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1.
J Chem Phys ; 151(24): 244101, 2019 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-31893895

RESUMO

We present density functional theory (DFT) calculations of atomic ionization potentials and lattice constants of simple solids from low atomic numbers Z to the large-Z limit. We compare different kinetic energy functional approximations [Kohn-Sham (KS) vs simple orbital-free functionals] and, in the case of orbital free, also different methods for including the nuclear potential (all-electron with the projector augmented wave method vs local pseudopotentials). For both ionization potentials and lattice constants, all-electron orbital-free DFT does yield the general trend of KS DFT for moderate values of the atomic number Z. For large values of Z, all-electron orbital-free DFT deviates from the KS DFT results. Local pseudopotentials give a better qualitative description by adding shell oscillations to the orbital-free DFT model. We show that both all-electron orbital-free DFT and KS DFT have a finite value for nonrelativistic lattice constants in the large-Z limit.

2.
J Phys Chem Lett ; 9(16): 4789-4794, 2018 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-30079734

RESUMO

Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag+-mediated guanine duplex with two nucleobases per strand, G2-Ag2+-G2. We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G2-Ag2+-G2 is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.

3.
Int J Mol Sci ; 19(8)2018 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-30096923

RESUMO

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree⁻Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag + -mediated DNA species.


Assuntos
DNA/química , Nanoestruturas/química , Dicroísmo Circular , DNA/genética , Simulação de Dinâmica Molecular , Teoria Quântica , Prata/química
4.
J Chem Phys ; 147(23): 234102, 2017 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-29272932

RESUMO

Our manuscript investigates a self-consistent solution of the statistical atom model proposed by Berthold-Georg Englert and Julian Schwinger (the ES model) and benchmarks it against atomic Kohn-Sham and two orbital-free models of the Thomas-Fermi-Dirac (TFD)-λvW family. Results show that the ES model generally offers the same accuracy as the well-known TFD-15vW model; however, the ES model corrects the failure in the Pauli potential near-nucleus region. We also point to the inability of describing low-Z atoms as the foremost concern in improving the present model.

5.
Sci Rep ; 7(1): 6982, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28765548

RESUMO

Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.

6.
J Chem Theory Comput ; 13(8): 3432-3441, 2017 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-28715635

RESUMO

We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr2+/3+, V2+/3+, Ru(NH3)62+/3+, Sn2+/4+, Cu1+/2+, FcMeOH0/1+, and Fe2+/3+ (in aqueous solution) and Fc0/1+ (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations.

7.
ACS Omega ; 2(10): 7343-7348, 2017 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-30023548

RESUMO

The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.

8.
J Chem Phys ; 145(24): 244504, 2016 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-28049340

RESUMO

We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.

9.
Sci Rep ; 5: 10163, 2015 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-25973536

RESUMO

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag(+)-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag(+) bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag(+)-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.


Assuntos
Pareamento de Bases/genética , DNA/química , Conformação de Ácido Nucleico , Prata/química , Dicroísmo Circular , Citosina/química , Guanina/química , Modelos Moleculares , Nanotecnologia , Espectrometria de Massas por Ionização por Electrospray , Termodinâmica
10.
J Phys Condens Matter ; 27(24): 245901, 2015 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-26000892

RESUMO

We present a computational study of spontaneous polarization and piezoelectricity in Sc(x)Al(1-x)N alloys in the compositional range from x = 0 to x = 0.5, obtained in the context of density functional theory and the Berry-phase theory of electric polarization using large periodic supercells. We report composition-dependent values of piezoelectric coefficients e(ij), piezoelectric moduli d(ij) and elastic constants C(ij). The theoretical findings are complemented with experimental measurement of e33 for a series of sputtered ScAlN films carried out with a piezoelectric resonator. The rapid increase with Sc content of the piezoelectric response reported in previous studies is confirmed for the available data. A detailed description of the full methodology required to calculate the piezoelectric properties of ScAlN, with application to other complex alloys, is presented. In particular, we find that the large amount of internal strain present in ScAlN and its intricate relation with electric polarization make configurational sampling and the use of large supercells at different compositions necessary in order to accurately derive the piezoelectric response of the material.

11.
J Phys Chem Lett ; 6(20): 4061-6, 2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26722777

RESUMO

DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.


Assuntos
Citosina/química , Prata/química , Dicroísmo Circular , Gases/química , Ligação de Hidrogênio , Modelos Moleculares , Teoria Quântica
12.
J Chem Phys ; 141(23): 234102, 2014 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-25527914

RESUMO

We present a computational scheme for orbital-free density functional theory (OFDFT) that simultaneously provides access to all-electron values and preserves the OFDFT linear scaling as a function of the system size. Using the projector augmented-wave method (PAW) in combination with real-space methods, we overcome some obstacles faced by other available implementation schemes. Specifically, the advantages of using the PAW method are twofold. First, PAW reproduces all-electron values offering freedom in adjusting the convergence parameters and the atomic setups allow tuning the numerical accuracy per element. Second, PAW can provide a solution to some of the convergence problems exhibited in other OFDFT implementations based on Kohn-Sham (KS) codes. Using PAW and real-space methods, our orbital-free results agree with the reference all-electron values with a mean absolute error of 10 meV and the number of iterations required by the self-consistent cycle is comparable to the KS method. The comparison of all-electron and pseudopotential bulk modulus and lattice constant reveal an enormous difference, demonstrating that in order to assess the performance of OFDFT functionals it is necessary to use implementations that obtain all-electron values. The proposed combination of methods is the most promising route currently available. We finally show that a parametrized kinetic energy functional can give lattice constants and bulk moduli comparable in accuracy to those obtained by the KS PBE method, exemplified with the case of diamond.

13.
J Chem Phys ; 135(9): 094701, 2011 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-21913777

RESUMO

Ligand-stabilized aluminum clusters are investigated by density functional theory calculations. Analysis of Kohn-Sham molecular orbitals and projected density of states uncovers an electronic shell structure that adheres to the superatom complex model for ligand-stabilized aluminum clusters. In this current study, we explain how the superatom complex electron-counting rule is influenced by the electron-withdrawing ligand and a dopant atom in the metallic core. The results may guide the prediction of new stable ligand-stabilized (superatom) complexes, regardless of core and electron-withdrawing ligand composition.

14.
J Am Chem Soc ; 133(11): 3752-5, 2011 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-21348523

RESUMO

Optical absorption of a gold nanocluster of 102 Au atoms protected by 44 para-mercaptobenzoic acid (p-MBA) ligands is measured in the range of 0.05-6.2 eV (mid-IR to UV) by a combination of several techniques for purified samples in solid and solution phases. The results are compared to calculations for a model cluster Au(102)(SMe)(44) based on the time-dependent density functional theory in the linear-response regime and using the known structure of Au(102)(p-MBA)(44). The measured and calculated molar absorption coefficients in the NIR-vis region are comparable, within a factor of 2, in the absolute scale. Several characteristic features are observed in the absorption in the range of 1.5-3.5 eV. The onset of the electronic transitions in the mid-IR region is experimentally observed at 0.45 ± 0.05 eV which compares well with the lowest calculated transition at 0.55 eV. Vibrations in the ligand layer give rise to fingerprint IR features below the onset of low-energy metal-to-metal electronic transitions. Partial exchange of the p-MBA ligand to glutathione does not affect the onset of the electronic transitions, which indicates that the metal core of the cluster is not affected by the ligand exchange. The full spectroscopic characterization of the Au(102)(p-MBA)(44) reported here for the first time gives benchmarks for further studies of manipulation and functionalization of this nanocluster to various applications.


Assuntos
Ouro/química , Ligantes , Espectroscopia de Luz Próxima ao Infravermelho
15.
Nat Chem ; 2(4): 329-34, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21124516

RESUMO

Finely dispersed nanometre-scale gold particles are known to catalyse several oxidation reactions in aerobic, ambient conditions. The catalytic activity has been explained by various complementary mechanisms, including support effects, particle-size-dependent metal-insulator transition, charging effects, frontier orbital interactions and geometric fluxionality. We show, by considering a series of robust and structurally well-characterized ligand-protected gold clusters with diameters between 1.2 and 2.4 nm, that electronic quantum size effects, particularly the magnitude of the so-called HOMO-LUMO energy gap, has a decisive role in binding oxygen to the nano-catalyst in an activated form. This can lead to the oxidation reaction 2CO + O(2) â†’ 2CO(2) with low activation barriers. Binding of dioxygen is significant only for the smallest particles with a metal core diameter clearly below 2 nm. Our results suggest a potentially viable route to practical applications using ligand-protected gold clusters for green chemistry.

16.
J Am Chem Soc ; 132(23): 8210-8, 2010 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-20499877

RESUMO

Structural, electronic, and optical properties of the thiolate-protected Au(38)(SR)(24) cluster are studied by density-functional theory computations (R = CH(3) and R = C(6)H(13)) and by powder X-ray crystallography (R = C(12)H(25)). A low-energy structure which can be written as Au(23)@(Au(SR)(2))(3)(Au(2)(SR)(3))(6) having a bi-icosahedral core and a chiral arrangement of the protecting gold-thiolate Au(x)(SR)(y) units yields an excellent match between the computed (for R = C(6)H(13)) and measured (for R = C(12)H(25)) powder X-ray diffraction function. We interpret in detail the electronic structure of the Au(23) core by using a particle-in-a-cylinder model. Although the alkane thiolate ligands are achiral, the chiral structure of the ligand layer yields strong circular dichroism (CD) in the excitations below 2.2 eV for Au(38)(SCH(3))(24). Our calculated CD spectrum is in quantitative agreement with the previously measured low-energy CD signal of glutathione-protected Au(38)(SG)(24). Our study demonstrates a new mechanism for the strong chiral response of thiolate-protected gold clusters with achiral metal cores and ligands.


Assuntos
Elétrons , Ouro/química , Nanoestruturas/química , Compostos de Sulfidrila/química , Absorção , Dicroísmo Circular , Modelos Moleculares , Conformação Molecular , Fenômenos Ópticos , Teoria Quântica , Estereoisomerismo , Difração de Raios X
17.
Phys Chem Chem Phys ; 11(33): 7123-9, 2009 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-19672520

RESUMO

Structure, electronic properties, optical absorption and charging properties of methylthiolate-protected bimetal PdAu(24)(SR)(18)(z) (R = Me) clusters with various charge states (-3

18.
J Am Chem Soc ; 131(35): 12573-5, 2009 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-19681617

RESUMO

Ligand-stabilized nanometer-sized gold particles are interesting building blocks for molecular electronics, precursors for catalysts, optical labels for biomolecules and diagnosis, and potential nontoxic carriers for therapeutics. In this work we characterize for the first time, by means of near-infrared and Raman spectroscopy and time-dependent density functional calculations, gold clusters protected with iron-carbonyl ligands, such as {Au(22)[Fe(CO)(4)](12)}(6-) shown in the figure. Surprisingly, our results show that these novel compounds bear many analogues to another, well-studied, class of gold clusters, namely those of thiolate-monolayer-protected gold clusters. Our work adds a new dimension to the rich chemistry of gold-based clusters that can be characterized as "molecular metals".


Assuntos
Aldeídos/química , Ouro/química , Ferro/química , Elétrons , Modelos Lineares , Modelos Moleculares , Conformação Molecular , Fosfinas/química , Teoria Quântica , Espectrofotometria Infravermelho , Análise Espectral Raman , Fatores de Tempo
19.
Proc Natl Acad Sci U S A ; 105(27): 9157-62, 2008 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-18599443

RESUMO

Synthesis, characterization, and functionalization of self-assembled, ligand-stabilized gold nanoparticles are long-standing issues in the chemistry of nanomaterials. Factors driving the thermodynamic stability of well documented discrete sizes are largely unknown. Herein, we provide a unified view of principles that underlie the stability of particles protected by thiolate (SR) or phosphine and halide (PR(3), X) ligands. The picture has emerged from analysis of large-scale density functional theory calculations of structurally characterized compounds, namely Au(102)(SR)(44), Au(39)(PR(3))(14)X(6)(-), Au(11)(PR(3))(7)X(3), and Au(13)(PR(3))(10)X(2)(3+), where X is either a halogen or a thiolate. Attributable to a compact, symmetric core and complete steric protection, each compound has a filled spherical electronic shell and a major energy gap to unoccupied states. Consequently, the exceptional stability is best described by a "noble-gas superatom" analogy. The explanatory power of this concept is shown by its application to many monomeric and oligomeric compounds of precisely known composition and structure, and its predictive power is indicated through suggestions offered for a series of anomalously stable cluster compositions which are still awaiting a precise structure determination.

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