dependent DFT techniques, to investigate the origin and the effect of local electric fields on the optical properties of organic dye-sensitized heterointerfaces, examining the case of the indoline D149 sensitizer on TiO2. On the one hand, we give precise information about the anchoring mode of D149 and its orientation with respect to the TiO2 surface, and on the other hand, we provide the computational framework model to interpret the Stark shifts experimentally observed by PIA spectroscopy. Our results show that the presence of oxidized dye molecules induces major spectral changes on the adjacent neutral dyes, which, along with the simulated effect of injected charge into TiO2, provide Stark shifts nicely reproducing the experimental observations.
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Affiliation(s)
- Mariachiara Pastore
- Istituto CNR di Scienze e Tecnologie Molecolari c/o Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari c/o Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy
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La Penna G, Furlan S, Solà M. Measuring electron sharing between atoms in first-principle simulations. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0955-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Abbotto A, Sauvage F, Barolo C, De Angelis F, Fantacci S, Graetzel M, Manfredi N, Marinzi C, Nazeeruddin MK. Panchromatic ruthenium sensitizer based on electron-rich heteroarylvinylene π-conjugated quaterpyridine for dye-sensitized solar cells. Dalton Trans 2011; 40:234-42. [DOI: 10.1039/c0dt01190h] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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De Angelis F, Armelao L. Optical properties of ZnO nanostructures: a hybrid DFT/TDDFT investigation. Phys Chem Chem Phys 2011; 13:467-75. [DOI: 10.1039/c0cp01234c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Furlan S, Hureau C, Faller P, La Penna G. Modeling the Cu+ Binding in the 1−16 Region of the Amyloid-β Peptide Involved in Alzheimer’s Disease. J Phys Chem B 2010; 114:15119-33. [DOI: 10.1021/jp102928h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sara Furlan
- LCC (Laboratoire de Chimie de Coordination), CNRS, 205 route de Narbonne, F-31077 Toulouse, France; UPS, INPT, LCC, Université de Toulouse, F-31077 Toulouse, France; and ICCOM (Institute for Chemistry of Organo-metallic Compounds), CNR (National Research Council), via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Christelle Hureau
- LCC (Laboratoire de Chimie de Coordination), CNRS, 205 route de Narbonne, F-31077 Toulouse, France; UPS, INPT, LCC, Université de Toulouse, F-31077 Toulouse, France; and ICCOM (Institute for Chemistry of Organo-metallic Compounds), CNR (National Research Council), via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Peter Faller
- LCC (Laboratoire de Chimie de Coordination), CNRS, 205 route de Narbonne, F-31077 Toulouse, France; UPS, INPT, LCC, Université de Toulouse, F-31077 Toulouse, France; and ICCOM (Institute for Chemistry of Organo-metallic Compounds), CNR (National Research Council), via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Giovanni La Penna
- LCC (Laboratoire de Chimie de Coordination), CNRS, 205 route de Narbonne, F-31077 Toulouse, France; UPS, INPT, LCC, Université de Toulouse, F-31077 Toulouse, France; and ICCOM (Institute for Chemistry of Organo-metallic Compounds), CNR (National Research Council), via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
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Pastore M, Angelis FD. Aggregation of organic dyes on TiO2 in dye-sensitized solar cells models: an ab initio investigation. ACS NANO 2010; 4:556-562. [PMID: 20020758 DOI: 10.1021/nn901518s] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A density functional theory (DFT), time-dependent DFT, and ab initio second order Møller-Plesset perturbation theory study of the aggregation of the metal free indoline D102 and D149 dyes on extended TiO(2) models is reported. By selecting the relevant dimeric arrangements on the TiO(2) surface and evaluating, at the same time, the associated spectroscopic response, an almost quantitative description of the extremely different aggregation behavior of the two dyes is provided. Nicely reproducing the experimental evidence, the present results predict strong aggregation interactions and a sizable red-shift of the absorption band in the case of D102, while negligible effects for D149. Our results open the possibility of computationally screening the various aggregation patterns and predicting the corresponding optical response, thus paving the way to an effective molecular engineering of further enhanced sensitizers for solar cell applications.
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Affiliation(s)
- Mariachiara Pastore
- Dipartimento di Chimica, Istituto CNR di Scienze e Tecnologie Molecolari, Universita di Perugia, I-06123, Perugia, Italy
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Giannozzi P, Baroni S, Bonini N, Calandra M, Car R, Cavazzoni C, Ceresoli D, Chiarotti GL, Cococcioni M, Dabo I, Dal Corso A, de Gironcoli S, Fabris S, Fratesi G, Gebauer R, Gerstmann U, Gougoussis C, Kokalj A, Lazzeri M, Martin-Samos L, Marzari N, Mauri F, Mazzarello R, Paolini S, Pasquarello A, Paulatto L, Sbraccia C, Scandolo S, Sclauzero G, Seitsonen AP, Smogunov A, Umari P, Wentzcovitch RM. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:395502. [PMID: 21832390 DOI: 10.1088/0953-8984/21/39/395502] [Citation(s) in RCA: 5769] [Impact Index Per Article: 384.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
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Affiliation(s)
- Paolo Giannozzi
- CNR-INFM Democritos National Simulation Center, 34100 Trieste, Italy. Dipartimento di Fisica, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy
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Scandolo S, Giannozzi P, Cavazzoni C, de Gironcoli S, Pasquarello A, Baroni S. First-principles codes for computational crystallography in the Quantum-ESPRESSO package. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.220.5.574.65062] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The Quantum-ESPRESSO package is a multi-purpose and multi-platform software for ab-initio calculations of condensed matter (periodic and disordered) systems. Codes in the package are based on density functional theory and on a plane wave/pseudopotential description of the electronic ground state and are ideally suited for structural optimizations (both at zero and at finite temperature), linear response calculations (phonons, elastic constants, dielectric and Raman tensors, etc.) and high-temperature molecular dynamics. Examples of applications of the codes included in the package are briefly discussed.
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Chen P, Yum JH, De Angelis F, Mosconi E, Fantacci S, Moon SJ, Baker RH, Ko J, Nazeeruddin MK, Grätzel M. High open-circuit voltage solid-state dye-sensitized solar cells with organic dye. NANO LETTERS 2009; 9:2487-92. [PMID: 19438193 DOI: 10.1021/nl901246g] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Solid-state dye-sensitized solar cells were fabricated using an organic dye, 2-cyanoacrylic acid-4-(bis-dimethylfluoreneaniline)dithiophene (JK2), which exhibits more than 1 V open-circuit potential (V(oc)). To scrutinize the origin of high voltage in these cells, transient V(oc) decay measurements and density functional theroy calculations of the interacting dye/semiconductor surface were performed. A negative conduction band shift was observed due to the favorable dipolar field exerted by the JK2 sensitizer to the TiO(2) surface, at variance with heteroleptic Ru(II)-dyes for which an opposite dipole effect was found, providing an increased V(oc).
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Affiliation(s)
- Peter Chen
- Laboratory for Photonics and Interfaces, Institute of Chemical Sciences and Engineering, School of Basic Sciences, Swiss Federal Institute of Technology, CH - 1015 Lausanne, Switzerland
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Furlan S, La Penna G. Modeling of the Zn2+ binding in the 1–16 region of the amyloid β peptide involved in Alzheimer’s disease. Phys Chem Chem Phys 2009; 11:6468-81. [DOI: 10.1039/b822771c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Modeling the interplay of glycine protonation and multiple histidine binding of copper in the prion protein octarepeat subdomains. J Biol Inorg Chem 2008; 14:361-74. [PMID: 19048309 DOI: 10.1007/s00775-008-0454-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 11/14/2008] [Indexed: 11/26/2022]
Abstract
The octarepeat region of the prion protein can bind Cu(2+) ions up to full occupancy (one ion per octarepeat) at neutral pH. While crystallographic data show that the HGGG octarepeat subdomain is the basic binding unit, multiple histidine coordination at lower Cu occupancy has been reported by X-ray absorption spectroscopy, EPR, and potentiometric experiments. In this paper we investigate, with first principles Car-Parrinello simulations, the first step for the formation of the Cu low-level binding mode, where four histidine side chains are coordinated to the same Cu(2+) ion. This step involves the further binding of a second histidine to an already HGGG domain bonded Cu(2+) ion. The influence of the pH on the ability of Cu to bind two histidine side chains was taken into account by simulating different protonation states of the amide N atoms of the two glycines lying nearest to the first histidine. Multiple histidine coordination is also seen to occur when glycine deprotonation occurs and the presence of the extra histidine stabilizes the Cu-peptide complex. Though the stabilization effect slightly decreases with the number of deprotonated glycines (reaching a minimum when both N atoms of the two nearest glycines are available as Cu ligands), the system is still capable of binding the second histidine in a 4N tetrahedral (though slightly distorted) coordination, whose energy is very near to that of the crystallographic square-planar 3N1O coordination. This result suggests that at low metal concentration the reorganization energy associated with Cu(II)/Cu(I) reduction is small also at pH approximately 7, when glycines are deprotonated.
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Li HB, Tian SX, Yang J. Theoretical Study of the Stepwise Protonation of the Dioxo Manganese(V) Porphyrin. J Phys Chem B 2008; 112:15807-12. [DOI: 10.1021/jp808443n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Bei Li
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, 230026, China
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De Angelis F, Fantacci S, Selloni A. Alignment of the dye's molecular levels with the TiO(2) band edges in dye-sensitized solar cells: a DFT-TDDFT study. NANOTECHNOLOGY 2008; 19:424002. [PMID: 21832662 DOI: 10.1088/0957-4484/19/42/424002] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a theoretical study of the lineup of the LUMO of Ru(II)-polypyridyl (N3 and N719) molecular dyes with the conduction band edge of a TiO(2) anatase nanoparticle. We use density functional theory (DFT) and the Car-Parrinello scheme for efficient optimization of the dye-nanoparticle systems, followed by hybrid B3LYP functional calculations of the electronic structure and time-dependent DFT (TDDFT) determination of the lowest vertical excitation energies. The electronic structure and TDDFT calculations are performed in water solution, using a continuum model. Various approximate procedures to compute the excited state oxidation potential of dye sensitizers are discussed. Our calculations show that the level alignment for the interacting nanoparticle-sensitizer system is very similar, within about 0.1 eV, to that for the separated TiO(2) and dye. The excellent agreement of our results with available experimental data indicates that the approach of this work could be used as an efficient predictive tool to help the optimization of dye-sensitized solar cells.
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Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM-CNR), c/o Dipartimento di Chimica, Università di Perugia, Via elce di Sotto 8, I-06213 Perugia, Italy
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26
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Shapir E, Cohen H, Calzolari A, Cavazzoni C, Ryndyk DA, Cuniberti G, Kotlyar A, Di Felice R, Porath D. Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy. NATURE MATERIALS 2008; 7:68-74. [PMID: 18037894 DOI: 10.1038/nmat2060] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 10/15/2007] [Indexed: 05/25/2023]
Abstract
Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and reproducibility. Here, by using scanning tunnelling spectroscopy at cryogenic temperature, we disclose the energy spectrum of poly(G)-poly(C) DNA molecules deposited on gold. The tunnelling current-voltage (I-V) characteristics and their derivative (dI/dV-V) curves at 78 K exhibit a clear gap and a peak structure around the gap. Limited fluctuations in the I-V curves are observed and statistically characterized. By means of ab initio density functional theory calculations, the character of the observed peaks is generally assigned to groups of orbitals originating from the different molecular components, namely the nucleobases, the backbone and the counterions.
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Affiliation(s)
- Errez Shapir
- Physical Chemistry Department and Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
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27
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De Angelis F, Fantacci S, Selloni A, Nazeeruddin MK, Grätzel M. Time-dependent density functional theory investigations on the excited states of Ru(II)-dye-sensitized TiO2 nanoparticles: the role of sensitizer protonation. J Am Chem Soc 2007; 129:14156-7. [PMID: 17960934 DOI: 10.1021/ja076293e] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM), c/o Dipartimento di Chimica, Università di Perugia, Perugia, Italy.
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28
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Furlan S, La Penna G, Guerrieri F, Morante S, Rossi GC. Studying the Cu binding sites in the PrP N-terminal region: a test case for ab initio simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:841-5. [PMID: 17492282 DOI: 10.1007/s00249-007-0162-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/09/2007] [Accepted: 03/20/2007] [Indexed: 11/25/2022]
Abstract
First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as a test case a study of the Cu coordination mode at the Prion Protein binding sites localized in the N-terminal octarepeat region. Using medium size PC-clusters, we are able to deal with systems with up to about 350 atoms and 10(3) electrons for as long as approximately 2 ps. With a foreseeable forthcoming scaling up of the available CPU times by a factor 10(3), one can hope to be soon able to simulate systems of biological interest of realistic size and for physical times of the order of the nanosecond.
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Affiliation(s)
- S Furlan
- Consiglio Nazionale delle Ricerche, ISMAC, Via De Marini 6, Genoa, Italy.
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29
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Furlan S, Penna GL, Banci L, Mealli C. Ab initio molecular dynamics of heme in cytochrome c. J Phys Chem B 2007; 111:1157-64. [PMID: 17266270 DOI: 10.1021/jp062609d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.
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Affiliation(s)
- Sara Furlan
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Firenze, Italy
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De Angelis F, Jin N, Car R, Groves JT. Electronic structure and reactivity of isomeric oxo-Mn(V) porphyrins: effects of spin-state crossing and pKa modulation. Inorg Chem 2007; 45:4268-76. [PMID: 16676990 DOI: 10.1021/ic060306s] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactivity of the isomeric oxo-Mn(V)-2-tetra-N-methylpyridyl (2-TMPyP) and oxo-Mn(V)-4-tetra-N-methylpyridyl (4-TMPyP) porphyrins has been investigated by a combined experimental and theoretical approach based on density functional theory. The unusual higher reactivity of the more electron-rich 4-TMPyP species appears to be related to both the higher basicity of its oxo ligand, compared to that of the 2-TMPyP isomer, and the smaller low-spin-high-spin promotion energy of 4-TMPyP, compared to that of 2-TMPyP, because of the stabilization of the A2u orbital in the latter isomer. Therefore, in a two-state energy profile involving crossing of the initial singlet and final quintet potential energy surfaces, the 4-TMPyP isomer should be kinetically favored. The calculated differences in the singlet-quintet gaps for the 2-TMPyP and 4-TMPyP systems compare well with the measured differences in the activation energies for two isomeric porphyrins. Both effects, proton affinity and electron-promotion energy, contribute to reduce the reactivity of the more electrophilic oxidant when electron-withdrawing groups are closer to the active site, contrary to the usual expectations based on simple chemical reactivity correlations. These theoretical results are in accord with new experimental data showing O=Mn(V)-O-H pK(a)s of 7.5 and 8.6 for the isomeric 2-TMPyP and 4-TMPyP systems, respectively.
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Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM), c/o Dipartimento di Chimica, ISTM-CNR Perugia, Via elce di Sotto 8, I-06213, Perugia, Italy.
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31
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Bagno A, D'Amico F, Saielli G. Computing the1H NMR Spectrum of a Bulk Ionic Liquid from Snapshots of Car–Parrinello Molecular Dynamics Simulations. Chemphyschem 2007; 8:873-81. [PMID: 17366643 DOI: 10.1002/cphc.200600725] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have investigated the performance of several computational protocols in predicting the NMR spectrum of a molecular ion in a complex liquid phase such as an ionic liquid. To do this, we computed the proton NMR chemical shifts of the 1-ethyl-3-methylimidazolium cation [emim](+) in [emim][Cl]. Environmental effects on the imidazolium ring proton chemical shifts are quite significant and must be taken into account explicitly. Calculations performed on the isolated imidazolium cation as well as on the [emim][Cl] ion pair grossly fail to reproduce the correct spacing between proton signals. In contrast, calculations performed on clusters extracted from the trajectory of a Car-Parrinello molecular dynamics simulation yield very good results.
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Affiliation(s)
- Alessandro Bagno
- Dipartimento di Scienze Chimiche, Università di Padova via Marzolo, 135131 Padova, Italy.
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De Angelis F, Fantacci S, Sgamellotti A. An integrated computational tool for the study of the optical properties of nanoscale devices: application to solar cells and molecular wires. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0224-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Kulik HJ, Cococcioni M, Scherlis DA, Marzari N. Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach. PHYSICAL REVIEW LETTERS 2006; 97:103001. [PMID: 17025809 DOI: 10.1103/physrevlett.97.103001] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2006] [Indexed: 05/11/2023]
Abstract
Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlated-electron quantum chemistry calculations in test cases that range from the ground state of Fe2 and Fe2- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach.
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Affiliation(s)
- Heather J Kulik
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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34
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De Angelis F, Fantacci S, Sgamellotti A. Ab initio molecular dynamics simulations of organometallic reactivity. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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De Angelis F, Tarantelli F, Alunni S. Ab Initio Molecular Dynamics Simulations of Elimination Reactions in Water Solution: Exploring the Borderline Region between the E1cb and E2 Reaction Mechanisms. J Phys Chem B 2006; 110:11014-9. [PMID: 16771355 DOI: 10.1021/jp061321l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.
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Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari, c/o Dipartimento di Chimica, Università di Perugia, Via elce di Sotto 8, I-06213, Perugia, Italy.
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36
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Rega N, Brancato G, Barone V. Non-periodic boundary conditions for ab initio molecular dynamics in condensed phase using localized basis functions. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.02.051] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Wang M, Wong CF. Calculation of Solvation Free Energy from Quantum Mechanical Charge Density and Continuum Dielectric Theory. J Phys Chem A 2006; 110:4873-9. [PMID: 16599457 DOI: 10.1021/jp0565195] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have combined ultrasoft pseudopotential density functional theory utilizing plane wave basis with a Poisson-Boltzmann/solvent-accessible surface area (PB/SA) model to calculate the solvation free energy of small neutral organic compounds in water. The solute charge density obtained from density functional theory was directly used in solving the Poisson-Boltzmann equation to obtain the reaction field. The polarized electronic wave function of the solute in the solvent was solved by including the reaction field in the density functional Hamiltonian. The quantum mechanical and Poisson-Boltzmann equations were solved self-consistently until the charge density and reaction field converged. Using the solute charge density directly instead of a point-charge representation permitted asymmetric distortion and spreading out of the electron cloud. Because the electron density could leave the van der Waals surface to penetrate into the high-dielectric solvent, the reaction field generated by this density was generally smaller than that obtained by using the point-charge representation. In applying this model to calculate the solvation free energy of 31 small neutral organic molecules spanning a range of 25 kcal/mol, we obtained a root-mean-square error of only 1.3 kcal/mol if we allowed one adjustable parameter to shift the calculated solvation free energy.
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Affiliation(s)
- Mingliang Wang
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, One University Boulevard, 63121, USA
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38
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Pavone M, Cimino P, De Angelis F, Barone V. Interplay of Stereoelectronic and Enviromental Effects in Tuning the Structural and Magnetic Properties of a Prototypical Spin Probe: Further Insights from a First Principle Dynamical Approach. J Am Chem Soc 2006; 128:4338-47. [PMID: 16569010 DOI: 10.1021/ja0574872] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.
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Affiliation(s)
- Michele Pavone
- Dipartimento di Chimica, Università di Napoli FedericoII, Complesso Universitario di Monte Sant'Angelo Via Cintia, Italy
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Pavone M, Crescenzi O, Morelli G, Rega N, Barone V. Solvent Effects on the UV (n → π*) and NMR (17O) Spectra of Acetone in Aqueous Solution: Development and Validation of a Modified AMBER Force Field for an Integrated MD/DFT/PCM Approach. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0098-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Fantacci S, De Angelis F, Sgamellotti A, Marrone A, Re N. Photophysical Properties of [Ru(phen)2(dppz)]2+ Intercalated into DNA: An Integrated Car−Parrinello and TDDFT Study. J Am Chem Soc 2005; 127:14144-5. [PMID: 16218583 DOI: 10.1021/ja054368d] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined Car-Parrinello and time-dependent DFT calculations performed on [Ru(phen)2dppz]2+ intercalated into an adenine-thymine tetramer reveal a remarkable influence of the base pairs in determining the electronic structure and the character of the excited states involved in the absorption and emission processes.
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Affiliation(s)
- Simona Fantacci
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM-CNR), c/o Dipartimento di Chimica, Università di Perugia, I-06213 Perugia, Italy.
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41
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Andruniów T, Fantacci S, De Angelis F, Ferré N, Olivucci M. Mechanism of the Initial Conformational Transition of a Photomodulable Peptide. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Andruniów T, Fantacci S, De Angelis F, Ferré N, Olivucci M. Mechanism of the Initial Conformational Transition of a Photomodulable Peptide. Angew Chem Int Ed Engl 2005; 44:6077-81. [PMID: 16108079 DOI: 10.1002/anie.200501145] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tadeusz Andruniów
- Dipartimento di Chimica, Università degli Studi di Siena via Aldo Moro, 53100 Siena, Italy
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43
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Kanai Y, Takeuchi N, Car R, Selloni A. Role of Molecular Conjugation in the Surface Radical Reaction of Aldehydes with H−Si(111): First Principles Study. J Phys Chem B 2005; 109:18889-94. [PMID: 16853431 DOI: 10.1021/jp0527610] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).
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Affiliation(s)
- Yosuke Kanai
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
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44
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Iozzi MF, Cossi M. Ab Initio Theoretical Study of Substituted Dicarboxylic Acids Adsorbed on GaAs Surfaces: Correlation between Microscopic Properties and Observed Electrical Behavior. J Phys Chem B 2005; 109:15383-90. [PMID: 16852951 DOI: 10.1021/jp052855+] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Five substituted tartaric acid derivatives are studied using density functional theory, both isolated and adsorbed onto an oxidized GaAs cluster, to model molecular layers on semiconductor surfaces. The structures, energies, and electronic properties are computed to clarify the interactions responsible for the electric behavior of the modified surfaces, used in semiconductor/metal junction devices. The chemical structure of the molecule/GaAs adducts is optimized ab initio and discussed for the first time. A strong binding scheme is found, providing useful insights about the microscopic structure of the molecular layer. A widely used model based on molecular dipole layers is discussed and verified, by computing the dipole moment for the isolated systems and estimating the charge separation in the adducts; moreover the molecular orbitals energies are analyzed and correlated to the experimental measures of the modified surface electron affinity.
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Affiliation(s)
- Maria Francesca Iozzi
- Dipartimento di Chimica, Università di Napoli Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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45
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De Angelis F, Sgamellotti A, Re N, Fantacci S. Intramolecular Coupling of η2-Iminoacyls on Zirconium Bis(aryloxides) and Calix[4]arenes: Revised Mechanism by DFT Calculations and Car−Parrinello Molecular Dynamics Simulations. Organometallics 2005. [DOI: 10.1021/om0491591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo De Angelis
- Istituto di Scienze e Tecnologie Molecolari (ISTM-CNR), Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy, and Facoltà di Farmacia, Università G. D'Annunzio, I-66100 Chieti, Italy
| | - Antonio Sgamellotti
- Istituto di Scienze e Tecnologie Molecolari (ISTM-CNR), Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy, and Facoltà di Farmacia, Università G. D'Annunzio, I-66100 Chieti, Italy
| | - Nazzareno Re
- Istituto di Scienze e Tecnologie Molecolari (ISTM-CNR), Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy, and Facoltà di Farmacia, Università G. D'Annunzio, I-66100 Chieti, Italy
| | - Simona Fantacci
- Istituto di Scienze e Tecnologie Molecolari (ISTM-CNR), Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy, and Facoltà di Farmacia, Università G. D'Annunzio, I-66100 Chieti, Italy
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Scherlis DA, Marzari N. π-Stacking in Thiophene Oligomers as the Driving Force for Electroactive Materials and Devices. J Am Chem Soc 2005; 127:3207-12. [PMID: 15740161 DOI: 10.1021/ja043557d] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pi-stacking between aromatic oligomers has been extensively studied for many years, although the notion of exploiting this phenomenon as the driving force for molecular actuation has only recently emerged. In this work we examine with MP2 and Car-Parrinello ab initio calculations the actuation properties of a novel class of thiophene-based materials introduced by Swager et al. (Adv. Mater. 2002, 14, 368; J. Am. Chem. Soc. 2003, 125, 1142). The chemical ingredients of the assembly, calix[4]arenes and oligothiophenes, are screened separately to characterize the actuation mechanisms and design optimal architectures. In particular, ab initio methods are used to study pi-stacking in mixed-valence oligothiophene dimers, revealing strong interactions that can be turned on and off as a function of the electrochemical potential. We show how these interactions could be harnessed to achieve molecular actuation and investigate the response of an active unit in real time with first-principles molecular dynamics simulations.
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Affiliation(s)
- Damian A Scherlis
- Department of Materials Science and Engineering and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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De Angelis F, Jarzecki AA, Car R, Spiro TG. Quantum Chemical Evaluation of Protein Control over Heme Ligation: CO/O2 Discrimination in Myoglobin. J Phys Chem B 2005; 109:3065-70. [PMID: 16851321 DOI: 10.1021/jp0451851] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Control of O2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8 degrees ) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O2 decreased by 0.8 and 4.1 kcal/mol for MbCO and MbO2, in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO2 that may play a key role in MbO2 photodynamics.
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Affiliation(s)
- Filippo De Angelis
- Chemistry Department, Princeton University, Princeton, New Jersey 08544, USA
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Hammond PS, Wu Y, Harris R, Minehardt TJ, Car R, Schmitt JD. Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car–Parrinello) molecular dynamics. J Comput Aided Mol Des 2005; 19:1-15. [PMID: 16059663 DOI: 10.1007/s10822-005-0096-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Accepted: 12/29/2004] [Indexed: 11/26/2022]
Abstract
A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.
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Affiliation(s)
- Philip S Hammond
- Targacept, Inc., 200 East First Street, Suite 300, Winston-Salem, NC 27101-4165, USA.
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Crescenzi O, Pavone M, De Angelis F, Barone V. Solvent Effects on the UV (n → π*) and NMR (13C and 17O) Spectra of Acetone in Aqueous Solution. An Integrated Car−Parrinello and DFT/PCM Approach. J Phys Chem B 2004; 109:445-53. [PMID: 16851035 DOI: 10.1021/jp046334i] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accurate reproduction of ultraviolet and nuclear magnetic resonance spectra of acetone in aqueous solution is used as a test of an integrated computational tool rooted in the density functional theory, the polarizable continuum model, and the Car-Parrinello dynamics. The analysis and solution of several conceptual and practical issues results in a robust and effective approach, which also can be used by nonspecialists and provides a general and powerful complement to experimental techniques.
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Affiliation(s)
- Orlando Crescenzi
- Dipartimento di Chimica, Università di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Napoli, Italy
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De Angelis F, Tilocca A, Selloni A. Time-Dependent DFT Study of [Fe(CN)6]4- Sensitization of TiO2 Nanoparticles. J Am Chem Soc 2004; 126:15024-5. [PMID: 15547988 DOI: 10.1021/ja045152z] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-dependent DFT calculations have been performed on the absorption spectrum of [Fe(CN)6]4- adsorbed on a TiO2 anatase nanoparticle model to provide a detailed description of the electronic structure for this prototype system and to understand the character of the states involved in the molecule --> semiconductor charge transfer process. Our results show that a direct charge injection process from an occupied dye molecular state to a nanoparticle excited state localized on a few Ti atoms, rather than to a delocalized conduction state, effectively takes place in this system, in agreement with recent experimental evidence.
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Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM), Dipartimento di Chimica, Università di Perugia, I-06213, Perugia, Italy.
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