Evaluation of AgNCs@PEI and their integrated hydrogel for colorimetric and fluorometric detection of ascorbic acid.

A dual-mode colorimetric and fluorometric sensor based on water soluble silver nanoclusters (AgNCs@PEI) is developed for quantitative and visual detection of ascorbic acid (Asc A). The detection method relies on the Asc A induced aggregation of AgNCs@PEI, which resulted in fluorecsence quenching of the sensor. The clusters exhibited a unique combination of static and collisional quenching with a wide range of dynamic detection (1-105 µM) Linear relationship was observed in the concentration range 102-103 µM using fluorescence and 0.2 × 102-5 × 103 µM using absorbance spectroscopy with respective detection limits of 10.65 µM and 2.49 µM. The corresponding colorimetric and fluorometric changes can be easily monitored by the naked eye with a visual detection limit of 103 µM. AgNCs@PEI were further integrated within a hydrogel for developing a solid-state visual detection platform. Notably, the sensing response of the clusters towards Asc A remained unaltered even after hydrogel integration. Additionally, digital image analysis was adopted, which improved the sensitivity of instrument-free fluorescence detection of Asc A. Analysis by the developed sensor showed excellent recovery percentages of Asc A in spiked urine samples, which further underscores the practical applicability of the sensor.

PMAA-CeO2 nanoparticle-based paper microfluidic device with customized image processing software for antioxidant assay.

Despite recent advancements in the field of microfluidic paper-based analytical devices (µPADs), a key challenge remains in developing a simple and efficient µPAD with customized imaging capabilities for antioxidant assays. In the present study, we report a facile approach for µPAD fabrication through the application of transparent nail paint leading to creation of hydrophobic barriers and well-defined channels. The resultant µPADs were then characterized through scanning electron microscopy and contact angle measurements. The resolution and functional features of the fabricated µPAD were amenable to the intended assay. The µPAD's impregnated poly(methacrylic acid) (PMAA)-coated cerium oxide (CeO2) nanoparticles oxidized the 3,3',5,5'-tetramethylbenzidine (TMB) leading to the formation of a blue-colored charge-transfer complex. The addition of different antioxidant standard solutions resulted in a reduction in the blue color in a dose-dependent manner which could be observed visually. The color intensity of the PMAA-CeO2 nanoparticle@TMB oxidation product was inversely proportional to the antioxidant concentration and was measured using customized in-house MATLAB-based image processing software. Importantly, PMAA-CeO2 nanoparticle-based µPADs demonstrated good analytical characteristics and were able to be stored for long periods without any loss of activity. Moreover, potential interferents did not pose any threat to the colorimetric signal read-out for determination of antioxidant activity. The developed method was further applied for the assessment of antioxidant activity in a variety of tea samples and performed satisfactorily in comparison with a commonly used antioxidant detection method. Collectively, the developed µPAD-based platform holds great potential as a low-cost, convenient, portable and reliable method for pursuing various on-site antioxidant assays. Graphical Abstract.

NECI: N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods.

We present NECI, a state-of-the-art implementation of the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) algorithm, a method based on a stochastic application of the Hamiltonian matrix on a sparse sampling of the wave function. The program utilizes a very powerful parallelization and scales efficiently to more than 24 000 central processing unit cores. In this paper, we describe the core functionalities of NECI and its recent developments. This includes the capabilities to calculate ground and excited state energies, properties via the one- and two-body reduced density matrices, as well as spectral and Green's functions for ab initio and model systems. A number of enhancements of the bare FCIQMC algorithm are available within NECI, allowing us to use a partially deterministic formulation of the algorithm, working in a spin-adapted basis or supporting transcorrelated Hamiltonians. NECI supports the FCIDUMP file format for integrals, supplying a convenient interface to numerous quantum chemistry programs, and it is licensed under GPL-3.0.

First-order properties from internally contracted multireference coupled-cluster theory with particular focus on hyperfine coupling tensors.

Internally contracted multireference coupled-cluster (icMRCC) theory is extended to the computation of first-order properties (expectation values). We use the previously defined Lagrange formulation of the energy functional to derive the required equations for the Lagrange multipliers and arrive at an expression for first-order properties according to the generalized Hellmann-Feynman theorem, analogous to single-reference coupled-cluster theory. The present formulation does not include orbital relaxation, but in line with previous experience in coupled-cluster theory, the single-excitation cluster operator can recover a significant portion of orbital relaxation. Further aspects of the theory that arise from the internal contraction approach are discussed. Using automated derivation techniques, we have implemented a pilot code for icMRCCSD and icMRCCSDT for testing the method numerically. We find good agreement with full configuration interaction for several properties of boron monohydride and dipole moment curves of hydrogen fluoride and chromium hydride. A particular focus is given to spin-dependent properties: The hyperfine coupling tensors of Σ and Π radicals have been computed and compared to experiment and previous computations. We discuss the problem of describing spin polarization with properly spin-adapted wavefunctions, which requires either including pseudo-triple excitations or employing sufficiently flexible reference functions.

Response Formalism within Full Configuration Interaction Quantum Monte Carlo: Static Properties and Electrical Response.

We formulate a general, arbitrary-order stochastic response formalism within the full configuration interaction quantum Monte Carlo framework. This modified stochastic dynamic allows for the exact response properties of correlated multireference electronic systems to be systematically converged upon for systems far out of reach of traditional exact treatments. This requires a simultaneous coupled evolution of a response state alongside the zero-order state, which is shown to be stable, nontransient, and unbiased. We demonstrate this with application to the static dipole polarizability of molecular systems and, in doing so, resolve a discrepancy between restricted and unrestricted high-level coupled-cluster linear response results which were the high-accuracy benchmark in the literature.

Quantum tunneling during interstellar surface-catalyzed formation of water: the reaction H + H2O2 → H2O + OH.

The final step of the water formation network on interstellar grain surfaces starting from the H + O2 route is the reaction between H and H2O2. This reaction is known to have a high activation energy and therefore at low temperatures it can only proceed via tunneling. To date, however, no rate constants are available at temperatures below 200 K. In this work, we use instanton theory to compute rate constants for the title reaction with and without isotopic substitutions down to temperatures of 50 K. The calculations are based on density functional theory, with additional benchmarks for the activation energy using unrestricted single-reference and multireference coupled-cluster single-point energies. Gas-phase bimolecular rate constants are calculated and compared with available experimental data not only for H + H2O2 → H2O + OH, but also for H + H2O2 → H2 + HO2. We find a branching ratio where the title reaction is favored by at least two orders of magnitude at 114 K. In the interstellar medium this reaction predominantly occurs on water surfaces, which increases the probability that the two reactants meet. To mimic this, one, two, or three spectator H2O molecules are added to the system. Eley-Rideal bimolecular and Langmuir-Hinshelwood unimolecular rate constants are presented here. The kinetic isotope effects for the various cases are compared to experimental data as well as to expressions commonly used in astrochemical models. Both the rectangular barrier and the Eckart approximations lead to errors of about an order of magnitude. Finally, fits of the rate constants are provided as input for astrochemical models.

Unitary group adapted state specific multireference perturbation theory: Formulation and pilot applications.

We present here a comprehensive account of the formulation and pilot applications of the second-order perturbative analogue of the recently proposed unitary group adapted state-specific multireference coupled cluster theory (UGA-SSMRCC), which we call as the UGA-SSMRPT2. We also discuss the essential similarities and differences between the UGA-SSMRPT2 and the allied SA-SSMRPT2. Our theory, like its parent UGA-SSMRCC formalism, is size-extensive. However, because of the noninvariance of the theory with respect to the transformation among the active orbitals, it requires the use of localized orbitals to ensure size-consistency. We have demonstrated the performance of the formalism with a set of pilot applications, exploring (a) the accuracy of the potential energy surface (PES) of a set of small prototypical difficult molecules in their various low-lying states, using natural, pseudocanonical and localized orbitals and compared the respective nonparallelity errors (NPE) and the mean average deviations (MAD) vis-a-vis the full CI results with the same basis; (b) the efficacy of localized active orbitals to ensure and demonstrate manifest size-consistency with respect to fragmentation. We found that natural orbitals lead to the best overall PES, as evidenced by the NPE and MAD values. The MRMP2 results for individual states and of the MCQDPT2 for multiple states displaying avoided curve crossings are uniformly poorer as compared with the UGA-SSMRPT2 results. The striking aspect of the size-consistency check is the complete insensitivity of the sum of fragment energies with given fragment spin-multiplicities, which are obtained as the asymptotic limit of super-molecules with different coupled spins.

Identification of differentially expressed transcripts associated with bast fibre development in Corchorus capsularis by suppression subtractive hybridization.

MAIN CONCLUSION: The present study documented the predominant role of WRKY transcription factor in controlling genes of different pathways related to fibre formation in jute and could be a candidate gene for the improvement of jute fiber. Understanding of molecular mechanism associated with bast fibre development is of immense significance to achieve desired improvement in jute (Corchorus sp.). Therefore, suppression subtractive hybridization was successfully applied to identify genes involved in fibre developmental process in jute. The subtracted library of normal Corchorus capsularis as tester with respect to its fibre-deficient mutant as driver resulted in 2,685 expressed sequence tags which were assumed to represent the differentially expressed genes between two genotypes. The identified expressed sequence tags were assembled and clustered into 225 contigs and 231 singletons. Among these 456 unigenes, 377 were classified into 15 different functional categories while others were of unknown functional category. Reverse Northern analysis of the unigenes showed distinct variation in hybridization intensity of 11 transcripts between two genotypes tested. The findings were also documented by Northern and real-time PCR analysis. Varied expression level of these transcripts suggested their crucial involvement in fibre development in this species. Among these transcripts, WRKY transcription factor was documented to be a most important transcript which was in agreement with its known role in other plant species in possible regulation related to cell wall biosynthesis, expansion and lignification. This report constitutes first systematic analysis of genes involved in fibre development process in jute. It may be suggested that the information generated in this study would be useful for genetic improvement of fibre traits in this plant species.

Excited states with internally contracted multireference coupled-cluster linear response theory.

In this paper, the linear response (LR) theory for the variant of internally contracted multireference coupled cluster (ic-MRCC) theory described by Hanauer and Köhn [J. Chem. Phys. 134, 204211 (2011)] has been formulated and implemented for the computation of the excitation energies relative to a ground state of pronounced multireference character. We find that straightforward application of the linear-response formalism to the time-averaged ic-MRCC Lagrangian leads to unphysical second-order poles. However, the coupling matrix elements that cause this behavior are shown to be negligible whenever the internally contracted approximation as such is justified. Hence, for the numerical implementation of the method, we adopt a Tamm-Dancoff-type approximation and neglect these couplings. This approximation is also consistent with an equation-of-motion based derivation, which neglects these couplings right from the start. We have implemented the linear-response approach in the ic-MRCC singles-and-doubles framework and applied our method to calculate excitation energies for a number of molecules ranging from CH2 to p-benzyne and conjugated polyenes (up to octatetraene). The computed excitation energies are found to be very accurate, even for the notoriously difficult case of doubly excited states. The ic-MRCC-LR theory is also applicable to systems with open-shell ground-state wavefunctions and is by construction not biased towards a particular reference determinant. We have also compared the linear-response approach to the computation of energy differences by direct state-specific ic-MRCC calculations. We finally compare to Mk-MRCC-LR theory for which spurious roots have been reported [T.-C. Jagau and J. Gauss, J. Chem. Phys. 137, 044116 (2012)], being due to the use of sufficiency conditions to solve the Mk-MRCC equations. No such problem is present in ic-MRCC-LR theory.

Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis.

Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 µg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future.