Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure.

Drug resistance in HIV type 1 (HIV-1) is a pervasive problem that affects the lives of millions of people worldwide. Although records of drug-resistant mutations (DRMs) have been extensively tabulated within public repositories, our understanding of the evolutionary kinetics of DRMs and how they evolve together remains limited. Epistasis, the interaction between a DRM and other residues in HIV-1 protein sequences, is key to the temporal evolution of drug resistance. We use a Potts sequence-covariation statistical-energy model of HIV-1 protein fitness under drug selection pressure, which captures epistatic interactions between all positions, combined with kinetic Monte-Carlo simulations of sequence evolutionary trajectories, to explore the acquisition of DRMs as they arise in an ensemble of drug-naive patient protein sequences. We follow the time course of 52 DRMs in the enzymes protease, RT, and integrase, the primary targets of antiretroviral therapy. The rates at which DRMs emerge are highly correlated with their observed acquisition rates reported in the literature when drug pressure is applied. This result highlights the central role of epistasis in determining the kinetics governing DRM emergence. Whereas rapidly acquired DRMs begin to accumulate as soon as drug pressure is applied, slowly acquired DRMs are contingent on accessory mutations that appear only after prolonged drug pressure. We provide a foundation for using computational methods to determine the temporal evolution of drug resistance using Potts statistical potentials, which can be used to gain mechanistic insights into drug resistance pathways in HIV-1 and other infectious agents.

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.

The ability of HIV-1 to rapidly mutate leads to antiretroviral therapy (ART) failure among infected patients. Drug-resistance mutations (DRMs), which cause a fitness penalty to intrinsic viral fitness, are compensated by accessory mutations with favorable epistatic interactions which cause an evolutionary trapping effect, but the kinetics of this overall process has not been well characterized. Here, using a Potts Hamiltonian model describing epistasis combined with kinetic Monte Carlo simulations of evolutionary trajectories, we explore how epistasis modulates the evolutionary dynamics of HIV DRMs. We show how the occurrence of a drug-resistance mutation is contingent on favorable epistatic interactions with many other residues of the sequence background and that subsequent mutations entrench DRMs. We measure the time-autocorrelation of fluctuations in the likelihood of DRMs due to epistatic coupling with the sequence background, which reveals the presence of two evolutionary processes controlling DRM kinetics with two distinct time scales. Further analysis of waiting times for the evolutionary trapping effect to reverse reveals that the sequences which entrench (trap) a DRM are responsible for the slower time scale. We also quantify the overall strength of epistatic effects on the evolutionary kinetics for different mutations and show these are much larger for DRM positions than polymorphic positions, and we also show that trapping of a DRM is often caused by the collective effect of many accessory mutations, rather than a few strongly coupled ones, suggesting the importance of multiresidue sequence variations in HIV evolution. The analysis presented here provides a framework to explore the kinetic pathways through which viral proteins like HIV evolve under drug-selection pressure.

Calculating and Characterizing the Charge Distributions in Solids.

Accurate estimation of the partial atomic charges on metal centers is useful for understanding electronic and catalytic properties of materials. However, different methods of calculating these charges may give quite different results; this issue has been more widely studied for molecules than for solids. Here we study the charges on the metal centers of a test set of 18 solids containing transition metals by using density functional theory with several density functionals (PBE, PBE+U, TPSS, revTPSS, HLE17, revM06-L, B3LYP, B3LYP*, and other exchange-modified B3LYP functionals) and four charge models (Bader, Hirshfeld, CM5, and DDEC6). The test set contains 12 systems with nonmagnetic metal centers (eight metal oxides (MO2), two metal sulfides (MS2), and two metal selenides (MSe2)) and six ferromagnetic transition metal complexes. Our study shows that, among the four types of charges, Bader charges are the highest and Hirshfeld charges are the lowest for all the systems, regardless of the functional being used. The CM5 charges are bigger than DDEC6 charges for MX2 with M = Ti or Mo and X = S or Se, but for the other 14 cases they are lower. We found that the most of the systems are sensitive to the Hubbard U parameters in PBE+U and to the percentage X of Hartree-Fock exchange in exchange-modified B3LYP; as we increase U or X, the charges on the metal atoms in MX2 increase steadily. Testing different density functionals shows charges calculated with higher Hubbard U parameters in PBE+U are comparable to B3LYP (with 20% Hartree-Fock exchange). Among four meta-GGA functionals studied, the charges with HLE17 have the closest agreement with B3LYP. The variation of charges with choice of charge model is greater than the variation with choice of density functional.

Improved Predictive Tools for Structural Properties of Metal-Organic Frameworks.

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal-organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

Ferromagnetism in magnesium chloride monolayer with an unusually large spin-up gap.

The primary research target of the rapidly evolving spintronic industry is to design highly efficient novel materials that consume very low power and operate with high speed. Main group based ferromagnetic half-metallic materials are very promising due to their long spin-relaxation time. In recent years, the discovery of superconducting state with high critical temperature in a magnesium based system (MgB2) invigorated researchers due to its simple crystal structure and intriguing results, leading to its use as a good material for large scale application in electronic devices. Here, we report ferromagnetism and strong half-metallicity in another Mg-based system, which can be a promising material for spintronics based devices rather than for electronic devices (such as MgB2). Based on the first principle calculations, we report here a series of magnetic half-metallic magnesium chloride based monolayers [Mg0.89δ0.11Cl2, Mg0.78δ0.22Cl2, and Mg0.67δ0.33Cl2 (MgCl3)]. This MgCl3 phase has a similar pattern as that in CrI3, which has drawn remarkable attention worldwide as the first intrinsic 2D magnet. These magnesium chloride monolayer based systems are 100% spin-polarized, and promising for scattering-less transport due to strong half-metallicity and large spin-up gap (∼6.135-6.431 eV). The unusually large spin-up gap in our proposed system may shield spin current leakage even in nanoscale device. Further investigation explores a ferromagnetic ordering in Mg0.89δ0.11Cl2 with a Curie temperature of 250 K, which makes the system viable for operation at temperatures slightly lower than the room temperature. High magnetic anisotropy energy (MAE) in Mg0.89δ0.11Cl2 (452.84 µeV) indicates that the energy required to flip the spin is high, and therefore inhibits spin fluctuation. These results suggest a promising way to discover MgCl2-based 2D spin valves, GMR, TMR and other spintronics devices.

High Curie temperature and half-metallicity in an atomically thin main group-based boron phosphide system: long range ferromagnetism.

Transition metal-free magnetism and half-metallicity are currently drawing remarkable attention due to their potential future applications in spintronics devices. Using state-of-the-art density functional theory (DFT) calculations, we have considered Be and Mg incorporated in atomically thin boron phosphide (BP) systems for possible spintronics applications. Interestingly, our results reveal that Mg and Be substitution at P-sites exhibits ferromagnetism and half-metallicity. We also found long range ferromagnetism and a high Curie temperature (TC = ∼494 K) in the MgP@BP system; this Curie temperature is remarkably high amongst the existing main group-based 2D materials reported to date. The calculated magnetic anisotropy energy (MAE) is as high as 21.6 µeV per Mg. The stability study of the Mg-doped BP systems shows excellent dynamical, thermal and mechanical properties. Thus, a material with this high Curie temperature can function at elevated temperatures for future nano-spintronics device applications.

Ferromagnetism and Half-Metallicity in a High-Band-Gap Hexagonal Boron Nitride System.

Metal-free half-metallicity is the subject of intense research in the field of spintronics devices. Using density functional theoretical calculations, atom-thin hexagonal boron nitride (h-BN)-based systems are studied for possible spintronics applications. Ferromagnetism is observed in patterned C-doped h-BN systems. Interestingly, such a patterned C-doped h-BN exhibits half-metallicity with a Curie temperature of approximately 324 K at a particular C-doping concentration. It shows half-metallicity more than metal-free systems studied to date. Thus, such a BN-based system can be used to achieve a 100 % spin-polarised current at the Fermi level. Furthermore, this C-doped system shows excellent dynamical, thermal, and mechanical properties. Therefore, a stable metal-free planar ferromagnetic half-metallic h-BN-based system is proposed for use in room-temperature spintronics devices.

Stanene based gas sensors: effect of spin-orbit coupling.

Density functional theory calculations are performed to investigate the gas sensing properties (NO, NO2, NH3 and N2O) of pure and doped (B@, N@, and B-N@) stanene. Dispersion corrected (DFT-D3) density functional calculations show that doping improves the interaction between stanene and gas molecules. The extent of interaction between the system and gas molecules is further studied through charge density difference (CDD), electrostatic potential (ESP) and Bader charge analysis. The electronic properties of pure stanene + gases are studied with and without the effect of spin-orbit coupling. Stanene + gas systems show the Rashba-type of spin-splitting under spin-orbit coupling (SOC), which is very promising for spintronic applications. Interestingly, the doped systems (B@-, N@-, and B-N@stanene) show higher selectivity and sensitivity toward gas molecules compared to pure stanene. Therefore, the B@-, N@-, and B-N@stanene systems are promising for semiconductor based gas sensors.

Ferromagnetism and Half-Metallicity in Atomically Thin Holey Nitrogenated Graphene Based Systems.

Metal-free half-metallicity has been the subject of immense research focus in the field of spintronic devices. By using density functional theoretical (DFT) calculations, atomically thin holey nitrogenated graphene (C2 N) based systems are studied for possible spintronic applications. Ferromagnetism is observed in all the C-doped holey nitrogenated graphene. Interestingly, the holey nitrogenated graphene (C2 N) based system shows strong half-metallicity with a Curie temperature of approximately 297 K when a particular C-doping concentration is reached. It shows a strong half-metallicity compared with any metal-free systems studied to date. Thus, such carbon nitride based systems can be used for a 100 % spin polarized current. Furthermore, such C-doped systems show excellent dynamical, thermal, and mechanical properties. Thus, we predict a metal-free planar ferromagnetic half-metallic holey nitrogenated graphene based system for room-temperature spintronic devices.

Room-Temperature Magneto-dielectric Effect in LaGa0.7Fe0.3O3+γ; Origin and Impact of Excess Oxygen.

We report an observation of room-temperature magneto-dielectric (RTMD) effect in LaGa0.7Fe0.3O3+γ compound. The contribution of intrinsic/resistive sources in the presently observed RTMD effect was analyzed by measuring direct-current (dc) magnetoresistance (MR) in four-probe geometry and frequency-dependent MR via impedance spectroscopy (MRIS). Present MRIS analysis reveals that at frequencies corresponding to grain contribution (≥1 × 106 Hz for present sample), the observed MD phenomenon is MR-free/intrinsic, whereas at lower probing frequencies (<1 × 106 Hz), the observed MD coupling appears to be MR-dominated possibly due to oxygen excess, that is, due to coexistence of Fe3+ and Fe4+. The magnetostriction is anticipated as a mechanism responsible for MR-free/intrinsic MD coupling, whereas the MR-dominated part is attributed to hopping charge transport along with Maxwell-Wagner and space charge polarization. The multivalence of Fe ions in LaGa0.7Fe0.3O3+γ was validated through iodometric titration and Fe K-edge X-ray absorption near-edge structure measurements. The excess of oxygen, that is, coexistence of Fe3+ and Fe4+, was understood in terms of stability of Fe4+ by means of "bond-valence-sum" analysis and density functional theory-based first-principles calculations. The cation vacancies at La/Ga site (or at La and Ga both) were proposed as the possible origin of excess oxygen in presently studied compound. Present investigation suggests that, to justify the intrinsic/resistive origin of MD phenomenon, frequency-dependent MR measurements are more useful than measuring only dc MR or comparing the trends of magnetic-field-dependent change in dielectric constant and tan δ. Presently studied Fe-doped LaGaO3 can be a candidate for RTMD applications.

Band gap opening in stanene induced by patterned B-N doping.

Stanene is a quantum spin Hall insulator and a promising material for electronic and optoelectronic devices. Density functional theory (DFT) calculations are performed to study the band gap opening in stanene by elemental mono-doping (B, N) and co-doping (B-N). Different patterned B-N co-doping is studied to change the electronic properties of stanene. A patterned B-N co-doping opens the band gap in stanene and its semiconducting nature persists under strain. Molecular dynamics (MD) simulations are performed to confirm the thermal stability of such a doped system. The stress-strain study indicates that such a doped system is as stable as pure stanene. Our work function calculations show that stanene and doped stanene have a lower work function than graphene and thus are promising materials for photocatalysts and electronic devices.

Transition-metal embedded carbon nitride monolayers: high-temperature ferromagnetism and half-metallicity.

High-temperature ferromagnetic materials with planar surfaces are promising candidates for spintronics applications. Using state-of-the-art density functional theory (DFT) calculations, transition metal (TM = Cr, Mn, and Fe) incorporated graphitic carbon nitride (TM@gt-C3N4) systems are investigated as possible spintronics devices. Interestingly, ferromagnetism and half-metallicity were observed in all of the TM@gt-C3N4 systems. We find that Cr@gt-C3N4 is a nearly half-metallic ferromagnetic material with a Curie temperature of ∼450 K. The calculated Curie temperature is noticeably higher than other planar 2D materials studied to date. Furthermore, it has a steel-like mechanical stability and also possesses remarkable dynamic and thermal (500 K) stability. The calculated magnetic anisotropy energy (MAE) in Cr@gt-C3N4 is as high as 137.26 µeV per Cr. Thereby, such material with a high Curie temperature can be operated at high temperatures for spintronics devices.

Octahedral Ni-nanocluster (Ni85) for Efficient and Selective Reduction of Nitric Oxide (NO) to Nitrogen (N2).

Nitric oxide (NO) reduction pathways are systematically studied on a (111) facet of the octahedral nickel (Ni85) nanocluster in the presence/absence of hydrogen. Thermodynamic (reaction free energies) and kinetic (free energy barriers, and temperature dependent reaction rates) parameters are investigated to find out the most favoured reduction pathway for NO reduction. The catalytic activity of the Ni-nanocluster is investigated in greater detail toward the product selectivity (N2 vs. N2O vs. NH3). The previous theoretical (catalyzed by Pt, Pd, Rh and Ir) and experimental reports (catalyzed by Pt, Ag, Pd) show that direct N-O bond dissociation is very much unlikely due to the high-energy barrier but our study shows that the reaction is thermodynamically and kinetically favourable when catalysed by the octahedral Ni-nanocluster. The catalytic activity of the Ni-nanocluster toward NO reduction reaction is very much efficient and selective toward N2 formation even in the presence of hydrogen. However, N2O (one of the major by-products) formation is very much unlikely due to the high activation barrier. Our microkinetic analysis shows that even at high hydrogen partial pressures, the catalyst is very much selective toward N2 formation over NH3.

Targeted water soluble copper-tetrazolate complexes: interactions with biomolecules and catecholase like activities.

Two new mononuclear water soluble copper(II) complexes, [Cu{(5-pyrazinyl)tetrazolate}2(1,10-phenanthroline)] 1 and [Cu{(5-pyrazinyl)tetrazolate}(1,10-phenanthroline)2](NO3)0.5(N3)0.5 2, have been synthesized using the metal mediated [2 + 3] cycloaddition reaction between copper bound azide and pyrazinecarbonitrile. The interactions of these copper tetrazolate complexes 1 and 2 with biomolecules like DNA and bovine serum albumin (BSA) are studied and the catecholase like catalytic activity of compound 2 is also explored. Structural determination reveals that both compounds 1 and 2 are octahedral in nature. Screening tests were conducted to quantify the binding ability of complexes (1 and 2) towards DNA and it was revealed that complex 2 has a stronger affinity to bind to CT-DNA. DFT studies indicated that a lower HOMO-LUMO energy gap between the DNA fragment and metal complexes might be the reason for this type of stronger interaction. DNA cleavage activity was explored by gel-electrophoresis and moderate to strong DNA cleavage properties were observed in the presence and absence of co-reagents. Inhibition of cleavage in the presence of sodium azide indicates the propagation of the activity through the production of singlet molecular oxygen. Furthermore enzyme kinetic studies reflect that complex 2 is also effective in mimicking catecholase like activities. An ESI-MS spectral study indicates the probable involvement of dimeric species [(phen)2Cu-(OH)2-Cu(phen)2](2+) in the catalytic cycle.

A cuboctahedral platinum (Pt79) nanocluster enclosed by well defined facets favours di-sigma adsorption and improves the reaction kinetics for methanol fuel cells.

The methanol dehydrogenation steps are studied very systematically on the (111) facet of a cuboctahedral platinum (Pt79) nanocluster enclosed by well-defined facets. The various intermediates formed during the methanol decompositions are adsorbed at the edge and bridge site of the facet either vertically (through C- and O-centres) or in parallel. The di-sigma adsorption (in parallel) on the (111) facet of the nanocluster is the most stable structure for most of the intermediates and such binding improves the interaction between the substrate and the nanocluster and thus the catalytic activity. The reaction thermodynamics, activation barrier, and temperature dependent reaction rates are calculated for all the successive methanol dehydrogenation steps to understand the methanol decomposition mechanism, and these values are compared with previous studies to understand the catalytic activity of the nanocluster. We find the catalytic activity of the nanocluster is excellent while comparing with any previous reports and the methanol dehydrogenation thermodynamics and kinetics are best when the intermediates are adsorbed in a di-sigma manner.

Direct vs. indirect pathway for nitrobenzene reduction reaction on a Ni catalyst surface: a density functional study.

Density functional theory (DFT) calculations are performed to understand and address the previous experimental results that showed the reduction of nitrobenzene to aniline prefers direct over indirect reaction pathways irrespective of the catalyst surface. Nitrobenzene to aniline conversion occurs via the hydroxyl amine intermediate (direct pathway) or via the azoxybenzene intermediate (indirect pathway). Through our computational study we calculated the spin polarized and dispersion corrected reaction energies and activation barriers corresponding to various reaction pathways for the reduction of nitrobenzene to aniline over a Ni catalyst surface. The adsorption behaviour of the substrate, nitrobenzene, on the catalyst surface was also considered and the energetically most preferable structural orientation was elucidated. Our study indicates that the parallel adsorption behaviour of the molecules over a catalyst surface is preferable over vertical adsorption behaviour. Based on the reaction energies and activation barrier of the various elementary steps involved in direct or indirect reaction pathways, we find that the direct reduction pathway of nitrobenzene over the Ni(111) catalyst surface is more favourable than the indirect reaction pathway.