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computational chemistry

Tsuyoshi Kato, Masayuku Nakagaki, Antoine Baceiredo, Shigeyoshi Sakaki
Although oxidative addition (O.A.) and reductive elimination (R.E.) are exceedingly important processes in organometallic chemistry, such processes are still extremely rare for main group element species. Here we report a theoretical study on the reaction of phosphine-stabilized silylenes with silanes which proceeds via reversible O.A./R.E. at room temperature. Of particular interest, this theoretical approach highlights the important role of the ligand, which can greatly affect kinetics and energy balance of the reaction...
May 22, 2018: Chemistry: a European Journal
Ruifeng Li, Hein J Wijma, Lu Song, Yinglu Cui, Marleen Otzen, Yu'e Tian, Jiawei Du, Tao Li, Dingding Niu, Yanchun Chen, Jing Feng, Jian Han, Hao Chen, Yong Tao, Dick B Janssen, Bian Wu
Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts...
May 21, 2018: Nature Chemical Biology
Naoki Ogasawara, Kota Kasahara, Ryosuke Iwai, Takuya Takahashi
Elucidating the molecular mechanism of helix-coil transitions of short peptides is a long-standing conundrum in physical chemistry. Although the helix-coil transitions of poly-glutamic acid (PGA) have been extensively studied, the molecular details of its unfolding process still remain unclear. We performed all-atom canonical molecular dynamics simulations for a 20-residue PGA, over a total of 19 μs, in order to investigate its helix-unfolding processes in atomic resolution. Among the 28 simulations, starting with the α-helical conformation, all showed an unfolding process triggered by the unwinding of terminal residues, rather than by kinking and unwinding of the middle region of the chain...
2018: PeerJ
Natasha K Maddigan, Andrew Tarzia, David M Huang, Christopher J Sumby, Stephen G Bell, Paolo Falcaro, Christian J Doonan
The durability of enzymes in harsh conditions can be enhanced by encapsulation within metal-organic frameworks (MOFs) via a process called biomimetic mineralisation. Herein we show that the surface charge and chemistry of a protein determines its ability to seed MOF growth. We demonstrate that chemical modification of amino acids on the protein surface is an effective method for systematically controlling biomimetic mineralisation by zeolitic imidazolate framework-8 (ZIF-8). Reaction of surface lysine residues with succinic (or acetic) anhydride facilitates biomimetic mineralisation by increasing the surface negative charge, whereas reaction of surface carboxylate moieties with ethylenediamine affords a more positively charged protein and hinders the process...
May 14, 2018: Chemical Science
Alexander V Vorontsov, Evgeny V Tretyakov
Graphene quantum dots (GQDs) are important for a variety of applications and designs, and the shapes of GQDs rely on the energy of their boundaries. Presently, many methods have been developed for the preparation of GQDs with the required boundaries, shapes and edge terminations. However, research on the properties of GQDs and their applications is limited due to the unavailability of these compounds in pure form. In the present computational study, the standard enthalpy of formation, the standard enthalpy of formation of edges and the standard enthalpy of hydrogenation are studied for hexagonal GQDs with purely zigzag and armchair edges in non-passivated and H-passivated forms using the semiempirical quantum chemistry method pm7...
May 18, 2018: Physical Chemistry Chemical Physics: PCCP
Daniel G A Smith, Lori A Burns, Dominic A Sirianni, Daniel R Nascimento, Ashutosh Kumar, Andrew M James, Jeffrey B Schriber, Tianyuan Zhang, Boyi Zhang, Adam S Abbott, Eric J Berquist, Marvin H Lechner, Leonardo A Cunha, Alexander G Heide, Jonathan M Waldrop, Tyler Y Takeshita, Asem Alenaizan, Daniel Neuhauser, Rollin A King, Andrew C Simmonett, Justin M Turney, Henry F Schaefer, Francesco A Evangelista, A Eugene DePrince, T Daniel Crawford, Konrad Patkowski, C David Sherrill
Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory...
May 17, 2018: Journal of Chemical Theory and Computation
Joanna Kisała, Kinga I Heclik, Krzysztof Pogocki, Dariusz Pogocki
The blood-brain barrier (BBB) is a complex system controlling two-way substances traffic between circulatory (cardiovascular) system and central nervous system (CNS). It is almost perfectly crafted to regulate brain homeostasis and to permit selective transport of molecules that are essential for brain function. For potential drug candidates, the CNS-oriented neuropharmaceuticals as well as for those of primary targets in the periphery, the extent to which a substance in the circulation gains access to the CNS seems crucial...
May 16, 2018: Current Medicinal Chemistry
Rachel Crespo-Otero, Mario Barbatti
Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency...
May 16, 2018: Chemical Reviews
Leonard Bezinge, Richard M Maceiczyk, Ioannis Lignos, Maksym V Kovalenko, Andrew J deMello
Recent advances in the development of hybrid organic-inorganic lead halide perovskite (LHP) nanocrystals (NCs) have demonstrated their versatility and potential application as photovoltaics and light emitters through compositional tuning of optical properties. That said, due to their compositional complexity, the targeted synthesis of mixed-cation, mixed-halide LHP NCs still represents an immense challenge for traditional batch scale chemistry. To address this limitation, we herein report the integration of a high-throughput segmented-flow microfluidic reactor and self-optimizing algorithm for the synthesis of nanocrystals with defined emission properties...
May 16, 2018: ACS Applied Materials & Interfaces
Francis Claret, Sylvain Grangeon, Annick Loschetter, Christophe Tournassat, Wout De Nolf, Nicholas Harker, Faiza Boulahya, Stéphane Gaboreau, Yannick Linard, Xavier Bourbon, Alejandro Fernandez-Martinez, Jonathan Wright
To understand the main properties of cement, a ubiquitous material, a sound description of its chemistry and mineralogy, including its reactivity in aggressive environments and its mechanical properties, is vital. In particular, the porosity distribution and associated sample carbonation, both of which affect cement's properties and durability, should be quantified accurately, and their kinetics and mechanisms of formation known both in detail and in situ . However, traditional methods of cement mineralogy analysis ( e...
March 1, 2018: IUCrJ
Mario Motta, Shiwei Zhang
We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules...
May 14, 2018: Journal of Chemical Physics
Ioannis Skarmoutsos, Mohamed Eddaoudi, Guillaume Maurin
Force field based-Molecular dynamics simulations were deployed to systematically explore the dynamics of confined molecules of different shapes and sizes, i.e. linear (CO2 and N2) and spherical (CH4) fluids, in a model small pore system, i.e. the Metal-Organic Framework SIFSIX-2-Cu-i. These computations unveil an unprecedented molecular symmetry dependence of the translational and rotational dynamics of fluids confined in channel-like nanoporous materials. In particular this peculiar behaviour is reflected by the extremely slow decay of the Legendre reorientational correlation functions of even-parity order for the linear fluids which is associated to jump-like orientation flips, while the spherical fluid shows a very fast decay taking place in a sub-picosecond time scale...
May 15, 2018: Journal of Physical Chemistry Letters
Evgeny Putin, Arip Asadulaev, Yan Ivanenkov, Vladimir Aladinskiy, Benjamin Sánchez-Lengeling, Alán Aspuru-Guzik, Alex Zhavoronkov
In silico modeling is a crucial milestone in modern drug design & development. Although computer-aided approaches in this field are well-studied, the application of deep learning methods in this research area is at the beginning. In this work, we present an original deep neural network (DNN) architecture named RANC (Reinforced Adversarial Neural Computer) for the de novo design of novel small-molecule organic structures based on generative adversarial network (GAN) paradigm and reinforcement learning (RL)...
May 15, 2018: Journal of Chemical Information and Modeling
Dmitry N Makarov
A system of two coupled quantum harmonic oscillators with the Hamiltonian H[over ̂]=1/2(1/m_{1}p[over ̂]_{1}^{2}+1/m_{2}p[over ̂]_{2}^{2}+Ax_{1}^{2}+Bx_{2}^{2}+Cx_{1}x_{2}) can be found in many applications of quantum and nonlinear physics, molecular chemistry, and biophysics. The stationary wave function of such a system is known, but its use for the analysis of quantum entanglement is complicated because of the complexity of computing the Schmidt modes. Moreover, there is no exact analytical solution to the nonstationary Schrodinger equation H[over ̂]Ψ=iℏ∂Ψ/∂t and Schmidt modes for such a dynamic system...
April 2018: Physical Review. E
Elliot J Taffet, Gregory D Scholes
The nature of intramolecular charge transfer (ICT) and the mechanism of intramolecular singlet fission (SF) in peridinin remain open research questions. Obtaining an understanding of the population evolution from the bright state to dark states following a photoinduced electronic transition is critical. Unambiguously describing this evolution in peridinin, and light-harvesting carotenoids in general, has proven elusive experimentally and computationally. To offer a balanced description of bright- and dark-state electronic structure, we here apply ab initio multireference perturbation theory quantum chemistry-the density matrix renormalization group self-consistent-field (DMRG-SCF) and complete-active space self-consistent field (CASSCF) with second-order N-electron valence perturbation theory (NEVPT2)...
May 14, 2018: Journal of Physical Chemistry. B
J Stuart Grossert, Donatella Boschi, Marco L Lolli, Robert L White
RATIONALE: The gas-phase fragmentation chemistry of multifunctional cations is highly influenced by the site of protonation. Possible relationships between protonation site and fragmentation processes were studied using 4-aminoalkyl-3-hydroxyfurazans. For these heterocyclic amines, the starting points for competing fragmentation pathways varied with protonation at multiple sites in two tautomers. METHODS: Mass spectra were acquired using electrospray ionization (ESI, positive mode) coupled to triple quadrupole and ion trap mass spectrometers; precursor-product ion relationships were studied by collision induced dissociation (CID)...
May 14, 2018: Rapid Communications in Mass Spectrometry: RCM
Xiao Hu, Irene Maffucci, Alessandro Contini
BACKGROUND: The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions...
May 13, 2018: Current Medicinal Chemistry
Insook Choi
Sonification is an open-ended design task to construct sound informing a listener of data. Understanding application context is critical for shaping design requirements for data translation into sound. Sonification requires methodology to maintain reproducibility when data sources exhibit non-linear properties of self-organization and emergent behavior. This research formalizes interactive sonification in an extensible model to support reproducibility when data exhibits emergent behavior. In the absence of sonification theory, extensibility demonstrates relevant methods across case studies...
2018: Frontiers in Neuroscience
Mohammad Abu-Laban, Raju R Kumal, Jonathan Casey, Jeff Becca, Daniel LaMaster, Carlos N Pacheco, Dan G Sykes, Lasse Jensen, Louis H Haber, Daniel J Hayes
The present study explores alternate pericyclic chemistries for tethering amine-terminal biomolecules onto silver nanoparticles. Employing the versatile tool of the retro-Diels-Alder (rDA) reaction, three thermally-labile cycloadducts are constructed that cleave at variable temperature ranges. While the reaction between furan and maleimide has widely been reported, the current study also evaluates the reverse reaction kinetics between thiophene-maleimide, and pyrrole-maleimide cycloadducts. Density Functional Theorem (DFT) calculations used to model and plan the experiments, predict energy barriers for the thiophene-maleimide reverse reaction to be greatest, and the pyrrole-maleimide barriers the lowest...
April 24, 2018: Journal of Colloid and Interface Science
Wiktor Pronobis, Alexandre Tkatchenko, Klaus-Robert Müller
Machine learning (ML) based prediction of molecular properties across chemical compound space is an important and alternative approach to efficiently estimate the solutions of highly complex many-electron problems in chemistry and physics. Statistical methods represent molecules as descriptors that should encode molecular symmetries and interactions between atoms. Many such descriptors have been proposed; all of them have advantages and limitations. Here, we propose a set of general two-body and three-body interaction descriptors which are invariant to translation, rotation and atomic indexing...
May 11, 2018: Journal of Chemical Theory and Computation
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