Proximal disruptor aided ligation (ProDAL) of kilobase-long RNAs

<p>RNA with site-specific modification is a useful tool for RNA biology studies. However, generating kilobase (kb) -long RNA with internal modification at a site distant from RNA termini remains challenging. Here we report an enhanced splint ligation technique, proximal disruptor aided ligation (ProDAL), which allows adequate efficiency toward this purpose. The key to our approach is using multiple DNA oligonucleotides, ‘proximal disruptors’, to target the RNA substrate sequence next to the ligation site. The binding of disruptors helps to free the ligation site from intramolecular RNA basepairing, and consequently promotes more efficient formation of the pre-ligation complex and a higher overall ligation yield. We used naturally occurring 1.0 kb renilla and 1.9 kb firefly luciferase mRNA sequences to test the efficacy of our approach. ProDAL yielded 9–14% efficiency for the ligation between two RNA substrates, both of which were between 414 and 1313 nucleotides (nt) long. ProDAL also allowed similarly high efficiency for generating kb-long RNA with site-specific internal modification by a simple three-part ligation between two long RNA substrates and a modification-carrying RNA oligonucleotide. In comparison, classical splint ligation yielded a significantly lower efficiency of 0–2% in all cases. We expect that ProDAL will benefit studies involving kb-long RNAs, including translation, long non-coding RNAs, RNA splicing and modification, and large ribonucleoprotein complexes.</p

Atom Condensed Fukui Functions Calculated for 2973 Organic Molecules

<p>Data set Fukui_2973</p> <p>==================</p> <p>Atomic NBO charges for non-hydrogen atoms in 2973 small organic molecules at the B3LYP/6-31G*//DFTB level of theory.</p> <p> </p> <p> </p> <p>Related publication:</p> <p>* Qingyou Zhang, Fangfang Zheng, Tanfeng Zhao, Xiaohui Qu, João Aires-de-Sousa:</p> <p>Machine Learning Estimation of Atom Condensed Fukui Functions.</p> <p>Molecular Informatics (2015)</p> <p>DOI: 10.1002/minf.201500113</p> <p> </p> <p>This data set is publicly available at</p> <p>http://dx.doi.org/10.6084/m9.figshare.1400514</p> <p> </p> <p>Files</p> <p>-----</p> <p>Fukui_2973_sdf.tar.gz - 2973 molecules in the MDL SDFile format</p> <p>charges_Fukui_2973.xlsx - NBO atomic charges for the non-hydrogen atoms in neutral and charged species</p> <p> </p> <p>Molecules</p> <p>---------</p> <p>For a subset of the fragment-like ZINC database [1] consisting of 2973 neutral organic molecules composed from elements H,C,N,O,S, molecular geometries were relaxed by DFTB+ [2] and atomic charges were calculated by the NBO 5.9 program [3] from a natural population analysis on the B3LYP/6-31G* wavefunction. Charged species (+1:cation and -1:anion) were calculated with the geometry obtained for the corresponding neutral species.</p> <p> </p> <p>Format</p> <p>------</p> <p>Each molecule is stored in its own file, ending in ".sdf".</p> <p>The format is the standard MDL SDFile generated with the Marvin/JChem 5.8.2, 2012, software [5].</p> <p>Atomic charges are stored in the charges_Fukui_2973.xlsx file. Three different sheets are used for the neutral, cation and anion species respectively.</p> <p> </p> <p>Column Content</p> <p>------ -------</p> <p>1 Molecule ID (as appears in the corresponding .sdf file name and in the ZINC database)</p> <p>2,... Atomic charge (in elementary charge units) for atoms in the same sequence as in the corresponding .sdf file</p> <p> </p> <p>References</p> <p>----------</p> <p>[1] Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG: ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012, 52: 1757-1768.</p> <p>[2] Aradi B, Hourahine B, Frauenheim T: DFTB+, a sparse matrix-based implementation of the DFTB method. J Phys Chem A 2007, 111:2678-5684.</p> <p>[3] NBO 5.9. Glendening ED, Badenhoop JK, Reed AE, JCarpenter JE, Bohmann JA, Morales CM, Weinhold F: Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 2011; [http://www.chem.wisc.edu/~nbo5].</p> <p>[4] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA: General atomic and molecular electronic structure system. J Comput Chem 1993, 14:1347-1363. GAMESS Version 11 Aug 2011 (R1)</p> <p>[5] ChemAxon [http://www.chemaxon.com/]</p

A Quantum Mechanical Study on the Formation of PCDD/Fs from 2-Chlorophenol as Precursor

The most direct route to the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in combustion and thermal processes is the gas-phase reaction of chemical precursors such as chlorinated phenols. Detailed insight into the mechanism and kinetics properties is a prerequisite for understanding the formation of PCDD/Fs. In this paper, we carried out molecular orbital theory calculations for the homogeneous gas-phase formation of PCDD/Fs from 2-chlorophenol (2-CP). The profiles of the potential energy surface were constructed, and the possible formation pathways are discussed. The single-point energy calculation was carried out at the MPWB1K/6−311+G(3f,2p) level. Several energetically favorable formation pathways were revealed for the first time. The rate constants of crucial elementary steps were deduced over a wide temperature range of 600∼1200 K using canonical variational transition-state theory (CVT) with small curvature tunneling contribution (SCT). The rate-temperature formulas were fitted. The ratio of PCDD to PCDF formed shows strong dependency on the reaction temperature and chlorophenoxy radicals (CPRs) concentration

Accurate, Uncertainty-Aware Classification of Molecular Chemical Motifs from Multimodal X‑ray Absorption Spectroscopy

Accurate classification of molecular chemical motifs from experimental measurement is an important problem in molecular physics, chemistry, and biology. In this work, we present neural network ensemble classifiers for predicting the presence (or lack thereof) of 41 different chemical motifs on small molecules from simulated C, N, and O K-edge X-ray absorption near-edge structure (XANES) spectra. Our classifiers not only achieve class-balanced accuracies of more than 0.95 but also accurately quantify uncertainty. We also show that including multiple XANES modalities improves predictions notably on average, demonstrating a “multimodal advantage” over any single modality. In addition to structure refinement, our approach can be generalized to broad applications with molecular design pipelines

Mechanistic and Kinetic Studies on the Homogeneous Gas-Phase Formation of PCDD/Fs from 2,4,5-Trichlorophenol

An understanding of the reaction mechanism of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) formation is crucial for any attempt to prevent PCDD/Fs formation. Among the polychlorophenols, 2,4,5-trichlorophenol (2,4,5-TCP) has the minimum number of Cl atoms needed to form 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (2,3,7,8-TeCDD), which is the most toxic among all 210 PCDD/F isomers. Experiments on the formation of PCDD/Fs from the 2,4,5-TCP precursor have been hindered by the strong toxicity of 2,3,7,8-TeCDD. In this work, we carried out molecular orbital theory calculations for the homogeneous gas-phase formation of PCDD/Fs from the 2,4,5-TCP precursor. Several energetically favorable formation pathways were revealed for the first time. The rate constants of crucial elementary steps were deduced over a wide temperature range of 600∼1200 K, using canonical variational transition state theory with small curvature tunneling contribution. The rate temperature formulas were fitted. This study shows that the formation of polychlorinated dibenzo-p-dioxins (PCDDs) from the 2,4,5-TCP precursor is preferred over the formation of polychlorinated dibenzofurans (PCDFs). The chlorine substitution pattern has a significant effect on the dimerization of chlorophenoxy radicals

Kinetic Properties for the Complete Series Reactions of Chlorophenols with OH RadicalsRelevance for Dioxin Formation

The chlorophenoxy radical (CPR) is a key intermediate species in the formation of polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). In municipal waste incinerators, the reactions of chlorophenols with OH radicals play the most central role in the formation of chlorophenoxy radicals. In this paper, molecular orbital theory calculations have been performed to investigate the formation of chlorophenoxy radicals from the complete series reactions of 19 chlorophenol congeners with OH radicals. The single-point energy calculation was carried out at the MPWB1K/6-311+G(3df,2p) level on the basis of the MPWB1K/6-31+G(d,p) optimized geometries. The kinetic modeling of the PCDD/PCDF (PCDD/F for short) formation demands the knowledge of the rate parameters for the formation of chlorophenoxy radicals from chlorophenols. So, the kinetic properties of the reactions of chlorophenols with OH radicals were deduced over a wide temperature range of 600−1200 K using canonical variational transition-state theory (CVT) with small curvature tunneling contribution (SCT). This study shows that the chlorine substitution at the ortho position in chlorophenol not only has a significant effect on the structures of chlorophenols, prereactive intermediates, the transition states, and chlorophenoxy radicals, but also plays a decisive role in determining the rate parameters

The Coupling between Stability and Ion Pair Formation in Magnesium Electrolytes from First-Principles Quantum Mechanics and Classical Molecular Dynamics

In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg²⁺ → Mg⁺), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI^– exhibits a significant bond weakening while paired with the transient, partially reduced Mg⁺. In contrast, BH₄^– and BF₄^– are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt

Mechanism and Thermal Rate Constants for the Complete Series Reactions of Chlorophenols with H

Reactions of chlorophenols with atomic H are important initial steps for the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in incinerators. Detailed insight into the mechanism and kinetic properties of crucial elementary steps is a prerequisite for understanding the formation of PCDD/Fs. In this paper, the complete series reactions of 19 chlorophenol congeners with atomic H have been studied theoretically using the density functional theory (DFT) method and the direct dynamics method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. Modeling of the PCDD/Fs formation requires kinetic information about the elemental reactions. The rate constants were deduced over a wide temperature range of 600∼1200 K using canonical variational transition-state theory (CVT) with small curvature tunneling contribution (SCT). The rate-temperature formulas were fitted for the first time. This study shows that the substitution pattern of the phenol has a significant effect on the strength and reactivity of the OH bonds in chlorophenols. Intramolecular hydrogen bonding plays a decisive role in determining the reactivity of the OH bonds for ortho-substituted phenols

Probing Oxidation-Driven Amorphized Surfaces in a Ta(110) Film for Superconducting Qubit

Recent advances in superconducting qubit technology have led to significant progress in quantum computing, but the challenge of achieving a long coherence time remains. Despite the excellent lifetime performance that tantalum (Ta) based qubits have demonstrated to date, the majority of superconducting qubit systems, including Ta-based qubits, are generally believed to have uncontrolled surface oxidation as the primary source of the two-level system loss in two-dimensional transmon qubits. Therefore, atomic-scale insight into the surface oxidation process is needed to make progress toward a practical quantum processor. In this study, the surface oxidation mechanism of native Ta films and its potential impact on the lifetime of superconducting qubits were investigated using advanced scanning transmission electron microscopy (STEM) techniques combined with density functional theory calculations. The results suggest an atomistic model of the oxidized Ta(110) surface, showing that oxygen atoms tend to penetrate the Ta surface and accumulate between the two outermost Ta atomic planes; oxygen accumulation at the level exceeding a 1:1 O/Ta ratio drives disordering and, eventually, the formation of an amorphous Ta2O5 phase. In addition, we discuss how the formation of a noninsulating ordered TaO1−δ (δ < 0.1) suboxide layer could further contribute to the losses of superconducting qubits. Subsurface oxidation leads to charge redistribution and electric polarization, potentially causing quasiparticle loss and decreased current-carrying capacity, thus affecting superconducting qubit coherence. The findings enhance the comprehension of the realistic factors that might influence the performance of superconducting qubits, thus providing valuable guidance for the development of future quantum computing hardware

Accelerating Electrolyte Discovery for Energy Storage with High-Throughput Screening

Computational screening techniques have been found to be an effective alternative to the trial and error of experimentation for discovery of new materials. With increased interest in development of advanced electrical energy storage systems, it is essential to find new electrolytes that function effectively. This Perspective reviews various methods for screening electrolytes and then describes a hierarchical computational scheme to screen multiple properties of advanced electrical energy storage electrolytes using high-throughput quantum chemical calculations. The approach effectively down-selects a large pool of candidates based on successive property evaluation. As an example, results of screening are presented for redox potentials, solvation energies, and structural changes of ∼1400 organic molecules for nonaqueous redox flow batteries. Importantly, on the basis of high-throughput screening, <i>in silico</i> design of suitable candidate molecules for synthesis and electrochemical testing can be achieved. We anticipate that the computational approach described in this Perspective coupled with experimentation will have a significant role to play in the discovery of materials for future energy needs