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Ab Initio

Hao Wang, Weitao Yang
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computational costs of QM methods. In order to overcome these two difficulties, here we developed the residue-based systematic molecular fragmentation method to partition general proteins into only twenty types of amino acid dipeptides and one type of peptide bond at Level 1...
December 14, 2018: Journal of Chemical Theory and Computation
Fabrice Pointillart, Jiang-Kun Ou-Yang, Guglielmo Fernandez Garcia, Vincent Montigaud, Jessica Flores Gonzalez, Rémi Marchal, Ludovic Favereau, Federico Totti, Jeanne Crassous, Olivier Cador, Lahcène Ouahab, Boris Le Guennic
The design of a coordination complex that involves a ligand combining both a tetrathiafulvalene core and a helicene fragment was achieved thanks to the reaction between the new 2-{1-[2-methyl[6]helicene]-4,5-[4,5-bis(propylthio)tetrathiafulvalenyl]-1 H-benzimidazol-2-yl}pyridine ligand (L) and the Dy(hfac)3 ·2H2 O metalloprecursor. Magnetic investigations showed field-induced single-molecule-magnet (SMM) behavior under an applied magnetic field of 1000 Oe for [Dy(hfac)3 (L)]·0.5CH2 Cl2 , while experimentally oriented single-crystal magnetic measurements allowed for determination of the magnetic anisotropy orientation...
December 14, 2018: Inorganic Chemistry
Xin Wu, Pavlo O Dral, Axel Koslowski, Walter Thiel
Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.3 billion two-electron (2-e) integrals...
December 14, 2018: Journal of Computational Chemistry
Lorenz Drescher, Geert Reitsma, Tobias Witting, Serguei Patchkovskii, Jochen Mikosch, Marc J J Vrakking
We report an experimental study of iodomethane attosecond transient absorption spectroscopy (ATAS) in the region of iodine 4d core-to-valence/Rydberg excitation. Similar to previous atomic experiments, XUV-NIR delay-dependent absorbance changes reflect a light-induced phase due to an NIR-field driven AC Stark shift of the excited states, as well as pathway interferences arising from couplings between neighboring states. As a novel aspect of molecular ATAS, we observe pronounced differences between the ATAS signatures of valence and Rydberg states...
December 14, 2018: Journal of Physical Chemistry Letters
Aleksandra Łachmańska, Paweł Tecmer, Örs Legeza, Katharina Boguslawski
Understanding the binding mechanism in neptunyl clusters formed due to cation-cation interactions is of crucial importance in nuclear waste reprocessing and related areas of research. Since experimental manipulations with such species are often rather limited, we have to rely on quantum-chemical predictions of their electronic structures and spectroscopic parameters. In this work, we present a state-of-the-art quantum chemical study of the T-shaped and diamond-shaped neptunyl(v) and neptunyl(vi) dimers. Specifically, we scrutinize their molecular structures, (implicit and explicit) solvation effects, the interplay of static and dynamical correlation, and the influence of spin-orbit coupling on the ground state and lowest-lying excited states for different total spin states and total charges of the neptunyl dications...
December 14, 2018: Physical Chemistry Chemical Physics: PCCP
Rosa Pujales-Paradela, Fabio Carniato, Rocío Uzal-Varela, Isabel Brandariz, Emilia Iglesias, Carlos Platas-Iglesias, Mauro Botta, David Esteban-Gómez
We report a pentadentate ligand containing a 2,2'-azanediyldiacetic acid moiety functionalized with a picolinate group at the nitrogen atom (H3paada), as well as a lipophylic derivative functionalized with a dodecyloxy group at position 4 of the pyridyl ring (H3C12Opaada). The protonation constants of the paada3- ligand and the stability constant of the Mn(ii) complex were determined using a combination of potentiometric and spectrophotometric titrations (25 °C, 0.15 M NaCl). A detailed relaxometric characterisation was accomplished by recording 1H Nuclear Magnetic Relaxation Dispersion (NMRD) profiles and 17O chemical shifts and relaxation rates...
December 14, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Kristie Darrah, Ting Wang, Ian Cook, Mary Cacace, Alexander Deiters, Thomas S Leyh
Catecholamine neurotransmitter levels in the synapses of the brain shape human disposition - cognitive flexibility, aggression, depression, reward seeking… - and manipulating these levels is a major objective of the pharmaceutical industry. Certain neurotransmitters are extensively sulfonated and inactivated by human sulfotransferase 1A3 (SULT1A3). To our knowledge, sulfonation as therapeutic means of regulating transmitter activity has not been explored. Here we describe the discovery of a SULT1A3 allosteric site that can be used to inhibit the enzyme...
December 13, 2018: Journal of Biological Chemistry
Ruge Quhe, Junchen Liu, Jinxiong Wu, Jie Yang, Yangyang Wang, Qiuhui Li, Tianran Li, Ying Guo, Jinbo Yang, Hailin Peng, Ming Lei, Jing Lu
A successful two-dimensional (2D) semiconductor successor of silicon for high-performance logic in the post-silicon era should have both excellent performance and air stability. However, air-stable 2D semiconductors with high performance were quite elusive until the air-stable Bi2O2Se with high electron mobility was fabricated very recently (J. Wu, H. Yuan, M. Meng, C. Chen, Y. Sun, Z. Chen, W. Dang, C. Tan, Y. Liu, J. Yin, Y. Zhou, S. Huang, H. Q. Xu, Y. Cui, H. Y. Hwang, Z. Liu, Y. Chen, B. Yan and H. Peng, Nat...
December 13, 2018: Nanoscale
Xiuxiu Wu, Johannes Ehrmaier, Andrzej L Sobolewski, Tolga N V Karsili, Wolfgang Domcke
The mechanisms of photoinduced reactions of adenine with water molecules in hydrogen-bonded adenine-water complexes were investigated with ab initio wave-function-based electronic-structure calculations. Two excited-state electron/proton transfer reaction mechanisms have been characterized: H-atom abstraction from water by photoexcited adenine as well as H-atom transfer from photoexcited adenine or the (adenine+H) radical to water. In the water-to-adenine H-atom transfer reaction, an electron from one of the p orbitals of the water molecule fills the hole in the n (π) orbital of the nπ* (ππ*) excited state of adenine, resulting in a charge-separated electronic state...
December 13, 2018: Physical Chemistry Chemical Physics: PCCP
Hedieh Torabifard, G Andrés Cisneros
Ten-eleven translocation 2 (TET2) is an Fe/α-ketoglutarate (α-KG) dependent enzyme that dealkylates 5-methylcytosine (5mC). The reaction mechanism involves a series of three sequential oxidations that convert 5mC to 5-hydroxy-methylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Our previous biochemical and computational studies uncovered an active site scaffold that is required for wild-type (WT) stepwise oxidation ( Nat. Chem. Bio. , 13 , 181). We showed that the mutation of a single residue, T1372 to some amino acids, such as Glu, can impact the iterative oxidation steps and stop the oxidation of 5hmC to 5fC/caC...
November 28, 2018: Chemical Science
Sita Nirupama Nishtala, Avish Arora, Jorge Reyes, Myles H Akabas
Infection with Plasmodium species parasites causes malaria. Plasmodium parasites are purine auxotrophic. They import purines via an equilibrative nucleoside transporter (ENT). In P. falciparum , the most virulent species, the equilibrative nucleoside transporter 1 (PfENT1) represents the primary purine uptake pathway. This transporter is a potential target for the development of antimalarial drugs. In the absence of a high-resolution structure for either PfENT1 or a homologous ENT, we used the substituted cysteine accessibility method (SCAM) to investigate the membrane-spanning domain structure of PfENT1 to identify potential inhibitor-binding sites...
December 12, 2018: Journal of Biological Chemistry
Marcin Rybicki, Joachim Sauer
A hybrid of high level and low level quantum mechanics (QM) methods has been employed to predict intrinsic and apparent energy barriers for the direct proton exchange mechanism of methane, ethane, propane, n-butane, and i-butane on Brønsted sites of H-MFI. The specific hybrid MP2:PBE+D2 + ΔCC implementation used is known to yield the so-called "chemical accuracy" (±4 kJ/mol). Whereas the apparent enthalpy barriers decrease with increasing C number from 104 to 63 kJ/mol, in line with the decreasing heat of adsorption, the intrinsic enthalpy barriers are constant within 124-127 kJ/mol at 500 K...
December 12, 2018: Journal of the American Chemical Society
Latévi M Lawson Daku
We report a detailed ab initio molecular dynamics (AIMD) study of the structural and vibrational properties of aqueous [Fe(tpy)2]2+ (tpy = 2,2':6',2''-ter-pyridine) in the low-spin (LS) and high-spin (HS) states, which extends our previous work on aqueous [Fe(bpy)3]2+ (bpy = 2,2'-bipyridine) [L. M. Lawson Daku and A. Hauser, J. Phys. Chem. Lett., 2010, 1, 1830-1835; L. M. Lawson Daku, Phys. Chem. Chem. Phys., 2018, 20, 6236-6253]. Upon the LS → HS change of states, the axial and distal Fe-N bonds of aqueous [Fe(tpy)2]2+ are predicted to lengthen by 0...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
Xiao Tang, Weiguo Sun, Cheng Lu, Liangzhi Kou, Changfeng Chen
Two-dimensional (2D) Dirac materials have attracted extensive research interest due to their high carrier mobility and ballistic charge transport, and they hold great promise for next-generation nanoscale devices. Here, we report a computational discovery of a stable 2D Dirac material, an NiB6 monolayer, which is identified by an extensive structure search, and its dynamic and thermal stabilities are confirmed by phonon and ab initio molecular dynamics (AIMD) simulations. This monolayer structure possesses anisotropic elastic properties with a Young's modulus of 189 N m-1, which is higher than that of phosphorene or silicene...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
Darren Bellshaw, Russell S Minns, Adam Kirrander
The choice of ab initio electronic structure method is an important factor in determining the fidelity of nonadiabatic dynamics simulations. We present an in-depth comparison of two simulations of photodissociation in the CS2 molecule following excitation to the 11B2 state. The simulations account for nonadiabatic and spin-orbit coupling, and are performed using the SHARC surface-hopping approach combined with state-averaged SA8-CASSCF(8,6)/SVP and SA8-CASSCF(10,8)/SVP ab initio calculations, with additional reference calculations at the MRCI(14,10)/aug-cc-pvTZ level...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
Hao Wang, Masanori Kohyama, Shingo Tanaka, KaiJin Wang, Ying Chen
A first-principles computational tensile test (FPCTT) is a powerful tool
 to investigate intrinsic strength and failure processes of grain
 boundaries (GBs), according to atomic and
 electronic behaviors based on density-functional theory, while
 careful interpretation is required in comparison with experiments,
 because of ideal conditions used in FPCTTs. We
 observed serious effects of a bulk-region size in FPCTTs of
 the {001} Σ5 GB in Al.
 For a GB supercell with enough thick bulk regions, the energy-strain curve shows spontaneous failure with catastrophic energy release just after the maximum stress point, which we name Type-A failure...
December 11, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Farzad Peyravi, Alimohammad Latif, Seyed Mohammad Moshtaghioun
The biological function of protein depends mainly on its tertiary structure which is determined by its amino acid sequence via the process of protein folding. Prediction of protein structure from its amino acid sequence is one of the most prominent problems in computational biology. Two basic methodologies on protein structure prediction are combined: ab initio method (3-D space lattice) and fold recognition method (hidden Markov model). The primary structure of proteins and 3-D coordinates of amino acid residues are put together in one hidden Markov model to learn the path of amino acid residues in 3-D space from the first atom to the last atom of each protein of each fold...
December 10, 2018: Bulletin of Mathematical Biology
Jamal Dabachi, Monique Body, Jens Dittmer, Aydar Rakhmatullin, Franck Fayon, Christophe Legein
Solid state NMR signals are very sensitive to the local environment of the observed nucleus; however, their interpretation is not straightforward. On the other hand, first-principles DFT calculations of NMR parameters can now be applied to periodic compounds to predict NMR parameters. Thus, ab initio calculations can help to interpret the NMR spectra exhibited by complex materials, to assign NMR lines to structural environments, and even to enlighten the environmental factors influencing the NMR parameters for a given nucleus...
December 11, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Sebastian P Sitkiewicz, Daniel Rivero, Josep M Oliva-Enrich, Alfonso Saiz-Lopez, Daniel Roca-Sanjuán
The electronic-structure properties of the low-lying electronic states and the absorption cross sections (σ(E)) of mercury halides HgCl2, HgBr2, HgI2, HgBrCl, HgClI, and HgBrI have been determined within the UV-vis spectrum range (170 nm ≤ λphoton ≤ 600 nm) by means of the DKH3-MS-CASPT2/SO-RASSI quantum-chemical methodology (with the ANO-RCC basis set) and a semi-classical computational strategy based on nuclear sampling for simulating the band shapes. Computed band energies show a good agreement with the available experimental data for HgX2 with errors around 0...
December 11, 2018: Physical Chemistry Chemical Physics: PCCP
Daniel C Elton, Michelle Fritz, Marivi Fernández-Serra
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy...
December 10, 2018: Physical Chemistry Chemical Physics: PCCP
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