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computational chemistry

Rakesh Radhakrishnan, Kumaran G Sreejalekshmi
Probing chemical space of luminescent organic materials built on novel cores is highly imperative for its potential to expand the horizons of advanced functional materials. Small organic fluorophores possessing therapeutic traits can contribute to theranostics. We coupled computational and classical synthetic chemistry strategies for the rational design of 5-(hetero-2-yl)-1,3-thiazoles as colour tunable fluorophore core. With the aid of DFT and TD-DFT, we prove multiheterocyclic system built on thiazole-het core with three inherent tunable sites on thiazole (C2, C4 and C5) capable of accommodating panoply of substituents, as a multifunctional molecular materials' platform...
January 15, 2018: Journal of Organic Chemistry
Lateefat Temitope Afolabi, Faisal Saeed, Haslinda Hashim, Olutomilayo Olayemi Petinrin
Pharmacologically active molecules can provide remedies for a range of different illnesses and infections. Therefore, the search for such bioactive molecules has been an enduring mission. As such, there is a need to employ a more suitable, reliable, and robust classification method for enhancing the prediction of the existence of new bioactive molecules. In this paper, we adopt a recently developed combination of different boosting methods (Adaboost) for the prediction of new bioactive molecules. We conducted the research experiments utilizing the widely used MDL Drug Data Report (MDDR) database...
2018: PloS One
Florent Calvo, Marie-Christine Bacchus-Montabonel
Recent photochemistry experiments provided evidence for the formation of hydantoin by irradiation of interstellar ice analogues. The significance of these results and the importance of hydantoin in prebiotic chemistry and polypeptide synthesis motivate the present theoretical investigation, in which we analyzed the effects of stepwise hydration on the structures, electronic and thermodynamical properties of microhydrated hydantoin using a variety of computational approaches. We generally find microhydration to proceed around the hydantoin heterocycle until 5 water molecules are reached, at which stage hydration becomes segregated with a water cluster forming aside the heterocycle...
January 12, 2018: Journal of Physical Chemistry. A
Bartomeu Monserrat
The interaction between electrons and phonons underlies multiple phenomena in physics, chemistry, and materials science. Examples include superconductivity, electronic transport, and the temperature dependence of optical spectra. A first-principles description of electron-phonon coupling enables the study of the above phenomena with accuracy and material specificity, which can be used to understand experiments and to predict novel effects and functionality. In this topical review, we describe the first-principles calculation of electron-phonon coupling from finite differences...
January 12, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Siddharth Sai Matikonda, Jessica M Fairhall, Franziska Fiedler, Suchaya Sanhajariya, Robert A J Tucker, Sarah Hook, Anna L Garden, Allan B Gamble
Bioorthogonal prodrug activation/decaging strategies need to be selective, rapid and release the drug from the masking group upon activation. The rates of the 1,3-dipolar cycloaddition between a trans-cyclooctene (TCO) and a series of fluorine-substituted azido-PABC self-immolative spacers caging two model drugs, and subsequent release from the 1,2,3-triazoline are reported. As the number of fluorine substituents on the PABC linker increases from one to four, the rate of cycloaddition increases by almost one-order of magnitude...
January 12, 2018: Bioconjugate Chemistry
A A Heller, S Y Lockwood, T M Janes, D M Spence
The creation of a pharmacokinetic (PK) curve, which follows the plasma concentration of an administered drug as a function of time, is a critical aspect of the drug development process and includes such information as the drug's bioavailability, clearance, and elimination half-life. Prior to a drug of interest gaining clearance for use in human clinical trials, research is performed during the preclinical stages to establish drug safety and dosing metrics from data obtained from the PK studies. Both in vivo animal models and in vitro platforms have limitations in predicting human reaction to a drug due to differences in species and associated simplifications, respectively...
January 11, 2018: Annual Review of Analytical Chemistry
Stefanie A Mewes, Felix Plasser, Anna Krylov, Andreas Dreuw
Benchmarking is an every-day task in computational chemistry, yet making meaningful comparisons between different methods is non-trivial. Benchmark studies often focus on the most obvious quantities such as energy differences. But to gain insight, it is desirable to explain the discrepancies between theoretical methods in terms of underlying wavefunctions and, consequently, physically relevant quantities. We present a new strategy of benchmarking excited-state calculations, which goes beyond excitation energies and oscillator strengths and involves the analysis of exciton properties based on the one-particle transition density matrix...
January 11, 2018: Journal of Chemical Theory and Computation
Petr Melichar, Drahomír Hnyk, Jindřich Fanfrlík
This paper presents a systematic study of multicenter and classical bonding on a broad series of experimentally known heteroboranes covering closo, nido, arachno and hypho types of cages with incorporated tetrel, pnictogen or chalcogen heterovertices up to the third-row elements. The nature of bonding is studied using a novel quantum-chemical tool, the intrinsic atomic/bond orbital (IAO/IBO) approach, which provides a direct connection between quantum chemistry and chemical concepts. We also discuss how the computed IBO properties are related to molecular observables such as interatomic distances, molecular electrostatic potential surfaces and dipole moments...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
Paul L A Popelier
Atomic multipole moments associated with a spherical volume fully residing within a topological atom (i.e., the β sphere) can be obtained analytically. Such an integration is thus free of quadrature grids. A general formula for an arbitrary rank spherical harmonic multipole moment is derived, for an electron density comprising Gaussian primitives of arbitrary angular momentum. The closed expressions derived here are also sufficient to calculate the electrostatic potential, the two types of kinetic energy, as well as the potential energy between atoms...
January 10, 2018: Journal of Computational Chemistry
Austin J Parish, Kevin W Boyack, John P A Ioannidis
We aimed to assess which factors correlate with collaborative behavior and whether such behavior associates with scientific impact (citations and becoming a principal investigator). We used the R index which is defined for each author as log(Np)/log(I1), where I1 is the number of co-authors who appear in at least I1 papers written by that author and Np are his/her total papers. Higher R means lower collaborative behavior, i.e. not working much with others, or not collaborating repeatedly with the same co-authors...
2018: PloS One
Nieves Lavado, Juan García de la Concepción, Reyes Babiano, Pedro Cintas
The condensation of cyanamide and glyoxal, two well-known prebiotic monomers, in aqueous phase has been investigated in great detail, demonstrating the formation of oligomeric species of varied structure, though consistent with generalizable patterns. This chemistry involving structurally simple substances also illustrates the ability of building molecular complexity under prebiotically plausible conditions, not only on Earth but also on extraterrestrial scenarios. We show that cyanamide-glyoxal reactions in water lead to mixtures comprising both acyclic and cyclic fragments, largely based on fused five- and six-membered rings, which can be predicted by computation...
January 10, 2018: Chemistry: a European Journal
Daniel Merk, Lukas Friedrich, Francesca Grisoni, Gisbert Schneider
Generative artificial intelligence offers a fresh view on molecular design. We present the first-time prospective application of a deep learning model for designing new druglike compounds with desired activities. For this purpose, we trained a recurrent neural network to capture the constitution of a large set of known bioactive compounds represented as SMILES strings. By transfer learning, this general model was fine-tuned on recognizing retinoid X and peroxisome proliferator-activated receptor agonists. We synthesized five top-ranking compounds designed by the generative model...
January 10, 2018: Molecular Informatics
Evan Hepler-Smith
In two books published in 1969 and 1973, the philosopher François Dagognet articulated a sharp contrast between the verbal and the visual in the history of chemical representation. Ursula Klein took up Dagognet's argument as both inspiration and foil in her account of Berzelian formulas as productive "paper tools." Building on Klein's work, I show how Dagognet portrayed chemical names and formulas not just as representations and paper tools, but as material abstractions that were objects of inquiry in themselves...
January 10, 2018: Ambix
Łukasz Szeleszczuk, Dariusz Maciej Pisklak, Monika Zielińska-Pisklak
Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD)...
January 5, 2018: Journal of Computational Chemistry
Min Zheng, Mark P Waller
Herein, we describe the implementation details of our interaction-based partitioning API (application programming interface) called Yoink for QM/MM modeling and fragment-based quantum chemistry studies. Interactions are detected by computing density descriptors such as reduced density gradient, density overlap regions indicator, and single exponential decay detector. Only molecules having an interaction with a user-definable QM core are added to the QM region of a hybrid QM/MM calculation. Moreover, a set of molecule pairs having density-based interactions within a molecular system can be computed in Yoink, and an interaction graph can then be constructed...
January 5, 2018: Journal of Computational Chemistry
Mathias Siggaard Jørgensen, Uffe Furlig Larsen, Karsten W Jacobsen, Bjørk Hammer
The ability to navigate vast energy landscapes of molecules, clusters, and solids is a necessity for discovering novel compounds in computational chemistry and materials science. For high-dimensional systems it is only computationally feasibly to search a small portion of the landscape, and hence the search strategy is of critical importance. Introducing Bayesian optimization concepts in an evolutionary algorithm framework, we quantify the concepts of exploration and exploitation in global minimum searches...
January 9, 2018: Journal of Physical Chemistry. A
Andres Fernandez-Reche, Eva S Cobos, Irene Luque, Javier Ruiz-Sanz, Jose C Martinez
In 1972 Christian B. Anfinsen received the Nobel Prize in Chemistry for "…his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation." The understanding of this principle is crucial for physical biochemistry students, since protein folding studies, bio-computing sciences and protein design approaches are founded on such a well-demonstrated connection. Herein, we describe a detailed and easy-to-follow experiment to reproduce the most relevant assays carried out at Anfinsen's laboratory in the 60s...
January 4, 2018: Biochemistry and Molecular Biology Education
Zhongming Jiang, Malgorzata Biczysko, Nigel W Moriarty
Unusual local arrangements of protein in Ramachandran space is not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. By contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. For conformations along transition regions - ϕ from -60 to 60° - a very good agreement with representative high-resolution experimental X-ray (≤1...
January 4, 2018: Proteins
Dimitrios Maganas, Serena DeBeer, Frank Neese
In this work, the efficiency of first principles calculations of X-ray absorption spectra of large chemical systems is drastically improved. The approach is based on the previously developed restricted open shell configuration interaction singles (ROCIS) method and its parameterized version, based on a density functional theory (DFT) ground state determinant ROCIS/DFT. The combination of the ROCIS or DFT/ROCIS methods with the well-known machinery of the pair natural orbitals (PNOs) leads to the new PNO-ROCIS and PNO-ROCIS/DFT variants...
January 9, 2018: Journal of Physical Chemistry. A
Milad Radiom, Plinio Maroni, Tomasz A Wesolowski
Using MP2, CCSD, and B3LYP methods of computational chemistry, we show length dependence in the intrinsic elastic properties of short alkane fragments. For isolated alkane fragments of finite length in the gas phase and zero temperature, the intrinsic elasticity constants are found to vary with the number of carbon atoms and its parity. From extrapolation of the elasticity constants calculations to infinite chain length, and by comparing with in-situ elasticity constant of single poly(ethylene) molecule obtained with atomic force microscopy, we estimate the softening effect of environment on the extension response of the polymer...
January 8, 2018: Journal of Molecular Modeling
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