Noa Marom

Tulane University, New Orleans, Louisiana, United States

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Publications (25)87.71 Total impact

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    ABSTRACT: Zinc oxide is often used as a popular inexpensive transparent conducting oxide. Here, we employ density functional theory and local density approximation to examine the effects of quantum confinement in doped nanocrystals of this material. Specifically, we examine the addition of Ga and Al dopants to ZnO nanocrystals on the order of 1.0 nm. We find that the inclusion of these dopants is energetically less favorable in smaller particles and that the electron binding energy, which is associated with the dopant activation, decreases with the nanocrystal size. We find that the introduction of impurities does not alter significantly the Kohn-Sham eigenspectrum for small nanocrystals of ZnO. The added electron occupies the lowest existing state, i.e., no new bound state is introduced in the gap. We verify this assertion with hybrid functional calculations.
    The Journal of chemical physics. 09/2014; 141(9):094309.
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    ABSTRACT: Hemozoin is a crystalline byproduct formed upon hemoglobin digestion in Plasmodium-infected blood cells. Based on X-ray powder diffraction (XRPD), hemozoin and its synthetic analogue β-hematin are very similar in structure, consisting of cyclic dimers (cd) of ferriprotoporphyrin IX [Fe(3+)-PPIX] molecules coordinated via Fe–O(propionate) bonds. Enantiofacial symmetry of Fe(3+)-PPIX implies formation of four different stereoisomeric dimers, two centrosymmetric (1̅), labeled cd1̅1 and cd1̅2, and two enantiomeric, cd2(+) and cd2(−), in which the Fe(3+)PPIX moieties are related by pseudo-2-fold symmetry. Only the cd1̅1 stereoisomer was reported as the repeat unit in the initial structural elucidation of β-hematin and refinement of hemozoin. Our recent study of β-hematin, employing a combination of XRPD and density functional theory (DFT), revealed besides the published phase, characterized in terms of a disordered cd1̅1/cd2(±) mixture, which is diffractionally equivalent to a cd1̅1/cd1̅2 mixture, a minor phase considered to comprise mainly cd1̅2 dimers. As a consequence single-phase β-hematin powders were recently reanalyzed in terms of a cd1̅1/cd1̅2 mixture, yielding an average occupancy 75:25. Here, we present evidence enhancing the biphase model of β-hematin. The primary focus is on a reexamination of the hemozoin structure in light of a biochemically based dimerization mechanism that we recently hypothesized. We suggest that upon hemoglobin degradation, the heme byproduct retains the O2 molecule bound to Fe on the Re side of the heme until Fe–O(propionate) coordination between such heme molecules occurs across their unbound Si sides yielding the cd2(+) dimer. We report Rietveld refinement of the hemozoin structure using data measured on an all-in-vacuum powder diffractometer assuming the following models: cd1̅1, cd1̅2, cd2(+), and the two mixtures cd1̅1/cd1̅2 and cd1̅1/cd2(+). The best figures of merit were obtained for the mixture cd1̅1/cd2(+) with a 50:50 occupancy, followed by the cd1̅1/cd1̅2 mixture with an occupancy 75:25, which we interpret as a structure that comprises the cd1̅1, cd2(+), cd2(−), and cd1̅2 isomers with occupancies 58:17:17:8. In this model system, the cd1̅1 “host” molecule is uniformly distributed throughout the crystal, whereas the enantiomeric molecules cd2(+) and cd2(−) are preferentially occluded in different crystalline sectors, which are thus enantiomorphous, related by overall centrosymmetric symmetry. Various arguments appear to favor the 50:50 cd1̅1/cd2(+) mixture, namely, a hemozoin crystal of overall chiral symmetry, consistent with our hypothesis. However, we cannot overrule the alternative model.
    Crystal Growth & Design 03/2014; 14(4):1543–1554. · 4.69 Impact Factor
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    ABSTRACT: Molecular crystals: The structures and relative energies of glycine polymorphs are determined using dispersion corrections to PBE and PBEh density functionals. The picture shows a potential-energy surface for the a-b plane of γ-glycine obtained with density functional theory including many-body dispersion interactions.
    Angewandte Chemie International Edition 05/2013; · 11.34 Impact Factor
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    ABSTRACT: Despite the success of the GW method in describing the photoemission spectra of solids, molecules and clusters, challenges remain. For aromatic molecules for example absolute as well as relative positions of ionisation energies and affinities are not well reproduced in perturbative G0W0 schemes with different starting points as well as in self-consistent GW [1], sometimes even giving the wrong orbital order. Motivated by renormalized second-order perturbation theory [2] for the ground-state energy, we propose a second-order screened exchange correction (SOSEX) to the GW self-energy. This correction follows the spirit of the SOSEX correction to the random-phase approximation for the electron correlation energy and reduces the self-correlation error. The performance of the GW+SOSEX scheme has been benchmarked for a set of molecular systems, including the G2 set, commonly used acceptor molecules, benzene and the azabenzene molecules. We find that the SOSEX correction improves the description of the spectral properties including the orbital order with respect to the different GW schemes, highlighting the importance of reducing the self-correlation error.[4pt] [1] N. Marom et al., arXiv:1211.0416[0pt] [2] X. Ren et al., J. Mater. Sci. 47, 7447 (2012)
    03/2013;
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    ABSTRACT: The electronic structure of cobalt-phthalocyanine (CoPc) molecules adsorbed on Ag(100) is investigated by photoemission spectroscopy. The results are compared to first-principles electronic structure calculations, based on many-body perturbation theory in the GW approximation. The photoemission data, obtained from both multilayer and monolayer films of CoPc, show that charge transfer occurs between the first molecular layer and the metal surface. Varying the photon energy, to tune the photoionization cross sections, reveals that the charge-transfer-related interface states mainly involve the Co 3d atomic orbitals of the Co central atom. GW calculations for the neutral CoPc molecule and its anion compare well with the experimental observations for a multilayer and a monolayer CoPc film, respectively. They confirm the major role played by the Co atom in the charge-transfer process and elucidate the complex energy rearrangement of the molecular electronic levels upon metal adsorption.
    Physical review. B, Condensed matter 02/2013; 87(7). · 3.66 Impact Factor
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    ABSTRACT: Many-body perturbation theory in the GW approximation is a useful method for describing electronic properties associated with charged excitations. A hierarchy of GW methods exists, starting from non-self-consistent G0W0, through partial self-consistency in the eigenvalues and in the Green's function (scGW0), to fully self-consistent GW (scGW). Here, we assess the performance of these methods for benzene, pyridine, and the diazines. The quasiparticle spectra are compared to photoemission spectroscopy (PES) experiments with respect to all measured particle removal energies and the ordering of the frontier orbitals. We find that the accuracy of the calculated spectra does not match the expectations based on their level of self-consistency. In particular, for certain starting points G0W0 and scGW0 provide spectra in better agreement with the PES than scGW.
    Physical review. B, Condensed matter 12/2012; 86(24):245127. · 3.66 Impact Factor
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    ABSTRACT: We show that electrodynamic dipolar interactions, responsible for long-range fluctuations in matter, play a significant role in the stability of molecular crystals. Density functional theory calculations with van der Waals interactions determined from a semilocal "atom-in-a-molecule" model result in a large overestimation of the dielectric constants and sublimation enthalpies for polyacene crystals from naphthalene to pentacene, whereas an accurate treatment of non-local electrodynamic response leads to an agreement with the measured values for both quantities. Our findings suggest that collective response effects play a substantial role not only for optical excitations, but also for cohesive properties of non-covalently bound molecular crystals.
    Physical review. B, Condensed matter 11/2012; 87(6). · 3.66 Impact Factor
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    ABSTRACT: Long-range corrected hybrid functionals that employ a nonempirically tuned range-separation parameter have been demonstrated to yield accurate ionization potentials and fundamental gaps for a wide range of finite systems. Here, we address the question of whether this high level of accuracy is limited to the highest occupied/lowest unoccupied energy levels to which the range-separation parameter is tuned or whether it is retained for the entire valence spectrum. We examine several π-conjugated molecules and find that orbitals of a different character and symmetry require significantly different range-separation parameters and fractions of exact exchange. This imbalanced treatment of orbitals of a different nature biases the resulting eigenvalue spectra. Thus, the existing schemes for the tuning of range-separated hybrid functionals, while providing for good agreement between the highest occupied energy level and the first ionization potential, do not achieve accuracy comparable to reliable G0W0 computations for the entire quasiparticle spectrum.
    Physical review. B, Condensed matter 11/2012; 86(20):205110. · 3.66 Impact Factor
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    ABSTRACT: Polymorphs in molecular crystals are often very close in energy, yet they may possess markedly different physical and chemical properties. The understanding and prediction of polymorphism is of paramount importance for a variety of applications, including pharmaceuticals, non-linear optics, and hydrogen storage. Here, we show that the non-additive many-body dispersion (MBD) energy beyond the standard pairwise approximation is crucial for the correct qualitative and quantitative description of polymorphism in molecular crystals. This is rationalized by the sensitive dependence of the MBD energy on the polymorph geometry and the ensuing dynamic electric fields inside molecular crystals. We use the glycine crystal as a fundamental and stringent benchmark case to demonstrate the accuracy of the DFT+MBD method.
    10/2012;
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    Thomas Körzdörfer, Noa Marom
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    ABSTRACT: Many-body perturbation theory in the G0W0 approximation is an increasingly popular tool for calculating electron removal energies and fundamental gaps for molecules and solids. However, the predictive power of G0W0 is limited by its sensitivity to the density functional theory (DFT) starting point. We introduce a nonempirical scheme, which allows us to find a reliable DFT starting point for G0W0 calculations. This is achieved by adapting the amount of Hartree-Fock exchange in a hybrid DFT functional. The G0W0 spectra resulting from this starting point reliably predict experimental photoelectron spectra for a test set of 13 typical organic semiconductor molecules.
    Physical review. B, Condensed matter 07/2012; 86(4). · 3.66 Impact Factor
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    ABSTRACT: We propose a new substitutional impurity complex in diamond composed of a lithium atom that is tetrahedrally coordinated by four nitrogen atoms (LiN_4). Density functional calculations are consistent with the hydrogenic impurity model, both supporting the prediction that this complex is a shallow donor with an activation energy of 0.27 +/- 0.06 eV. Three paths to the experimental realization of the LiN_4 complex in diamond are proposed and theoretically analyzed.
    Physical Review Letters 05/2012; 108(22). · 7.73 Impact Factor
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    ABSTRACT: We study the structure and electronic properties of (TiO2)(2-10) clusters by using basin hopping based on density functional theory, combined with many-body perturbation theory. We show that in photoemission experiments performed on anions isomers with high electron affinity are selectively observed rather than those with the lowest energy. These isomers possess a highly reactive Ti3+ site. The selectivity for highly reactive clusters may be exploited for applications in catalysis.
    Physical Review Letters 03/2012; 108(10):106801. · 7.73 Impact Factor
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    ABSTRACT: The development of new types of solar cells is driven by the need for clean and sustainable energy. In this respect dye-sensitized solar cells (DSC) are considered as a promising route for departing from the traditional solid state cells. The physical insight provided by computational modeling may help develop improved DSCs. To this end, it is important to obtain an accurate description of the electronic structure, including the fundamental gaps and level alignment at the dye-TiO2 interface. This requires a treatment beyond ground-state density functional theory (DFT). We present a many-body perturbation theory study, within the G0W0 approximation, of two of the crystalline phases of dye-sensitized TiO2 clusters, reported by Benedict and Coppens, [ J. Am. Chem. Soc. 132 2938 (2010)]. We obtain geometries in good agreement with the experiment by using DFT with the Tkatchenko-Scheffler van der Waals correction. We demonstrate that even when DFT gives a good description of the valence spectrum and a qualitatively correct picture of the electronic structure of the dye-TiO2 interface, G0W0 calculations yield more valuable quantitative information regarding the fundamental gaps and level alignment. In addition, we systematically investigate the issues pertaining to G0W0 calculations, namely: (i) convergence with respect to the number of basis functions, (ii) dependence on the mean-field starting point, and (iii) the validity of the assumption that the DFT wave function is a good approximation to the quasiparticle wave function. We show how these issues are manifested for dye molecules and for dye-sensitized TiO2 clusters.
    Physical review. B, Condensed matter 12/2011; 84(24). · 3.66 Impact Factor
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    ABSTRACT: We present all-electron G0W0 calculations for the electronic structure of the organic semiconductor copper phthalocyanine, based on semilocal and hybrid density-functional theory (DFT) starting points. We show that G0W0 calculations improve the quantitative agreement with high resolution photoemission and inverse photoemission experiments. However, the extent of the improvement provided by G0W0 depends significantly on the choice of the underlying DFT functional, with the hybrid functional serving as a much better starting point than the semilocal one. In particular, strong starting-point dependence is observed in the energy positions of highly localized molecular orbitals. This is attributed to self-interaction errors (SIE), due to which the orbitals obtained from semilocal DFT do not approximate the quasi-particle (QP) orbitals as well as those obtained from hybrid DFT. Our findings establish the viability of the G0W0 approach for describing the electronic structure of metal-organic systems, given a judiciously chosen DFT-based starting point.
    Physical review. B, Condensed matter 11/2011; 84(19). · 3.66 Impact Factor
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    ABSTRACT: We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko–Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth–Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the Heyd–Scuseria–Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections.
    11/2011;
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    ABSTRACT: Malaria, an infectious disease once considered eradicated, has reemerged in recent years, primarily due to parasite resistance to commonly used synthetic antimalarial drugs. These drugs act by inhibiting crystallization of the malaria pigment, hemozoin (HZ). Thus, there is a vital need for understanding the process of HZ nucleation. In a companion paper, the pseudopolymorphic behavior of β-hematin, the synthetic form of HZ, has been characterized by X-ray diffraction (XRD) (Straasø, T.; Kapishnikov, S.; Kato, K.; Takata, M.; Als-Nielsen, J.; Leiserowitz, L. Cryst. Growth Des. 2011, 11, DOI: 10.1021/cg200410b). Here, we employ van der Waals (vdW)-corrected density functional theory (DFT) to study the two β-hematin crystal structures and their repeat unit, a heme dimer. We find that vdW interactions play a major role in the binding of the heme dimer and the β-hematin crystal. In addition, accounting for the periodic nature of the system is essential to obtaining the correct geometry of the heme dimer, which is affected by vdW interactions with adjacent dimers in the β-hematin crystal. The different stereoisomers of the heme dimer and their molecular crystals are close in energy, which is consistent with pseudopolymorphism in β-hematin, in agreement with recent XRD experiments. Finally, we use our results to comment on β-hematin crystallization mechanisms. This work demonstrates the viability of vdW-corrected DFT as a tool for gaining valuable insight into pertinent problems involving biological systems.
    07/2011;
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    ABSTRACT: We present a real-space method for exact-exchange Kohn-Sham calculations of periodic systems. The method is based on self-consistent solutions of the optimized effective potential (OEP) equation on a three-dimensional non-orthogonal grid, using norm conserving pseudopotentials. These solutions can be either exact, using the S-iteration approach, or approximate, using the Krieger, Li, and Iafrate (KLI) approach. We demonstrate, using a variety of systems, the importance of singularity corrections and use of appropriate pseudopotentials.
    03/2011;
  • Physical review. B, Condensed matter 09/2010; 82(12). · 3.66 Impact Factor
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    ABSTRACT: The interlayer sliding energy landscape of hexagonal boron nitride (h-BN) is investigated via a van der Waals corrected density functional theory approach. It is found that the main role of the van der Waals forces is to anchor the layers at a fixed distance, whereas the electrostatic forces dictate the optimal stacking mode and the interlayer sliding energy. A nearly free-sliding path is identified, along which band gap modulations of ∼0.6  eV are obtained. We propose a simple geometric model that quantifies the registry matching between the layers and captures the essence of the corrugated h-BN interlayer energy landscape. The simplicity of this phenomenological model opens the way to the modeling of complex layered structures, such as carbon and boron nitride nanotubes.
    Physical Review Letters 07/2010; 105(4):046801. · 7.73 Impact Factor
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    ABSTRACT: Noncovalent interactions, of which London dispersion is an important special case, are essential to many fields of chemistry. However, treatment of London dispersion is inherently outside the reach of (semi)local approximations to the exchange-correlation functional as well as of conventional hybrid density functionals based on semilocal correlation. Here, we offer an approach that provides a treatment of both dispersive interactions and the electronic structure within a computationally tractable scheme. The approach is based on adding the leading interatomic London dispersion term via pairwise ion-ion interactions to a suitably chosen nonempirical hybrid functional, with the dispersion coefficients and van der Waals radii determined from first-principles using the recently proposed “TS-vdW” scheme (Tkatchenko, A.; Scheffler, M. Phys. Rev. Lett. 2009, 102, 073005). This is demonstrated via the important special case of weakly bound metal-phthalocyanine dimers. The performance of our approach is additionally compared to that of the semiempirical M06 functional. We find that both the PBE-hybrid+vdW functional and the M06 functional predict the electronic structure and the equilibrium geometry well, but with significant differences in the binding energy and in their asymptotic behavior.
    Journal of Chemical Theory and Computation 03/2010; · 5.39 Impact Factor