pinecone/core-2020-05-10-deduplication huggingface dataset:
Computational Study of the Phosphoryl Donor Activity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate

Adenosine triphosphate (ATP) is the main biological phosphoryl donor required in many enzymes including dihydroxyacetone kinases (DHAKs) that convert dihydroxyacetone (Dha) into dihydroxyacetone phosphate (Dha-P), a key species with potential applications in synthesis. Herein, we present a theoretical study of the molecular mechanism for the phosphoryl transfer reaction from an inorganic polyphosphate to Dha catalyzed by DHAK from C. freundii. This is part of a project devoted to modify the phosphoryl donor specificity of this enzyme avoiding the use of the problematic direct addition of ATP. Based on the use of hybrid QM/MM potentials, with the QM region described by semiempirical and DFT methods, the reaction mechanism of the wild-type enzyme and the most active experimentally measured mutant (Glu526Lys) with poly-P as phosphoryl donor has been explored to elucidate the origin of the activity of this mutant. The similar energy barriers obtained in both systems confirm our previous studies on the binding step (Sánchez-Moreno et al., Int. J. Mol. Sci. 2015, 16, 27835) suggesting that this mutation favors a more adequate position of the poly-P in the active site for the following step, the chemical reaction, to take place
Performance of SCAN density functional for a set of ionic liquid ion
  pairs

Computational chemistry is a powerful tool for the discovery of novel
materials. In particular, it is used to simulate ionic liquids in search of
electrolytes for electrochemical applications. Herein, the choice of the
computational method is not trivial, as it has to be both efficient and
accurate. Density functional theory (DFT) methods with appropriate corrections
for the systematic weaknesses can give precision close to that of the
post-Hartree--Fock coupled cluster methods with a fraction of their cost.
Thence, we have evaluated the performance of a recently developed non-empirical
Strongly Constrained and Appropriately Normed (SCAN) density functional on
electronic structure calculations of ionic liquid ion pairs. The performance of
SCAN and other popular functionals (PBE, M06-L, B2PLYP) among with Grimme's
dispersion correction and Boys-Bernardi basis set superposition error
correction was compared to DLPNO-CCSD(T)/CBS. We show that SCAN reproduces
coupled-cluster results for describing the employed dataset of 48 ion pairs.Comment: 24 pages, 6 figure
Thermodynamic properties of diatomic molecules systems under anharmonic
  Eckart potential

Due to one of the most representative contributions to the energy in diatomic
molecules being the vibrational, we consider the generalized Morse potential
(GMP) as one of the typical potential of interaction for one-dimensional
microscopic systems, which describes local anharmonic effects. From Eckart
potential (EP) model, it is possible to find a connection with the GMP model,
as well as obtain the analytical expression for the energy spectrum because it
is based on $S\,O\left(2,1\right)$ algebras. In this work we find the
macroscopic properties such as vibrational mean energy $U$, specific heat $C$,
Helmholtz free energy $F$ and entropy $S$ for a heteronuclear diatomic system,
along with the exact partition function and its approximation for the high
temperature region. Finally, we make a comparison between the graphs of some
thermodynamic functions obtained with the GMP and the Morse potential (MP) for
$H\,Cl$ molecules.Comment: 12 pages, 8 figures, 1 table, submitted to the Int. J. Quantum. Che
Analysis of bonding properties in molecular ground and excited states by a Cohen-type bond order

A Cohen-type bond-order (I. Cohen, 1972) anal. in terms of orthogonalized at. basis functions is given, which can be used to analyze neglect-of-differential-overlap wave functions of large org. and organometallic mols. For small mols., the results from this method agreed with the results obtained with the same anal. based on ab-initio STO-3G wave functions. For large planar arom. systems, these AVE bond orders are a consistent generalization of the p-bond order. A simple relation between these bond orders and the corresponding covalent bond energies was established. The method can be easily extended to study excited state MC wave functions. Calcns. were done for C2H2, C2H4, C2H6, and Mn2(CO)10. The results indicate that the method can be used to discuss the photochem. of org. and organometallic compds
Continuous-Variable Quantum Key Distribution with Gaussian Modulation --
  The Theory of Practical Implementations

Quantum key distribution using weak coherent states and homodyne detection is
a promising candidate for practical quantum-cryptographic implementations due
to its compatibility with existing telecom equipment and high detection
efficiencies. However, despite the actual simplicity of the protocol, the
security analysis of this method is rather involved compared to
discrete-variable QKD. In this article we review the theoretical foundations of
continuous-variable quantum key distribution (CV-QKD) with Gaussian modulation
and rederive the essential relations from scratch in a pedagogical way. The aim
of this paper is to be as comprehensive and self-contained as possible in order
to be well intelligible even for readers with little pre-knowledge on the
subject. Although the present article is a theoretical discussion of CV-QKD,
its focus lies on practical implementations, taking into account various kinds
of hardware imperfections and suggesting practical methods to perform the
security analysis subsequent to the key exchange. Apart from a review of well
known results, this manuscript presents a set of new original noise models
which are helpful to get an estimate of how well a given set of hardware will
perform in practice.Comment: 71 pages, 9 figures, 1 tabl
Adaptive weight estimator for quantum error correction

Quantum error correction of a surface code or repetition code requires the
pairwise matching of error events in a space-time graph of qubit measurements,
such that the total weight of the matching is minimized. The input weights
follow from a physical model of the error processes that affect the qubits.
This approach becomes problematic if the system has sources of error that
change over time. Here we show how the weights can be determined from the
measured data in the absence of an error model. The resulting adaptive decoder
performs well in a time-dependent environment, provided that the characteristic
time scale $\tau_{\mathrm{env}}$ of the variations is greater than $\delta
t/\bar{p}$, with $\delta t$ the duration of one error-correction cycle and
$\bar{p}$ the typical error probability per qubit in one cycle.Comment: 5 pages, 4 figure
Quantifiable simulation of quantum computation beyond stochastic
  ensemble computation

In this study, a distinctive feature of quantum computation (QC) is
characterized. To this end, a seemingly-powerful classical computing model,
called "stochastic ensemble machine (SEnM)," is considered. The SEnM runs with
an ensemble consisting of finite copies of a single probabilistic machine,
hence is as powerful as a probabilistic Turing machine (PTM). Then the
hypothesis--that is, the SEnM can effectively simulate a general circuit model
of QC--is tested by introducing an information-theoretic inequality, named
readout inequality. The inequality is satisfied by the SEnM and imposes a
critical condition: if the hypothesis holds, the inequality should be satisfied
by the probing model of QC. However, it is shown that the above hypothesis is
not generally accepted with the inequality violation, namely, such a simulation
necessarily fails, implying that PTM $\subseteq$ QC.Comment: 8 pages, 4 figures, Advanced Quantum Technologies (2018
Enhanced Quantum Synchronization via Quantum Machine Learning

We study the quantum synchronization between a pair of two-level systems
inside two coupled cavities. By using a digital-analog decomposition of the
master equation that rules the system dynamics, we show that this approach
leads to quantum synchronization between both two-level systems. Moreover, we
can identify in this digital-analog block decomposition the fundamental
elements of a quantum machine learning protocol, in which the agent and the
environment (learning units) interact through a mediating system, namely, the
register. If we can additionally equip this algorithm with a classical feedback
mechanism, which consists of projective measurements in the register,
reinitialization of the register state and local conditional operations on the
agent and environment subspace, a powerful and flexible quantum machine
learning protocol emerges. Indeed, numerical simulations show that this
protocol enhances the synchronization process, even when every subsystem
experience different loss/decoherence mechanisms, and give us the flexibility
to choose the synchronization state. Finally, we propose an implementation
based on current technologies in superconducting circuits
Quantitative determination of paroxetine and its 4-hydroxy-3-methoxy metabolite in plasma by high-performance liquid chromatography/electrospray ion trap mass spectrometry: application to pharmacokinetic studies

7 pages, 4 figures, 3 tables.-- PMID: 12820211 [PubMed].-- Printed version published Jul, 22, 2003.A high-performance liquid chromatography (HPLC) method with tandem mass spectrometric detection is described for the determination of paroxetine, an antidepressant drug, and its metabolite (3S,4R)-4-(4-fluorophenyl)-3-(4-hydroxy-3-methoxyphenoxymethyl)piperidine (HM paroxetine) in human plasma. Plasma samples were hydrolysed with hydrochloric acid and then analytes were extracted with ethyl acetate at alkaline pH. Extracts were analysed by HPLC coupled to an atmospheric pressure ionisation-electrospray (ESI) interface and an ion trap mass spectrometer. Chromatography was performed on a reversed-phase column using acetonitrile/0.02% formic acid (66:34, v/v) as a mobile phase. The mass spectrometer was operated in the multiple reaction monitoring mode. The method was validated over concentration ranges of 0.75-100 g/L and 5-100 g/L for paroxetine and HM paroxetine, respectively. Mean recoveries of 77% for paroxetine and 76% for HM paroxetine were found, with precision always better than 15%. The limits of detection and quantification were 0.20 and 0.70 g/L for paroxetine, and 0.70 and 2.20 g/L for its metabolite. The method was applied to the analysis of plasma samples obtained from nine healthy male volunteers administered with a single oral dose of 20 mg paroxetine. After the 20-mg dose, the mean peak plasma concentration was 8.60 g/L for paroxetine and 92.40 g/L for HM paroxetine showing a tenfold ratio between the metabolite and the parent drug along the entire time-concentration curve.This study was supported by Area Progetto Droga from Istituto Superiore di Sanità, Roma (Italy), Fondo de Investigación Sanitaria, Madrid, Spain (grants FIS 97/1198, FIS 98/0181, FIS 00/0777 and FIS 01/1336) and Generalitat de Catalunya, Barcelona, Spain (GENCAT-CIRIT, grant 2001SGR00407).Peer reviewe
新規プロテオーム解析法の開発とそのバイオマーカー探索への応用

This is the author's version of a work that was accepted for publication in Proteomics-Clinical Applications. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Proteomics-Clinical Applications, 4: 925-935 (2008), http://doi.org/10.1002/prca.200780111This is the author's version of a work that was accepted for publication in Rapid Communications in Mass Spectrometry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Rapid Communications in Mass Spectrometry. 20: 31.38 (2006), http://doi.org/10.1002/rcm.2262This is the author's version of a work that was accepted for publication in Proteomics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Proteomics, 6:2042-2049 (2006), http://doi.org/10.1002/pmic.200500575This is the author's version of a work that was accepted for publication in Rapid Communications in Mass Spectrometry. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Rapid Communications in Mass Spectrometry, 17: 1642.1650 (2003), http://doi.org/10.1002/rcm.110
Kinetics of gas-phase hydrogen/deuterium exchange and gas-phase structure of protonated phenylalanine, proline, tyrosine and tryptophan

Site-specific rate constants for the gas-phase hydrogen/deuterium (H/D) exchange of four, three, five and five hydrogen atoms in protonated phenylalanine (Phe), proline (Pro), tyrosine (Tyr) and tryptophan (Trp), respectively, were determined from matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) experiments with D2O, D2S, and CH3OD as deuterating agents. No H/D exchange was observed with D2S. For exchange with both CD3OD and D2O, which is about ten times slower in the latter, results indicate for all compounds protonation of the -amino group in agreement with theoretical results. Also, with both reagents, all compounds exchange at the COOH site more than ten times faster than at the protonation site, with OH and NH sites of Tyr and Trp, respectively, exchanging slowest. The observation of H/D exchange despite the high differences in proton affinities between the amino acids and deuterating agent exceeding 200 kJ mol-1 is in agreement with lowering of the barrier for proton transfer through hydrogen bonding proposed by Lebrilla and coworkers
Identifying acetylated lignin units in non-wood fibers using pyrolysis-gas chromatography/mass spectrometry

1Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, P.O. Box 1052, E-41080-Seville, Spain\ud
2Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040-Madrid, Spain\ud
E-mail address: delrio@irnase.csic.esA series of non-wood plant fibers, namely kenaf, jute, sisal and abaca, have been analyzed upon Py-GC/MS of the whole material. The pyrolysis products mainly arise from the carbohydrate and lignin moieties of the fibers. The lignin-derived phenols belonged to the p-hydroxyphenylpropanoid (H), guaiacylpropanoid (G) and syringylpropanoid (S) structures, and showed a high S/G ratio of between 2.0 and 5.4, the highest corresponding to kenaf. Among the lignin-derived phenols released, small amounts of sinapyl and coniferyl acetates (in both cis- and trans- forms) were identified for the first time upon Py-GC/MS of lignocellulosic materials. Acetylation of the sinapyl and coniferyl alcohols was at the γ-position of the side-chain. The release of these alcohols derived from intact acetylated lignin units upon pyrolysis seems to indicate that the native lignin in the fibers selected for this study is at least partially acetylated. Sinapyl (and coniferyl) acetates have recently been suggested to be authentic lignin precursors involved in the polymerization of lignin along with the normal sinapyl and coniferyl alcohols. Py-GC/MS will offer a convenient and rapid tool for analyzing naturally acetylated lignins, as well as to screen plant materials for the presence of acetylated units in lignin.This study has been supported by the Spanish Ministerio de Ciencia y Tecnología (MCyT) (project AGL2002-00393). A.G. acknowledges a "Ramón y Cajal" contract of the Spanish MCyT. We also thank J.M. Gras and G. Artal (CELESA, Spain) for providing the plant samples.Peer reviewe
Identification of intact long-chain p-hydroxycinnamate esters in leaf fibers of abaca (Musa textilis) using gas chromatography/mass spectrometry

Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, P.O. Box 1052, 41080-Seville, Spain; E-mail address: delrio@irnase.csic.es (J.C. del Río)The study of acetone extractable components from the leaf fibers of the non-wood plant abaca (Musa textilis) resulted in the isolation and identification of series of intact hydroxycinnamate esters consisting of ferulic and p-coumaric acids esterified to long chain fatty alcohols (C20 to C28) and ω-hydroxyfatty acids (C22 to C28). These series of compounds were characterized by high temperature gas chromatography-mass spectrometry (GC/MS) using capillary columns (12 m length) with thin films that allowed the analysis of hydroxycinnamate esters without prior saponification nor derivatization. Characterization of intact individual compounds was achieved based on the mass spectra obtained by GC/MS of the underivatized and their methyl and/or TMS ether derivatives.This study has been supported by the Spanish Ministerio de Ciencia y Tecnología (MCyT) (project AGL2002-00393). A.G. acknowledges a "Ramón y Cajal" contract of the Spanish MCyT. We also thank J.M. Gras and G. Artal (CELESA, Spain) for providing the abaca leaf fibers.Peer reviewe
Study of peptide on-line complexation with transition-metal ions generated from sacrificial electrodes in thin-chip polymer microsprays

A miniaturized polymer electrospray-type interface is used to study metal-ion chelation with model peptides. Taking advantage of the intrinsic electrochemical behavior of electrospray, a sacrificial electrode is used to generate at the same time electrospray and transition-metal ions coming from the anodic dissolution of the electrode. The microspray interface provides enhanced mass transport due to its small dimensions, increasing the yield of possible reactions, in particular complex formation. Transition-metal electrodes, e.g. copper, zinc, nickel, iron and silver, are used to obtain on-line complexation with model peptides. It is demonstrated that the use of in-reservoir sacrificial electrodes is an efficient way to generate metal ions in order to form and study complexes with peptides, avoiding the addition of metallic salts
Tandem mass spectrometry of deprotonated iodothyronines

In order to assist with the development of more selective and sensitive methods for thyroid hormone analysis the \[M-H](-) anions of the iodothyronines T4, T3, rT3, (3,5)-T2 and the non-iodinated thyronine (TO) have been generated by negative ion electrospray mass spectrometry. Tandem mass spectra of these ions were recorded on a triple-quadrupole mass spectrometer and show a strong analogy with the fragmentation pathways of the parent compound, tyrosine. All iodothyronines also show significant abundances of the iodide anion in their tandem mass spectra, which represents an attractive target for multiple reaction monitoring (MRM) analysis, given that iodothyronines are the only iodine bearing endogenous molecules. Characteristic fragments are observed at m/z 359.7 and 604.5 for rT3 but are absent in the spectrum of T3, thus differentiating the two positional isomers. The striking difference in the fragmentation patterns of these regioisomeric species is attributed to the increased acidity of the phenol moiety in rT3 compared with T3. Copyright (C) 2005 John Wiley & Sons, Ltd
From mass to structure: An aromaticity index for high-resolution mass data of natural organic matter

Recent progress in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) provided extensive molecular mass data for complex natural organic matter (NOM). Structural information can be deduced solely from the molecular masses for ions with extreme molecular element ratios, in particular low H/C ratios, which are abundant in thermally altered NOM (e.g. black carbon). In this communication we propose a general aromaticity index (AI) and two threshold values as unequivocal criteria for the existence of either aromatic (AI > 0.5) or condensed aromatic structures (AI >= 0.67) in NOM. AI can be calculated from molecular formulae which are derived from exact molecular masses of naturally occurring compounds containing C, H, O, N, S and P and is especially applicable for substances with aromatic cores and few alkylations. In order to test the validity of our model index, AI is applied to FTICRMS data of a NOM deep-water sample from the Weddell Sea (Antarctica), a fulvic acid standard and an artificial dataset of all theoretically possible molecular formulae. For graphical evaluation a ternary plot is suggested for four-dimensional data representation. The proposed aromaticity index is a step towards structural identification of NOM and the molecular identification of black carbon in the environment
The fragmentation pathways of protonated Amiton in the gas phase : towards the structural characterisation of organophosphorus chemical warfare agents by electrospray ionisation tandem mass spectrometry

Amiton (O,O-diethyl-S-[2-(diethylamino)ethyl]phosphorothiolate), otherwise known as VG, is listed in schedule 2 of the Chemical Weapons Convention (CWC) and has a structure closely related to VX (O-ethyl-S-(2-diisopropylamino)ethylmethylphosphonothiolate). Fragmentation of protonated VG in the gas phase was performed using electrospray ionisation ion trap mass spectrometry (ESI-ITMS) and revealed several characteristic product ions. Quantum chemical calculations provide the most probable structures for these ions as well as the likely unimolecular mechanisms by which they are formed. The decomposition pathways predicted by computation are consistent with deuterium-labeling studies. The combination of experimental and theoretical data suggests that the fragmentation pathways of VG and analogous organophosphorus nerve agents, such as VX and Russian VX, are predictable and thus ESI tandem mass spectrometry is a powerful tool for the verification of unknown compounds listed in the CWC. Copyright (c) 2006 Commonwealth of Australia. Published by John Wiley & Sons, Ltd
Surfactant-mediated matrix-assisted laser desorption/\ud
ionization time-of-flight mass spectrometry\ud
of small molecules

A variety of surfactants have been tested as matrix-ion suppressors for the analysis of small molecules\ud
by matrix-assisted laser desorption/ionization time-of flight mass spectrometry. Their addition to the\ud
common matrix a-cyano-4-hydroxycinnamic acid (CHCA) greatly reduces the presence of matrixrelated\ud
ions when added at the appropriate mole ratio of CHCA/surfactant, while still allowing the\ud
analyte signal to be observed. A range of cationic quaternary ammonium surfactants, as well as a\ud
neutral and anionic surfactant, was tested for the analysis of phenolics, phenolic acids, peptides and\ud
caffeine. It was found that the cationic surfactants, particularly cetyltrimethylammonium bromide\ud
(CTAB), were suitable for the analysis of acidic analytes. The anionic surfactant, sodium dodecyl\ud
sulfate, showed promise for peptide analysis. For trialanine, the detection limit was observed to be in\ud
the 100 femtomole range. The final matrix/surfactant mole ratio was a critical parameter for matrix ion\ud
suppression and resulting intensity of analyte signal. It was also found that the mass resolution of\ud
analytes was improved by 25–75%. Depth profiling of sample spots, by varying the number of laser\ud
shots, revealed that the surfactants tend to migrate toward the top of the droplet during crystallization,\ud
and that it is likely that the analyte is also enriched in this surface region. Here, higher\ud
analyte/surfactant concentration would reduce matrix-matrix interactions (known to be a source of\ud
matrix-derived ions). Copyright # 2007 John Wiley & Sons, Ltd