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This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence. [ABSTRACT FROM AUTHOR]

A pseudospectral implementation of nonadiabatic derivative couplings in the Tamm–Dancoff approximation is reported, and the accuracy and efficiency of the pseudospectral nonadiabatic derivative couplings are studied. Our results demonstrate that the pseudospectral method provides mean absolute errors of 0.2%–1.9%, while providing a significant speedup. Benchmark calculations on fullerenes (Cn, n up to 100) using B3LYP achieved 10- to 15-fold, 8- to 17-fold, and 43- to 75-fold speedups for 6-31G**, 6-31++G**, and cc-pVTZ basis sets, respectively, when compared to the conventional spectral method. [ABSTRACT FROM AUTHOR]

The accuracy and efficiency of time-dependent density functional theory (TDDFT) excited state gradient calculations using the pseudospectral method are presented. TDDFT excited state geometry optimizations of the G2 test set molecules, the organic fluorophores with large Stokes shifts, and the Pt-complexes show that the pseudospectral method gives average errors of 0.01–0.1 kcal/mol for the TDDFT excited state energy, 0.02–0.06 pm for the bond length, and 0.02–0.12° for the bond angle when compared to the results from conventional TDDFT. TDDFT gradient calculations of fullerenes (Cn, n up to 540) with the B3LYP functional and 6-31G** basis set show that the pseudospectral method provides 8- to 14-fold speedups in the total wall clock time over the conventional methods. The pseudospectral TDDFT gradient calculations with a diffuse basis set give higher speedups than the calculations for the same basis set without diffuse functions included. [ABSTRACT FROM AUTHOR]

CXC chemokine receptor 4 (CXCR4) is a promising therapeutic target. Previous studies have shown that intracellular delivery of siRNA to knockdown CXCR4 expression in cancer cells is an effective therapeutic strategy. To prepare efficient magnetic nucleic acid carriers, it is now necessary to improve the endocytosis efficiency of PEGylated magnetic nanoparticles. In our work, Heptafluorobutyryl-polyethylene glycol-polyethyleneimine (FPP) was first prepared and then used to coat magnetic nanoparticles (MNPs) to obtain magnetic nanocarriers FPP@MNPs. The materials were characterized by 19 F-Nuclear Magnetic Resonance (NMR), transmission electron microscope (TEM), energy dispersive spectroscopy (EDS), and dynamic light scattering (DLS). The biosecurity of FPP@MNPs was confirmed by cell viability and apoptosis experiments. Cellular uptake of FPP@MNPs and siRNA transfection enhanced by external magnetic fields were detected by fluorescence microscopy, confocal laser microscopy, and flow cytometry. The results show that the cellular uptake efficiency of FPP@MNPs was significantly improved, and transfection efficiency reached more than 90%. The knockdown of CXCR4 on the 4 T1 cell membrane was confirmed by real-time polymerase chain reaction (RT-PCR) and flow cytometry. In conclusion, the fluorinated cationic polymer-coated magnetic nanoparticles FPP@MNPs can be loaded with siRNA to reduce CXCR4 expression as well as be expected to be efficient universal siRNA carriers. [ABSTRACT FROM AUTHOR]

We have implemented pseudospectral density‐functional theory (DFT) with long‐range corrected DFT functionals (PS‐LRC) in quantum mechanics package Jaguar, and applied it in the calculations of geometry optimizations, dimmer interaction energies, polarizabilities and first‐order hyperpolarizabilities, harmonic vibrational frequencies, S1 and T1 excitation energies, singlet‐triplet gaps, charge transfer numbers, oscillator strengths, reaction barrier heights, electron‐transfer couplings, and charge‐transfer excitation energies. From our accuracy benchmark analysis, PS grids, PS dealiasing functions, PS atomic corrections, PS multigrid strategy, PS length scales, and PS cutoff scheme perform well in PS DFT with LRC density functionals with very small and ignorable deviations when compared to the conventional spectral (CS) method. The timing benchmark study of S1 excitation energy calculations of fullerenes (Cn, n up to 540) demonstrates that PS‐LRC achieves 1.4–8.4‐fold speedups in SCF, 22–32‐fold speedups in Tamm‐Dancoff approximation, and 6–15‐fold speedups in total wall clock time with an average error 0.004 eV of excitation energies compared to the CS method. [ABSTRACT FROM AUTHOR]

This correction notice addresses an error in a previous publication regarding the citation of a study on the immune regulator CXCR4 as a target for gastric cancer. The corrected citation has been inserted in the introduction section of the publication. The authors assure that this correction does not impact the scientific conclusions of the study. The original publication has been updated to reflect this correction. [Extracted from the article]

We have developed an algorithm based upon pseudospectral (PS) ab initio electronic structure methods for evaluating nuclear magnetic shielding constants using gauge-including atomic orbitals (GIAOs) in the spin-restricted and spin-unrestricted formalisms of Hartree–Fock (HF) theory and density-functional theory (DFT). The nuclear magnetic shielding constants for both 1H and 13C calculated using PS methodology for 21 small molecules have absolute mean errors of less than 0.3 ppm in comparison with analytic integral results. CPU timing comparisons between PS methods and conventional methods carried out for seven large molecules ranging from 510 to 1285 basis functions demonstrate that the PS methods are an order of magnitude more efficient than the conventional methods. PS-HF was between 9 and 26 times faster than conventional integral technology, and PS-DFT (Becke three-parameter Lee–Yang–Parr) was between 6 and 21 times faster. [ABSTRACT FROM AUTHOR]

We have developed algorithms based on pseudospectral (PS) ab initio electronic structure methods for solving the first- and second-order Hartree–Fock/Kohn–Sham equations and evaluating molecular polarizabilities and first- and second-order hyperpolarizabilities in the spin-restricted and spin-unrestricted formalisms at the Hartree–Fock (HF) and density functional theory (DFT) levels. We carry out calculations on 50 small molecules to test the accuracy of the PS approach. Our results demonstrate that the molecular polarizability α computed by the PS method is essentially identical to the value obtained from conventional methods for both HF and DFT calculations, while the first-order hyperpolarizability β and second-order hyperpolarizability γ have mean unsigned percentage differences of 1.26% and 0.62% (HF) and 0.78% and 0.65% (DFT), respectively. We also present CPU timing comparisons between the PS and conventional methods at the 6-31 G** level for 14 molecules having 185 to 1185 basis functions. The timing results show that the PS method is 25 (PS-HF) and 13 (PS-DFT) times faster than the conventional method for a system with 500 basis functions. The PS methods are found scale as N2.70 (PS-HF) and N2.40 (PS-DFT), while the conventional methods scale as N2.93 (PRISM-HF) and N2.87 (PRISM-DFT), where N is the number of basis functions. [ABSTRACT FROM AUTHOR]

Thermal cracking is a widespread distress for asphalt pavement in cold regions. The main reason causing thermal cracking is due to the contraction of asphalt concrete. Once thermally induced contraction stress exceeds the fracture resistance of the asphalt concrete, cracks start to develop. Comparing to aggregate, asphalt mastic is believed to have much larger thermal coefficient of contraction, therefore play a more significant role in determining the thermal cracking resistance of asphalt pavement. To modify the inherent thermal property of asphalt mastic, a new-developed material, zirconium tungstate (ZT), was utilized in this study. Different from normal material’s heated expansion and cooled contraction properties, ZT has a negative thermal expansion property of heated contraction and cooled expansion. Being as a substitute for mineral filler, the physical properties of ZT fillers and performances of asphalt mastics made with ZT fillers were investigated. Results show that ZT can better absorb and adhere asphalt binder when comparing with mineral filler. The addition of ZT is able to decrease the thermal coefficients of volume contraction and creep stiffness, improve the adhesive bond between filler and asphalt binder and reduce the complex modulus of asphalt mastic. [ABSTRACT FROM AUTHOR]

We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G** show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G** basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G** basis set with up to 8100 basis functions show that PS-FLR-TDDFT CPU time scales as N2.05 with the number of basis functions. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

An accurate prediction model for surface wear in planetary gear systems is essential to decipher wear fault mechanisms and facilitate model-driven failure prognosis. A high-fidelity dynamic wear model relies on the appropriate characterization and updating strategy of the tooth macro-geometry, contact parameters and dynamic load. A geometrically adaptive-loaded tooth contact analysis (GA-LTCA) method is proposed to "bridge" wear morphology and dynamic behaviours. The finite element method and run-to-failure test are adopted to verify the GA-LTCA method and wear prediction model, respectively. Based on the proposed wear model, the life-cycle wear characteristics and the updating strategy of wear geometry are investigated. Owing to the consideration of the micro-cycle of the contact stress and geometrical updating, the predicted wear profile exhibits a desirable agreement with experimental results. The tooth profile deviation vector should be updated more frequently than the finite element model of worn gears. Only the finite element grid of the sun-planet gear pair should be updated because the wear of the sun-planet is much more serious than that of the ring-planet. Numerical results indicate the potential of the proposed high-fidelity model for digital twin-based wear prediction and life cycle failure prognosis. [Display omitted] • A high-fidelity wear degradation model is proposed to realize the life-cycle dynamic wear prediction. • The geometry updating and micro-cycle of contact stress are taken into consideration. • GA-LTCA method is proposed to "bridge" wear morphology and dynamic behaviours. • The proposed wear model is verified both numerically and experimentally. • Life-cycle wear characteristics and the updating strategy of wear geometry are investigated. [ABSTRACT FROM AUTHOR]

This paper describes an empirical localized orbital correction model which improves the accuracy of density functional theory (DFT) methods for the prediction of thermochemical properties for molecules of first and second row elements. The B3LYP localized orbital correction version of the model improves B3LYP DFT atomization energy calculations on the G3 data set of 222 molecules from a mean absolute deviation (MAD) from experiment of 4.8 to 0.8 kcal/mol. The almost complete elimination of large outliers and the substantial reduction in MAD yield overall results comparable to the G3 wave-function-based method; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. The following four classes of correction parameters are applied to a molecule based on standard valence bond assignments: corrections to atoms, corrections to individual bonds, corrections for neighboring bonds of a given bond, and radical environmental corrections. Although the model is heuristic and is based on a 22 parameter multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation. [ABSTRACT FROM AUTHOR]

We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1752–1780, 2005 [ABSTRACT FROM AUTHOR]

Objective: To establish an uncertainty analysis method for content determination of sodium bicarbonate ear drops by acid-base titration. Methods : By establishing a mathematical model, the source of uncertainty was analysed, and the combined standard uncertainty and the extended uncertainty were calculated. Results :The main factors contributing to the total uncertainty were the volume and calibration of the hydrochloric acid titration solution and the sample volume. The combined stardard uncertainty was 0.129% and the extended uncertainty was 0.258% (k = 2) under the 95% confidence interval. Conclusion: The method is suitable for the uncertainty analysis of the content of sodium bicarbonate ear drops by acid-base titration, thus make the evaluation results more objective and reliable. [ABSTRACT FROM AUTHOR]

• The strain CZ-2 was identified as a novel species of the genus Sphingobacterium. • Three specific genes contribute to the environmental adaptability of strain CZ-2. • Gene family contraction may be a major process in the evolution of strain genome. • Gene structural changes as a potential mechanism for adaptive evolution of strain. • The strain CZ-2 has the potential to degrade aminobenzoates. Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium. [ABSTRACT FROM AUTHOR]

In crops, RNA editing is one of the most important post-transcriptional processes in which specific cytidines (C) in virtually all mitochondrial protein-coding genes are converted to uridines (U). Despite extensive recent research in RNA editing, exploring all of the C-to-U editing events efficiently on the genomic scale remains challengeable. Developing accurate prediction methods for the detection of RNA editing sites would dramatically reduce experimental determination. Therefore, we propose a novel method, iPReditor-CMG (improved predictive RNA editor for crop mitochondrial genomes), to predict crop mitochondrial editing sites using genome sequence and an optimised support vector machine (SVM). We first selected three mitochondrial genomes with known RNA editing sites from Arabidopsis thaliana , Brassica napus and Oryza sativa , released by NCBI, as the training and test sets. The genes and their transcripts from self-sequenced tobacco mitochondrial ATPase were selected as the validation set. The iPReditor-CMG first coded the genome sequences as numerical vectors and then performed an efficient feature selection on the high-dimensional feature space, where the SVM was employed in feature selection and following modelling. The average independent prediction accuracy of intraspecific editing sites across three species was 0.85, and up to 0.91 in A. thaliana , which outperformed the reference models. For the interspecific independent prediction, the prediction accuracy between dicotyledons was 0.78 and the accuracy between dicotyledons and monocotyledons was 0.56, which implies that there might be similarity in the C-to-U editing mechanism in close relatives. Finally, the best model was identified with an independent test accuracy of 0.91 and an AUC of 0.88, which suggested that five unreported feature sequences, i.e. TGACA, ACAAC, GTAGA, CCGTT and TAACA, are closely associated with the editing phenomenon. Multiple tests supported that the iPReditor-CMG could be effectively applied to predict editing sites in crop mitochondria, which may further contribute to understanding the mechanisms of site editing and post-transcriptional events in crop mitochondria. The iPReditor-CMG performed excellently in the independent prediction of intraspecific editing sites, and its findings in interspecies supported that the RNA editing mechanisms might be species-specific. [Display omitted] • The intraspecific prediction accuracy for editing sites across three species was 0.85–0.91 • The accuracy of mutual prediction between dicotyledons and monocotyledons was 0.56. • Similarity in the C-to-U editing mechanism in close relatives is suggested. • The best model was identified with an independent test accuracy of 0.91 and an AUC of 0.88 • It is suggested that five unreported feature sequences are closely associated with the editing phenomenon. [ABSTRACT FROM AUTHOR]