Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives

Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.

Unravelling the atomistic mechanisms underpinning the morphological evolution of Al-alloyed hematite

Hydrothermal synthesis based upon the use of Al3+ as the dopant and/or ethanol as the solvent is effective in promoting the growth of hematite into nanoplates rich in the (001) surface, which is highly active for a broad range of catalytic applications. However, the underpinning mechanism for the flattening of hematite crystals is still poorly comprehended. To close this knowledge gap, in this work, we have attempted intensive computational modelling to construct a binary phase diagram for Fe2O3-Al2O3 under typical hydrothermal conditions, as well as to quantify the surface energy of hematite crystal upon coverage with Al3+ and ethanol molecules. An innovative coupling of density functional theory calculation, cluster expansion and Monte Carlo simulations in analogy to machine learning and prediction was attempted. Upon successful validation by experimental observation, our simulation results suggest an optimum atomic dispersion of Al3+ within hematite in cases when its concentration is below 4 at% otherwise phase separation occurs, and discrete Al2O3 nano-clusters can be preferentially formed. Computations also revealed that the adsorption of ethanol molecules alone can reduce the specific surface energy of the hematite (001) surface from 1.33 to 0.31 J m-2. The segregation of Al3+ on the (001) surface can further reduce the specific surface energy to 0.18 J m-2. Consequently, the (001) surface growth is inhibited, and it becomes dominant after the disappearance of other surfaces upon their continual growth. This work provides atomistic insights into the synergistic effect between the aluminium textural promoter and the ethanol capping agent in determining the morphology of hematite nanoparticles. The established computation approach also applies to other oxide-based catalysts in controlling their surface growth and morphology, which are critical for their catalytic applications.

Matched Ligands for Small, Stable Colloidal Nanoparticles of Copper, Cuprous Oxide and Cuprous Sulfide

This work applies organometallic routes to copper(0/I) nanoparticles and describes how to match ligand chemistries with different material compositions. The syntheses involve reacting an organo-copper precursor, mesitylcopper(I) [CuMes]z (z=4, 5), at low temperatures and in organic solvents, with hydrogen, air or hydrogen sulfide to deliver Cu, Cu2 O or Cu2 S nanoparticles. Use of sub-stoichiometric quantities of protonated ligand (pro-ligand; 0.1-0.2 equivalents vs. [CuMes]z ) allows saturation of surface coordination sites but avoids excess pro-ligand contaminating the nanoparticle solutions. The pro-ligands are nonanoic acid (HO2 CR1 ), 2-[2-(2-methoxyethoxy)ethoxy]acetic acid (HO2 CR2 ) or di(thio)nonanoic acid, (HS2 CR1 ), and are matched to the metallic, oxide or sulfide nanoparticles. Ligand exchange reactions reveal that copper(0) nanoparticles may be coordinated by carboxylate or di(thio)carboxylate ligands, but Cu2 O is preferentially coordinated by carboxylate ligands and Cu2 S by di(thio)carboxylate ligands. This work highlights the opportunities for organometallic routes to well-defined nanoparticles and the need for appropriate ligand selection.

Theory of Anisotropic Metal Nanostructures

A significant challenge in the development of functional materials is understanding the growth and transformations of anisotropic colloidal metal nanocrystals. Theory and simulations can aid in the development and understanding of anisotropic nanocrystal syntheses. The focus of this review is on how results from first-principles calculations and classical techniques, such as Monte Carlo and molecular dynamics simulations, have been integrated into multiscale theoretical predictions useful in understanding shape-selective nanocrystal syntheses. Also, examples are discussed in which machine learning has been useful in this field. There are many areas at the frontier in condensed matter theory and simulation that are or could be beneficial in this area and these prospects for future progress are discussed.

Twinned-Au-tip-induced growth of plasmonic Au-Cu Janus nanojellyfish in upconversion luminescence enhancement

The metallic Janus nanoparticle is an emerging plasmonic nanostructure that has attracted attention in the fields of materials science and nanophotonics. The instability of the Cu nanostructure leads to very complex nucleation and growth kinetics, and synthesis of Cu Janus nanoparticle has challenges. Here, we report a new method for synthesis of Au-Cu Janus nanojellyfish (JNF) by using twinned tips of Au nanoflower (NF) as seeds. The twinned nanotip of the Au NF and the large lattice mismatch between Au and Cu can induce formation of twin defects during the growth process, resulting in asymmetric deposition of Cu atoms. The symmetry-breaking using different sizes of Au NF and Cu nanodomains within the Au-Cu JNF can controllably change the localized surface plasmon resonance (LSPR) modes. The asymmetric Au-Cu JNF can induce plasmon coupling between dipolar and multipolar modes, which leads to clear electric-field enhancement in the near-infrared region. An Au-Cu JNF with multiple LSPR modes was chosen to simultaneously match the excitation and emission bands of the lanthanide-doped upconversion nanoparticles (UCNPs). A 5000-fold enhancement of the upconversion luminescence was achieved by using single plasmonic Au-Cu JNF. The Au-Cu JNF can also provide a guide for new metallic Janus nanoparticles in the fields of plasmonic, photothermal conversion, and nanomotors.

Solution-Phase Growth of Cu Nanowires with Aspect Ratios Greater Than 1000: Multiscale Theory

Penta-twinned metal nanowires are finding widespread application in existing and emerging technologies. However, little is known about their growth mechanisms. We probe the origins of chloride- and alkylamine-mediated, solution-phase growth of penta-twinned Cu nanowires from first-principles using multiscale theory. Using quantum density functional theory (DFT) calculations, we characterize the binding and surface diffusion of Cu atoms on chlorine-covered Cu(100) and Cu(111) surfaces. We find stronger binding and slower diffusion of Cu atoms on chlorinated Cu(111) than on chlorinated Cu(100), which is a reversal of the trend for bare Cu surfaces. We also probe interfacet diffusion and find that this proceeds faster from Cu(100) to Cu(111) than the reverse. Using the DFT rates for hopping between individual sites at Ångstrom scales, we calculate coarse-grained, interfacet rates for nanowires of various lengths─up to hundreds of micrometers─and diameters in the 10 nm range. We predict nanowires with aspect ratios of ∼100, based on surface diffusion alone. We also account for the influence of a self-assembled alkylamine layer that covers most of the {100} facets, but is absent or thin and disordered on the {111} facets and in an "end zone" near the {100}/{111} boundary. With an end zone, we predict a wide range of nanowire aspect ratios in the experimental ranges. Our work reveals the mechanisms by which a halide─chloride─promotes the growth of high-aspect-ratio nanowires.

Adsorption of alkylamines on Cu surfaces: identifying ideal capping molecules using first-principles calculations

We used dispersion-corrected density-functional theory to perform an in silico search over a series of primary alkylamines, including linear, branched, and cyclic molecules, to identify capping molecules for shape-selective Cu nanocrystal synthesis. We identify several attributes associated with successful capping agents. Generally, molecules with good geometric matching to the Cu surfaces possessed the strongest molecule-surface chemical bonds. However, non-bonding van der Waals interactions and molecular packing constraints can play a more significant role in determining the overall binding energy, the surface coverage, and the likely efficacy of the capping molecule. Though nearly all the molecules exhibited stronger binding to Cu(100) than to Cu(111), all predicted Wulff shapes are primarily {111}-faceted, based on ab initio thermodynamics calculations. From predicted capping-molecule densities on Cu(100) and Cu(111) for various solution environments, we identified several candidate molecules to produce {100}- or {111}-faceted nanocrystals with kinetic shapes, based on synthesis conditions used to grow Cu nanowires with ethylenediamine capping agent. Our study reveals the complexity of capping-molecule binding and important considerations that go into the selection of a successful capping agent.

Adsorption of ethylenediamine on Cu surfaces: attributes of a successful capping molecule using first-principles calculations

The shape-controlled synthesis of Cu nanocrystals can benefit a wide range of applications, though challenges exist in achieving high and selective yields to a particular shape. Capping agents play a pivotal role in controlling shape, but their exact role remains ambiguous. In this study, the adsorption of ethylenediamine (EDA) on Cu(100) and Cu(111) was investigated with quantum density functional theory (DFT) to reveal the complex roles of EDA in promoting penta-twinned Cu nanowire growth. We find EDA has stronger binding on Cu(100) than on Cu(111), which agrees the general expectation that penta-twinned Cu nanowires express facets with stronger capping-molecule binding. Despite this stronger binding, ab initio thermodynamics reveals the surface energy of EDA-covered Cu(111) is lower than that EDA-covered Cu(100) at all solution-phase EDA chemical potentials, so there is no thermodynamic driving force for penta-twinned nanowires. We also investigated the capability of EDA to protect Cu surfaces from oxidation in water by quantifying energy barriers for a water molecule to diffuse through EDA layers on Cu(100) and Cu(111). The energy barrier on Cu(100) is significantly lower, which supports observations of faster oxidation of Cu(100) in electrochemical experiments. Thus, we elucidate another possible function of a capping agent - to enable selective oxidation of crystal facets. This finding adds to the general understanding of successful attributes of capping agents for shape-selective nanocrystal growth.

Self-Assembly of a Linear Alkylamine Bilayer around a Cu Nanocrystal: Molecular Dynamics

Copper nanocrystals are often grown with the help of alkylamine capping agents, which direct the nanocrystal shape. However, the role of these molecules is still unclear. We characterized the assembly of aqueous tetradecylamine (TDA) around a Cu nanocrystal and found that TDA exhibits a temperature-dependent bilayer structure. The bilayer involves an inner layer, in which TDA binds to Cu via the amine group and tends to orient the alkyl tail perpendicular to the surface, and an outer layer whose structure depends on temperature. At low temperatures, alkylamines in the inner layer form bundles with no apparent relation to the crystal facets. Alkylamines in the outer layer tend to orient their long axes perpendicular to the Cu surfaces, with interdigitation into the inner layer. At high temperatures, alkylamines in the inner layer lose their bundle structure, and outer-layer alkylamines tend to orient themselves tangential to the Cu surfaces, forming a "web" above inner-layer TDA. TDA exhibits a rapid interlayer exchange at typical synthesis temperatures, consistent with experiment. The variety in the assemblies seen here and in other studies of alkanethiols around gold nanocrystals indicates a richness in the assemblies that can be achieved by modulating the interaction between the strongly binding end group and the surface.

Understanding the Solution-Phase Growth of Cu and Ag Nanowires and Nanocubes from First Principles

In this feature article, we provide an account of the Langmuir Lecture delivered by Kristen Fichthorn at the Fall 2020 Virtual Meeting of the American Chemical Society. We discuss how multiscale theory and simulations based on first-principles DFT were useful in uncovering the intertwined influences of kinetics and thermodynamics on the shapes of Ag and Cu cubes and nanowires grown in solution. We discuss how Ag nanocubes can form through PVP-modified deposition kinetics and how the addition of chloride to the synthesis can promote thermodynamic cubic shapes for both Ag and Cu. We discuss kinetic factors contributing to nanowire growth: in the case of Ag, we show that high-aspect-ratio nanowires can form as a consequence of Ag atom surface diffusion on the strained surfaces of Marks-like decahedral seeds. On the other hand, solution-phase chloride enhances Cu nanowire growth due to a synergistic interaction between adsorbed chloride and hexadecylamine (HDA), which leaves the {111} nanowire ends virtually bare while the {100} sides are fully covered with HDA. For each of these topics, a synergy between theory and experiment led to significant progress.

Electrochemical investigations of metal nanostructure growth with single crystals

Control over the nanoscopic structure of a material allows one to tune its properties for a wide variety of applications. Colloidal synthesis has become a convenient way to produce anisotropic metal nanostructures with a desired set of properties, but in most syntheses, the facet-selective surface chemistry causing anisotropic growth is not well-understood. This review highlights the recent use of electrochemical methods and single-crystal electrodes to investigate the roles of organic and inorganic additives in modulating the rate of atomic addition to different crystal facets. Differential capacitance and chronocoulometric techniques can be used to extract thermodynamic data on how additives selectively adsorb, while mixed potential theory can be used to observe the effect of additives on the rate of atomic addition to a specific facet. Results to date indicate that these experimental methods can provide new insights into the role capping agents and halides play in controlling anisotropic growth.

Antimicrobial Zn-Based "TSOL" for Citrus Greening Management: Insights from Spectroscopy and Molecular Simulation

Huanglongbing (HLB), also known as citrus greening, is a bacterial disease that poses a devastating threat to the citrus industry worldwide. To manage this disease efficiently, we developed and characterized a ternary aqueous solution (TSOL) that contains zinc nitrate, urea, and hydrogen peroxide. We report that TSOL exhibits better antimicrobial activity than commercial bactericides for growers. X-ray fluorescence analysis demonstrates that zinc is delivered to citrus leaves, where the bacteria reside. FTIR and Raman spectroscopy, molecular dynamics simulations, and density functional theory calculations elucidate the solution structure of TSOL and reveal a water-mediated interaction between Zn²⁺ and H₂O₂, which may facilitate the generation of highly reactive hydroxyl radicals contributing to superior antimicrobial activity of TSOL. Our results not only suggest TSOL as a potent antimicrobial agent to suppress bacterial growth in HLB-infected trees, but also provide a structure-property relationship that explains the superior performance of TSOL.

Retarding oxidation of copper nanoparticles without electrical isolation and the size dependence of work function

Copper nanoparticles (CuNPs) are attractive as a low-cost alternative to their gold and silver analogues for numerous applications, although their potential has hardly been explored due to their higher susceptibility to oxidation in air. Here we show the unexpected findings of an investigation into the correlation between the air-stability of CuNPs and the structure of the thiolate capping ligand; of the eight different ligands screened, those with the shortest alkyl chain, -(CH2)2-, and a hydrophilic carboxylic acid end group are found to be the most effective at retarding oxidation in air. We also show that CuNPs are not etched by thiol solutions as previously reported, and address the important fundamental question of how the work function of small supported metal particles scales with particle size. Together these findings set the stage for greater utility of CuNPs for emerging electronic applications.

Theory of the thermodynamic influence of solution-phase additives in shape-controlled nanocrystal synthesis

Though many experimental studies have documented that certain solution-phase additives can play a key role in the shape-selective synthesis of metal nanocrystals, the origins and mechanisms of this shape selectivity are still unclear. One possible role of such molecules is to thermodynamically induce the equilibrium shape of a nanocrystal by altering the interfacial free energies of the facets. Using a multi-scheme thermodynamic integration method that we recently developed [J. Chem. Phys., 2016, 145, 194108], we calculate the solid-liquid interfacial free energies γ_sl and investigate the propensity to achieve equilibrium shapes in such syntheses. We first apply this method to Ag(100) and Ag(111) facets in ethylene glycol solution containing polyvinylpyrrolidone (PVP), to mimic the environment in polyol synthesis of Ag nanocrystals. We find that although PVP has a preferred binding to Ag(100), its selectivity is not sufficient to induce a thermodynamic preference for {100}-faceted nanocubes, as has been observed experimentally. This indicates that PVP promotes Ag nanocube formation kinetically rather than thermodynamically. We further quantify the thermodynamic influence of adsorbed solution-phase additives for generic molecules, by building a γ_sl ratio/nanocrystal shape map as a function of zero-temperature binding energies. This map can be used to gauge the efficacy of candidate additive molecules for producing targeted thermodynamic nanocrystal shapes. The results indicate that only additives with a strong facet selectivity can impart significant thermodynamic-shape change. Therefore, many of the nanocrystals observed in experiments are likely kinetic products.