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β2-microglobulin is a paradigmatic amyloidogenic protein responsible fordialysis-related amyloidosis, a disease associated to long-term hemodialyzedpatients and characterized by accumulation of amyloid deposits in the osteoar-ticular tissues. In the early stages of amyloid fibril formation, β2-microglobulinassociates into dimers and higher oligomers, but clarifications are still neededfor the triggering conditions, mechanisms and specificity of dimer forma-tion. To characterize the dimeric association process, the protein-proteininteractions between three different species are investigated: namely, thenative protein and the two amyloidogenic variants ΔN6 and D76N. Thedimerization process is rationalized relying on state of the art computationalmethods. A comparative mechanism for how different mutations in the threevariants can affect protein dimerization and thus fibril formation is proposed. The number of salt bridges involved at the protein-protein interface correlateswith the degree of amyloidogenicity of each individual species. The findingscan offer possible strategies in controlling the dimerization mechanism basedon different β2-microglobulin protein mutations, which have significant rolesin the fibrillogenical process.

Control over supramolecular recognition between proteins and nanoparticles (NPs) is of fundamental importance in therapeutic applications and sensor development. Most NP-protein binding approaches use 'tags' such as biotin or His-tags to provide high affinity; protein surface recognition provides a versatile alternative strategy. Generating high affinity NP-protein interactions is challenging however, due to dielectric screening at physiological ionic strengths. We report here the co-engineering of nanoparticles and protein to provide high affinity binding. In this strategy, 'supercharged' proteins provide enhanced interfacial electrostatic interactions with complementarily charged nanoparticles, generating high affinity complexes. Significantly, the co-engineered protein-nanoparticle assemblies feature high binding affinity even at physiologically relevant ionic strength conditions. Computational studies identify both hydrophobic and electrostatic interactions as drivers for these high affinity NP-protein complexes.

The biological functions of proteins closely depend on their conformational dynamics. This aspect is especially relevant for intrinsically disordered proteins (IDP) for which structural ensembles often offer more useful representations than individual conformations. Here we employ extensive enhanced sampling temperature replica-exchange atomistic simulations (TREMD) and deep learning dimensionality reduction to study the conformational ensembles of the human heat shock protein B8 and its pathological mutant K141E, for which no experimental 3D structures are available. First, we combined homology modelling with TREMD to generate high-dimensional data sets of 3D structures. Then, we employed a recently developed machine learning based post-processing algorithm, EncoderMap, to project the large conformational data sets into meaningful two-dimensional maps that helped us interpret the data and extract the most significant conformations adopted by both proteins during TREMD. These studies provide the first 3D structural characterization of HSPB8 and reveal the effects of the pathogenic K141E mutation on its conformational ensembles. In particular, this missense mutation appears to increase the compactness of the protein and its structural variability, at the same time rearranging the hydrophobic patches exposed on the protein surface. These results offer the possibility of rationalizing the pathogenic effects of the K141E mutation in terms of conformational changes.

Understanding protein interactions with inorganic nanoparticle is central to the rational design of new tools in biomaterial sciences, nanobiotechnology, and nanomedicine. Theoretical modeling and simulations provide complementary approaches for experimental studies and are applied for exploring protein–particle surface-binding mechanisms, the determinants of binding specificity toward different surfaces, and the thermodynamics and kinetics of adsorption. The use of multiscale approaches is inevitable because the adsorption events extend over a wide range of time and length scales, which require the system to be addressed at different resolution levels. Here, we review the latest advances in coarse-grained treatment of these systems, usually addressed using residue-level resolution for proteins and mesoscale for the nanoparticle. We illustrate the parameterization strategies, focusing on those combining experimental and atomistic simulation data, within the theoretical framework of multiscale approaches.

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.

Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere with the formation of protein dimers and multimers in solution. A very special class of interactors are nanoparticles thanks to the extremely efficient extension of their interaction surface. In particular citrate-coated gold nanoparticles (cit-AuNPs) were recently investigated with amyloidogenic protein $\beta$2-microglobulin ($\beta$2m). Here we present the computational studies on two challenging models known for their enhanced amyloidogenic propensity, namely $\Delta$N6 and D76N $\beta$2m naturally occurring variants, and disclose the role of cit-AuNPs on their fibrillogenesis. The proposed interaction mechanism lies in the interference of the cit-AuNPs with the protein dimers at the early stages of aggregation, that induces dimer disassembling. As a consequence, natural fibril formation can be inhibited. Relying on the comparison between atomistic simulations at multiple levels (enhanced sampling molecular dynamics and Brownian dynamics) and protein structural characterisation by NMR, we demonstrate that the cit-AuNPs interactors are able to inhibit protein dimer assembling. As a consequence, the natural fibril formation is also inhibited, as found in experiment., Comment: Published by RSC, under a Creative Commons Attribution 3.0 Unported Licence

The impact of nanotechnologies in biomedicine and biotechnology is becoming more and more evident. It imposes practical challenges, for instance, raising specific issues on the biocompatibility of nanostructures. Nanoparticles are characterized by a high surface-to-volume ratio, which makes them reactive to foreign species. Thus, when proteins or peptides approach an inorganic nanoparticle, as well as a flat surface, they are likely to interact with the substrate to some extent. This interaction is crucial for applications in drug delivery, imaging, diagnostics, implants, and other medical devices. Specifically, gold nanoparticles are highly versatile and particularly appealing. It is widely accepted that the surfaces of nanoparticles adsorb proteins either transiently in the soft corona layer or permanently in the hard corona layer. As a consequence, the protein structure and/or function may undergo profound adjustments or remain conserved. Detailing the interaction of different inorganic substrates with proteins and peptides at the atomic level, and designing ways to control the interaction, is the key for biomedical applications of nanoparticles, both from a fundamental viewpoint and for practical implementations. In the last decade, we have addressed protein–nanoparticle interactions, focusing on interfaces of gold surfaces and nanoparticles with amyloidogenic peptides and protein models. We have developed classical force fields, performed advanced molecular dynamics simulations, and compared computational outcomes with data from nuclear magnetic resonance experiments. Protein–gold complexes with differently coated gold nanoparticles have been modeled to explore the effects of charge and size on the protein structure. Our work unravels that a complex interplay between surface properties and characteristics of the biological adsorbate determines whether peptide conformation is influenced and whether protein aggregation is accelerated or inhibited by the presence of the substrate. General guidelines to cope with amyloidogenic proteins could be inferred: these can be essentially summarized with the necessity of balancing the hydrophobic and electrostatic interactions that the amyloidogenic proteins establish with the coating moieties.

Nanoparticles have repeatedly been shown to enhance fibril formation when assayed with amyloidogenic proteins. Recently, however, evidence casting some doubt about the generality of this conclusion started to emerge. Therefore, to investigate further the influence of nanoparticles on the fibrillation process, we used a naturally occurring variant of the paradigmatic amyloidogenic protein β

Nanoparticles have repeatedly been shown to enhance fibril formation when assayed with amyloidogenic proteins. Recently, however, evidence casting some doubt about the generality of this conclusion started to emerge. Therefore, to investigate further the influence of nanoparticles on the fibrillation process, we used a naturally occurring variant of the paradigmatic amyloidogenic protein β2-microglobulin (β2m), namely D76N β2m where asparagine replaces aspartate at position 76. This variant is responsible for aggressive systemic amyloidosis. After characterizing the interaction of the variant with citrate-stabilized gold nanoparticles (Cit-AuNPs) by NMR and modeling, we analyzed the fibril formation by three different methods: thioflavin T fluorescence, native agarose gel electrophoresis and transmission electron microscopy. The NMR evidence indicated a fast-exchange interaction involving preferentially specific regions of the protein that proved, by subsequent modeling, to be consistent with a dimeric adduct interacting with Cit-AuNPs. The fibril detection assays showed that AuNPs are able to hamper D76N β2m fibrillogenesis through an effective interaction that competes with protofibril formation or recruitment. These findings open promising perspectives for the optimization of the nanoparticle surface to design tunable interactions with proteins.

Indoles represent a structural element in a myriad of natural products and biologically active molecules. Of special importance are 2,3-disubstituted indoles. Thus, a number of methods for their synthesis have been described. However, these are often hampered by a number of limitations: they often offer poor regioselectivity and suboptimal functional group tolerance. Also, they can normally be adapted to the procurement of a small subclass of indoles only. We have developed an approach to 2,3-disubstituted indoles overcoming these obstacles. By selectively activating the amide carbonyl in isatin-derived oxindoles, we obtained a number of the title compounds in a regiospecific and functional group-tolerant manner. The methodology is normally characterized by excellent yields. The reaction proceeds by chemoselective partial reduction of the amide moiety to an iminium salt and a subsequent nucleophilic addition followed by dehydration, which furnishes the target indole. A number of nucleophiles, including C- and S-nucleophiles, have been examined. The obtained compounds were studied towards acetylcholinesterase (AChE) inhibitory activity, as the indole skeleton is often seen in the struc-ture of enzyme inhibitors. Cholinesterase inhibitors are used in the treatment of Alzheimer's disease, increasing available acetylcholine by decreasing the AChE activity. For the tested agents, properties like logP, logBBB (Blood-Brain Barier penetration) and Caco2 permeabilities were also calculated. Based on the predicted values, only two of them are able to penetrate into the CNS (central nervous system). Molecular docking was performed on the whole set of the syntesized indole derivatives, resulting in a wide range of AChE inhibitory activity. Molecular docking binding interactions reported the lowest energy conformations of the syntesized compounds and the key amino acid residues at the active binding site of AChE. The current synergy between computations and experiments provided the identification of the indole derivatives exhibiting the highest inhibitory activity. The presented results will provide theoretical guidance for further modification and optimization of the indole derivatives.

We present a combined investigation of the dynamics and optics of triplex DNA, based on classical molecular dynamics and time-dependent density functional theory. Our approach is devised to include the effects of conformational fluctuations on the electronic structure and optical excitations of the system. We find that the structural flexibility has a strong role in the determination of the optical signals. Our results allow us to unravel the peculiar fingerprints of Watson-Crick and Hoogsteen H-bonding in the optical absorption spectra. We find a specific optical absorption feature that is due to the simultaneous presence of the two H-bonding patterns in C(+)GC triplets. While this peculiar triplet signal is wiped out in some structures that are representative of the finite-temperature dynamics, it can be recovered in an average view, so that it is a pristine result of this work.

Biodriven self-organization of α-quinquethiophene (t5): Cast films of 5′TA3′-t5 are electroactive, photoluminescent, and chiral. Their growth is not directed by intermolecular Watson–Crick hydrogen bonding between the A⋅⋅⋅T moieties of interacting molecules, but is governed by intra- and intermolecular thiophene–nucleobase stacking interactions. The synthesis and properties of 5′TA3′-t5 (8 a) and 5′CG3′-t5 (8 b) conjugates, in which the self-complementary dinucleotides TA and CG are covalently bound to the central ring of α-quinquethiophene (t5), are described. According to molecular mechanics calculations, the preferred conformation of both 8 a and 8 b is that with the dinucleotide folded over the planar t5 backbone, with the nucleobases facing t5 at stacking distance. The calculations show that the aggregation process of 8 a and 8 b is driven by a mix of nucleobase-thiophene interactions, hydrogen bonding between nucleobases (non Watson–Crick (W&C) in TA, and W&C in CG), van der Waals, and electrostatic interactions. While 8 b is scarcely soluble in any solvents, 8 a is soluble in water, indicating that the aggregates of the former are more stable than those of the latter. Microfluidic-induced self-assembly studies of 8 a showed the formation of lamellar, spherulitic, and dendritic supramolecular structures, depending on the concentration and solvent evaporation time. The self-assembled structures displayed micrometer dimensions in the xy plane of the substrate and nanometer dimensions in the z direction. Spatially resolved confocal microscopy and spectroscopy showed that the aggregates were characterized by intense fluorescence emission. Cast films of 8 a from water solutions showed chirality transfer from the dinucleotide to t5. The hole mobility of the cast films of 8 a was estimated using a two-electrode device under high vacuum and found to be up to two orders of magnitude greater than those previously measured for dinucleotide–quarterthiophene conjugates under the same experimental conditions.

The electronic properties of several metal-modified Watson-Crick guanine-cytosine base pairs are investigated by rneans of first-principle density functional theory calculations. Focus is placed on a new structure recently proposed as a plausible model for building an antiparallel duplex with Zn-guanine-cytosine pairs, but we also inspect several other conformations and the incorporation of Ag and Cu ions. We analyze the effects induced by the incorporation of one metal cation per base pair by comparing the structures and the electronic properties of the metalated pairs to those of the natural guanine-cytosine pair, particularly for what concerns the modifications of energy levels and charge density distributions of the frontier orbitals. Our results reveal the establishment of covalent bonding between the metal cation and the nucleobases, identified in the presence of hybrid metal-guanine and metal-cytosine orbitals. Attachment of the cation can occur either at the N1 or the N7 site of guanine and is compatible with altering or not altering the H-bond pattern of the natural pair. Cu(II) strongly contributes to the hybridization of the orbitals around the band gap, whereas Ag(l) and Zn(II) give hybrid states farther from the band gap. Most metalated pairs have smaller band gaps than the natural guanine-cytosine pair. The band gap shrinking along with the metal-base coupling suggests interesting consequences for electron transfer through DNA double helices.

Nanoparticles (NPs) are known to exhibit distinct physical and chemical properties compared with the same materials in bulk form. NPs have been repeatedly reported to interact with proteins, and this interaction can be exploited to affect processes undergone by proteins, such as fibrillogenesis. Fibrillation is common to many proteins, and in living organisms, it causes tissue-specific or systemic amyloid diseases. The nature of NPs and their surface chemistry is crucial in assessing their affinity for proteins and their effects on them. Here we present the first detailed structural characterization and molecular mechanics model of the interaction between a fibrillogenic protein, ? 2 -microglobulin, and a NP, 5 nm hydrophilic citrate-capped gold nanoparticles. NMR measurements and simulations at multiple levels (enhanced sampling molecular dynamics, Brownian dynamics, and PoissonÀBoltzmann electrostatics) explain the origin of the observed protein perturbations mostly localized at the amino-terminal region. Experiments show that the proteinÀNP interaction is weak in the physiological-like, conditions and do not induce protein fibrillation. Simulations reproduce these findings and reveal instead the role of the citrate in destabilizing the lower pH protonated form of ? 2 -microglobulin. The results offer possible strategies for controlling the desired effect of NPs on the conformational changes of the proteins, which have significant roles in the fibrillation process.

Protein-nanoparticle associations have important applications in nanoscienceand nanotechnology but the recognition mechanisms and the determinantsof specificity are still poorly understood at the microscopic level. Crucialquestions remain open, related to the association mechanisms, control ofbinding events, and preservation of functionality. Gold is a promising materialin nanoparticles for nanobiotechnology applications because of the ease ofits functionalization and its tunable optical properties. We present a conciseoverview of recent computational modeling advances which were pursued inthe quest for a theoretical framework elucidating the association mechanismsand the ability to design and control the recognition events of a specificclass of systems, namely, interfaces between polypeptides/proteins and a goldsurface in the presence of water. We select two different methodologicaladvances, the first related to the effect of surfactants covering the surfaceof nanoparticles and altering their interactions with proteins and the secondrelated to the immobilization of proteins on inorganic surfaces and conservingtheir functionality. Both cases, demonstrate how the understanding of thepolypeptide-surface coupling mechanisms is essential to the control of theprocess and exploitation for biotechnological and nanotechnological purposes.

The preferential sites for lithium doping in hydrogen-rich amorphous carbon materials are investigated by considering, as a model, a large polycyclic aromatic hydrocarbon (PAH): hexa-peri-hexabenzocoronene. Quantum-chemical calculations are carried out with B3LYP/6-31G* density functional theory to study the lowest energy configurations of the PAH doped with two lithium atoms. Infrared and Raman activities are computed for the most stable configurations and compared with the spectra of the pristine material to disclose the effect of doping on the vibrational spectra of hydrogen-rich amorphous carbon materials. It is shown that interaction with lithium atoms perturbs appreciably the atomic and electronic structure of the nanometric graphene sheet and leads to new marker bands in the spectra.

The synthesis and properties of (5')TA(3')-t5 (8a) and (5')CG(3')-t5 (8b) conjugates, in which the self-complementary dinucleotides TA and CG are covalently bound to the central ring of alpha-quinquethiophene (t5), are described. According to molecular mechanics calculations, the preferred conformation of both 8 a and 8b is that with the dinucleotide folded over the planar t5 backbone, with the nucleobases facing t5 at stacking distance. The calculations show that the aggregation process of 8 a and 8b is driven by a mix of nucleobase-thiophene interactions, hydrogen bonding between nucleobases (non Watson-Crick (W&C) in TA, and W&C in CG), van der Waals, and electrostatic interactions. While 8b is scarcely soluble in any solvents, 8a is soluble in water, indicating that the aggregates of the former are more stable than those of the latter. Microfluidic-induced self-assembly studies of 8a showed the formation of lamellar, spherulitic, and dendritic supramolecular structures, depending on the concentration and solvent evaporation time. The self-assembled structures displayed micrometer dimensions in the. v plane of the substrate and nanometer dimensions in the z direction. Spatially resolved confocal microscopy and spectroscopy showed that the aggregates were characterized by intense fluorescence emission. Cast films of 8a from water solutions showed chirality transfer from the dinucleotide to t5. The hole mobility of the cast films of 8a was estimated using a two-electrode device under high vacuum and found to be up to two orders of magnitude greater than those previously measured for dinucleotide-quarterthiophene conjugates under the same experimental conditions.

Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au₂₅L₁₈(-) (L = S(CH₂)₂Ph) on the β₂-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β₂-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion.

Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au25L18- (L S(CH2)(2)Ph) on the beta(2)-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length-and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of beta(2)-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion.

Structural and electronic properties of pristine and lithium-intercalated, phenyl-capped aniline dimers as a model for the lithium-polyaniline system have been studied by photoelectron spectroscopy and quantum chemical calculations. It was found that the electronic structure of reduced and oxidized forms of oligoanilines is only weakly affected by isomerism. Upon intercalation, charge transfer from the Li-atoms is remarkable and highly localized at N-atomic sites, where configurations are energetically favored in which both N atoms of the dimers are bound to Li atoms. Conversion of nitrogen sites is different for the two forms of aniline dimers and incomplete up to high intercalation levels, indicating a pronounced role of solid-state effects in the formation of such compounds.

We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.

We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge transport model. The influence of solvent- and DNA-mediated structural fluctuations is encoded in the obtained time series of the electronic charge transfer parameters. Within the Landauer approach to charge transport, we perform a detailed analysis of the conductance and current time series obtained by sampling the electronic structure along the molecular dynamics trajectory, and find that the inclusion of 8-oxoG damages into the DNA sequence can induce a change in the electrical response of the system. However, solvent-induced fluctuations tend to mask the effect, so that a detection of such sequence modifications via electrical transport measurements in a liquid environment seems to be difficult to achieve.

Protein-nanoparticle associations have important applications in nanoscience and nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnology applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by nuclear magnetic resonance (NMR). To reveal the molecular basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical molecular dynamics and Brownian dynamics) and compared the results with experimental data (circular dichroism and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the association process, and the origin of the perturbations in the NMR chemical shifts.

The electrical properties of single double-stranded DNA (dsDNA) molecules, and in particular conductivity through dsDNA, have several implications in the contexts of biology and nanotechnology. This importance led to a series of investigations [ 1 − 3 ] into the conduction properties and the conduction mechanisms through this 1D wire. [ 4 – 6 ] To expand our fi ndings on dsDNA [ 7 ] , we report comparative scanning tunneling spectroscopy (STS) results showing an interesting consistent discrepancy in the gap width between the dsDNA and the corresponding dsDNA complexed with metal ions (M-DNA). [ 8 ] Electronic structure calculations support the data. The STS study of this novel DNA-based molecule has high scientifi c and technological signifi cance and nicely complements other work in this fi eld, [ 7 , 9–13 ] which was limited to the canonical dsDNA. A poly(dG)-poly(dC) DNA sample was deposited on a gold substrate by electrostatic attraction. Right after the deposition the sample was imaged using atomic force microscopy (AFM) to inspect the DNA topography and to measure the concentration of the molecules on the surface, which was detected as ≈ 1–10 molecules in 1 × 1 μ m 2 . The sample was then inserted into the scanning tunneling microscopy (STM) ultrahigh vacuum (UHV) chamber for measurement. M-DNA molecules were obtained by dipping a DNA sample in a Cu + -ion solution. AFM images were fi rst recorded right after poly(dG)-poly(dC) deposition and then again after metallization of the sample, just before inserting into the UHV chamber. The AFM images show that the surface remains rather clean after the metallization procedure. Figure 1 shows images of DNA and M-DNA molecules scanned at room temperature (RT). Figure 1 a shows an example

The structural, tautomeric, hydrogen-bonding, stacking, and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar, and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical "keto" form is the most stable tautomer, in the gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e., a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in interplane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT...A stacked base pairs are larger than those determined for similarly stacked natural T...A pairs.

Quaterthiophene-dinucleotide conjugates (5')TA(3')-t4-(3')AT(5'), (5')AA(3')- t4-(3')AA(5'), and (TT3')-T-5'-t4-(TT5')-T-3' (TA: thymidine-adenosine, AA: adenosine-adenosine, TT: thymidine-thymidine) were synthesized and analyzed by a combination of spectroscopy and microscopy, electrical characterization, and theoretical calculations. Circular dichroism (CD) experiments demonstrated a transfer of chirality from the dinucleotides to quaterthiophene at high ionic strength and in cast films. The films were photoluminescent and electroactive. CD and photoluminescence spectra and current density/voltage plots (measured under dynamic vacuum) displayed significant variation on changing the dinucleotide scaffold. Molecular mechanics and molecular dynamics calculations indicated that the conformation and packing modes of the conjugates are the result of a balance between intra- and intermolecular nucleobase-thiophene stacking interactions and intramolecular hydrogen bonding between the nucleobases.

We report on the synthesis and self-assembly of a guanosine derivative bearing an alkyloxy side group under different environmental conditions. This derivative was found to spontaneously form ordered supramolecular nanoribbons in which the individual nucleobases are interacting through H-bonds. In toluene and chloroform solutions the formation of gel-like liquid-crystalline phases was observed. Sub-molecularly resolved scanning tunneling microscopic imaging of monolayers physisorbed at the graphite-solution interface revealed highly ordered two-dimensional networks. The recorded intramolecular contrast can be ascribed to the electronic properties of the different moieties composing the molecule, as proven by quantum-chemical calculations. This self-assembly behavior is in excellent agreement with that of 5'-O-acylated guanosines, which are also characterized by a self-assembled motif of guanosines that resembles parallel ribbons. Therefore, for guanosine derivatives (without sterically demanding groups on the guanine base) the formation of supramolecular nanoribbons in solution, in the solid state, and on flat surfaces is universal. This result is truly important in view of the electronic properties of these supramolecular anisotropic architectures and thus for potential applications in the fields of nano- and opto-electronics.

The CHARMM force field is used to calculate 36 minima along the potential energy surface of the helix -coil conversion of Ac-A14KG3A14K + 2H+ and to interconnect them through 35 transition states. The energy barriers are used to give the rate constants of interconversion between the conformers and the relevant kinetic equations are then solved. Fair to good agreement with the data obtained by drift time spectrometry experiments (D. T.Kaleta,M. F. Jarrold, J.Am.Chem. Soc . 125:7186, 2003) is obtained under a simple hypothesis of the initial conformer distribution.

We present a quantum chemical study on the effect of lithium doping in hydrogen rich carbon nanostructures. To model the hydrogen rich carbon nanostructure we selected hexa‐peri‐hexabenzocoronene, a well‐known polycyclic aromatic hydrocarbon whose UPS spectra have been recorded recently. This study shows that lithium interacts strongly with the carbon nanostructure and does not simply transfer charge to the PAH. As a result, the unusual features observed in the UPS spectra of lithium‐doped HBC are correctly reproduced by the calculations.

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.