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Going Beyond the GW Approximation Using the Time-Dependent Hartree-Fock Vertex. J Chem Theory Comput 2024. [PMID: 38772396 DOI: 10.1021/acs.jctc.4c00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The time-dependent Hartree-Fock (TDHF) vertex of many-body perturbation theory (MBPT) makes it possible to extend TDHF theory to charged excitations. Here we assess its performance by applying it to spherical atoms in their neutral electronic configuration. On a theoretical level, we recast the TDHF vertex as a reducible vertex, highlighting the emergence of a self-energy expansion purely in orders of the bare Coulomb interaction; then, on a numerical level, we present results for polarizabilities, ionization energies (IEs), and photoemission satellites. We confirm the superiority of THDF over simpler methods such as the random phase approximation for the prediction of atomic polarizabilities. We then find that the TDHF vertex reliably provides better IEs than GW and low-order self-energies do in the light-atom, few-electron regime; its performance degrades in heavier, many-electron atoms instead, where an expansion in orders of an unscreened Coulomb interaction becomes less justified. New relevant features are introduced in the satellite spectrum by the TDHF vertex, but the experimental spectra are not fully reproduced due to a missing account of nonlinear effects connected to hole relaxation. We also explore various truncations of the self-energy given by the TDHF vertex, but do not find them to be more convenient than low-order approximations such as GW and second Born (2B), suggesting that vertex corrections should be carried out consistently both in the self-energy and in the polarizability.
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2
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Excitonic Effects in Energy-Loss Spectra of Freestanding Graphene. NANO LETTERS 2023; 23:11835-11841. [PMID: 38088831 DOI: 10.1021/acs.nanolett.3c03863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
In this work, we perform electron energy-loss spectroscopy (EELS) of freestanding graphene with high energy and momentum resolution to disentangle the quasielastic scattering from the excitation gap of Dirac electrons close to the optical limit. We show the importance of many-body effects on electronic excitations at finite transferred momentum by comparing measured EELS to ab initio calculations at increasing levels of theory. Quasi-particle corrections and excitonic effects are addressed within the GW approximation and the Bethe-Salpeter equation, respectively. Both effects are essential in the description of the EEL spectra to obtain a quantitative agreement with experiments, with the position, dispersion, and shape of both the excitation gap and the π plasmon being significantly affected by excitonic effects.
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Distinguishing Different Stackings in Layered Materials via Luminescence Spectroscopy. PHYSICAL REVIEW LETTERS 2023; 131:206902. [PMID: 38039447 DOI: 10.1103/physrevlett.131.206902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/12/2023] [Indexed: 12/03/2023]
Abstract
Despite its simple crystal structure, layered boron nitride features a surprisingly complex variety of phonon-assisted luminescence peaks. We present a combined experimental and theoretical study on ultraviolet-light emission in hexagonal and rhombohedral bulk boron nitride crystals. Emission spectra of high-quality samples are measured via cathodoluminescence spectroscopy, displaying characteristic differences between the two polytypes. These differences are explained using a fully first-principles computational technique that takes into account radiative emission from "indirect," finite-momentum excitons via coupling to finite-momentum phonons. We show that the differences in peak positions, number of peaks, and relative intensities can be qualitatively and quantitatively explained, once a full integration over all relevant momenta of excitons and phonons is performed.
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Numerically Precise Benchmark of Many-Body Self-Energies on Spherical Atoms. J Chem Theory Comput 2022; 18:3703-3717. [PMID: 35561415 PMCID: PMC9202310 DOI: 10.1021/acs.jctc.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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We investigate the
performance of beyond-GW approaches in many-body
perturbation theory by addressing atoms described within the spherical
approximation via a dedicated numerical treatment based on B-splines
and spherical harmonics. We consider the GW, second Born (2B), and
GW + second order screened exchange (GW+SOSEX) self-energies and use
them to obtain ionization potentials from the quasi-particle equation
(QPE) solved perturbatively on top of independent-particle calculations.
We also solve the linearized Sham–Schlüter equation
(LSSE) and compare the resulting xc potentials against exact data.
We find that the LSSE provides consistent starting points for the
QPE but does not present any practical advantage in the present context.
Still, the features of the xc potentials obtained with it shed light
on possible strategies for the inclusion of beyond-GW diagrams in
the many-body self-energy. Our findings show that solving the QPE
with the GW+SOSEX self-energy on top of a PBE or PBE0 solution is
a viable scheme to go beyond GW in finite systems, even in the atomic
limit. However, GW shows a comparable performance if one agrees to
use a hybrid starting point. We also obtain promising results with
the 2B self-energy on top of Hartree–Fock, suggesting that
the full time-dependent Hartree–Fock vertex may be another
viable beyond-GW scheme for finite systems.
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Abstract
Spontaneous condensation of excitons is a long-sought phenomenon analogous to the condensation of Cooper pairs in a superconductor. It is expected to occur in a semiconductor at thermodynamic equilibrium if the binding energy of the excitons-electron (e) and hole (h) pairs interacting by Coulomb force-overcomes the band gap, giving rise to a new phase: the "excitonic insulator" (EI). Transition metal dichalcogenides are excellent candidates for the EI realization because of reduced Coulomb screening, and indeed a structural phase transition was observed in few-layer systems. However, previous work could not disentangle to which extent the origin of the transition was in the formation of bound excitons or in the softening of a phonon. Here we focus on bulk [Formula: see text] and demonstrate theoretically that at high pressure it is prone to the condensation of genuine excitons of finite momentum, whereas the phonon dispersion remains regular. Starting from first-principles many-body perturbation theory, we also predict that the self-consistent electronic charge density of the EI sustains an out-of-plane permanent electric dipole moment with an antiferroelectric texture in the layer plane: At the onset of the EI phase, those optical phonons that share the exciton momentum provide a unique Raman fingerprint for the EI formation. Finally, we identify such fingerprint in a Raman feature that was previously observed experimentally, thus providing direct spectroscopic confirmation of an ideal excitonic insulator phase in bulk [Formula: see text] above 30 GPa.
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Abstract
The dispersion of the electronic states of epitaxial graphene (Gr) depends significantly on the strength of the bonding with the underlying substrate. We report on empty electron states in cobalt-intercalated Gr grown on Ir(111), studied by angle-resolved inverse photoemission spectroscopy and x-ray absorption spectroscopy, complemented with density functional theory calculations. The weakly bonded Gr on Ir preserves the peculiar spectroscopic features of the Gr band structure, and the empty spectral densities are almost unperturbed. Upon intercalation of a Co layer, the electronic response of the interface changes, with an intermixing of the Gr π* bands and Co d states, which breaks the symmetry of π/σ states, and a downshift of the upper part of the Gr Dirac cone. Similarly, the image potential of Ir(111) is unaltered by the Gr layer, while a downward shift is induced upon Co intercalation, as unveiled by the image state energy dispersion mapped in a large region of the surface Brillouin zone.
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Surface chemistry effects on work function, ionization potential and electronic affinity of Si(100), Ge(100) surfaces and SiGe heterostructures. Phys Chem Chem Phys 2020; 22:25593-25605. [PMID: 33164017 DOI: 10.1039/d0cp04013d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We combine density functional theory and many body perturbation theory to investigate the electronic properties of Si(100) and Ge(100) surfaces terminated with halogen atoms (-I, -Br, -Cl, -F) and other chemical functionalizations (-H, -OH, -CH3) addressing the absolute values of their work function, electronic affinity and ionization potential. Our results point out that electronic properties of functionalized surfaces strongly depend on the chemisorbed species and much less on the surface crystal orientation. The presence of halogens at the surface always leads to an increment of the work function, ionization potential and electronic affinity with respect to fully hydrogenated surfaces. On the contrary, the presence of polar -OH and -CH3 groups at the surface leads to a reduction of the aforementioned quantities with respect to the H-terminated system. Starting from the work functions calculated for the Si and Ge passivated surfaces, we apply a simple model to estimate the properties of functionalized SiGe surfaces. The possibility of modulating the work function by changing the chemisorbed species and composition is predicted. The effects induced by different terminations on the band energy line-up profile of SiGe surfaces are then analyzed. Interestingly, our calculations predict a type-II band offset for the H-terminated systems and a type-I band offset for the other cases.
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A monolayer transition-metal dichalcogenide as a topological excitonic insulator. NATURE NANOTECHNOLOGY 2020; 15:367-372. [PMID: 32123382 DOI: 10.1038/s41565-020-0650-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Monolayer transition-metal dichalcogenides in the T' phase could enable the realization of the quantum spin Hall effect1 at room temperature, because they exhibit a prominent spin-orbit gap between inverted bands in the bulk2,3. Here we show that the binding energy of electron-hole pairs excited through this gap is larger than the gap itself in the paradigmatic case of monolayer T' MoS2, which we investigate from first principles using many-body perturbation theory4. This paradoxical result hints at the instability of the T' phase in the presence of spontaneous generation of excitons, and we predict that it will give rise to a reconstructed 'excitonic insulator' ground state5-7. Importantly, we show that in this monolayer system, topological and excitonic order cooperatively enhance the bulk gap by breaking the crystal inversion symmetry, in contrast to the case of bilayers8-16 where the frustration between the two orders is relieved by breaking time reversal symmetry13,15,16. The excitonic topological insulator is distinct from the bare topological phase because it lifts the band spin degeneracy, which results in circular dichroism. A moderate biaxial strain applied to the system leads to two additional excitonic phases, different in their topological character but both ferroelectric17,18 as an effect of electron-electron interaction.
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Many-body perturbation theory calculations using the yambo code. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:325902. [PMID: 30943462 DOI: 10.1088/1361-648x/ab15d0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo's capabilities include the calculation of linear response quantities (both independent-particle and including electron-hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron-phonon interactions to the implementation of a real-time propagation scheme for simulating linear and non-linear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools.
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Abstract
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The definition of plasmon at the
microscopic scale is far from
being understood. Yet, it is very important to recognize plasmonic
features in optical excitations, as they can inspire new applications
and trigger new discoveries by analogy with the rich phenomenology
of metal nanoparticle plasmons. Recently, the concepts of plasmonicity
index and the generalized plasmonicity index (GPI) have been devised
as computational tools to quantify the plasmonic nature of optical
excitations. The question may arise whether any strong absorption
band, possibly with some sort of collective character in its microscopic
origin, shares the status of plasmon. Here we demonstrate that this
is not always the case, by considering a well-known class of systems
represented by J-aggregates molecular crystals, characterized by the
intense J band of absorption. By means of first-principles simulations,
based on a many-body perturbation theory formalism, we investigate
the optical properties of a J-aggregate made of push–pull organic
dyes. We show that the effect of aggregation is to lower the GPI associated
with the J-band with respect to the isolated dye one, which corresponds
to a nonplasmonic character of the electronic excitations. In order
to rationalize our finding, we then propose a simplified one-dimensional
theoretical model of the J-aggregate. A useful microscopic picture
of what discriminates a collective molecular crystal excitation from
a plasmon is eventually obtained.
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Interplay between Intra- and Intermolecular Charge Transfer in the Optical Excitations of J-Aggregates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:6831-6838. [PMID: 30949274 PMCID: PMC6443228 DOI: 10.1021/acs.jpcc.8b11709] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/13/2019] [Indexed: 05/17/2023]
Abstract
In a first-principles study based on density functional theory and many-body perturbation theory, we address the interplay between intra- and intermolecular interactions in a J-aggregate formed by push-pull organic dyes by investigating its electronic and optical properties. We find that the most intense excitation dominating the spectral onset of the aggregate, i.e., the J-band, exhibits a combination of intramolecular charge transfer, coming from the push-pull character of the constituting dyes, and intermolecular charge transfer, due to the dense molecular packing. We also show the presence of a pure intermolecular charge-transfer excitation within the J-band, which is expected to play a relevant role in the emission properties of the J-aggregate. Our results shed light on the microscopic character of optical excitations of J-aggregates and offer new perspectives to further understand the nature of collective excitations in organic semiconductors.
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12
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Interaction-Driven Giant Orbital Magnetic Moments in Carbon Nanotubes. PHYSICAL REVIEW LETTERS 2018; 121:127704. [PMID: 30296145 DOI: 10.1103/physrevlett.121.127704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 06/08/2023]
Abstract
Carbon nanotubes continue to be model systems for studies of confinement and interactions. This is particularly true in the case of so-called "ultraclean" carbon nanotube devices offering the study of quantum dots with extremely low disorder. The quality of such systems, however, has increasingly revealed glaring discrepancies between experiment and theory. Here, we address the outstanding anomaly of exceptionally large orbital magnetic moments in carbon nanotube quantum dots. We perform low temperature magnetotransport measurements of the orbital magnetic moment and find it is up to 7 times larger than expected from the conventional semiclassical model. Moreover, the magnitude of the magnetic moment monotonically drops with the addition of each electron to the quantum dot directly contradicting the widely accepted shell filling picture of single-particle levels. We carry out quasiparticle calculations, both from first principles and within the effective-mass approximation, and find the giant magnetic moments can only be captured by considering a self-energy correction to the electronic band structure due to electron-electron interactions.
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13
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Ferromagnetic and Antiferromagnetic Coupling of Spin Molecular Interfaces with High Thermal Stability. NANO LETTERS 2018; 18:2268-2273. [PMID: 29558616 DOI: 10.1021/acs.nanolett.7b04836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report an advanced organic spin-interface architecture with magnetic remanence at room temperature, constituted by metal phthalocyanine molecules magnetically coupled with Co layer(s), mediated by graphene. Fe- and Cu-phthalocyanines assembled on graphene/Co have identical structural configurations, but FePc couples antiferromagnetically with Co up to room temperature, while CuPc couples ferromagnetically with weaker coupling and thermal stability, as deduced by element-selective X-ray magnetic circular dichroic signals. The robust antiferromagnetic coupling is stabilized by a superexchange interaction, driven by the out-of-plane molecular orbitals responsible of the magnetic ground state and electronically decoupled from the underlying metal via the graphene layer, as confirmed by ab initio theoretical predictions. These archetypal spin interfaces can be prototypes to demonstrate how antiferromagnetic and/or ferromagnetic coupling can be optimized by selecting the molecular orbital symmetry.
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Theoretical S1 ← S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green’s Function Theory. J Chem Theory Comput 2017; 13:4357-4367. [DOI: 10.1021/acs.jctc.7b00505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Abstract
Despite most of the applications of anatase nanostructures rely on photoexcited charge processes, yet profound theoretical understanding of fundamental related properties is lacking. Here, by means of ab initio ground and excited-state calculations, we reveal, in an unambiguous way, the role of quantum confinement effect and of the surface orientation, on the electronic and optical properties of anatase nanosheets (NSs). The presence of bound excitons extremely localized along the (001) direction, whose existence has been recently proven also in anatase bulk, explains the different optical behavior found for the two orientations - (001) and (101) - when the NS thickness increases. We suggest also that the almost two-dimensional nature of these excitons can be related to the improved photoconversion efficiency observed when a high percentage of (001) facet is present in anatase nanocrystals.
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Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Ground state structures and electronic excitations of biological chromophores at Quantum Monte Carlo/Many Body Green’s Function Theory level. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Ab Initio Geometry and Bright Excitation of Carotenoids: Quantum Monte Carlo and Many Body Green's Function Theory Calculations on Peridinin. J Chem Theory Comput 2014; 10:501-6. [PMID: 26580027 PMCID: PMC4864508 DOI: 10.1021/ct400943a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree-Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO-LUMO major contribution of the Bu(+)-like (S2) bright excited state. Many Body Green's Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu(+)-like state for the VMC structure (VMC/MBGFT) provide an excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed.
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19
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Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities. J Chem Phys 2014; 140:054102. [DOI: 10.1063/1.4863213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Protein Field Effect on the Dark State of 11- cis Retinal in Rhodopsin by Quantum Monte Carlo/Molecular Mechanics. J Chem Theory Comput 2013; 9:8-12. [PMID: 24611033 PMCID: PMC3943175 DOI: 10.1021/ct3007502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate determination of the geometrical details of the dark state of 11-cis retinal in rhodopsin represents a fundamental step for the rationalization of the protein role in the optical spectral tuning in the vision mechanism. We have calculated geometries of the full retinal protonated Schiff base chromophore in the gas phase and in the protein environment using the correlated variational Monte Carlo method. The bond length alternation of the conjugated carbon chain of the chromophore in the gas phase shows a significant reduction when moving from the β-ionone ring to the nitrogen, whereas, as expected, the protein environment reduces the electronic conjugation. The proposed dark state structure is fully compatible with solid-state NMR data reported by Carravetta et al. [J. Am. Chem. Soc. 2004, 126, 3948-3953]. TDDFT/B3LYP calculations on such geometries show a blue opsin shift of 0.28 and 0.24 eV induced by the protein for S1 and S2 states, consistently with literature spectroscopic data. The effect of the geometrical distortion alone is a red shift of 0.21 and 0.16 eV with respect to the optimized gas phase chromophore. Our results open new perspectives for the study of the properties of chromophores in their biological environment using correlated methods.
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Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory. J Phys Chem B 2012; 116:10693-702. [DOI: 10.1021/jp304818s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Dielectric and Thermal Effects on the Optical Properties of Natural Dyes: A Case Study on Solvated Cyanin. J Am Chem Soc 2011; 133:15425-33. [PMID: 21905678 DOI: 10.1021/ja201733v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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On the intrinsic optical absorptions by tetrathiafulvalene radical cations and isomers. Chem Commun (Camb) 2011; 47:6900-2. [DOI: 10.1039/c1cc11936b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fingerprints of bonding motifs in DNA duplexes of adenine and thymine revealed from circular dichroism: synchrotron radiation experiments and TDDFT calculations. J Phys Chem B 2009; 113:9614-9. [PMID: 19537699 DOI: 10.1021/jp9032029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synchrotron radiation circular dichroism (SRCD) spectra were recorded for a family of 12 DNA duplexes that all contain nine adenines (A) and nine thymines (T) in each strand but in different combinations. The total number of AT Watson-Crick (WC) base pairs is constant (18), but the number of cross-strand (CS) hydrogen bonds between A and T varies between 0 and 16, the maximum possible. Eleven of the duplexes have one or more A tracts, and one duplex has T tracts. The signals due to hybridization were found from subtraction of spectra of single strands from spectra of the duplexes. The residual spectrum of the T-tract duplex T(9)A(9):A(9)T(9) (5'-3':3'-5') significantly differs from that of the A-tract duplex A(9)T(9):T(9)A(9), but only below 210 nm, which suggests that the signal in this region depends on the superhelicity of the duplex. A principal component analysis of all residual spectra reveals that spectra of A-tract duplexes can be obtained to a good approximation as a linear combination of just two basis spectra. The first component is assigned to the spectrum of 18 WC and 8 CS pairs, whereas the second component is that of 8 CS pairs. This interpretation is supported by separate experiments on duplexes of varying lengths but with similar arrangements of the A and T's and by experiments on two other duplex families of 14 and 30 base pairs. The best correlation is obtained by the assumption that cross-strand interactions occur as long as there are two adenine neighbors in a strand. Our data indicate that a circular dichroism spectrum of a duplex containing only A and T can simply be inferred from the number of WC base pairs and the number of CS interactions, and we provide reference spectra for these two interactions. Finally, time dependent density functional theory calculations of the circular dichroism spectra for an isolated WC base pair and two different CS base pairs (between adenine N-6 amine and thymine O-4 or between adenine C-2-H and thymine O-2) were performed to provide some additional support for the interpretation of the experimental spectra. We find large differences between the two calculated CS spectra. However, there is a reasonable qualitative agreement between the calculated WC and the C-2-H...O-2 CS spectra and those deduced from the experimental data.
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First principles effective electronic couplings for hole transfer in natural and size-expanded DNA. J Phys Chem B 2009; 113:9402-15. [PMID: 19537767 DOI: 10.1021/jp904295q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in pi-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level.
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Photoexcitation of a light-harvesting supramolecular triad: a time-dependent DFT study. J Phys Chem B 2009; 113:5345-9. [PMID: 19331406 DOI: 10.1021/jp900820q] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the first time-dependent density functional theory (TDDFT) calculation on a light-harvesting triad carotenoid-diaryl-porphyrin-C(60). Besides the numerical challenge that the ab initio study of the electronic structure of such a large system presents, we show that TDDFT is able to provide an accurate description of the excited-state properties of the system. In particular, we calculate the photoabsorption spectrum of the supramolecular assembly, and we provide an interpretation of the photoexcitation mechanism in terms of the properties of the component moieties. The spectrum is in good agreement with experimental data, and provides useful insight on the photoinduced charge-transfer mechanism which characterizes the system.
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Towards a gauge invariant method for molecular chiroptical properties in TDDFT. Phys Chem Chem Phys 2009; 11:4481-9. [DOI: 10.1039/b903200b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Optical saturation driven by exciton confinement in molecular chains: a time-dependent density-functional theory approach. PHYSICAL REVIEW LETTERS 2008; 101:133002. [PMID: 18851443 DOI: 10.1103/physrevlett.101.133002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Indexed: 05/26/2023]
Abstract
We identify excitonic confinement in one-dimensional molecular chains (i.e., polyacetylene and H2) as the main driving force for the saturation of the chain polarizability as a function of the number of molecular units. This conclusion is based on first principles time-dependent density-functional theory calculations using a recently developed exchange-correlation kernel that accounts for excitonic effects. The failure of simple local and semilocal functionals is shown to be linked to the lack of memory effects, spatial ultranonlocality, and self-interaction corrections. These effects get smaller as the gap reduces, in which case such simple approximations do perform better.
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30
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Ab Initio Optical Absorption Spectra of Size-Expanded xDNA Base Assemblies. J Phys Chem B 2007; 111:14012-21. [DOI: 10.1021/jp075711z] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Abstract
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.
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32
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Time-dependent density-functional approach for biological chromophores: the case of the green fluorescent protein. PHYSICAL REVIEW LETTERS 2003; 90:258101. [PMID: 12857170 DOI: 10.1103/physrevlett.90.258101] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Indexed: 05/24/2023]
Abstract
We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.
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33
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Abstract
Benign masseteric hypertrophy in a young child is presented. Diagnosis was confirmed by sonography and computed tomography. Recognition of this disorder obviates the need for further invasive investigations.
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34
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Transient focal headaches with persistent ipsilateral EEG disturbances. Headache 1986; 26:30-2. [PMID: 3781823 DOI: 10.1111/j.1526-4610.1986.hed2601030.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Abstract
A 5-month-old infant presented with severe dyspnea and dysphagia resulting from a right-sided cervical mass. At 5 months of age, a large aberrant thymus was excised, resulting in the disappearance of all symptoms. Pathological examination showed normal thymus tissue. Since the preoperative chest X-ray film showed a normal thymic shadow and the T-lymphocyte functions were normal, we conclude that this was not an ectopic gland but an undescended thymic implant.
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36
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Abstract
Two children were admitted for clinical and radiologic signs of small-bowel obstruction. Examination revealed an abdominal mass that was suspected of being a mass of intussusception. Bowel obstruction caused by Ascaris lumbricoides was found at surgery. The laboratory, radiologic, and surgical findings are presented with a short review of the literature with emphasis on diagnosis, incidence, complications, and treatment.
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37
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Pseudo-precocious puberty in a young boy due to interstitial cell adenomas of the testis. HELVETICA PAEDIATRICA ACTA 1984; 39:79-87. [PMID: 6724998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A case of pseudo-precocious puberty in a 2 4/12-year-old boy, due to Leydig cell adenomas of the testicle, is described. The special endocrine investigations revealed high levels of plasma testosterone and other androgens together with suppressed plasma gonadotropins unresponsive to stimulation. After operation the hormones returned to normal. The growth velocity and bone age were only gradually decreased, during a period of one year, while the sexual manifestations were the last to disappear, in the third year.
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38
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[A new focus of the sickle cell gene in Israel]. HAREFUAH 1983; 104:9-10. [PMID: 6654216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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39
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[Clinical expression of congenital malformations of the aortic arch and/or its major branches in childhood]. HAREFUAH 1981; 101:169-71. [PMID: 7037571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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40
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Intramural esophageal diverticulosis in an infant. ISRAEL JOURNAL OF MEDICAL SCIENCES 1980; 16:604-6. [PMID: 6774955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the course of evaluating an infant with recurrent episodes of bronchiolitis, the esophagus was radiologically examined. A totally unexpected finding was the presence of intramural diverticulosis of the upper part of the esophagus. On reexamination four months later, the diverticula had disappeared.
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41
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Abstract
A newborn male referred for genetic investigation because of a large sized head and dysplastic ears, but with apparently normal male genitalia was found to have a deletion of all of the brightly fluorescent part of the long are of chromosome Y and absence of the Y fluorescent body on buccal smear. His father and his two brothers had normal Y chromosomes. Social and family history as well as marker investigation make illegitimacy most unlikely and leaves an occurrence of a new chromosomal mutation in the father the most probably interpretation. Follow-up of the infant to the age of 9 months revealed a large baby with normal development.
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42
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Treatment of cystinuria in childhood with penicillamine. ISRAEL JOURNAL OF MEDICAL SCIENCES 1967; 3:544-8. [PMID: 6060570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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43
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Idiopathic pericarditis without symptoms. JAMA 1967; 199:425-6. [PMID: 6071230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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