Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping.

Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 µg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

Development of an inoculation technique for rapidly evaluating maize inbred lines for resistance to stalk rot caused by Fusarium spp. in the field.

Maize (Zea mays L.) stalk rot, caused primarily by the soil-borne fungal pathogen Fusarium spp., reduces maize quality and yield worldwide. This study was undertaken to develop and utilize a rapid continuous injection inoculation technique to evaluate maize inbred lines for resistance to Fusarium spp. under field conditions, which could facilitate the identification and development of new sources of host resistance to manage the disease. Continuous injection inoculation is a rapid, stable, and simple method that can evaluate the resistance of maize inbred lines to Fusarium stalk rot (FSR) within 20 days. To verify the feasibility and reliability of inoculation method, Fusarium graminearum, F. proliferatum, and F. subglutinans were isolated, identified, and inoculated into maize at the six-leaf stage (V6) by a veterinary adjustable bottle continuous vaccination syringe. Our results showed that out of a total of 97 inbred maize lines, six (6.2%) showed high resistance to maize stalk rot, 20 showed resistance (20.6%), 32 were susceptible (33.0%), and 39 were very susceptible (40.2%). Based on simple sequence repeat (SSR) markers, an analysis of molecular variance indicated a significant correlation between population of the inbred maize line and resistance to FSR (P = 0.001). Overall, this study provided a systematic, rapid, stable, and simple identification method for maize inbred lines resistant to FSR in the field. At the same time, this method was also suitable for genetic diversity analysis of maize inbred lines resistant to FSR.

Empirical correction of nondynamical correlation energy for density functionals.

To provide an efficient means to address nondynamical correlation, an empirical correction for single and double hybrid density functionals has been formulated. The correction utilizes the highest doubly occupied, lowest unoccupied, and singly occupied generalized Kohn-Sham orbitals and, for potential energy curves, a few additional strongly correlated orbitals. Utilizing proposed nondynamical correlation corrections, hybrid BLYP predicted potential energy curves that fit well to those obtained by ab initio multireference methods for the torsional rotation of ethylene and the automerization of cyclobutadiene. The empirical nondynamical correlation corrections, calculated at the transition structures, also reduce the overall errors of B2K-PLYP for the DBH24 and BH76 barrier height data sets. The proposed empirical correction can efficiently enhance the utility of both single and double hybrid density functionals for chemical situations with moderate to significant nondynamical correlation.

Toward accurate theoretical thermochemistry of first row transition metal complexes.

The recently developed correlation consistent Composite Approach for transition metals (ccCA-TM) was utilized to compute the thermochemical properties for a collection of 225 inorganic molecules containing first row (3d) transition metals, ranging from the monohydrides to larger organometallics such as Sc(C(5)H(5))(3) and clusters such as (CrO(3))(3). Ostentatiously large deviations of ccCA-TM predictions stem mainly from aging and unreliable experimental data. For a subset of 70 molecules with reported experimental uncertainties less than or equal to 2.0 kcal mol(-1), regardless of the presence of moderate multireference character in some molecules, ccCA-TM achieves transition metal chemical accuracy of ±3.0 kcal mol(-1) as defined in our earlier work [J. Phys. Chem. A2007, 111, 11269-11277] by giving a mean absolute deviation of 2.90 kcal mol(-1) and a root-mean-square deviation of 3.91 kcal mol(-1). As subsets are constructed with decreasing upper limits of reported experimental uncertainties (5.0, 4.0, 3.0, 2.0, and 1.0 kcal mol(-1)), the ccCA-TM mean absolute deviations were observed to monotonically drop off from 4.35 to 2.37 kcal mol(-1). In contrast, such a trend is missing for DFT methods as exemplified by B3LYP and M06 with mean absolute deviations in the range 12.9-14.1 and 10.5-11.0 kcal mol(-1), respectively. Salient multireference character, as demonstrated by the T(1)/D(1) diagnostics and the weights (C(0)(2)) of leading electron configuration in the complete active self-consistent field wave function, was found in a significant amount of molecules, which can still be accurately described by the single reference ccCA-TM. The ccCA-TM algorithm has been demonstrated as an accurate, robust, and widely applicable model chemistry for 3d transition metal-containing species with versatile bonding features.

Multireference Character for 3d Transition-Metal-Containing Molecules.

Coupled cluster and configuration interaction diagnostics have been examined in order to assess the reliability of single reference quantum methods for a series of 3d transition metal species including hydrides, nitrides, chalcogenides, halides, small clusters, coordination complexes, and metal dimers. Several means of diagnostics have been considered including T1 and D1 diagnostics (the Frobenius norm and matrix 2-norm of coupled cluster amplitudes for single excitations, respectively), C0(2) (the weight of leading configuration of a complete active space wave function), and %TAE (percent total atomization energy). T1 and D1 diagnostics are strongly correlated for certain metal-ligand bonding types. The use of T1 and D1 together with %TAE can provide more reliable assessment of the severity of nondynamical correlation than a single indicator can provide. New criteria, namely T1 > 0.05, D1 > 0.15, and |%TAE| > 10, are suggested to identify inorganic species with substantial nondynamical correlation. For these systems, energies and spectroscopic properties computed using single reference electronic correlation methods may suffer from large errors and unpredictable behavior. Conversely, a computation where a molecule is below one or more of these thresholds does not always imply domination by a single reference. Some historically pathological molecules such as Mn2 and Cr2 show T1 < 0.05 and D1 < 0.15. Current implementations of coupled cluster diagnostics may still be insufficient for categorization of molecules that have pronounced nondynamical correlation.

Comparative Study of Single and Double Hybrid Density Functionals for the Prediction of 3d Transition Metal Thermochemistry.

The performance of 13 density functionals, including hybrid-GGA, hybrid-meta-GGA, and double-hybrid functionals, in combination with the correlation consistent basis sets, has been evaluated for the prediction of gas phase enthalpies of formation for a large set of 3d transition-metal-containing molecules with versatile bonding features. Of the methods studied, the hybrid B97-1 functional and the double hybrid functional mPW2-PLYP exhibit the best overall performance with mean absolute deviations (MAD) from experimental data of 7.2 and 7.3 kcal mol(-1), respectively. For single reference molecules, where dynamic correlation predominates, the results of the hybrid functionals B97-1, B98, and ωB97X and the double hybrid functionals B2-PLYP, B2GP-PLYP, and mPW2-PLYP yield the smallest deviations from the experimental enthalpies of formation. For the prediction of thermodynamic properties of coordination complexes including metal carbonyls, B97-1 and mPW2-PLYP are the most promising functionals of those investigated. When the size of the molecule is considered, B97-1 and B98 outperform mPW2-PLYP for diatomics and triatomics, while mPW2-PLYP yields the lowest MAD for larger molecules.

A pseudopotential-based composite method: the relativistic pseudopotential correlation consistent composite approach for molecules containing 4d transition metals (Y-Cd).

The correlation consistent composite approach (ccCA) has proven to be an effective first-principles-based composite approach for main group and first-row transition metal species. By combining relativistic pseudopotentials and ccCA, accurate energetic and thermodynamic data for heavier elements, including transition metals, is obtainable. Relativistic pseudopotential ccCA (rp-ccCA) was formulated and tested on 25 molecules from the G3∕05 set that contain 4p elements (Ga-Kr). A 32.5% time savings was obtained using rp-ccCA, relative to ccCA employing all-electron basis sets. When implementing rp-ccCA to compute dissociation energies and enthalpies of formation for molecules from the 4p block, rp-ccCA results in a mean absolute deviation of 0.89 kcal mol(-1) from experimental data. rp-ccCA was also applied to a set of 30 4d transition metal-containing molecules, ranging from diatomics to Mo(CO)(6), and enthalpies of formation for these species were obtained with a mean absolute deviation of 2.89 kcal mol(-1) in comparison to experimental data. Based on quality of the experimentally available enthalpies of formation, where the average value of reported experimental error bars is 3.43 kcal mol(-1), rp-ccCA is within transition metal chemical accuracy for the 4d molecule set. rp-ccCA is a pseudopotential-based composite method for transition metals and is shown to yield accurate thermodynamic results for molecules containing heavy elements Ga-Kr and Y-Cd.

Theoretical study of the photodissociation of Li(2)+ in one-color intense laser fields.

A theoretical treatment of the photodissociation of the molecular ion Li(2) (+) in one-color intense laser fields, using the time-dependent wave packet approach in a Floquet Born-Oppenheimer representation, is presented. Six electronic states 1,2 (2)Σ(g)(+), 1,2 (2)Σ(u)(+), 1 (2)Π(g), and 1 (2)Π(u) are of relevance in this simulation and have been included. The dependences of the fragmental dissociation probabilities and kinetic energy release (KER) spectra on pulse width, peak intensity, polarization angle, wavelength, and initial vibrational level are analyzed to interpret the influence of control parameters of the external field. Three main dissociation channels, 1 (2)Σ(g)(+) (m = -1), 2 (2)Σ(g)(+) (m = -2), and 2 (2)Σ(u)(+) (m = -3), are seen to dominate the dissociation processes under a wide variety of laser conditions and give rise to well separated groups of KER features. Different dissociation mechanisms for the involved Floquet channels are discussed.

Multireference composite approaches for the accurate study of ground and excited electronic states: C2, N2, and O2.

A multireference analog of the correlation consistent composite approach (MR-ccCA) based on complete active space with second-order perturbation theory (CASPT2) has been utilized in an investigation of the ground and valence excited states of C(2), N(2), and O(2). The performance of different second-order multireference perturbation theory methods including second-order n-electron valence state perturbation theory, second-order multireference Møller-Plesset, and second-order generalized van Vleck perturbation theory has been analyzed as potential alternatives to CASPT2 within MR-ccCA. The MR-ccCA-P predicts spectroscopic constants with overall mean absolute deviations from experimental values of 0.0006 Å, 7.0 cm(-1), and 143 cm(-1) for equilibrium bond length (r(e)), harmonic frequency (ω(e)), and term values (T(e)), respectively, which are comparable to the predictions by more computationally costly multireference configuration interaction-based methods.

Configuration-driven unitary group approach for generalized Van Vleck variant multireference perturbation theory.

A new, efficient, configuration-driven algorithm utilizing the unitary group approach (UGA) was developed and implemented for the generalized van Vleck perturbation theory (GVVPT) variant of multireference perturbation theory. The computational speed has been improved by 1 or 2 orders of magnitude compared to the previous implementation based on the Table-CI technique. It is shown that the reformulation is applicable to both the second-order (GVVPT2) and third-order (GVVPT3) approximations. Calculations on model problems and on a chemically realistic description of cyclobutadiene are used to illustrate the performance of the method. The calculations on cyclobutadiene, using over 2.3 billion CSFs, provide results on geometric parameters and the barrier height of the automerization reaction in good agreement with established high accuracy results.

Theoretical study of electronic states of N22+in an intense radiation field.

The Floquet states of N(2) (2+) created by the interactions of the six lowest singlet (1 (1)Sigma(g) (+), 1 (1)Delta(g), 2 (1)Sigma(g) (+), 1 (1)Pi(u), 1 (1)Pi(g), and 1 (1)Sigma(u) (-)) states of the dication with intense (0.4 x 10(13) Wcm(2)) radiation have been studied using the recently developed multireference configuration interaction method with single and double excitations (MRCISD)-based approach. The adiabatic Floquet state coinciding near its minimum with the initial X (1)Sigma(g) (+) ground state and asymptotically correlating with A (1)Pi(u) (m = -1), i.e., with one less photon in the dressed state, is expected to be metastable, as is the ground state in the absence of a field, but to support up to the v(max) = 12 quasibound vibrational level in comparison with v(max) = 11 in the parent field-free X (1)Sigma(g) (+) ground state. The tunneling lifetimes of the highest vibrational levels in this adiabatic Floquet state are predicted to be several orders longer than those in the parent field-free state. Analysis of the complete basis set limit extrapolated MRCISD potential energy curve of the field-free X (1)Sigma(g) (+) state of N(2) (2+) calculated in the present work (R(e) = 1.130 A, omega(e) = 2011 cm(-1), omega(e)x(e) = 26.1 cm(-1)) is in good agreement with spectroscopic experimental data. Calculations on the field-free A (1)Pi(u) state (T(e) = 12 106 cm(-1), R(e) = 1.252 A, omega(e) = 1438 cm(-1), omega(e)x(e) = 23.5 cm(-1)) generally support earlier theoretical work and do not support reported experimental values.

Density functional study on the mechanism of bicyclic guanidine-catalyzed Strecker reaction.

As a direct and viable synthesis of amino acids, the small organic molecule catalyzed asymmetric Strecker reactions have been explored successfully in recent years. For these catalysts, the active sites may be a guanidine group or similarly a urea group. In an effort to elucidate the reaction mechanism, we have investigated the bicyclic guanidine-catalyzed Strecker reaction of HCN and methanimine using density functional theory with the B3LYP method. Assisted by guanidine, two competitive pathways to aminoacetonitrile were rationalized. The aminoisoacetonitrile may not form due to the instability of the product.