Covalent and non-covalent coupling of a Au102 nanocluster with a fluorophore: energy transfer, quenching and intracellular pH sensing.

Interactions between an atomically precise gold nanocluster Au102(p-MBA)44 (p-MBA = para mercaptobenzoic acid) and a fluorescent organic dye molecule (KU, azadioxatriangulenium) are studied. In solution, the constituents form spontaneously a weakly bound complex leading to quenching of fluorescence of the KU dye via energy transfer. The KU can be separated from the complex by lowering pH, leading to recovery of fluorescence, which forms a basis for an optical reversible pH sensor. However, the sensor is not a stable entity, which could be delivered inside cells. For this purpose, a covalently bound hybrid is synthesized by linking the KU dye to the ligand layer of the cluster via an ester bond. Covalent linking facilitates entry of the cluster-dye hybrids into cells via endocytosis. Inside cells, the hybrids accumulate in endosomes where Au102 releases its cargo via hydrolysis of the ester bond. Changes of the local pH inside endosomes regulate reversible fluorescence due to variations in the interactions between the Au102 cluster and the dye. This work presents a concept for delivering reporter molecules into cells by using atomically precise gold nanoclusters as carriers and paves the way for future developments of cluster-reporter sensors for in vivo measurements of e.g. absolute pH values or ion concentrations.

Dithiol-Induced Oligomerization of Thiol-Protected Gold Nanoclusters.

Controlled synthesis of nanostructure oligomers requires detailed understanding of their wet chemistry and the forces driving the polymerization process. In this paper, we report the main factors affecting the reaction yields of a dithiol-induced synthesis of covalently bound nanocluster dimers and oligomers and present a detailed analysis of possible reaction mechanisms. We synthesize the nanocluster oligomers using monodisperse para-mercaptobenzoic acid (p-MBA)-protected gold nanoclusters with a nominal composition of Au∼250(p-MBA) n to minimize ensemble effects on size, shape, and surface structure. Ligand exchange was performed on the nanoclusters with five different dithiol linkers: 5,5'-bis(mercaptomethyl)-2,2'-bipyridine, 4,4″-thiobisbenzenethiol, benzene-1,4-dithiol, 1,4-benzenedimethanethiol, and dimercaptostilbene. Oligomer yields depend strongly on the used dithiol and on the dithiol-to-nanocluster ratio. Detailed analysis of the reaction yields in combination with simulations suggests that the system reaches a dynamic equilibrium, where ligand exchange happens continuously forming and breaking nanocluster oligomers that are bound together by short chains of disulfide-bridged dithiols. Despite the dynamic nature of the system, dithiol-induced polymerization of nanoclusters is a general and straightforward approach to produce dimers and larger oligomers of thiol-protected nanoclusters. Our work provides physical insight into, offers tools for, and reveals challenges in the controlled synthesis of covalently bound nanoparticle assemblies.

Covalently linked multimers of gold nanoclusters Au102(p-MBA)44 and Au∼250(p-MBA)n.

We present the synthesis, separation, and characterization of covalently-bound multimers of para-mercaptobenzoic acid (p-MBA) protected gold nanoclusters. The multimers were synthesized by performing a ligand-exchange reaction of a pre-characterized Au102(p-MBA)44 nanocluster with biphenyl-4,4'-dithiol (BPDT). The reaction products were separated using gel electrophoresis yielding several distinct bands. The bands were analyzed by transmission electron microscopy (TEM) revealing monomer, dimer, and trimer fractions of the nanocluster. TEM analysis of dimers in combination with molecular dynamics simulations suggest that the nanoclusters are covalently bound via a disulfide bridge between BPDT molecules. The linking chemistry is not specific to Au102(p-MBA)44. The same approach yields multimers also for a larger monodisperse p-MBA-protected cluster of approximately 250 gold atoms, Au∼250(p-MBA)n. While the Au102(p-MBA)44 is not plasmonic, the Au∼250(p-MBA)n nanocluster supports localized surface plasmon resonance (LSPR) at 530 nm. Multimers of the Au∼250(p-MBA)n exhibit additional transitions in their UV-vis spectrum at 630 nm and 810 nm, indicating the presence of hybridized LSPR modes. Well-defined structures and relatively small sizes make these systems excellent candidates for connecting ab initio theoretical studies and experimental quantum plasmonics. Moreover, our work opens new possibilities in the controlled synthesis of advanced monodisperse nanocluster superstructures.

Plasmonic twinned silver nanoparticles with molecular precision.

Determining the structures of nanoparticles at atomic resolution is vital to understand their structure-property correlations. Large metal nanoparticles with core diameter beyond 2 nm have, to date, eluded characterization by single-crystal X-ray analysis. Here we report the chemical syntheses and structures of two giant thiolated Ag nanoparticles containing 136 and 374 Ag atoms (that is, up to 3 nm core diameter). As the largest thiolated metal nanoparticles crystallographically determined so far, these Ag nanoparticles enter the truly metallic regime with the emergence of surface plasmon resonance. As miniatures of fivefold twinned nanostructures, these structures demonstrate a subtle distortion within fivefold twinned nanostructures of face-centred cubic metals. The Ag nanoparticles reported in this work serve as excellent models to understand the detailed structure distortion within twinned metal nanostructures and also how silver nanoparticles can span from the molecular to the metallic regime.

Electronic structure and optical properties of the intrinsically chiral 16-electron superatom complex [Au20(PP3)4](4+).

The recently solved crystal structure of the [Au20(PP3)4]Cl4 cluster (PP3: tris(2-(diphenylphophino)ethyl)phosphine) is examined using density functional theory (DFT). The Au20 core of the cluster is intrinsically chiral by the arrangement of the Au atoms. This is in contrast to the chirality of thiolate-protected gold clusters, in which the protecting Au-thiolate units are arranged in chiral patterns on achiral cores. We interpret the electronic structure of the [Au20(PP3)4]Cl4 cluster in terms of the superatom complex model. The 16-electron cluster cannot be interpreted as a dimer of 8-electron clusters (which are magic). Instead, a superatomic electron configuration of 1S(2) 1P(6) 1D(6) 2S(2) is found. The 2S band is strongly stabilized, and the 1D states are nondegenerate with a large gap. Ligand protection of the (Au20)(4+) core leads to a significant increase of the HL-gap and thus stabilization. We also tested a charge of +II, which would give rise to an 18-electron superatom complex. Our results indicate that the 16-electron cluster is indeed more stable. We also investigate the optical properties of the cluster. The experimental absorption spectrum is well-reproduced by time-dependent DFT. Prominent transitions are analyzed by time-dependent density-functional perturbation theory. The intrinsic chirality of the cluster is compared to that of Au38(SR)24. We observe that the chiral arrangement of the protecting Au-SR units in Au38(SR)24 has very strong influence on the strength of the CD spectra, whereas phosphine protection in the title compound does not.

Superatomic S(2) silver clusters stabilized by a thiolate-phosphine monolayer: insight into electronic and optical properties of Ag14(SC6H3F2)12(PPh3)8 and Ag16(SC6H3F2)14(DPPE)4.

The electronic structure of two recently crystallographically solved, thiolate-phosphine protected silver clusters Ag14 and Ag16 are analyzed via density functional theory (DFT) and their optical excitations are analyzed from time-dependent DFT perturbation theory. Both clusters can be characterized as having the S(2) free-electron configuration in the metal core, which is the first time such a configuration is confirmed for structurally known ligand-protected noble metal clusters. However, their different core shapes and ligand layer induce significantly different optical spectra. Performance of gradient-corrected DFT functionals is discussed and it is shown that the asymptotically correct Leeuwen-Baerends LB94 functional reproduces the optical spectrum of Ag14 in a good agreement with experiment. Choice of the functional becomes important for clusters where the optical transitions are dominated by the electron-rich ligand layer.

A DFT Study of Linear Gold-Thiolate Superclusters Absorbing in the Therapeutic NIR Window.

A series of linear clusters up to an aspect ratio of 1:6, formed as multimers of smaller clusters with an icosahedral Au13(5+) core having an eight-electron superatom configuration, are computationally predicted to have a greatly enhanced size-dependent absorption in the near-infrared (NIR) region extending to the biologically important NIR window. A novel structural model is presented for the previously isolated thiol-stabilized Au54(SR)30 cluster, where the metal core is formed as a heterodimer of the cores of the known Au25(SR)18(-/0) and Au38(SR)24 clusters.

Supramolecular functionalization and concomitant enhancement in properties of Au(25) clusters.

We present a versatile approach for tuning the surface functionality of an atomically precise 25 atom gold cluster using specific host-guest interactions between ß-cyclodextrin (CD) and the ligand anchored on the cluster. The supramolecular interaction between the Au25 cluster protected by 4-(t-butyl)benzyl mercaptan, labeled Au25SBB18, and CD yielding Au25SBB18∩CDn (n = 1, 2, 3, and 4) has been probed experimentally using various spectroscopic techniques and was further analyzed by density functional theory calculations and molecular modeling. The viability of our method in modifying the properties of differently functionalized Au25 clusters is demonstrated. Besides modifying their optoelectronic properties, the CD moieties present on the cluster surface provide enhanced stability and optical responses which are crucial in view of the potential applications of these systems. Here, the CD molecules act as an umbrella which protects the fragile cluster core from the direct interaction with many destabilizing agents such as metal ions, ligands, and so on. Apart from the inherent biocompatibility of the CD-protected Au clusters, additional capabilities acquired by the supramolecular functionalization make such modified clusters preferred materials for applications, including those in biology.

Birth of the localized surface plasmon resonance in monolayer-protected gold nanoclusters.

Gold nanoclusters protected by a thiolate monolayer (MPC) are widely studied for their potential applications in site-specific bioconjugate labeling, sensing, drug delivery, and molecular electronics. Several MPCs with 1-2 nm metal cores are currently known to have a well-defined molecular structure, and they serve as an important link between molecularly dispersed gold and colloidal gold to understand the size-dependent electronic and optical properties. Here, we show by using an ab initio method together with atomistic models for experimentally observed thiolate-stabilized gold clusters how collective electronic excitations change when the gold core of the MPC grows from 1.5 to 2.0 nm. A strong localized surface plasmon resonance (LSPR) develops at 540 nm (2.3 eV) in a cluster with a 2.0 nm metal core. The protecting molecular layer enhances the LSPR, while in a smaller cluster with 1.5 nm gold core, the plasmon-like resonance at 540 nm is confined in the metal core by the molecular layer. Our results demonstrate a threshold size for the emergence of LSPR in these systems and help to develop understanding of the effect of the molecular overlayer on plasmonic properties of MPCs enabling engineering of their properties for plasmonic applications.

Electronic structure and optical properties of the thiolate-protected Au28(SMe)20 cluster.

The recently reported crystal structure of the Au28(TBBT)20 cluster (TBBT: p-tert-butylbenzenethiolate) is analyzed with (time-dependent) density functional theory (TD-DFT). Bader charge analysis reveals a novel trimeric Au3(SR)4 binding motif. The cluster can be formulated as Au14(Au2(SR)3)4(Au3(SR)4)2. The electronic structure of the Au14(6+) core and the ligand-protected cluster were analyzed, and their stability can be explained by formation of distorted eight-electron superatoms. Optical absorption and circular dichroism (CD) spectra were calculated and compared to the experiment. Assignment of handedness of the intrinsically chiral cluster is possible.

All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures.

Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag44(SR)30 and three Au12Ag32(SR)30 intermetallic nanoclusters stabilized with fluorinated arylthiols (SR=SPhF, SPhF2 or SPhCF3). The nanocluster forms a Keplerate solid of concentric icosahedral and dodecahedral atom shells, protected by six Ag2(SR)5 units. Positive counterions in the crystal indicate a high negative charge of 4(-) per nanoparticle, and density functional theory calculations explain the stability as an 18-electron superatom shell closure in the metal core. Highly featured optical absorption spectra in the ultraviolet-visible region are analysed using time-dependent density functional perturbation theory. This work forms a basis for further understanding, engineering and controlling of stability as well as electronic and optical properties of these novel nanomaterials.

Au40(SR)24 cluster as a chiral dimer of 8-electron superatoms: structure and optical properties.

We predict and analyze density-functional theory (DFT)-based structures for the recently isolated Au(40)(SR)(24) cluster. Combining structural information extracted from ligand-exchange reactions, circular dichroism and transmission electron microscopy leads us to propose two families of low-energy structures that have a chiral Au-S framework on the surface. These families have a common geometrical motif where a nonchiral Au(26) bi-icosahedral cluster core is protected by 6 RS-Au-SR and 4 RS-Au-SR-Au-SR oligomeric units, analogously to the "Divide and Protect" motif of known clusters Au(25)(SR)(18)(-/0), Au(38)(SR)(24) and Au(102)(SR)(44). The strongly prolate shape of the proposed Au(26) core is supported by transmission electron microscopy. Density-of-state-analysis shows that the electronic structure of Au(40)(SR)(24) can be interpreted in terms of a dimer of two 8-electron superatoms, where the 8 shell electrons are localized at the two icosahedral halves of the metal core. The calculated optical and chiroptical characteristics of the optimal chiral structure are in a fair agreement with the reported data for Au(40)(SR)(24).

High-pressure structures of disilane and their superconducting properties.

A systematic ab initio search for low-enthalpy phases of disilane (Si2H6) at high pressures was performed based on the minima hopping method. We found a novel metallic phase of disilane with Cmcm symmetry, which is enthalpically more favorable than the recently proposed structures of disilane up to 280 GPa, but revealing compositional instability below 190 GPa. The Cmcm phase has a moderate electron-phonon coupling yielding a superconducting transition temperature T(c) of around 20 K at 100 GPa, decreasing to 13 K at 220 GPa. These values are significantly smaller than previously predicted T(c))s for disilane at equivalent pressure. This shows that similar but different crystalline structures of a material can result in dramatically different T(c)'s and stresses the need for a systematic search for a crystalline ground state.

Nonadiabatic Ehrenfest molecular dynamics within the projector augmented-wave method.

We derive equations for nonadiabatic Ehrenfest molecular dynamics within the projector augmented-wave (PAW) formalism. The discretization of the electrons is time-dependent as the augmentation functions depend on the positions of the nuclei. We describe the implementation of the Ehrenfest molecular dynamics equations within the real-space PAW method. We demonstrate the applicability of our method by studying the vibration of NaCl, the torsional rotation of H(2)C=NH(2)(+) in both the adiabatic and the nonadiabatic regimes, and the hydrogen bombardment of C(40)H(16).

Crystal structure of cold compressed graphite.

Through a systematic structural search we found an allotrope of carbon with Cmmm symmetry which we predict to be more stable than graphite for pressures above 10 GPa. This material, which we refer to as Z-carbon, is formed by pure sp(3) bonds and it provides an explanation to several features in experimental x-ray diffraction and Raman spectra of graphite under pressure. The transition from graphite to Z-carbon can occur through simple sliding and buckling of graphene sheets. Our calculations predict that Z-carbon is a transparent wide band-gap semiconductor with a hardness comparable to diamond.

All-electron time-dependent density functional theory with finite elements: time-propagation approach.

We present an all-electron method for time-dependent density functional theory which employs hierarchical nonuniform finite-element bases and the time-propagation approach. The method is capable of treating linear and nonlinear response of valence and core electrons to an external field. We also introduce (i) a preconditioner for the propagation equation, (ii) a stable way to implement absorbing boundary conditions, and (iii) a new kind of absorbing boundary condition inspired by perfectly matched layers.

Simple preconditioning for time-dependent density functional perturbation theory.

By far, the most common use of time-dependent density functional theory is in the linear-reponse regime, where it provides information about electronic excitations. Ideally, the linear-response equations should be solved by a method that avoids the use of the unoccupied Kohn-Sham states--such as the Sternheimer method--as this reduces the complexity and increases the precision of the calculation. However, the Sternheimer equation becomes ill-conditioned near and indefinite above the first resonant frequency, seriously hindering the use of efficient iterative solution methods. To overcome this serious limitation, and to improve the general convergence properties of the iterative techniques, we propose a simple preconditioning strategy. In our method, the Sternheimer equation is solved directly as a linear equation using an iterative Krylov subspace method, i.e., no self-consistent cycle is required. Furthermore, the preconditioner uses the information of just a few unoccupied states and requires simple and minimal modifications to existing implementations. In this way, convergence can be reached faster and in a considerably wider frequency range than the traditional approach.

A density functional investigation of thiolate-protected bimetal PdAu(24)(SR)(18)(z) clusters: doping the superatom complex.

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

All-electron density functional theory and time-dependent density functional theory with high-order finite elements.

We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite-element bases. Our mesh generation scheme, in which structured atomic meshes are merged to an unstructured molecular mesh, allows a highly nonuniform discretization of the space. Thus it is possible to represent the core and valence states using the same discretization scheme, i.e., no pseudopotentials or similar treatments are required. The nonuniform discretization also allows the use of large simulation cells, and therefore avoids any boundary effects.

Time-dependent density-functional theory in the projector augmented-wave method.

We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we found perfect agreement in the calculated photoabsorption spectra. We discuss the strengths and weaknesses of the two methods as well as their convergence properties. We demonstrate different applications of the methods by calculating excitation energies and excited state Born-Oppenheimer potential surfaces for a set of atoms and molecules with the linear-response method and by calculating nonlinear emission spectra using the time-propagation method.