Performance of density functionals for the structure and energetics of (M–O)0,± (M=Al,Si, Sc–Zn)

We report the results of the performance of 20 exchange–correlation functionals of density functional theory (DFT) in the structure (Metal–Oxygen bond length) and energetical properties (bond dissociation energy, adiabatic ionisation energy, and adiabatic electron affinity) of twelve metal monoxides (M–O, M=Al, Si, Sc–Zn). The calculated results show that the selected DFT functionals have the ability to reproduce the M–O bond length with a mean deviation of 0.01–0.05 Å, the energy values are reproduced with a mean deviation of 0.20–1.00?eV. In general, the functionals with significant HF exchange show decent performance in the calculation of bond length and harmonic vibrational frequency. These functionals show poor performance in energetics. Our calculated results show that the M06-L, B3LYP, and TPSSh functionals give good performance in both structure and energetical properties of metal monoxides. These functionals are recommended for the studies of structure and energetics in metal oxide systems. Further, our studies indicate that M06-L can be used for the studies in larger molecular systems. Among the 20 DFT functionals, the recently developed N12 functional gives poor performance in the studies of metal monoxides. Hence this functional is not recommended for the studies of structure and energetics in metal oxide systems.     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

Spin states of Mn(III) meso-tetraphenylporphyrin chloride assessed by density functional methods

The present work assessed several exchange-correlation functionals (including GGA, meta-GGA and hybrid functionals), in combination with a variety of basis sets and effective core potentials (ECP) for their ability to predict the ground spin state of Mn(III) meso-tetraphenylporphyrin chloride complex, labeled Mn(III)TPPCl, for which experimental data support the quintet high spin state. Geometry optimization of Mn(III)TPPCl was performed for three possible spin states (singlet state, LS; triplet state, IS; and quintet state, HS) at the TPSSh level using the LANL2DZ ECP for Mn and the 6-311G(d) basis set for C, N, Cl and H. Afterwards, single-point energy calculations were conducted by applying 18 exchange-correlation functionals (BLYP, B3LYP, PW91, BPW91, BP86, OLYP, OPBE, OPW91, O3LYP, PBE0, PBEh1PBE, HSEH1PBE, TPSS, TPSSh, M06 L, M06, M062X and M06HF). The influence of the basis set for the metal center was assessed using a smaller group of functionals and varying between the Pople basis set 6-31G(d), its newer formulation m6-31G(d) and the larger Def2-QZVP basis set. All functionals in combination with Pople basis sets predict the quintet state as the ground spin state. In addition, the BLYP, BP86, BPW91, PW91, PBEh1PBE, TPSS and TPSSh functionals predicted the IS lying at most ~60 kJ mol^?1 above the HS, which agrees with the reference data. Results including Def2-QZVP basis set were inconsistent, since only BLYP and B3LYP predict HS as the ground spin state. The recommended methodology for the treatment of such systems seems to be exchange-correlations functionals with few or none Hartree-Fock exchange and modest size basis sets.

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Graphical Abstract MnTPPCl molecule and the energy ordering of its spin states assessed by 18 functionals

     

d(A)<Subscript>3</Subscript>d(T)<Subscript>3</Subscript> and d(G)<Subscript>3</Subscript>d(C)<Subscript>3</Subscript> B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)₃·d(T)₃ and d(G)₃·d(C)₃ nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)₃d(T)₃ and d(G)₃d(C)₃ duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.     

DFT study of structure and vibrational spectra of ceramide 3: comparison to experimental data

The Fourier transform Raman and infrared (IR) spectra of the Ceramide 3 (CER3) have been recorded in the regions 200–3500 cm^? 1 and 680–4000 cm^? 1, respectively. We have calculated the equilibrium geometry, harmonic vibrational wavenumbers, electrostatic potential surfaces, absolute Raman scattering activities and IR absorption intensities by the density functional theory with B3LYP functionals having extended basis set 6-311G. This work is undertaken to study the vibrational spectra of CER3 completely and to identify the various normal modes with better wavenumber accuracy. Good consistency is found between the calculated results and experimental data for the IR and Raman spectra.     

On the potential application of DFT methods in predicting the interaction-induced electric properties of molecular complexes. Molecular H-bonded chains as a case of study

A detailed analysis of the selected DFT functionals for the calculations of interaction-induced dipole moment, polarizability and first-order hyperpolarizability has been carried out. The hydrogen-bonded model chains consisting of HF, H(2)CO and H(3)N molecules have been chosen as a case study. The calculations of the components of the static electric properties using the diffuse Dunning's basis set (aug-cc-pVDZ) have been performed employing different types of density functionals (B3LYP, LC-BLYP, PBE0, M06-2X and CAM-B3LYP). Obtained results have been compared with those gained at the CCSD(T) level of theory. The counterpoise correction scheme, namely site-site function counterpoise, has been applied in order to eliminate basis set superposition error. The performed tests allow to conclude that the DFT functionals can provide a useful tool for prediction of the interaction-induced electric properties, however a caution has to be urged to their decomposition to the two- and many-body terms.     

DFT study of isomers of the ruthenium dihydride complex RuH<Subscript>2</Subscript>(CO)<Subscript>2</Subscript>(AsMe<Subscript>2</Subscript>Ph)<Subscript>2</Subscript>

A density functional theory (DFT) study of cct-As, ccc, and cct-CO isomers of the ruthenium dihydride complex RuH₂(CO)₂(AsMe₂Ph)₂ is reported (see Scheme for the labeling isomer 34 structures of RuH₂(CO)₂(AsMe₂Ph)₂). Complex geometries and relative energies of different isomers have been calculated with both B3LYP and M06-2X functionals. The results show that the B3LYP calculated Boltzmann populations of cct-As, ccc, and cct-CO isomers are 65.5, 34.2, and 0.3%, respectively. These are in better agreement with the experimental data than those calculated at the M06-2X level. However, the calculations of ¹H NMR chemical shifts were found to be better described with M06-2X than with B3LYP or with HF level of theories. In addition, a transition state between the two most stable isomers was determined through DFT/(B3LYP or M06-2X) calculations.

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Graphical Abstract Scheme: Labeling structure of RuH₂(CO)₂(AsMe₂Ph)₂

     

Assessing the quantum mechanical level of theory for prediction of linear and nonlinear optical properties of push-pull organic molecules

In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability (〈α〉) and total static first hyperpolarizability (β_t) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with β ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.

Evaluation of density functional methods on the geometric and energetic descriptions of species involved in Cu+-promoted catalysis

We have evaluated the performance of 15 density functionals of diverse complexity on the geometry optimization and energetic evaluation of model reaction steps present in the proposed reaction mechanisms of Cu(I)-catalyzed indole synthesis and click chemistry of iodoalkynes and azides. The relative effect of the Cu⁺ ligand on the relative strength of Cu⁺-alkyne interactions, and the strong preference for a π-bonding mode is captured by all functionals. The best energetic correlations with MP2 are obtained with PBE0, M06-L, and PBE1PW91, which also provide good quality geometries. Furthermore, PBE0 and PBE1PW91 afford the best agreement with the high-level CCSD(T) computations of the deprotonation energies of Cu⁺-coordinated eneamines, where MP2 strongly disagrees with CCSD(T) and the examined DFT functionals. PBE0 also emerged as the most suitable functional for the study of the energetics and geometries of Cu⁺ hydrides, while at the same time correctly capturing the influence of the Cu⁺ ligands on the metal reactivity.     

Comparative Effects of Hydrogen Sulfide-Releasing Compounds on [<Superscript>3</Superscript>H]D-Aspartate Release from Bovine Isolated Retinae

We investigated the pharmacological actions of a slow-releasing H₂S donor, GYY 4137; a substrate for the biosynthesis of H₂S, l-cysteine and its precursor, N-acetylcysteine on potassium (K⁺; 50 mM)-evoked [³H]D-aspartate release from bovine isolated retinae using the Superfusion Method. GYY 4137 (10 nM–10 µM), l-cysteine (100 nM–10 µM) and N-acetylcysteine (10 µM–1 mM) elicited a concentration-dependent decrease in K⁺-evoked [³H]D-aspartate release from isolated bovine retinae without affecting basal tritium efflux. At equimolar concentration of 10 µM, the rank order of activity was as follows: l-cysteine?>?GYY 4137?>?N-acetylcysteine. A dual inhibitor of the biosynthetic enzymes for H₂S, cystathionine β-synthase (CBS) and cystathionine γ-lyase (CSE), amino-oxyacetic acid (AOA; 3 mM) reversed the inhibitory responses caused by GYY 4137, l-cysteine and N-acetylcysteine on K⁺-evoked [³H]D-aspartate release. Glibenclamide (300 µM), an inhibitor of K_ATP channels blocked the inhibitory action of GYY 4137 and l-cysteine but not that elicited by N-acetylcysteine on K⁺-induced [³H]D-aspartate release. The inhibitory effect of GYY 4137 and l-cysteine on K⁺-evoked [³H]D-aspartate release was reversed by the non-specific inhibitor of nitric oxide synthase (NOS), l-NAME (300 µM). Furthermore, a specific inhibitor of inducible NOS (iNOS), aminoguanidine (10 µM) blocked the inhibitory action of l-cysteine on K⁺-evoked [³H]D-aspartate release. We conclude that both donors and substrates for H₂S production can inhibit amino acid neurotransmission in bovine isolated retinae, an effect that is dependent, at least in part, upon the intramural biosynthesis of this gas, and on the activity of K_ATP channels and NO synthase.     

Linkage isomerism of pentaammine(dimethylsulfoxide)ruthenium(II/III) complexes: A theoretical study

Density functional theory (DFT) calculations have been performed for understanding the linkage isomerism of [Ru^II/III(NH₃)₅(dmso)]^2+/3+ (dmso = dimethylsulfoxide) from a theoretical point of view. In particular, we focus on the interchange between O-bonded and S-bonded structures of the dmso ligand by oxidation/reduction. We have examined five different exchange-correlation functionals (SVWN, BP86, mPWPW91, B3PW91, and B3LYP) in our DFT calculations and found that the relative stabilities of the O-bonded and S-bonded structures are largely dependent on the functional employed. From detailed analyses of atomic charge distributions, it has been found that the calculated atomic charges on the central metal ions are strongly correlated with the relative energies. We also studied the effect of solvation on the linkage isomerism using continuum solvation models.     

DFT study of linear and nonlinear optical properties of donor-acceptor substituted stilbenes, azobenzenes and benzilideneanilines

A theoretical analysis of the linear and nonlinear optical properties of six push–pull π-conjugated molecules with stilbene, azobenzene and benzilideneaniline as a backbone is presented. The photophysical properties of the investigated systems were determined by using response functions combined with density functional theory (DFT). Several different exchange-correlation potentials were applied in order to determine parameters describing the one- and two-photon spectra of the studied molecules. In particular, the recently proposed Coulomb-attenuated model (CAM-B3LYP) was used to describe charge-transfer (CT) excited states. In order to compare theoretical predictions with available experimental data, calculations with inclusion of solvent effects were performed. The BLYP and the CAM-B3LYP functionals were found to yield values of two-photon absorption (TPA) probabilities closer to experimental values than the B3LYP functional or the HF wavefunction. Moreover, molecular static hyperpolarisabilities were determined using both DFT and second-order Møller-Plesset perturbation (MP2) theory. Likewise, the CAM-B3LYP functional was found to outperform other applied exchange-correlation potentials in determining first hyperpolarisability (β). Moreover, it was confirmed on a purely theoretical basis that the presence of a –C=C– bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a –N=N– bridge.     

Absolute configuration of (−)-myrtenal by vibrational circular dichroism

The VCD spectrum of the monoterpene (−)-myrtenal (1) was compared with theoretical spectra using ab initio density functional theory (DFT) calculations at the B3LYP/6-31G(d,p), B3LYP/6-31G+(d,p), B3LYP/6-311G+(d,p), B3LYP/DGDZVP, and B3PW91/DGTZVP levels of theory. Conformational analysis of 1 indicated that the lowest energy conformer was s-trans-C2-C10, which contributes more than 98.5% to the total conformational population regardless of the employed level of theory. The use of a recently developed confidence level algorithm demonstrated that VCD spectra calculated for the main conformer, using the indicated hybrid functionals and basis set, gave no significant changes, from where it follows that B3LYP/DGDZVP calculations provide a superior balance between computer cost and VCD spectral accuracy. The DGDZVP basis set demanded around a quarter the time than the 6-311G+(d,p) basis set while providing similar results. The spectral comparison also provided evidence that the levorotatory enantiomer of myrtenal has the 1R absolute configuration.     

Quantum-mechanical computations on the electronic structure of trans-resveratrol and trans-piceatannol: a theoretical study of the stacking interactions in trans-resveratrol dimers

Accurate quantum-chemical calculations based on the second-order M?ller-Plesset perturbation method (MP2) and density functional theory (DFT) were performed for the first time to investigate the electronic structures of trans-resveratrol and trans-piceatannol, as well as to study the stacking interaction between trans-resveratrol molecules. Ab initio MP2 calculations performed with using standard split-valence Pople basis sets led us to conclude that these compounds have structures that deviate strongly from planarity, whereas the DFT computations for the same basis sets revealed that the equilibrium geometries of these bioactive polyphenols are planar. Furthermore, the results obtained at the MP2(full)/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ levels indicated that the geometries of trans-resveratrol and trans-piceatannol are practically planar at their absolute energy minima. The relative energies of the equilibrium geometries of trans-resveratrol on its potential energy surface were computed at the MP2(full)/aug-cc-pVTZ level. According to the results obtained, a T-shaped (edge-to-phase) conformer of trans-resveratrol dimer is the most stable in vacuum. This T-shaped conformer is mainly stabilized by strong hydrogen bonding and weak C-H...π interactions. Stacked structures with parallel-displaced trans-stilbene skeletons were also found to be energetically stable. The vertical separation and twist angle dependencies of the stacking energy were investigated at the MP2(full)/aug-cc-pVTZ, B3LYP/aug-cc-pVTZ, and HF/aug-cc-pVTZ levels. The standard B3LYP functional and the Hartree-Fock method neglect long-range attractive dispersion interactions. The MP2 computations revealed that the London dispersion energy cannot be neglected at long or short distances. The stacked model considered here may be useful for predicting the quantum nature of the interactions in π-stacked systems of other naturally occurring stilbenoids, and can help to enhance our understanding of the antioxidant and anticancer activities of trans-resveratrol.     

Exploring potential applications of a novel extracellular polymeric substance synthesizing bacterium (<Emphasis Type="Italic">Bacillus licheniformis</Emphasis>) isolated from gut contents of earthworm (<Emphasis Type="Italic">Metaphire posthuma</Emphasis>) in environmental remediation

The aim was to isolate, characterize, and explore potentials of gut bacteria from the earthworm (Metaphire posthuma) and imply these bacteria for remediation of Cu(II) and Zn(II). An extracellular polymeric substance (EPS) producing gut bacteria (Bacillus licheniformis strain KX657843) was isolated and identified based on 16S rRNA sequencing and phylogenetic analysis. The strain showed maximum tolerance of 8 and 6 mM for Cu(II) and Zn(II) respectively. It removed 34.5% of Cu(II) and 54.4% of Zn(II) at 25 mg L^?1 after 72 and 96 h incubation respectively. The bacteria possessed a great potential to produce indole acetic acid (38.49 μg mL^?1) at 5 mg mL^?1 l-tryptophan following 12 days incubation. The sterilized seeds of mung beans (Vigna radiata) displayed greater germination and growth under bacterium enriched condition. We observed that the bacterial strain phosphate solubilization ability with a maximum of 204.2 mg L^?1 in absence of Cu(II) and Zn(II). Endowed with biosurfactant property the bacterium exhibited 24% emulsification index. The bacterium offered significant potential of plant growth promotion, Cu(II) and Zn(II) removal, and as such this study is the first report on EPS producing B. licheniformis KX657843 from earthworm which can be applied as powerful tool in remediation programs of Cu(II) and Zn(II) contaminated sites.     

Genome shuffling and high-throughput screening of <Emphasis Type="Italic">Brevibacterium flavum</Emphasis> MDV1 for enhanced <Emphasis Type="SmallCaps">l</Emphasis>-valine production

l-valine is an essential branched-amino acid that is widely used in multiple areas such as pharmaceuticals and special dietary products and its use is increasing. As the world market for l-valine grows rapidly, there is an increasing interest to develop an efficient l-valine-producing strain. In this study, a simple, sensitive, efficient, and consistent screening procedure termed 96 well plate-PC-HPLC (96-PH) was developed for the rapid identification of high-yield l-valine strains to replace the traditional l-valine assay. l-valine production by Brevibacterium flavum MDV1 was increased by genome shuffling. The starting strains were obtained using ultraviolet (UV) irradiation and binary ethylenimine treatment followed by preparation of protoplasts, UV irradiation inactivation, multi-cell fusion, and fusion of the inactivated protoplasts to produce positive colonies. After two rounds of genome shuffling and the 96-PH method, six l-valine high-yielding mutants were selected. One genetically stable mutant (MDVR2-21) showed an l-valine yield of 30.1 g/L during shake flask fermentation, 6.8-fold higher than that of MDV1. Under fed-batch conditions in a 30 L automated fermentor, MDVR2-21 accumulated 70.1 g/L of l-valine (0.598 mol l-valine per mole of glucose; 38.9% glucose conversion rate). During large-scale fermentation using a 120 m³ fermentor, this strain produced?>?66.8 g/L l-valine (36.5% glucose conversion rate), reflecting a very productive and stable industrial enrichment fermentation effect. Genome shuffling is an efficient technique to improve production of l-valine by B. flavum MDV1. Screening using 96-PH is very economical, rapid, efficient, and well-suited for high-throughput screening.     

DFT/TDDFT computational study of the structural,electronic and optical properties of rhodium (III) and iridium (III) complexes based on tris-picolinate bidentate ligands

The electronic structures and spectroscopic properties of two complexes [M(pic)₃] (M = Ir, Rh) containing picolinate as bidentate ligands have been calculated by means density functional theory (DFT) and time-dependent DFT/TD-DFT using three hybrid functionals B3LYP, PBE0 and mPW1PW91. The PBE0 and mPW1PW91 functionals, which have the same HF exchange fraction (25%), give similar results and do not differ drastically from B3LYP results. Calculated geometric parameters of the complexes are in good agreement with the available experimental data. The UV absorptions observed in acetonitrile were assigned on the basis of singlet state transitions. The most intense band observed in the UV-C region corresponds to ligand-to-ligand charge transfer states (LLCT) in both complexes. The theoretical spectrum of the rhodium complex is characterized by a large degree of mixing between metal-to-ligand-charge-transfer (MLCT), LLCT and metal centered (MC) states in the UV-A region. The presence of low-lying excited states with MC character affects the absorption spectrum under spin-orbit coupling (SOC) effects and play important roles in the photochemical properties.

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Graphical abstract Frontier molecular orbital diagram of mer-M(pic)₃ (M=Ir, Rh).

     

Increased productivity of <Emphasis Type="SmallCaps">l</Emphasis>-2-aminobutyric acid and total turnover number of NAD<Superscript>+</Superscript>/NADH in a one-pot system through enhanced thermostability of <Emphasis Type="SmallCaps">l</Emphasis>-threonine deaminase

Objective

To strengthen NADH regeneration in the biosynthesis of l-2-aminobutyric acid (l-ABA).

Results

l-Threonine deaminase (l-TD) from Escherichia coli K12 was modified by directed evolution and rational design to improve its endurance to heat treatment. The half-life of mutant G323D/F510L/T344A at 42 °C increased from 10 to 210 min, a 20-fold increase compared to the wild-type l-TD, and the temperature at which the activity of the enzyme decreased by 50% in 15 min increased from 39 to 53 °C. The mutant together with thermostable l-leucine dehydrogenase from Bacillus sphaericus DSM730 and formate dehydrogenase from Candida boidinii constituted a one-pot system for l-ABA biosynthesis. Employing preheat treatment in the one-pot system, the biosynthesis of l-ABA and total turnover number of NAD⁺/NADH were 0.993 M and 16,469, in contrast to 0.635 M and 10,531 with wild-type l-TD, respectively.

Conclusions

By using the engineered l-TD during endured preheat treatment, the one-pot system has achieved a higher productivity of l-ABA and total turnover number of coenzyme.