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computational chemistry

Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro
The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger...
March 14, 2017: Sensors
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
Mengxi Yang, François P Gabbaï
As part of our fundamental interest in the chemistry of main-group Lewis acids, we have decided to target stibonium cations whose Lewis acidity is enhanced by the presence of a halogen substituent directly bound to antimony. Starting from Ph3Sb(OTf)2 (1) and Mes3Sb(OTf)2 (2), we successfully prepared the triflate derivatives Ph3SbF(OTf) (3) and Mes3SbF(OTf) (4). We also synthesized the hexachloroantimonate salt of [Mes3SbCl](+) (6), an analogue of the known [Ph3SbCl][SbCl6] (5). The structures of these complexes have been investigated experimentally as well as computationally using density functional theory methods...
March 22, 2017: Inorganic Chemistry
Pavel Majek, Jan Krupcik, Zachary S Breitbach, Milan K Dissanayake, Peter Kroll, Aaron A Ruch, LeGrande M Slaughter, Daniel W Armstrong
Dynamic high resolution liquid chromatography (DHPLC) was used to determine the kinetic and thermodynamic activation parameters of interconversion of three novel pentahelicene derivatives {3,5-bis(trifluoromethyl)benzo[i]pentahelicene, naphtho[1,2-i]pentahelicene and 4-methoxybenzo[i]pentahelicene}. DHPLC was performed on a chiral isopropyl - carbamate cyclofructan 6 (LARIHC CF6-P) column under normal phase conditions. Variation of the column temperature and flow rate was used to study the interconversion process...
December 21, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Sukrit Ranjan, Dimitar D Sasselov
The UV environment is a key boundary condition to abiogenesis. However, considerable uncertainty exists as to planetary conditions and hence surface UV at abiogenesis. Here, we present two-stream multilayer clear-sky calculations of the UV surface radiance on Earth at 3.9 Ga to constrain the UV surface fluence as a function of albedo, solar zenith angle (SZA), and atmospheric composition. Variation in albedo and latitude (through SZA) can affect maximum photoreaction rates by a factor of >10.4; for the same atmosphere, photoreactions can proceed an order of magnitude faster at the equator of a snowball Earth than at the poles of a warmer world...
March 2017: Astrobiology
Arndt R Finkelmann, Andreas H Göller, Gisbert Schneider
Machine learning models for site of metabolism (SoM) prediction offer the ability to identify metabolic soft spots in low molecular weight drug molecules at low computational cost and enable data-based reactivity prediction. SoM prediction is an atom classification problem. Successful construction of machine learning models requires atom representations that capture the reactivity-determining features of a potential reaction site. We have developed a descriptor scheme that characterizes an atom's steric and electronic environment and its relative location in the molecular structure...
March 21, 2017: ChemMedChem
Nicole V DelRosso, Sarah Hews, Lee Spector, Nathan D Derr
The predictable chemistry of Watson-Crick base-pairing imparts a unique structural programmability to DNA, enabling the facile design of molecular reactions that perform computations. However, many of the current architectures limit devices to a single operational cycle. Herein, we introduce the design of the "regenerator", a device based on coupled enthalpic and entropic reactions that permits the regeneration of molecular circuit components.
March 21, 2017: Angewandte Chemie
Aleix Comas-Vives, Kim Larmier, Christophe Copéret
The characterization of the active sites in heterogeneous catalysts is highly challenging and hinders the rational development and design of better catalysts. One approach to achieve this goal is Surface Organometallic Chemistry (SOMC), which allows generation of well-defined active sites characterized at the molecular level using spectroscopic methods. Due to many advances in the field and the increase of computational power, Computational Chemistry (CompChem) plays a key role in providing an atomistic understanding of these systems and the nature of the active sites...
March 21, 2017: Chemical Communications: Chem Comm
Riccardo Spezia, Emilio Martínez-Nuñez, Saulo Vazquez, William L Hase
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
David R Glowacki, W J Rodgers, Robin Shannon, Struan H Robertson, Jeremy N Harvey
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Francesca Peccati, Sebastian Mai, Leticia González
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Alvaro Muñoz-Castro, Wilson Caimanque-Aguilar, Cesar Morales-Verdejo
Corannulene, C20H10, exhibits a concave surface in the ground state which is able to experience a bowl-to-bowl inversion through a planar conformation. Such structure is the smaller example resembling an isolated-pentagon motif, as a relevant fragment in Fullerene chemistry. Here, we explored the differences between bowl and planar conformations involving both energetic and 13C-NMR properties, for the neutral and tetraanionic species by using DFT methods. This allows to understand the variation of the chemical environment at the carbon atoms upon planarization of this representive motif...
March 20, 2017: Journal of Physical Chemistry. A
Dylan J Sures, Stefano A Serapian, Károly Kozma, Pedro I Molina, Carles Bo, May Nyman
Ion pairs and solubility related to ion-pairing in water influence many processes in nature and in synthesis including efficient drug delivery, contaminant transport in the environment, and self-assembly of materials in water. Ion pairs are difficult to observe spectroscopically because they generally do not persist unless extreme solution conditions are applied. Here we demonstrate two advanced techniques coupled with computational studies that quantify the persistence of ion pairs in simple solutions and offer explanations for observed solubility trends...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
Mohamed F Attia, Sidy M Dieng, Mayeul Collot, Andrey S Klymchenko, Caroline Bouillot, Christophe A Serra, Marc Schmutz, Meriem Er-Rafik, Thierry F Vandamme, Nicolas Anton
Efficiency of drug administration is related to the inhibition of adverse effects, and can be improved by drug targeting through lipid nanocarriers encapsulation. Targeting technology generally goes along with the nanocarrier functionalization that can be surface modification and/or ligand grafting. The great advantage of nanoemulsions is their loading capability and the possibilities to encapsulate several entities in a single droplet, however, the decoration of the lipid droplets with strongly anchored reactive functions is challenging...
March 17, 2017: Macromolecular Bioscience
Stefan Ilic, Marija R Zoric, Usha Pandey Kadel, Yunjing Huang, Ksenija D Glusac
Metal-free motifs, such as graphitic carbon nitride, conjugated polymers, and doped nanostructures, are emerging as a new class of Earth-abundant materials for solar fuel devices. Although these metal-free structures show great potential, detailed mechanistic understanding of their performance remains limited. Here, we review important experimental and theoretical findings relevant to the role of metal-free motifs as either photoelectrodes or electrocatalysts. First, the light-harvesting characteristics of metal-free photoelectrodes (band energetics, exciton binding energies, charge carrier mobilities and lifetimes) are discussed and contrasted with those in traditional inorganic semiconductors (such as Si)...
March 15, 2017: Annual Review of Physical Chemistry
Guo P Chen, Vamsee K Voora, Matthew M Agee, Sreeganesh Balasubramani, Filipp Furche
Random-phase approximation (RPA) methods are rapidly emerging as costeffective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed...
March 16, 2017: Annual Review of Physical Chemistry
Tatsuya Ishiyama, Akihiro Morita
Vibrational sum frequency generation (VSFG) spectroscopy is a widely used probe of interfaces and, having ideal surface sensitivity and selectivity, is particularly powerful when applied to wet and soft interfaces. Although VSFG spectroscopy can sensitively detect molecular details of interfaces, interpretation of observed spectra has, until recently, been challenging and often ambiguous. The situation has been greatly improved by remarkable advances in computational VSFG analysis on the basis of molecular modeling and molecular dynamics simulation...
March 16, 2017: Annual Review of Physical Chemistry
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
Denis Jacquemin, Ivan Duchemin, Xavier Blase
Developing ab initio approaches able to provide accurate excited-state energies at a reasonable computational cost is one of the biggest challenges in theoretical chemistry. In that framework, the Bethe-Salpeter equation approach, combined with the GW exchange-correlation self-energy, which maintains the same scaling with system size as TD-DFT, has recently been the focus of a rapidly increasing number of applications in molecular chemistry. Using a recently proposed set encompassing excitation energies of many kinds [J...
March 21, 2017: Journal of Physical Chemistry Letters
Carin C C Johansson Seechurn, Theresa Sperger, Thomas G Scrase, Franziska Schoenebeck, Thomas J Colacot
The reduction of Pd(II) intermediates to Pd(0) is a key elementary step in a vast number of Pd-catalyzed processes, ranging from cross-coupling, C-H activation to Wacker chemistry. For one of the most powerful new generation phosphine ligands, PtBu3, oxidation state Pd(I), and not Pd(0), is generated upon reduction from Pd(II). The mechanism of the reduction of Pd(II) to Pd(I) has been investigated by means of experimental and computational studies for the formation of the highly active precatalyst [{Pd(μ-Br)(PtBu3)}2]...
March 16, 2017: Journal of the American Chemical Society
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