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Ab Initio

Jane S Richardson, Christopher J Williams, Lizbeth L Videau, Vincent B Chen, David C Richardson
We find that the overall quite good methods used in the CryoEM Model Challenge could still benefit greatly from several strategies for improving local conformations. Our assessments primarily use validation criteria from the MolProbity web service. Those criteria include MolProbity's all-atom contact analysis, updated versions of standard conformational validations for protein and RNA, plus two recent additions: first, flags for cis-nonPro and twisted peptides, and second, the CaBLAM system for diagnosing secondary structure, validating Cα backbone, and validating adjacent peptide CO orientations in the context of the Cα trace...
August 11, 2018: Journal of Structural Biology
Andrea Pérez-Villa, Antonino Marco Saitta, Thomas Georgelin, Jean-Francois Lambert, Francois Guyot, Marie-Christine Maurel, Fabio Pietrucci
Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-D-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides...
August 14, 2018: Journal of Physical Chemistry Letters
Veacheslav Vieru, Liviu Ungur, Valeriu Cemortan, Andrey Sukhanov, Amer Baniodeh, Christopher E Anson, Annie K Powell, Violeta Voronkova, Liviu Chibotaru
We investigate the magnetism and the magnetization blocking of a series of [Fe2Dy2(OH)2(teaH)2(RC6H4COO)6] complexes, where teaH3 = triethanolamine and R = meta-CN (1), para-CN (2), meta-CH3 (3), para-NO2 (4) and para-CH3 (5), by combining ab initio calculations and EPR measurements. BS-DFT calculations show that in all compounds the Fe-Fe exchange interaction is antiferromagnetic and by far stronger than Fe-Dy and Dy-Dy ones. As a result, the lowest two exchange doublets probed by EPR mostly originate from the Ising interaction of Dy ions in all compounds...
August 14, 2018: Chemistry: a European Journal
Qinghua Wu, Qianku Hu, Yiming Hou, Haiyan Wang, Aiguo Zhou, Libo Wang
Using the ab initio evolutionary algorithm, four thermodynamically stable C5N phases (P6 ̅2m, R3 ̅m-1, R3 ̅m-2 and C2/m) are uncovered. The structures of the P6 ̅2m, R3 ̅m-1 and R3 ̅m-2 phases possess layered features. The dense C2/m phase with three-dimensional strong covalent bond network is calculated to be superhard with hardness of 75.4 and 83.9 GPa by Chen and Gao models. The electronic properties of the C5N is diverse including conductor (P6 ̅2m), indirect semiconductor (R3 ̅m-1 and R3 ̅m-2) and direct semiconductor (C2/m)...
August 14, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Nanshu Liu, Si Zhou, Nan Gao, Jijun Zhao
Monolayer gallium selenide (GaSe), an emerging two-dimensional semiconductor, holds great promise for electronics and optoelectronics. In reality, the contact properties between a semiconductor and the electrodes play a vital role in device performance. Thus, selecting suitable electrode materials with zero contact resistance is critical and challenging. Here, we explore the contact properties and electronic transport of monolayer GaSe with a series of electrode materials (including transition metals and MXenes) by ab initio electronic calculations and quantum transport simulations...
August 14, 2018: Physical Chemistry Chemical Physics: PCCP
Marcin Czapla, Jack Simons, Piotr Skurski
The consequences of an excess electron attachment to HGaF4 (HF/GaF3) superacid are investigated on the basis of theoretical calculations employing ab initio methods. It is found that the dipole potential of HGaF4 plays an important role in the initial formation of a dipole-bound anionic state. Due to the kinetic instability of that initially formed anion, a fragmentation reaction occurs promptly and leads to (GaF4)- and H as the final products. The energy profile of this process, its rate, and mechanism are presented and discussed...
August 14, 2018: Physical Chemistry Chemical Physics: PCCP
Young-Jin Park, Yong-Un Jeong, Won-Sik Kong
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous...
August 13, 2018: International Journal of Molecular Sciences
Wei Wang, Fengxiang Guo, Zhigang Gai, Tao Zhang, Jianguo Tang, Xuelei Tian, Wenqing Liu
In order to investigate the competitive interaction between nanoparticles and twin, the eutectic Si microstructures in Al⁻10Si (wt. %) base alloys with exclusive and combined addition of Sr and Sb are characterized by combined TEM and atom probe tomography (APT). The chemical short range order in Sb⁻Sb and Sb⁻Sr pairs is revealed by ab initio molecular dynamics simulation, which promotes the formation of clusters and nanoparticles. The coexistence of nanoparticles and twins is observed in Sb containing alloys, with a negative correlation in the corresponding number density, owing to the competitive stacking of precursors and individual atoms at the solid⁻liquid interface...
August 10, 2018: Materials
Yuan Liu, Minsik Cho, Brenda Rubenstein
We present an ab initio auxiliary field quantum Monte Carlo method for studying the electronic structure of molecules, solids, and model Hamiltonians at finite temperature. The algorithm marries the ab initio phaseless auxiliary field quantum Monte Carlo algorithm known to produce high accuracy ground state energies of molecules and solids with its finite temperature variant, long used by condensed matter physicists for studying model Hamiltonian phase diagrams, to yield a phaseless, ab initio finite temperature method...
August 13, 2018: Journal of Chemical Theory and Computation
Silvia Pandolfi, Carlos Renero-Lecuna, Yann Le Godec, Benoit Baptiste, Nicolas Menguy, Michele Lazzeri, Christel Gervais, Kristina Spektor, Wilson A Crichton, Oleksandr O Kurakevych
Hexagonal Si allotropes are expected to enhance light absorption in the visible range as compared to common cubic Si with diamond structure. Therefore, synthesis of these materials is crucial for the development of Si-based optoelectronics. In this work we combine in- situ high-pressure high-temperature synthesis and vacuum heating to obtain hexagonal Si. High pressure is one of the most promising routes to stabilize these allotropes. It allows to obtain large-volume nanostructured ingots by a sequence of direct solid-solid transformations, ensuring high-purity samples for detailed characterization...
August 13, 2018: Nano Letters
Thuc Hue Ly, Qingming Deng, Manh-Ha Doan, Lain-Jong Li, Jiong Zhao
Two-dimensional (2D) materials have been emerging as potential candidates for the next generation materials in various technology fields. The performance of the devices based on these 2D materials depends on their intrinsic band structures as well as the extrinsic (doping) effects such as surrounding chemicals and environmental oxygen/moisture, which strongly determines their Fermi energy level. Herein, we report the UV treatments on the 2D transition metal dichalcogenides (TMdCs), to controllably dope the samples without damaging the crystal structures or quenching the luminescence properties...
August 13, 2018: ACS Applied Materials & Interfaces
Maria J Capitán, Jesus Alvarez, Felix Yndurain
We performed a systematic study of electron-acceptor molecules in two closely related organometallic solids, namely, CuTCNQ and AgTCNQ. These studies were performed using both an experimental approach, via the use of electron spectroscopies (XPS and UPS), and a theoretical approach, via the use of ab initio DFT calculations. From these results, a complete description of the electronic structure of these molecular solid-films could be given, identifying the characteristic electronic and structural features of each part of the molecules and their contribution to the final electronic structure...
August 13, 2018: Physical Chemistry Chemical Physics: PCCP
Johannes Stefanski, Christian Schmidt, Sandro Jahn
Hydrothermal diamond anvil cell experiments in combination with Raman spectroscopy and first principles molecular dynamics simulations were performed to investigate the structure and dynamics of aqueous NaOH solutions for temperatures up to 700 °C, pressures up to 850 MPa and two different solute concentrations. The significant changes observed in the O-H stretching region of the Raman spectra between ambient and supercritical conditions are explained by both dynamic effects and structural differences. Especially important are a Grotthuss-like proton transport process and the decreasing network connectivity of the water molecules with increasing temperature...
August 13, 2018: Physical Chemistry Chemical Physics: PCCP
Yan Jin, Juan Wang, Qian Gou, Zhining Xia, Gang Feng
The rotational spectrum of the formic acid-difluoromethane complex was measured by using supersonic-jet Fourier transform microwave spectrometer. Experimental results and ab initio calculations support a conformation formed through a relative strong OH⋯F and a bifurcated weak CH2 ⋯O hydrogen bonds. The distances of the non-bonding interactions were determined to be 1.960(2) Å and 2.797(3) Å for OH⋯F and CH2 ⋯O, respectively. The dissociation energy of the complex is estimated to be about 1346 cm-1 ...
August 6, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Carlo Caponecchia, Wu Yi Zheng, Michael A Regan
The WOMBAT pilot selection test is widely used to select candidates for pilot training programs. Despite use in many countries, little information is available regarding the predictive validity of the test. This study was designed to test the ability of the WOMBAT test to predict performance outcomes in a sample of ab-initio pilots. Sixty students commenced the study in 3 cohorts, and completed the WOMBAT test before their performance in the training program was evaluated through flight time to solo, flight time to licence level achievement, and instructor ratings of performance...
November 2018: Applied Ergonomics
Lars Meckbach, Ulrich Huttner, Lars Christian Bannow, Tineke Stroucken, Stephan W Koch
Combining \emph{ab initio} density functional theory with the Dirac-Bloch and gap equations, excitonic properties of transition-metal dichalcogenide hetero-bilayers with type-II band alignment are computed. The existence of interlayer excitons is predicted whose binding energies are as large as 350\,meV, only roughly 100\,meV less than those of the coexisting intralayer excitons. The oscillator strength of the interlayer excitons reaches a few percent of the intralayer exciton resonances and their radiative lifetime is two orders of magnitude larger than that of the intralayer excitons...
August 10, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Jinlu He, Wei-Hai Fang, Run Long
Lead bromide perovskites APbBr3 (A = Cs, MA, FA) hold great promise in optoelectronics and photovoltaics. Because the bandgap of the three materials are similar, and also because the A site cation does not contribute to band edges, leading one to expect minor influence of A site cation on the excited-state lifetime of the perovskites. Experiments defy the expectation. By performing ab initio nonadiabatic (NA) molecular dynamics combined with time-domain density functional simulations, we demonstrate that the nonradiative electron-hole recombination times are on the order FAPbBr3 > MAPbBr3 > CsPbBr3, which are determined by the NA electron-phonon coupling because decoherence times are similar...
August 10, 2018: Journal of Physical Chemistry Letters
Leo Yuxiu Li, Nathan A Seifert, Fan Xie, Matthias Heger, Yunjie Xu, Wolfgang Jäger
The microwave spectrum of the hydrogen-bonded hydrogen peroxide-formic acid complex was measured in the range from 4 to 17 GHz. Assignment of transitions and analyses of the spectrum were supported by ab initio wavefunction and density functional calculations. The detected conformer features a seven-membered hydrogen-bonded ring, in which the H-atom of one hydroxyl group of H2O2 and the O-atom of the other OH group are a hydrogen bond donor and acceptor, respectively, to the carboxyl group of formic acid. The rotational transitions show a tunnelling splitting, which is attributed to a wagging-like motion of the free H-atom of H2O2 from above to below the heavy atom plane of formic acid...
August 10, 2018: Physical Chemistry Chemical Physics: PCCP
Christina A Gatsiou, Claire S Adjiman, Constantinos C Pantelides
In lattice energy models that combine ab initio and empirical components, it is important to ensure consistency between these components so that meaningful quantitative results are obtained. A method for deriving parameters of atom-atom repulsion dispersion potentials for crystals, tailored to different ab initio models, is presented. It is based on minimization of the sum of squared deviations between experimental and calculated structures and energies. The solution algorithm is designed to avoid convergence to local minima in the parameter space by combining a deterministic low-discrepancy sequence for the generation of multiple initial parameter guesses with an efficient local minimization algorithm...
August 10, 2018: Faraday Discussions
Oleg D Feya, Qinggao Wang, Sergey V Lepeshkin, Vladimir S Baturin, Yurii A Uspenskii, Artem R Oganov
Crystalline silica (SiO2 ) is a major material used in many technologies, yet the exact surface structures of silica polymorphs are still mostly unknown. Here we perform a comprehensive study of surface reconstructions of α-cristobalite (001), α-quartz (001) and stishovite (110) and (100) using evolutionary algorithm USPEX in conjunction with ab initio calculations. We found the well-known "dense surface" to be among low-energy reconstructions of α-quartz (001), as well as its previously proposed distorted version, which we call "shifted surface"...
August 9, 2018: Scientific Reports
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