Self-assembly of diamondoid molecules and derivatives (MD simulations and DFT calculations)

Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response

BACKGROUND AND AIMS

Hepatoblastoma (HB) is the predominant form of pediatric liver cancer, though it remains exceptionally rare. While treatment outcomes for children with HB have improved, patients with advanced tumors face limited therapeutic choices. Additionally, survivors often suffer from long-term adverse effects due to treatment, including ototoxicity, cardiotoxicity, delayed growth, and secondary tumors. Consequently, there is a pressing need to identify new and effective therapeutic strategies for patients with HB. Computational methods to predict drug sensitivity from a tumor's transcriptome have been successfully applied for some common adult malignancies, but specific efforts in pediatric cancers are lacking because of the paucity of data.

APPROACH AND RESULTS

In this study, we used DrugSense to assess drug efficacy in patients with HB, particularly those with the aggressive C2 subtype associated with poor clinical outcomes. Our method relied on publicly available collections of pan-cancer transcriptional profiles and drug responses across 36 tumor types and 495 compounds. The drugs predicted to be most effective were experimentally validated using patient-derived xenograft models of HB grown in vitro and in vivo. We thus identified 2 cyclin-dependent kinase 9 inhibitors, alvocidib and dinaciclib as potent HB growth inhibitors for the high-risk C2 molecular subtype. We also found that in a cohort of 46 patients with HB, high cyclin-dependent kinase 9 tumor expression was significantly associated with poor prognosis.

CONCLUSIONS

Our work proves the usefulness of computational methods trained on pan-cancer data sets to reposition drugs in rare pediatric cancers such as HB, and to help clinicians in choosing the best treatment options for their patients.

Novel adamantane-based hole transport materials for perovskite solar cells: a computational approach

Adamantane derivatives have been subjected to quantum mechanical calculations to determine their capabilities as potential hole transport materials (HTMs) in perovskite solar cells (PSCs). Adamantane has been modified in two ways: multiple arm substitution and outermost substituent variation. It has been shown that tetra-substitution of adamantane gave the best characteristics as a HTM. Further modification showed tetra-ethyl substituted adamantane (ad-EtTPA) has the lowest HOMO, a small hole reorganization energy (λh), absorption in the UV region, and good stability. These appropriate properties mean that ad-EtTPA could be a promising HTM in PSCs. In addition, the relationship between λh and the electrostatic potential (ESP) maps of the cationic geometry has been studied. Three outcomes were drawn from the investigation: (1) the high positive potential in the ESP map is the region where more geometric distortions are occurring in going from the neutral to the cationic state, (2) large geometric distortions in this region lead to high λh, and (3) for tetra-substituted adamantane derivatives, delocalization of the positive potential leads to lower λh. The results showed that ESP maps can give insight into the molecular engineering of HTMs.

Optical Properties of Single- and Double-Functionalized Small Diamondoids

The rational control of the electronic and optical properties of small functionalized diamond-like molecules, the diamondoids, is the focus of this work. Specifically, we investigate the single- and double- functionalization of the lower diamondoids, adamantane, diamantane, and triamantane with -NH₂ and -SH groups and extend the study to N-heterocyclic carbene (NHC) functionalization. On the basis of electronic structure calculations, we predict a significant change in the optical properties of these functionalized diamondoids. Our computations reveal that -NH₂ functionalized diamondoids show UV photoluminescence similar to ideal diamondoids while -SH substituted diamondoids hinder the UV photoluminescence due to the labile nature of the S-H bond in the first excited state. This study also unveils that the UV photoluminescence nature of -NH₂ diamondoids is quenched upon additional functionalization with the -SH group. The double-functionalized derivative can, thus, serve as a sensitive probe for biomolecule binding and sensing environmental changes. The preserved intrinsic properties of the NHC and the ideal diamondoid in NHC-functionalized-diamondoids suggests its utilization in diamondoid-based self-assembled monolayers (SAM), whose UV-photoluminescent signal would be determined entirely by the functionalized diamondoids. Our study aims to pave the path for tuning the properties of diamondoids through a selective choice of the type and number of functional groups. This will aid the realization of optoelectronic devices involving, for example, large-area SAM layers or diamondoid-functionalized electrodes.

Tuning the HOMO-LUMO Energy Gap of Small Diamondoids Using Inverse Molecular Design

Functionalized diamondoids show great potential as building blocks for various new optoelectronic applications. However, until now, only simple mono and double substitutions were investigated. In this work, we considered up to 10 and 6 sites for functionalization of the two smallest diamondoids, adamantane and diamantane, respectively, in search for diamondoid derivatives with a minimal and maximal HOMO-LUMO energy gap. To this end, the energy gap was optimized systematically using an inverse molecular design methodology based on the best-first search algorithm combined with a Monte Carlo component to escape local optima. Adamantane derivatives were found with HOMO-LUMO gaps ranging from 2.42 to 10.63 eV, with 9.45 eV being the energy gap of pure adamantane. For diamantane, similar values were obtained. The structures with the lowest HOMO-LUMO gaps showed apparent push-pull character. The push character is mainly formed by sulfur or nitrogen dopants and thiol groups, whereas the pull character is predominantly determined by the presence of electron-withdrawing nitro or carbonyl groups assisted by amino and hydroxyl groups via the formation of intramolecular hydrogen bonds. In contrast, maximal HOMO-LUMO gaps were obtained by introducing numerous electronegative groups.

Self-assembly of glycine on Cu(001): the effect of temperature and polarity

Glycine on Cu(001) is studied as an example to illustrate the critical role of finite temperature and molecular polarity in the self-assembly of biomolecules at a metal surface.

Diamondoid-based molecular junctions: a computational study

In this work, we deal with the computational investigation of diamondoid-based molecular conductance junctions and their electronic transport properties. A small diamondoid is placed between the two gold electrodes of the nanogap and is covalently bonded to the gold electrodes through two different molecules, a thiol group and a N-heterocyclic carbene molecule. We have shown that the thiol linker is more efficient as it introduces additional electron paths for transport at lower energies. The influence of doping the diamondoid on the properties of the molecular junctions has been investigated. We find that using a nitrogen atom to dope the diamondoids leads to a considerable increase of the zero bias conductance. For the N-doped system we show an asymmetric feature of the I-V curve of the junctions resulting in rectification within a very small range of bias voltages. The rectifying nature is the result of the characteristic shift in the bias-dependent highest occupied molecular orbital state. In all cases, the efficiency of the device is manifested and is discussed in view of novel nanotechnological applications.

Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing

Small diamond-like particles, diamondoids, have been shown to effectively functionalize gold electrodes in order to sense DNA units passing between the nanopore-embedded electrodes. In this work, we present a comparative study of Au(111) electrodes functionalized with different derivatives of lower diamondoids. Focus is put on the electronic and transport properties of such electrodes for different DNA nucleotides placed within the electrode gap. The functionalization promotes a specific binding to DNA leading to different properties for the system, which provides a tool set to systematically improve the signal-to-noise ratio of the electronic measurements across the electrodes. Using quantum transport calculations, we compare the effectiveness of the different functionalized electrodes in distinguishing the four DNA nucleotides. Our results point to the most effective diamondoid functionalization of gold electrodes in view of biosensing applications.

Carbene-mediated self-assembly of diamondoids on metal surfaces

N-heterocyclic carbenes (NHC)s are emerging as an alternative class of molecules to thiol-based self-assembled monolayers (SAMs), making carbene-based SAMs much more stable under harsh environmental conditions. In this work, we have functionalized tiny diamondoids using NHCs in order to prepare highly stable carbene-mediated diamondoid SAMs on metal substrates. Using quantum-mechanical simulations and two different configurations for the carbene-functionalized diamondoids attached on gold, silver, and platinum surfaces we were able to study in detail these materials. Specifically, we focus on the binding characteristics, stability, and adsorption of the NHC-mediated diamondoid SAMs on the metal surfaces. A preferential binding to platinum surfaces was found, while a modulation of the work function in all cases was clear. The surface morphology of all NHC-based diamondoid SAMs was revealed through simulated STM images, which show characteristic features for each surface.

Towards double-functionalized small diamondoids: selective electronic band-gap tuning

Diamondoids are nanoscale diamond-like cage structures with hydrogen terminations, which can occur in various sizes and with a diverse type of modifications. In this work, we focus on the structural alterations and the effect of doping and functionalization on the electronic properties of diamondoids, from the smallest adamantane to heptamantane. The results are based on quantum mechanical calculations. We perform a self-consistent study, starting with doping the smallest diamondoid, adamantane. Boron, nitrogen, silicon, oxygen, and phosphorus are chosen as dopants at sites which have been previously optimized and are also consistent with the literature. At a next step, an amine- and a thiol- group are separately used to functionalize the adamantane molecule. We mainly focus on a double functionalization of diamondoids up to heptamantane using both these atomic groups. The effect of isomeration in the case of tetramantane is also studied. We discuss the higher efficiency of a double-functionalization compared to doping or a single-functionalization of diamondoids in tuning the electronic properties, such as the electronic band-gap, of modified small diamondoids in view of their novel nanotechnological applications.

The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases

It has been shown that diamondoids can interact with DNA by forming relatively strong hydrogen bonds to DNA units, such as nucleobases. For this interaction to occur the diamondoids must be chemically modified in order to provide donor/acceptor groups for the hydrogen bond. We show here that the exact arrangement of an amine-modified adamantane with respect to a neighboring nucleobase has a significant influence on the strength of the hydrogen bond. Whether the diamondoid acts as a hydrogen donor or acceptor in the hydrogen binding to the nucleobase affects the electronic structure and thereby the electronic band-gaps of the diamondoid-nucleobase complex. In a donor arrangement of the diamondoid close to a nucleobase, the interaction energies are weak, but the electronic band-gaps differ significantly. Exactly the opposite trend is observed in an acceptor arrangement of the diamondoid. In each of these cases the frontier orbitals of the diamondoid and the nucleobase play a different role in the binding. The results are discussed in view of a diamondoid-based biosensing device.

Stable boron nitride diamondoids as nanoscale materials

We predict the stability of diamondoids made up of boron and nitrogen instead of carbon atoms. The results are based on quantum-mechanical calculations within density functional theory (DFT) and show some very distinct features compared to the regular carbon-based diamondoids. These features are evaluated with respect to the energetics and electronic properties of the boron nitride diamondoids as compared to the respective properties of the carbon-based diamondoids. We find that BN-diamondoids are overall more stable than their respective C-diamondoid counterparts. The electronic band-gaps (E(g)) of the former are overall lower than those for the latter nanostructures but do not show a very distinct trend with their size. Contrary to the lower C-diamondoids, the BN-diamondoids are semiconducting and show a depletion of charge on the nitrogen site. Their differences in the distribution of the molecular orbitals, compared to their carbon-based counterparts, offer additional bonding and functionalization possibilities. These tiny BN-based nanostructures could potentially be used as nanobuilding blocks complementing or substituting the C-diamondoids, based on the desired properties. An experimental realization of boron nitride diamondoids remains to show their feasibility.