474 results match your criteria fragment densities


A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy.

J Chem Theory Comput 2021 Jul 19. Epub 2021 Jul 19.

Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain.

Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. Read More

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First report of Meloidogyne arenaria infecting Maidong (Ophiopogon japonicus) in China.

Plant Dis 2021 Jun 11. Epub 2021 Jun 11.

Southwest Foresttry UniversityKunming, Yunnan, China, 650224;

Maidong (Ophiopogon japonicus) is a perennial evergreen plant of the Asparagaceae, occurring mainly in China, Japan, Vietnam, and India. It grows in the damp place on the hillside below 2000 meters above sea level, under the forest or beside the stream;It has been widely cultivated in the Sichuan ofhina for medicinal uses; and it is included in the Chinese Pharmacopoeia. During April 2019, Maidong plants exhibiting symptoms of stunting, leaf wilting, and multiple galls in the roots associated with root-knot nematode (Meloidogyne sp. Read More

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Projector-Free Capped-Fragment Scheme within Density Functional Embedding Theory for Covalent and Ionic Compounds.

J Chem Theory Comput 2021 Jul 7;17(7):4105-4121. Epub 2021 Jun 7.

Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States.

Quantum-mechanics-(QM)-based simulations now routinely aid in understanding and even discovering new chemistries involving molecules and materials exhibiting desired functionalities. correlated wavefunction (CW) theories systematically improve QM methods, with many exhibiting high accuracy. However, execution of CW methods requires expensive computations that typically scale poorly with system size. Read More

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First report of on roots of in Guangdong Province, China.

Plant Dis 2021 May 31. Epub 2021 May 31.

Guangzhou Institute of Forestry and Landscape Architecture, Soil environmental investigation department, Guangzhou, Guangdong, China;

(), a perennial herbaceous legume, is widely distributed in southern China. . has antipyretic, antiseptic and expectorant properties and can therefore be used as a phytomedicine (Ghosal et al. Read More

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Structural insight into transmissive mutant huntingtin species by correlative light and electron microscopy and cryo-electron tomography.

Biochem Biophys Res Commun 2021 Jun 10;560:99-104. Epub 2021 May 10.

Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. Electronic address:

Aggregates of mutant huntingtin (mHTT) containing an expanded polyglutamine (polyQ) tract are hallmarks of Huntington's Disease (HD). Studies have shown that mHTT can spread between cells, leading to the propagation of misfolded protein pathology. However, the structure of transmissive mHTT species, and the molecular mechanisms underlying their transmission remain unknown. Read More

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Deformation Potentials: Towards a Systematic Way beyond the Atomic Fragment Approach in Orbital-Free Density Functional Theory.

Authors:
Kati Finzel

Molecules 2021 Mar 11;26(6). Epub 2021 Mar 11.

Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Bergstraße 66c, 01069 Dresden, Germany.

This work presents a method to move beyond the recently introduced atomic fragment approximation. Like the bare atomic fragment approach, the new method is an ab initio, parameter-free, orbital-free implementation of density functional theory based on the bifunctional formalism that treats the potential and the electron density as two separate variables, and provides access to the Kohn-Sham Pauli kinetic energy for an appropriately chosen Pauli potential. In the present ansatz, the molecular Pauli potential is approximated by the sum of the bare atomic fragment approach, and a so-called deformation potential that takes the interaction between the atoms into account. Read More

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A BCMAxCD3 bispecific T cell-engaging antibody demonstrates robust antitumor efficacy similar to that of anti-BCMA CAR T cells.

Blood Adv 2021 03;5(5):1291-1304

CD3-engaging bispecific antibodies (bsAbs) and chimeric antigen receptor (CAR) T cells are potent therapeutic approaches for redirecting patient T cells to recognize and kill tumors. Here we describe a fully human bsAb (REGN5458) that binds to B-cell maturation antigen (BCMA) and CD3, and compare its antitumor activities vs those of anti-BCMA CAR T cells to identify differences in efficacy and mechanism of action. In vitro, BCMAxCD3 bsAb efficiently induced polyclonal T-cell killing of primary human plasma cells and multiple myeloma (MM) cell lines expressing a range of BCMA cell surface densities. Read More

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Electronic Couplings for Photoinduced Charge Transfer and Excitation Energy Transfer Based on Fragment Particle-Hole Densities.

J Phys Chem Lett 2021 Jan 20;12(3):1032-1039. Epub 2021 Jan 20.

State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China.

A new scheme is proposed to calculate the electronic couplings for photoinduced charge transfer and excitation energy transfer for both singlet and triplet states. In this scheme, the locally excited and charge-transfer states are constructed from the adiabatic ones by maximally localizing the particle (i.e. Read More

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January 2021

Effect of the Electron Density of the Heme Fe Atom on the Nature of Fe-O Bonding in Oxy Myoglobin.

Inorg Chem 2021 Jan 28;60(2):1021-1027. Epub 2020 Dec 28.

Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, Sanyo-Onoda, Yamaguchi 756-0884, Japan.

Mössbauer spectroscopy has been used to characterize oxygenated myoglobins (oxy Mbs) reconstituted with native and chemically modified Fe-enriched heme cofactors with different electron densities of the heme Fe atom (ρ) and to elucidate the effect of a change in the ρ on the nature of the bond between heme Fe and oxygen (O), i.e., the Fe-O bond, in the protein. Read More

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January 2021

More than one million barriers fragment Europe's rivers.

Nature 2020 12 16;588(7838):436-441. Epub 2020 Dec 16.

European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Łódź, Poland.

Rivers support some of Earth's richest biodiversity and provide essential ecosystem services to society, but they are often fragmented by barriers to free flow. In Europe, attempts to quantify river connectivity have been hampered by the absence of a harmonized barrier database. Here we show that there are at least 1. Read More

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December 2020

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes.

J Chem Theory Comput 2020 Dec 24;16(12):7525-7555. Epub 2020 Nov 24.

Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland.

Direct optimization against experimental condensed-phase properties concerning small organic molecules still represents the most reliable way to calibrate the empirical parameters of a force field. However, compared to a corresponding calibration against quantum-mechanical (QM) calculations concerning isolated molecules, this approach is typically very tedious and time-consuming. The present article describes an integrated scheme for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library combinatorial isomer enumeration. Read More

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December 2020

Pervasive and persistent effects of ant invasion and fragmentation on native ant assemblages.

Ecology 2021 03 12;102(3):e03257. Epub 2021 Jan 12.

Department of Entomology, University of Illinois at Urbana-Champaign, 320 Morrill Hall, 505 S. Goodwin Avenue, Urbana, Illinois, 61801, USA.

Biological invasions are a leading cause of global change, yet their long-term effects remain hard to predict. Invasive species can remain abundant for long periods of time, or exhibit population crashes that allow native communities to recover. The abundance and impact of nonnative species may also be closely tied to temporally variable habitat characteristics. Read More

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Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations.

Phys Chem Chem Phys 2020 Dec;22(46):26852-26864

State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.

Inspired by the analysis of Kohn-Sham energy densities by Nakai and coworkers, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations. Using ethylene-tetrafluoroethylene and oxyluciferin-water complexes as examples, distinctive distribution patterns were demonstrated for the excitation energy densities of local excitations (within a molecular fragment) and charge-transfer excitations (between molecular fragments). It also provided a simple way to compute the effective energy of both hot carriers (particle and hole) from charge-transfer excitations via an integration of the excitation energy density over the donor and acceptor grid points. Read More

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December 2020

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations.

Phys Chem Chem Phys 2020 Dec;22(46):26838-26851

Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.

In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag4-N2 complexes as examples, it is shown that the grid-based Kohn-Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag4 and N2) can be obtained by partitioning the Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. Read More

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December 2020

Microplastic contamination in surface waters of the Küçükçekmece Lagoon, Marmara Sea (Turkey): Sources and areal distribution.

Environ Pollut 2021 Jan 10;268(Pt B):115801. Epub 2020 Oct 10.

Istanbul University-Cerrahpasa, Department of Environmental Engineering, Istanbul, Turkey. Electronic address:

The distribution of freshwater and marine microplastics (MPs) varies due to the difference in fresh and seawater densities and MP sources. This study aims to investigate the abundance of MPs and their possible sources in surface waters of different ecosystems, such as sea, lagoon, and lake. We classified MPs in terms of their color and type and established the relationship between the MPs in surface waters with different characteristics. Read More

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January 2021

Polarizable Density Embedding for Large Biomolecular Systems.

J Chem Theory Comput 2020 Oct 1;16(10):5999-6006. Epub 2020 Oct 1.

Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.

We present an efficient and robust fragment-based quantum-classical embedding model capable of accurately capturing effects from complex environments such as proteins and nucleic acids. This is realized by combining the molecular fractionation with conjugate caps (MFCC) procedure with the polarizable density embedding (PDE) model at the level of Fock matrix construction. The PDE contributions to the Fock matrix of the core region are constructed using the local molecular basis of the individual fragments rather than the supermolecular basis of the entire system. Read More

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October 2020

London dispersion forces without density distortion: a path to first principles inclusion in density functional theory.

Faraday Discuss 2020 12;224(0):145-165

Department of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.

We analyse a path to construct density functionals for the dispersion interaction energy from an expression in terms of the ground state densities and exchange-correlation holes of the isolated fragments. The expression is based on a constrained search formalism for a supramolecular wavefunction that is forced to leave the diagonal of the many-body density matrix of each fragment unchanged, and is exact for the interaction between one-electron densities. We discuss several aspects: the necessary features of a density functional approximation for the exchange-correlation holes of the monomers, the optimal choice of the one-electron basis (named "dispersals"), and the functional derivative with respect to monomer density variations. Read More

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December 2020

Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch].

BMC Plant Biol 2020 Sep 23;20(1):438. Epub 2020 Sep 23.

College of horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. Read More

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September 2020

Controlling the Biological Fate of Micellar Nanoparticles: Balancing Stealth and Targeting.

ACS Nano 2020 10 16;14(10):13739-13753. Epub 2020 Sep 16.

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia.

Integrating nanomaterials with biological entities has led to the development of diagnostic tools and biotechnology-derived therapeutic products. However, to optimize the design of these hybrid bionanomaterials, it is essential to understand how controlling the biological interactions will influence desired outcomes. Ultimately, this knowledge will allow more rapid translation from the bench to the clinic. Read More

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October 2020

In-Depth Investigation of a Donor-Acceptor Interaction on the [email protected] in Transition-Metal Tetrylone Complexes: Structure, Bonding, and Property.

ACS Omega 2020 Aug 14;5(33):21271-21287. Epub 2020 Aug 14.

Department of Chemistry, University of Sciences, Hue University, Hue City 530000, Vietnam.

Stabilization for tetrylone complexes, which carry ylidone(0) ligands [(CO)W-X (YCp*)] (X = Ge, Sn, Pb; Y = B-Tl), has become an active theoretical research because of their promising application. Structure, bonding, and quantum properties of the transition-metal donor-acceptor complexes were theoretically investigated at the level of theory BP86 with several types of basis sets including SVP, TZVPP, and TZ2P+. The optimized structures reveal that all ligands X (YCp*) are strongly bonded in tilted modes to the metal fragment W(CO), and Cp* rings are mainly η-bonded to atom X. Read More

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The discovery of a new antibody for BRIL-fused GPCR structure determination.

Sci Rep 2020 07 15;10(1):11669. Epub 2020 Jul 15.

R&D Division, Kyowa Kirin Co., Ltd., Shizuoka, Japan.

G-protein-coupled receptors (GPCRs)-the largest family of cell-surface membrane proteins-mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Read More

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Biomechanical comparison of three different compression screws for treatment of odontoid fractures evaluation of a new screw design.

Clin Biomech (Bristol, Avon) 2020 07 25;77:105049. Epub 2020 May 25.

Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany.

Background: Lag screw osteosynthesis in odontoid fractures shows a high rate of pseudarthrosis. Biomechanical properties may play a role with insufficient fragment compression or unnoticed screw stripping. A biomechanical comparison of different constructed lag-screws was carried out and the biomechanical properties determined. Read More

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A self-consistent coulomb bath model using density fitting.

J Comput Chem 2020 Jul 5;41(18):1698-1708. Epub 2020 May 5.

Shenzhen Bay Laboratory, Shenzhen, China.

A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Read More

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Directional allosteric regulation of protein filament length.

Phys Rev E 2020 Mar;101(3-1):032409

Green Center for Molecular, Computational, and Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

Cofilin and ADF are cytoskeleton remodeling proteins that cooperatively bind and fragment actin filaments. Bound cofilin molecules do not directly interact with each other, indicating that cooperative binding of cofilin is mediated by the actin filament lattice. Cofilactin is therefore a model system for studying allosteric regulation of self-assembly. Read More

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Elucidation of Bottom-Up Growth of CaCO Involving Prenucleation Clusters from Structure Predictions and Decomposition of Globally Optimized (CaCO) Nanoclusters.

ACS Nano 2020 Apr 13;14(4):4153-4165. Epub 2020 Apr 13.

Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States.

Low-energy minima structures for (CaCO), ≤ 28, are predicted using bottom-up genetic algorithms in conjunction with density functional theory electronic structure calculations, in comparison with the frozen and relaxed top-down clusters generated by cuts from the calcite, vaterite, and aragonite crystal structures. Similarities in structural motifs for the bottom-up and relaxed top-down are revealed using a fragment recognition technique. Fragment energy decomposition analysis shows that the bottom-up and relaxed top-down clusters belong to two classes of amorphous clusters with distinct intracluster energy distributions, despite their structural similarity. Read More

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Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.).

BMC Genomics 2020 Mar 4;21(1):206. Epub 2020 Mar 4.

Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.

Background: Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding. Read More

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TheoDORE: A toolbox for a detailed and automated analysis of electronic excited state computations.

Authors:
F Plasser

J Chem Phys 2020 Feb;152(8):084108

Department of Chemistry, Loughborough University, Loughborough LE11 3TU, United Kingdom.

The advent of ever more powerful excited-state electronic structure methods has led to a tremendous increase in the predictive power of computation, but it has also rendered the analysis of these computations much more challenging and time-consuming. TheoDORE tackles this problem through providing tools for post-processing excited-state computations, which automate repetitive tasks and provide rigorous and reproducible descriptors. Interfaces are available for ten different quantum chemistry codes and a range of excited-state methods implemented therein. Read More

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February 2020

Microplastic fragment and fiber contamination of beach sediments from selected sites in Virginia and North Carolina, USA.

Mar Pollut Bull 2020 Feb 29;151:110869. Epub 2020 Jan 29.

Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University, Norfolk, VA 23529, USA.

Microplastic particles (<5 mm) constitute a growing pollution problem within coastal environments. This study investigated the microplastic presence of estuarine and barrier island beaches in the states of Virginia and North Carolina, USA. Seventeen sediment cores were collected at four study sites and initially tested for microplastic presence by pyrolysis-gas chromatography-mass spectrometry. Read More

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February 2020

Para-acetabular Radiopaque Densities in Patients With Femoroacetabular Impingement: A Retrospective Assessment of Prevalence and Characteristics.

Orthop J Sports Med 2020 Jan 23;8(1):2325967119892330. Epub 2020 Jan 23.

Department of Orthopaedic Surgery, School of Medicine, University of South Carolina, Columbia, South Carolina, USA.

Background: Femoroacetabular impingement (FAI) syndrome is a common source of hip pain associated with chondrolabral injury. There is a subset of patients with FAI syndrome who present with radiopaque densities (RODs) adjacent to the acetabular rim.

Purpose: To evaluate the prevalence, characteristics, and patient-specific factors associated with RODs adjacent to the acetabulum in patients treated with hip arthroscopy for symptomatic FAI. Read More

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January 2020

Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model.

J Chem Theory Comput 2020 Feb 27;16(2):1039-1054. Epub 2020 Jan 27.

Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States.

The fully analytic gradient of the second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity (RI) approximation in the fragment molecular orbital (FMO) framework is derived and implemented using a hybrid multilevel parallel programming model, a combination of the general distributed data interface (GDDI) and the OpenMP API. The FMO/MP2 analytic gradient contains three parts, i.e. Read More

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February 2020