Evaluation of 1,10-phenanthroline-based hydroxamate derivative as dual histone deacetylases/ribonucleotide reductase inhibitor with antitumor activities.

BACKGROUND: Aberrant expression of histone deacetylases (HDACs) and ribonucleotide reductase (RR) enzymes are commonly observed in various cancers. Researchers are focusing on these enzymes in cancer studies with the aim of developing effective chemotherapeutic drugs for cancer treatment. Targeting both HDAC and RR simultaneously with a dual HDAC/RR inhibitor has exhibited enhanced effectiveness compared to monotherapy in cancer treatment, making it a promising strategy. OBJECTIVES: The objective of the study is to synthesize and assess the anti-cancer properties of a 1,10-phenanthroline-based hydroxamate derivative, characterizing it as a novel dual HDAC/RR inhibitor. METHODS: The N1-hydroxy-N8-(1,10-phenanthrolin-5-yl)octanediamide (PA), a 1,10-phenanthroline-based hydroxamate derivative, was synthesized and structurally characterized. The compound was subjected to in vitro assessments of its anti-cancer, HDAC, and RR inhibitory activities. In silico docking and molecular dynamics simulations were further studied to explore its interactions with HDACs and RRM2. RESULTS: The structurally confirmed PA exhibited antiproliferative activity in SiHa cells with an IC50 of 16.43 µM. It displayed potent inhibitory activity against HDAC and RR with IC50 values of 10.80 µM and 9.34 µM, respectively. Co-inhibition of HDAC and RR resulted in apoptosis-induced cell death in SiHa cells, mediated by the accumulation of reactive oxygen species (ROS). In silico docking studies demonstrated that PA can effectively bind to the active sites of HDAC isoforms and RRM2. Furthermore, PA demonstrated a more favorable interaction with HDAC7, displaying a docking score of -9.633 kcal/mol, as compared to the standard HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), which exhibited a docking score of -8.244 kcal/mol against HDAC7. CONCLUSION: The present study emphasizes the prospect of designing a potential 1,10-phenanthroline hydroxamic acid derivative as a novel dual HDAC and RR-inhibiting anti-cancer molecule.

Antiaromatic Molecules as Magnetic Couplers: A Computational Quest.

In this study, we investigate a set of organic diradical structures in which two oxo-verdazyl radicals are selected as radical spin centers that are connected (coupled) via six coupler molecules (CM), resulting in various magnetic (ferromagnetic (FM) or antiferromagnetic (AFM)) characteristics, as reflected by their exchange coupling constants (J). We have designed 12 diradicals with 6-antiaromatic couplers coupled with bis-oxo-verdazyl diradicals with meta-meta (m-m) and para-meta (p-m) positional connectivities. The nature of the magnetic coupling (ferromagnetic, nonmagnetic, or antiferromagnetic) and the magnitude of the exchange constant J depend on the type of coupler, the connecting point between each radical center and CM, the degree of aromaticity of the coupler, and the length of the through-bond distance between radical centers. The computed magnetic exchange coupling constants J for these diradicals at the B3LYP/6-311++G(d,p) and MN12SX/6-311++G(d,p) levels of theory are large for many of these structures, indicating strong ferromagnetic coupling (with positive J values). In some cases, magnetic couplings are observed with J > 1000 cm-1 (B3LYP/6-311++G(d,p)) and strong antiferromagnetic coupling (with negative J values) with J < -1000 cm-1 (B3LYP/6-311++G(d,p)). Similarly, in some cases, magnetic couplings are observed with J > 289 cm-1 (MN12SX/6-311++G(d,p)) and strong antiferromagnetic coupling (with negative J values) with J < -568 cm-1 (MN12SX/6-311++G(d,p)). Furthermore, while numerous studies have reported that the degree of aromaticity of molecular couplers often favors strong ferromagnetic coupling, displaying the high-spin character of diradicals in their ground states, the couplers chosen in this study are characterized as antiaromatic or nonaromatic. The current investigation provides evidence that, remarkably, antiaromatic couplers are able to enhance stability by favoring electronic diradical structures with very strong ferromagnetic coupling when the length of the through-bond distance and connectivity pattern between radical centers are selected in such a way that the FM coupling is optimized. The findings in this study offer new strategies in the design of novel organic materials with interesting magnetic properties for practical applications.

The effect of hetero-atoms on spin exchange coupling pathways (ECPs): a computational investigation.

The effect of heteroatoms on exchange coupling pathways and the presence of more than one coupling paths are investigated. The lone pairs of sp2-hybridized heteroatoms contribute to aromaticity but do not play any pivotal role in the spin coupling between two spin centers. A conceptual model to describe this behavior of heteroatoms has been introduced, and we name it as the hetero-atom blocking effect. With the occurrence of two π-orbital exchange coupling pathways (ECPs) via bridgehead heteroatoms (B-, N-, O-, or S-), the magnetic exchange coupling constants (J) can be viewed as a signed sum of different individual pathways. The effect of σ-electron coupling is also investigated in this work.

Metallocene-coupled cumulenes: a quest for chiral single-molecule magnets.

In this work, we computationally investigated nickelocene and chromocene-coupled linear carbon chains. The designed systems are [Ni]-Cn-Ni], [Cr]-Cn-[Cr] and [Cr]-Cn-[Ni] (n = 3 to 9), where [Ni], [Cr] and Cn represent nickelocene (NiCp2, Cp = cyclopentadienyl), chromocene (CrCp2) and linear carbon chains respectively. The magnetic properties of these systems were computationally investigated by a density functional theory-based method. Ferromagnetic ground states were observed for [Ni]-Cn-[Ni] and [Cr]-Cn-[Cr] complexes for couplers with odd numbers of carbon atoms (n = 3, 5, 7 and 9), whereas antiferromagnetic ground states result for couplers with even numbers of carbon atoms (n = 4, 6 and 8). However, a totally opposite trend is followed by [Cr]-Cn-[Ni] complexes due to the spin polarization inside the chromocene. The calculation and study of magnetic anisotropy for all the ferromagnetic complexes suggest that the [Ni]-Cn-[Ni] complexes with coupler of odd number of carbon atoms will be suitable for the synthesis of single-molecule magnets among the designed complexes.

Cobaltocene-Coupled Cumulene: A Perspective on Chiral Magnet and Spintronics Device Design.

We present a computational study of the magnetic and electronic transport properties of cumulene-based monocobaltocene and dicobaltocene complexes. We show that the odd cumulene-based dicobaltocene complexes are a potential candidate for the ferromagnetic material. The calculation of the zero-field splitting (ZFS) parameter D confirms that the odd cumulene-based dicobaltocene complexes can be used as potential single-molecule magnets. The monocobaltocene-based complexes are found to be a good spin filter, as demonstrated by the calculation of the transmission and current versus voltage curve. The orthogonal SOMOs of the dicobaltocene complexes make them weak or a nonspin filter despite having a high spin ground state.

A Protocol for Fast Prediction of Electronic and Optical Properties of Donor-Acceptor Polymers Using Density Functional Theory and the Tight-Binding Method.

The ability of donor-acceptor (D-A) type polymers to control the positions of the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals makes them a popular choice for organic solar cell applications. The alternating D-A pattern in a monomer leads to a weak electronic coupling between the constituent monomers within the polymer chain. Exploiting the weak electronic coupling characteristics, we developed a method to efficiently calculate (1) the electronic properties and (2) the optical gap of such polymer chains. The electronic properties (HOMO and LUMO energies, ionization potential, electron affinity, and quasiparticle gap of an oligomer of any length up to an infinitely long polymer) of the D-A polymers are predicted by combining density functional theory calculation results and a tight-binding model. The weak electronic coupling implies that the optical gap of the polymer is size-independent, and thus, it can be calculated using a monomer. We validated the methods using a set of 104 polymers by checking the consistency where the electronic gap of a polymer is larger than the optical gap. Furthermore, we establish relationships between the results obtained from more accurate, yet slower methods (i.e., B3LYP functional, singlet-ΔSCF) with those obtained from the faster counterparts (i.e., BLYP functional, triplet-ΔSCF). Leveraging the found relationships, we propose a way in which the electronic and optical properties of the polymers can be calculated efficiently while retaining high accuracy. The use of the tight-binding model combined with the approach to estimate more accurate results based on less expensive simulations is crucial in the applications where a large volume of computations needs to be carried out efficiently with sufficiently high accuracy, such as high-throughput computational screening or training a machine-learning model.

Machine learning-based screening of complex molecules for polymer solar cells.

Polymer solar cells admit numerous potential advantages including low energy payback time and scalable high-speed manufacturing, but the power conversion efficiency is currently lower than for their inorganic counterparts. In a Phenyl-C_61-Butyric-Acid-Methyl-Ester (PCBM)-based blended polymer solar cell, the optical gap of the polymer and the energetic alignment of the lowest unoccupied molecular orbital (LUMO) of the polymer and the PCBM are crucial for the device efficiency. Searching for new and better materials for polymer solar cells is a computationally costly affair using density functional theory (DFT) calculations. In this work, we propose a screening procedure using a simple string representation for a promising class of donor-acceptor polymers in conjunction with a grammar variational autoencoder. The model is trained on a dataset of 3989 monomers obtained from DFT calculations and is able to predict LUMO and the lowest optical transition energy for unseen molecules with mean absolute errors of 43 and 74 meV, respectively, without knowledge of the atomic positions. We demonstrate the merit of the model for generating new molecules with the desired LUMO and optical gap energies which increases the chance of finding suitable polymers by more than a factor of five in comparison to the randomised search used in gathering the training set.

Magnetic and transport properties of conjugated and cumulated molecules: the π-system enlightens part of the story.

We have investigated the intramolecular magnetic exchange coupling constants (J) for a series of nitronyl nitroxide diradicals connected by a range of linear conjugated and cumulene couplers focusing on the unusual π-interaction properties within the couplers. Distance between radical centers, spin density within the couplers, as well as the dihedral angles between the radical centers and the plane of the coupler influence the strength of magnetic coupling. We also establish that with the increase in the length of the coupler, the strength of magnetic interaction in conjugated and cumulated systems varies in a different way. Transport calculations show that with the increase in chain length, diradicals based on cumulene containing an even number of carbon atoms act as better conductors than cumulenes with an odd number of carbon atoms. It is also observed that with the increase in the length of the conjugated coupler based diradicals, transmission does not vary in a sequential way.

Performance of range-separated hybrid exchange-correlation functionals for the calculation of magnetic exchange coupling constants of organic diradicals.

The prediction of magnetic behavior is important for the design of new magnetic materials. Kohn-Sham density functional theory is popular for this purpose, although one should be careful about choosing the right exchange-correlation functional. Here, we perform a statistical analysis to test different range-separated hybrid density functionals for the calculation of magnetic exchange coupling constants J of fourteen organic diradicals. Our analysis suggests that in absolute terms the MN12SX functional performs best among the series of twelve functionals studied here (including the popular B3LYP), followed by N12SX functionals along with Scuseria's HSE series of functionals. LC- ωPBE was found to be the least accurate, which is in contrast with its good performance for calculating J for transition metal complexes. The HSE family of functionals and B3LYP are the only functionals to reproduce the qualitative trends of the coupling constants correctly for the ferromagnetically coupled diradicals under study. © 2017 Wiley Periodicals, Inc.

Toward Molecular Magnets of Organic Origin via Anion-π Interaction Involving m-Aminyl Diradical: A Theoretical Study.

Here we study a set of novel magnetic organic molecular species with different halide ions (fluoride, chloride, bromide) absorbed ∼2 Å above or below the center of an aromatic π-ring in an m-aminyl diradical. Focus is on the nature of anion-π interaction and its impact on magnetic properties, specifically on magnetic anisotropy and on intramolecular magnetic exchange coupling. In the development of single molecule magnets, magnetic anisotropy is considered to be the most influential factor. A new insight regarding the magnetic anisotropy that determines the barrier height for relaxation of magnetization of m-aminyl diradical-derived anionic complexes is obtained from calculations of the axial zero-field-splitting (ZFS) parameter D. The noncovalent anion-π interaction strongly influences magnetic anisotropy in m-aminyl-halide diradical complexes. In particular, the change of D values from positive (for the m-aminyl diradical, m-aminyl diradical/fluoride, and m-aminyl diradical/chloride complexes) to negative D-values in m-aminyl diradical complexes containing bromide signals a change from oblate to prolate type of spin-density distribution. Furthermore, the noncovalent halide-π interactions lead to large values of intramolecular magnetic exchange coupling coefficients J exhibiting a ferromagnetic sign. The magnitude of J steadily increases going from anionic complexes containing fluoride to chloride and then to bromide. Relations are sought between the magnetic exchange coupling coefficients J and aromaticity, namely structural HOMA (harmonic oscillator model of aromaticity) and magnetic NICS (nucleus independent chemical shift) aromaticity indices, in particular, the NICSzz(+1) component. Finally, possible numerical checks on the conditions relating to validity of the well-known Yamaguchi's formula for calculating the exchange coupling coefficient J in diradical systems are discussed.

A Perspective on Designing Chiral Organic Magnetic Molecules with Unusual Behavior in Magnetic Exchange Coupling.

A total of nine diradical-based organic chiral magnetic molecules with allene and cumulene couplers have been theoretically designed, and subsequently, their magnetic property has been studied by density functional theory. It is found that with an increase in length of the coupler, a remarkable increase in spin density within the coupler takes place. An increase in the length of the coupler reduces the energy of LUMO, and a smaller HOMO-LUMO gap facilitates stronger magnetic coupling and thereby a higher magnetic exchange coupling constant (J). This observation is supported by the occupation number of natural orbitals.

Increasing Magnetic Coupling through Oxidation of a Ferrocene Bridge.

Ferrocene is an interesting coupler for designing magnetic molecules because of its rich chemistry and controllable oxidation state. In this work we have calculated the exchange spin coupling of a ferrocene-coupled nitronyl nitroxide diradical in its neutral and oxidized state (in which an additional spin center is introduced on the metallocene subunit). We do so by carrying out spin-unrestricted Kohn-Sham density functional theory (KS-DFT) calculations with different approximate exchange-correlation functionals and basis sets. We find that the neutral complex is weakly ferromagnetically coupled (in contrast to experimental results on single crystals), whereas the spin centers in the cationic complex are strongly antiferromagnetically coupled, resulting in an overall ferrimagnetic arrangement of the spins. Our calculations suggest that the magnetic exchange occurs through a spin alternation mechanism and that the lowest unoccupied molecular orbital (LUMO) plays an important role. The ferromagnetic behavior of the neutral complex is very sensitive to rotating one Cp ring versus the other. In the case of the cationic complex, the magnetic coupling is nearly independent of such structural changes. Thus, oxidation allows for switching between a weakly coupled and a strongly coupled, robust overall ferrimagnetic spin arrangement.

A high-spin organic diradical as a spin filter.

Here, in this work we have designed a molecular bridge structure which can be used as a spin filter where the prototypical highly ferromagnetic m-phenylene connected bis(aminoxyl) diradical is used as a bridging fragment between two semi-infinitely widened gold (Au) electrodes along the [100] direction. A state-of-the-art non-equilibrium Green function's (NEGF) method coupled with the density functional theory (DFT) was carried out on this two-probe molecular bridge system to understand its electrical spin transport characteristics. The spin current at various bias voltages from 0.00 V to 4.00 V at intervals of 0.20 V for this Au-diradical-Au molecular junction is evaluated. We also quantify the bias-dependent spin injection coefficients (BDSIC) at different bias voltages and also the spin-filter efficiency at equilibrium, i.e., at zero bias voltage. Also plots of BDSIC vs. voltage, the up- and down-spin current vs. voltage (I-V) curves, and density of states (DOS) at zero bias voltage are evaluated.

Borazine: spin blocker or not?

The spin blocker capacity of borazine is investigated. Specifically, meta-B-B, meta-N-N and para-B-N connected borazines are used as spin-blocker couplers comprised of a pair of radicals: two iminonitroxides (IN); IN and tetrathiafulvalene radical cations (TTF); or two TTFs. Density functional theory (DFT) is used to elucidate the spin blocker capacity of the linkage-specific (meta or para) borazine-coupler and elaborate the role of the lowest unoccupied molecular orbital (LUMO) in magnetic-exchange. Furthermore, a qualitative relation between different magnetic aromaticity indices is made using both nuclear-independent chemical shift (NICS) and the harmonic oscillator model of aromaticity (HOMA). The NICS values are calculated at the centre of the borazine spacer fragment of these diradical species and then also at 0.5 Å increments of the virtual probe from this centre position up to an orthogonal distance of 2.0 Å from the centre. The HOMA values are calculated for the borazine ring fragment in these diradicals. Based on the HOMA and NICS values, it is evident that the borazine exhibits less aromatic character than benzene itself - due to the polar nature of B-N π-bonding. The LUMO mediated spin-exchange between the two consecutive singly occupied molecular orbitals (SOMOs) is explicitly discussed and confirmed to play a pivotal role. The parity of the coupler pathways, i.e. even or odd number of bonds along a selected pathway, between radical moieties is an important factor in predicting the nature and extent of magnetic exchange for these diradicals. Surprisingly, borazine does not always act as a spin-coupling blocker - rather in some cases the coupling is enhanced as compared to a homoatomic (carbon-based) benzene coupler.

Performance of the widely used Minnesota density functionals for the prediction of heat of formations, ionization potentials of some benchmarked first row transition metal complexes.

We have computed and investigated the performance of Minnesota density functionals especially the M05, M06, and M08 suite of complementary density functionals for the prediction of the heat of formations (HOFs) and the ionization potentials (IPs) of various benchmark complexes containing nine different first row transition metals. The eight functionals of M0X family, namely, the M05, M05-2X, M06-L, M06, M06-2X, M06-HF, M08-SO, and M08-HX are taken for the computation of the above-mentioned physical properties of such metal complexes along with popular Los Alamos National Laboratory 2 double-ζ (LANL2DZ) basis set. Total 54 benchmark systems are taken for HOF calculation, whereas the 47 systems among these benchmark complexes are chosen for the calculation of IPs because of lack of experimental results on rest of the seven systems. The computed values of HOFs and IPs are compared with the experimental results obtained from the literature. The deviation of these computed values from the actual experimental results is calculated for each eight different M0X functionals to judge their performances in evaluating these properties. Finally, a clear relationship between the exchange correlation energy of eight M0X functionals and their efficiency are made to predict the different physical properties.

A theoretical study on photomagnetic fluorescent protein chromophore coupled diradicals and their possible applications.

We have designed and theoretically studied three different pairs of green fluorescent protein chromophores and their different homologue-based diradicals coupled with imino nitroxides. To begin with, the geometries of all these diradicals have been optimized at high spin (HS) state in the gas phase, in a water medium and in a blood plasma medium. The process of calculations is straightforward and well-established in the case of the gas phase. However, for calculations in water, we have adopted our own N-layer integrated molecular orbital and molecular mechanics (ONIOM) method. Similarly for the blood phase calculations, the polarized continuum model (PCM) method has been adopted. With these optimized geometries the magnetic exchange coupling constant (J) values are estimated for these diradicals in different media using the broken symmetry (BS) approach in an unrestricted DFT framework. In order to obtain the BS solutions in the ONIOM method, we have carried out ONIOM-BS, where the BS calculations are done for the inner high-level layer (diradical system) keeping the outer water layer at low level. In a similar fashion, a PCM-BS technique has also been adopted for the BS calculations in the PCM method. We have found that these diradicals have an ability to change their magnetic nature from antiferromagnetic in the trans form to ferromagnetic in the cis form upon irradiation of light with the appropriate wavelength. Using a time-dependent DFT (TDDFT) technique, the required wavelengths of light by which non-fluorescent dark trans diradicals turn into their corresponding bright fluorescent cis isomers are determined for each pair of diradicals for the gas and water media. This color change is indeed a signature of the change in magnetic state of the diradicals concerned. Here, we have also calculated the zero field splitting (ZFS) parameter (D), rhombic ZFS parameter (E) and ZFS magnitude (a2). From our calculations we ambitiously expect that if these diradicals are synthesized then they might be used as a successful, non-hazardous magnetic resonance imaging contrast agent (MRICA) in place of other metal-based contrast agents.

A DFT study on the magnetostructural property of ferromagnetic heteroverdazyl diradicals with phenylene coupler.

We have theoretically designed five different m-phenylene coupled high-spin bis-heteroverdazyl diradicals and their analogous p-phenylene coupled low-spin positional isomers. The geometry-based aromaticity index, harmonic oscillator model of aromaticity (HOMA) values for both the couplers (local HOMA), and the whole diradicals (global HOMA) have been calculated for all the diradicals. We also qualitatively relate these HOMA values with the intramolecular magnetic exchange coupling constants (J), calculated using a broken symmetry approach within unrestricted density functional theory framework. Structural aromaticity index HOMA of linkage specific benzene rings in our designed diradical systems shows that the aromatic character depends on the planarity of the molecule and it controls the sign and magnitude of J. The predicted J values are explained on the basis of spin polarization maps, average dihedral angles, and magnetic orbitals. The effect of the spin leakage phenomenon on magnetic exchange coupling constant and that on HOMA values of certain phosphaverdazyl systems has been explicitly discussed. In addition, a similar comparison is made between the calculated exchange coupling constants and corresponding HOMA values. The main novelty of this work stands on the consideration of the aromatic behavior by means of the geometrical index HOMA. We also estimate another aromaticity index, nucleus independent chemical shift (NICS) values for the phenylene coupler in each diradical to measure aromaticity and compare its value with that of HOMA. The ground state stabilities of these diradicals have also been compared.

Photoinduced antiferromagnetic to ferromagnetic crossover in organic systems.

Magnetization reversal is important for different technological applications. Photoinduced magnetization reversal is easier to implement than conventional reversal methods. Here, we theoretically design and investigate the photomagnetic property of azobenzene based diradical systems, where trans isomers convert into corresponding cis forms upon irradiation with light of appropriate wavelength. The coupling constant values have been estimated using the broken symmetry approach in the density functional theory framework. In each case, the trans isomer is found to be antiferromagnetic, while the cis form is ferromagnetic in nature. Therefore, photoinduced magnetic crossover from antiferromagnetic to ferromagnetic regime would be observed. This is a new observation in case of the systems of organic origin. Importance of such systems for photomagnetic switches, sensors, high density data storage, spin valves, and semiconductor spintronic materials have also been discussed with support from density of state analysis, singly occupied molecular orbital-singly occupied molecular orbital energy gaps and spin density plots.